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Zootaxa, 4748(2). https://doi.org/10.11646/zootaxa.4748.2.3\n", "ot:studyYear": 2020, "studyID": "ot_3160", "treeID": "tree3"}, {"SHA": "", "comments": "SUBCLASS CALCARONEA", "compactRefText": "ALVIZU, 2019", "decision": "INCLUDED", "defaultSortOrder": 26, "name": "FIGURE 21. Phylogenetic reconstruction using Bayesian inference of 18S + C-region rDNA for chiactine/pugiole-bearing sponges (ALVIZU, 2019)", "ot:studyPublication": "https://doi.org/10.11646/zootaxa.4615.2.1", "ot:studyPublicationReference": "ALVIZU, A., XAVIER, J. R., & RAPP, H. T. (2019). Description of new chiactine-bearing sponges provides insights into the higher classification of Calcaronea (Porifera: Calcarea). Zootaxa, 4615(2). https://doi.org/10.11646/zootaxa.4615.2.1\n", "ot:studyYear": 2019, "studyID": "ot_3161", "treeID": "tree1"}, {"SHA": "", "comments": "SUBCLASS CALCARONEA", "compactRefText": "Alvizu, 2018", "decision": "INCLUDED", "defaultSortOrder": 27, "name": "Fig. 1. Phylogenetic reconstruction with Bayesian inference of 18S rRNA for Calcaronea (Alvizu, 2018)", "ot:focalCladeOTTTaxonName": "Calcaronea", "ot:studyPublication": "https://doi.org/10.1007/s13127-018-0368-4", "ot:studyPublicationReference": "Alvizu, A., Eilertsen, M. H., Xavier, J. R., & Rapp, H. T. (2018). Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea). Organisms Diversity &amp; Evolution, 18(3), 279\u2013290. https://doi.org/10.1007/s13127-018-0368-4\n", "ot:studyYear": 2018, "studyID": "ot_3156", "treeID": "tree1"}, {"SHA": "", "comments": "SUBCLASS CLATHRINIDA", "compactRefText": "Riesgo A, 2018", "decision": "INCLUDED", "defaultSortOrder": 28, "name": "Fig. 7. ML phylogenetic inter-relationships within Clathrinida using 18S rRNA and 28S rRNA (Riesgo A, 2018)", "ot:focalCladeOTTTaxonName": "Calcinea", "ot:studyPublication": "https://doi.org/10.1071/IS17033", "ot:studyPublicationReference": "Riesgo A, Cavalcanti FF, Kenny NJ, R\u00edos P, Cristobo J, Lanna E. (2018) Integrative systematics of clathrinid sponges: morphological, reproductive and phylogenetic characterisation of a new species of Leucetta from Antarctica (Porifera, Calcarea, Calcinea) with notes on the occurrence of flagellated sperm. Invertebrate Systematics 32, 827\u2013841. https://doi.org/10.1071/IS17033\n\n", "ot:studyYear": 2018, "studyID": "ot_3181", "treeID": "tree1"}, {"SHA": "", "comments": "SUBCLASS CALCINEA", "compactRefText": "VOIGT, 2018", "decision": "INCLUDED", "defaultSortOrder": 29, "name": "FIGURE 4. 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ML tree based on partial 28S rDNA sequences of Calcinea (Klautau, 2016)", "ot:focalCladeOTTTaxonName": "Calcarea", "ot:studyPublication": "https://doi.org/10.5852/ejt.2016.178", "ot:studyPublicationReference": "Klautau, M., Ime\u0161ek, M., Azevedo, F., Ple\u0161e, B., Nikoli\u0107, V., & \u0106etkovi\u0107, H. (2016). Adriatic calcarean sponges (Porifera, Calcarea), with the description of six new species and a richness analysis. European Journal of Taxonomy, 178. https://doi.org/10.5852/ejt.2016.178\n", "ot:studyYear": 2016, "studyID": "ot_3158", "treeID": "tree2"}, {"SHA": "", "comments": "SUBCLASS CALCARONEA", "compactRefText": "Klautau, 2016", "decision": "INCLUDED", "defaultSortOrder": 32, "name": "Fig. 19. ML tree based on partial 28S rDNA sequences of Calcaronea (Klautau, 2016)", "ot:focalCladeOTTTaxonName": "Calcarea", "ot:studyPublication": "https://doi.org/10.5852/ejt.2016.178", "ot:studyPublicationReference": "Klautau, M., Ime\u0161ek, M., Azevedo, F., Ple\u0161e, B., Nikoli\u0107, V., & \u0106etkovi\u0107, H. (2016). Adriatic calcarean sponges (Porifera, Calcarea), with the description of six new species and a richness analysis. European Journal of Taxonomy, 178. https://doi.org/10.5852/ejt.2016.178\n", "ot:studyYear": 2016, "studyID": "ot_3158", "treeID": "tree3"}, {"SHA": "", "comments": "SUBCLASS CLATHRINIDA", "compactRefText": "C\u00d3NDOR-LUJ\u00c1N, 2016", "decision": "INCLUDED", "defaultSortOrder": 33, "name": "FIGURE 3. Bayesian 50% consensus tree from ITS rDNA (C\u00d3NDOR-LUJ\u00c1N, 2016)", "ot:focalCladeOTTTaxonName": "Clathrinida", "ot:studyPublication": "https://doi.org/10.11646/zootaxa.4103.3.2", "ot:studyPublicationReference": "C\u00d3NDOR-LUJ\u00c1N, B., & KLAUTAU, M. (2016). Nicola gen. nov. with redescription of Nicola tetela (Borojevic &amp;amp; Peixinho, 1976) (Porifera: Calcarea: Calcinea: Clathrinida)\u00a0. Zootaxa, 4103(3). https://doi.org/10.11646/zootaxa.4103.3.2\n", "ot:studyYear": 2016, "studyID": "ot_3182", "treeID": "tree1"}, {"SHA": "", "comments": "SUBCLASS CALCINEA", "compactRefText": "Azevedo, 2015", "decision": "INCLUDED", "defaultSortOrder": 34, "name": "Figure 11. Bayesian 50% majority rule consensus tree from ITS rDNA alignment (Azevedo, 2015)", "ot:focalCladeOTTTaxonName": "Calcinea", "ot:studyPublication": "https://doi.org/10.1111/zoj.12213", "ot:studyPublicationReference": "Azevedo, F., C\u00f3ndor-Luj\u00e1n, B., Willenz, P., Hajdu, E., Hooker, Y., & Klautau, M. (2015). Integrative taxonomy of calcareous sponges (subclass Calcinea) from the Peruvian coast: morphology, molecules, and biogeography. Zoological Journal of the Linnean Society, 173(4), 787\u2013817. https://doi.org/10.1111/zoj.12213\n", "ot:studyYear": 2015, "studyID": "ot_3180", "treeID": "tree1"}, {"SHA": "", "comments": "ORDER AMPHIDISCOPHORA", "compactRefText": "Martin Dohrmann, 2017", "decision": "INCLUDED", "defaultSortOrder": 35, "name": "Fig. 8. Phylogeny of Amphidiscophora inferred with TNT (Martin Dohrmann, 2017)", "ot:focalCladeOTTTaxonName": "Hexactinellida", "ot:studyPublication": "http://dx.doi.org/10.1186/s12983-017-0191-3", "ot:studyPublicationReference": "Martin Dohrmann, Christopher Kelley, Michelle Kelly, Andrzej Pisera, John N. A. Hooper, Henry M. Reiswig, 2017, 'An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)', Frontiers in Zoology, vol. 14, no. 1", "ot:studyYear": 2017, "studyID": "ot_1068", "treeID": "tree7"}, {"SHA": "", "comments": "ORDER SCEPTRULOPHORA", "compactRefText": "Martin Dohrmann, 2017", "decision": "INCLUDED", "defaultSortOrder": 36, "name": "Fig. 9. Phylogeny of Sceptrulophora inferred with TNT (Martin Dohrmann, 2017)", "ot:focalCladeOTTTaxonName": "Hexactinellida", "ot:studyPublication": "http://dx.doi.org/10.1186/s12983-017-0191-3", "ot:studyPublicationReference": "Martin Dohrmann, Christopher Kelley, Michelle Kelly, Andrzej Pisera, John N. A. Hooper, Henry M. Reiswig, 2017, 'An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)', Frontiers in Zoology, vol. 14, no. 1", "ot:studyYear": 2017, "studyID": "ot_1068", "treeID": "tree8"}, {"SHA": "", "comments": "ORDER LEUCOSOLENIDA", "compactRefText": "Van Soest, 2015", "decision": "INCLUDED", "defaultSortOrder": 37, "name": "Figure 8. ML phylogenetic tree of 28S partial sequences of Leucosolenida calcareous sponges (Van Soest, 2015)", "ot:studyPublication": "https://doi.org/10.3897/zookeys.546.6122", "ot:studyPublicationReference": "Van Soest, R., Hoeksema, B. W., Reimer, J. D., & De Voogd, N. J. (2015). New records of the rare calcareous sponge Paragrantia waguensis H\u00f4zawa, 1940. ZooKeys, 546, 1\u201320. https://doi.org/10.3897/zookeys.546.6122\n", "ot:studyYear": 2015, "studyID": "ot_3162", "treeID": "tree1"}, {"SHA": "", "comments": "ORDER VERONGIIDA", "compactRefText": "D\u00cdAZ, 2015", "decision": "INCLUDED", "defaultSortOrder": 38, "name": "FIGURE 5. Phylogenetic relationships of genera of Verongida, summarizing four previously published phylogenies (D\u00cdAZ, 2015)", "ot:studyPublication": "https://doi.org/10.11646/zootaxa.3956.3.5", "ot:studyPublicationReference": "D\u00cdAZ, M. C., THACKER, R. W., REDMOND, N. E., PEREZ, T., & COLLINS, A. G. (2015). Vansoestia caribensis gen. nov., sp. nov.: first report of the family Ianthellidae (Verongida, Demospongiae) in the Caribbean\u00a0. Zootaxa, 3956(3). https://doi.org/10.11646/zootaxa.3956.3.5\n", "ot:studyYear": 2015, "studyID": "ot_3216", "treeID": "tree1"}, {"SHA": "", "comments": "ORDER HEXACTINOSIDA", "compactRefText": "Henkel, 2013", "decision": "INCLUDED", "defaultSortOrder": 39, "name": "Fig. 3. Order Hexactinosida: maximum parsimony tree (Henkel, 2013)", "ot:focalCladeOTTTaxonName": "Hexactinellida", "ot:studyPublication": "https://doi.org/10.1017/s0025315413000180", "ot:studyPublicationReference": "Henkel, D., Borkenhagen, K., & Janussen, D. (2013). Phylogeny of the Hexactinellida: phylogenetic reconstruction of the subclass Hexasterophora based on morphological characters. Journal of the Marine Biological Association of the United Kingdom, 95(7), 1365\u20131369. https://doi.org/10.1017/s0025315413000180\n", "ot:studyYear": 2013, "studyID": "ot_3139", "treeID": "tree3"}, {"SHA": "", "comments": "CLADE ANUNCINATARIA", "compactRefText": "Martin Dohrmann, 2017", "decision": "INCLUDED", "defaultSortOrder": 40, "name": "Fig. 10. 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Deep-Sea Carnivorous Sponges From the Mariana Islands. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00371\n", "ot:studyYear": 2019, "studyID": "ot_3163", "treeID": "tree1"}, {"SHA": "", "comments": "FAMILY LEUCONIIDAE\nDescribed new species of calcareous sponges and their relationships", "compactRefText": "Sanamyan, 2023", "decision": "INCLUDED", "defaultSortOrder": 42, "name": "Fig. 13. ML tree from C-region of 28S rRNA sequences (Sanamyan, 2023)", "ot:focalCladeOTTTaxonName": "Calcarea", "ot:studyPublication": "https://doi.org/10.15298/invertzool.20.2.03", "ot:studyPublicationReference": "Sanamyan, K. E., Sanamyan, N. P., Kukhlevskiy, A. D., & Shilov, V. A. (2023). New species of calcareous sponges of the family Leuconiidae (Porifera: Calcarea: Baeriida) from Kuril Islands, NW Pacific. Invertebrate Zoology, 20(2), 153\u2013179. https://doi.org/10.15298/invertzool.20.2.03\n", "ot:studyYear": 2023, "studyID": "ot_3153", "treeID": "tree1"}, {"SHA": "", "comments": "FAMILY OSCARELLIDAE", "compactRefText": "PEREZ, 2018", "decision": "INCLUDED", "defaultSortOrder": 43, "name": "FIGURE 8. ML Phylogenetic reconstruction of Oscarellidae (PEREZ, 2018)", "ot:studyPublication": "https://doi.org/10.11646/zootaxa.4369.4.3", "ot:studyPublicationReference": "PEREZ, T., & RUIZ, C. (2018). Description of the first Caribbean Oscarellidae (Porifera: Homoscleromorpha)\u00a0. Zootaxa, 4369(4). https://doi.org/10.11646/zootaxa.4369.4.3\n", "ot:studyYear": 2018, "studyID": "ot_3145", "treeID": "tree1"}, {"SHA": "", "comments": "FAMILY PLAKINIDAE", "compactRefText": "Cruz-Barraza, 2014", "decision": "INCLUDED", "defaultSortOrder": 44, "name": "Figure 8. 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Current Biology, 22(15), R593-R594.", "ot:studyYear": 2012, "studyID": "pg_1242", "treeID": "tree2507"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Rony Huys, Jacqueline Mackenzie-Dodds, Julia Llewellyn-Hughes, 2009, 'Cancrincolidae (Copepoda, Harpacticoida) associated with land crabs: A semiterrestrial leaf of the ameirid tree', Molecular Phylogenetics and Evolution, vol. 51, no. 2, pp. 143-156", "compactRefText": "Rony Huys, 2009", "decision": "INCLUDED", "defaultSortOrder": 91, "name": "Fig. 1 (Rony Huys, 2009)", "ot:focalCladeOTTTaxonName": "", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2008.12.007", "ot:studyPublicationReferenc": "Rony Huys, Jacqueline Mackenzie-Dodds, Julia Llewellyn-Hughes, 2009, 'Cancrincolidae (Copepoda, Harpacticoida) associated with land crabs: A semiterrestrial leaf of the ameirid tree', Molecular Phylogenetics and Evolution, vol. 51, no. 2, pp. 143-156", "ot:studyPublicationReference": "Rony Huys, Jacqueline Mackenzie-Dodds, Julia Llewellyn-Hughes, 2009, 'Cancrincolidae (Copepoda, Harpacticoida) associated with land crabs: A semiterrestrial leaf of the ameirid tree', Molecular Phylogenetics and Evolution, vol. 51, no. 2, pp. 143-156", "ot:studyYear": 2009, "studyID": "ot_1039", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Yuchi Zheng, John J. Wiens, 2016, 'Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species', Molecular Phylogenetics and Evolution, vol. 94, pp. 537-547", "compactRefText": "Yuchi Zheng, 2016", "decision": "INCLUDED", "defaultSortOrder": 92, "name": "Fig 2. appendix S3 ML tree calibrated in BEAST (Yuchi Zheng, 2016)", "ot:focalCladeOTTTaxonName": "", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2015.10.009", "ot:studyPublicationReferenc": "Yuchi Zheng, John J. Wiens, 2016, 'Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species', Molecular Phylogenetics and Evolution, vol. 94, pp. 537-547", "ot:studyPublicationReference": "Yuchi Zheng, John J. Wiens, 2016, 'Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species', Molecular Phylogenetics and Evolution, vol. 94, pp. 537-547", "ot:studyYear": 2016, "studyID": "ot_1041", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Sara Ruane, Christopher C. Austin, 2017, 'Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens', Molecular Ecology Resources", "compactRefText": "Sara Ruane, 2017", "decision": "INCLUDED", "defaultSortOrder": 93, "name": "Untitled (tree1) (Sara Ruane, 2017)", "ot:focalCladeOTTTaxonName": "", "ot:studyPublication": "http://dx.doi.org/10.1111/1755-0998.12655", "ot:studyPublicationReferenc": "Sara Ruane, Christopher C. 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Austin, 2017, 'Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens', Molecular Ecology Resources", "ot:studyYear": 2017, "studyID": "ot_1042", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Benjamin Ollomo, Patrick Durand, Franck Prugnolle, Emmanuel Douzery, Celine Arnathau, Dieudonne Nkoghe, Eric Leroy, Francois Renaud, 2009, 'A New Malaria Agent in African Hominids', PLoS Pathogens, vol. 5, no. 5, p. e1000446", "compactRefText": "Benjamin Ollomo, 2009", "decision": "INCLUDED", "defaultSortOrder": 94, "name": "Untitled (tree6417) (Benjamin Ollomo, 2009)", "ot:focalCladeOTTTaxonName": "Plasmodium", "ot:studyPublication": "http://dx.doi.org/10.1371/journal.ppat.1000446", "ot:studyPublicationReference": "Benjamin Ollomo, Patrick Durand, Franck Prugnolle, Emmanuel Douzery, Celine Arnathau, Dieudonne Nkoghe, Eric Leroy, Francois Renaud, 2009, 'A New Malaria Agent in African Hominids', PLoS Pathogens, vol. 5, no. 5, p. e1000446", "ot:studyYear": 2009, "studyID": "pg_2770", "treeID": "tree6417"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Rony Huys, Farrah Fatih, Susumu Ohtsuka, Julia Llewellyn-Hughes, 2012, 'Evolution of the bomolochiform superfamily complex (Copepoda: Cyclopoida): New insights from ssrDNA and morphology, and origin of umazuracolids from polychaete-infesting ancestors rejected', International Journal for Parasitology, vol. 42, no. 1, pp. 71-92", "compactRefText": "Rony Huys, 2012", "decision": "INCLUDED", "defaultSortOrder": 95, "name": "Fig. 2 (Rony Huys, 2012)", "ot:focalCladeOTTTaxonName": "", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ijpara.2011.10.009", "ot:studyPublicationReferenc": "Rony Huys, Farrah Fatih, Susumu Ohtsuka, Julia Llewellyn-Hughes, 2012, 'Evolution of the bomolochiform superfamily complex (Copepoda: Cyclopoida): New insights from ssrDNA and morphology, and origin of umazuracolids from polychaete-infesting ancestors rejected', International Journal for Parasitology, vol. 42, no. 1, pp. 71-92", "ot:studyPublicationReference": "Rony Huys, Farrah Fatih, Susumu Ohtsuka, Julia Llewellyn-Hughes, 2012, 'Evolution of the bomolochiform superfamily complex (Copepoda: Cyclopoida): New insights from ssrDNA and morphology, and origin of umazuracolids from polychaete-infesting ancestors rejected', International Journal for Parasitology, vol. 42, no. 1, pp. 71-92", "ot:studyYear": 2012, "studyID": "ot_1045", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Seong-il Eyun, 2017, 'Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies', BMC Evolutionary Biology, vol. 17, no. 1", "compactRefText": "Seong-il Eyun, 2017", "decision": "INCLUDED", "defaultSortOrder": 96, "name": "Fig. 3 (Seong-il Eyun, 2017)", "ot:focalCladeOTTTaxonName": "Crustacea", "ot:studyPublication": "http://dx.doi.org/10.1186/s12862-017-0883-5", "ot:studyPublicationReference": "Seong-il Eyun, 2017, 'Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies', BMC Evolutionary Biology, vol. 17, no. 1", "ot:studyYear": 2017, "studyID": "ot_1046", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from T. H. Oakley, J. M. Wolfe, A. R. Lindgren, A. K. Zaharoff, 2012, 'Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny', Molecular Biology and Evolution, vol. 30, no. 1, pp. 215-233", "compactRefText": "T. H. Oakley, 2012", "decision": "INCLUDED", "defaultSortOrder": 97, "name": "Fig. 1 (T. H. Oakley, 2012)", "ot:focalCladeOTTTaxonName": "Pancrustacea", "ot:studyPublication": "http://dx.doi.org/10.1093/molbev/mss216", "ot:studyPublicationReference": "T. H. Oakley, J. M. Wolfe, A. R. Lindgren, A. K. 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Peters, Lars Krogmann, Christoph Mayer, Alexander Donath, Simon Gunkel, Karen Meusemann, Alexey Kozlov, Lars Podsiadlowski, Malte Petersen, Robert Lanfear, Patricia A. Diez, John Heraty, Karl M. Kjer, Seraina Klopfstein, Rudolf Meier, Carlo Polidori, Thomas Schmitt, Shanlin Liu, Xin Zhou, Torsten Wappler, Jes Rust, Bernhard Misof, Oliver Niehuis, 2017, 'Evolutionary History of the Hymenoptera', Current Biology", "compactRefText": "Ralph S. Peters, 2017", "decision": "INCLUDED", "defaultSortOrder": 99, "name": "Figure 1 (Ralph S. Peters, 2017)", "ot:focalCladeOTTTaxonName": "Hymenoptera", "ot:studyPublication": "http://dx.doi.org/10.1016/j.cub.2017.01.027", "ot:studyPublicationReference": "Ralph S. Peters, Lars Krogmann, Christoph Mayer, Alexander Donath, Simon Gunkel, Karen Meusemann, Alexey Kozlov, Lars Podsiadlowski, Malte Petersen, Robert Lanfear, Patricia A. Diez, John Heraty, Karl M. Kjer, Seraina Klopfstein, Rudolf Meier, Carlo Polidori, Thomas Schmitt, Shanlin Liu, Xin Zhou, Torsten Wappler, Jes Rust, Bernhard Misof, Oliver Niehuis, 2017, 'Evolutionary History of the Hymenoptera', Current Biology", "ot:studyYear": 2017, "studyID": "ot_1053", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dahiana Arcila, Guillermo Ort\u00ed, Richard Vari, Jonathan W. Armbruster, Melanie L. J. Stiassny, Kyung D. Ko, Mark H. Sabaj, John Lundberg, Liam J. Revell, Ricardo Betancur-R., 2017, 'Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life', Nature Ecology & Evolution, vol. 1, p. 0020", "compactRefText": "Arcila, 2017", "decision": "INCLUDED", "defaultSortOrder": 100, "name": "Figure 3 (Arcila, 2017)", "ot:focalCladeOTTTaxonName": "Otophysi", "ot:studyPublication": "http://dx.doi.org/10.1038/s41559-016-0020", "ot:studyPublicationReference": "Arcila, Dahiana, Guillermo Ort\u00ed, Richard Vari, Jonathan W. 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Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biology 10 (1): 12", "ot:studyYear": 2012, "studyID": "ot_328", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Moreau C.S., & Bell C. 2013. Testing the museum versus cradle tropical biological diversity hypothesis: Phylogeny, diversification, and ancestral biogeographic range evolution of the ants. Evolution, 67(8): 2240-2257.", "compactRefText": "Moreau C.S., 2013", "decision": "INCLUDED", "defaultSortOrder": 102, "name": "MLT (Moreau C.S., 2013)", "ot:focalCladeOTTTaxonName": "", "ot:studyPublication": "http://dx.doi.org/10.1111/evo.12105", "ot:studyPublicationReferenc": "Moreau C.S., & Bell C. 2013. Testing the museum versus cradle tropical biological diversity hypothesis: Phylogeny, diversification, and ancestral biogeographic range evolution of the ants. Evolution, 67(8): 2240-2257.", "ot:studyPublicationReference": "Moreau C.S., & Bell C. 2013. Testing the museum versus cradle tropical biological diversity hypothesis: Phylogeny, diversification, and ancestral biogeographic range evolution of the ants. Evolution, 67(8): 2240-2257.", "ot:studyYear": 2013, "studyID": "ot_1056", "treeID": "Tr66754"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Allison K. Miller, Alexander M. Kerr, Gustav Paulay, Mike Reich, Nerida G. Wilson, Jose I. Carvajal, Greg W. Rouse, 2017, 'Molecular phylogeny of extant Holothuroidea (Echinodermata)', Molecular Phylogenetics and Evolution, vol. 111, pp. 110-131", "compactRefText": "Miller, 2017", "decision": "INCLUDED", "defaultSortOrder": 103, "name": "Figure 3 - first tree from supp. data 2 (Miller, 2017)", "ot:focalCladeOTTTaxonName": "Holothuroidea", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2017.02.014", "ot:studyPublicationReference": "Miller, Allison K., Alexander M. Kerr, Gustav Paulay, Mike Reich, Nerida G. Wilson, Jose I. Carvajal, Greg W. Rouse, 2017, 'Molecular phylogeny of extant Holothuroidea (Echinodermata)', Molecular Phylogenetics and Evolution, vol. 111, pp. 110-131", "ot:studyYear": 2017, "studyID": "ot_1058", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from William J.D. Iles, Chodon Sass, Laura Lagomarsino, Gracie Benson-Martin, Heather Driscoll, Chelsea D. Specht, 2016, 'The phylogeny of Heliconia (Heliconiaceae) and the evolution of floral presentation', Molecular Phylogenetics and Evolution", "compactRefText": "William J.D. Iles, 2016", "decision": "INCLUDED", "defaultSortOrder": 104, "name": "Heliconiaceae (William J.D. Iles, 2016)", "ot:focalCladeOTTTaxonName": "Heliconiaceae", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2016.12.001", "ot:studyPublicationReference": "William J.D. Iles, Chodon Sass, Laura Lagomarsino, Gracie Benson-Martin, Heather Driscoll, Chelsea D. 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Kiril\u2019chik, 2010, 'Molecular-phylogenetic analysis of cyclopoids (Copepoda: Cyclopoida) from Lake Baikal and its water catchment basin', Russian Journal of Genetics, vol. 46, no. 11, pp. 1373-1380", "ot:studyPublicationReference": "T. Yu. Mayor, N. G. Sheveleva, L. V. Sukhanova, O. A. Timoshkin, S. V. Kiril\u2019chik, 2010, 'Molecular-phylogenetic analysis of cyclopoids (Copepoda: Cyclopoida) from Lake Baikal and its water catchment basin', Russian Journal of Genetics, vol. 46, no. 11, pp. 1373-1380", "ot:studyYear": 2010, "studyID": "ot_1064", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from R. W. Thacker, A. L. Hill, M. S. Hill, N. E. Redmond, A. G. Collins, C. C. Morrow, L. Spicer, C. A. Carmack, M. E. Zappe, D. Pohlmann, C. Hall, M. C. Diaz, P. V. Bangalore, 2013, 'Nearly Complete 28S rRNA Gene Sequences Confirm New Hypotheses of Sponge Evolution', Integrative and Comparative Biology, vol. 53, no. 3, pp. 373-387", "compactRefText": "R. 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Pastore, Domingos Cardoso, Cristiane Snak, Ana Lu\u00edsa de C. Lima, Edeline Gagnon, Mohammad Vatanparast, Ailsa E. Holland, Ashley N. Egan, 2015, 'A multilocus phylogenetic analysis reveals the monophyly of a recircumscribed papilionoid legume tribe Diocleae with well-supported generic relationships', Molecular Phylogenetics and Evolution, vol. 90, pp. 1-19", "compactRefText": "Luciano Paganucci de Queiroz, 2015", "decision": "INCLUDED", "defaultSortOrder": 358, "name": "de Queiroz et al., 2015 Concatenated Bayesian (Luciano Paganucci de Queiroz, 2015)", "ot:focalCladeOTTTaxonName": "Dioclea", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2015.04.016", "ot:studyPublicationReference": "Luciano Paganucci de Queiroz, Jos\u00e9 Floriano B. Pastore, Domingos Cardoso, Cristiane Snak, Ana Lu\u00edsa de C. Lima, Edeline Gagnon, Mohammad Vatanparast, Ailsa E. Holland, Ashley N. 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Kawahara, Jesse W. Breinholt, Marianne Espeland, Caroline Storer, David Plotkin, Kelly M. Dexter, Emmanuel F.A. Toussaint, Ryan A. St Laurent, Gunnar Brehm, Sergio Vargas, Dimitri Forero, Naomi E. Pierce, David J. Lohman, 2018, 'Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set', Molecular Phylogenetics and Evolution, vol. 127, pp. 600-605", "compactRefText": "Akito Y. Kawahara, 2018", "decision": "INCLUDED", "defaultSortOrder": 364, "name": "Hedylidae (Kawahara et al. 2018) (Akito Y. Kawahara, 2018)", "ot:focalCladeOTTTaxonName": "Macrosoma (genus in superorder Amphiesmenoptera)", "ot:studyPublication": "http://dx.doi.org/10.1016/j.ympev.2018.06.002", "ot:studyPublicationReference": "Akito Y. Kawahara, Jesse W. Breinholt, Marianne Espeland, Caroline Storer, David Plotkin, Kelly M. Dexter, Emmanuel F.A. Toussaint, Ryan A. St Laurent, Gunnar Brehm, Sergio Vargas, Dimitri Forero, Naomi E. Pierce, David J. 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Sinn, Dylan D. Sedmak, Lawrence M. Kelly, John V. Freudenstein, 2018, 'Total duplication of the small single copy region in the angiosperm plastome: Rearrangement and inverted repeat instability in Asarum\n                    ', American Journal of Botany, vol. 105, no. 1, pp. 71-84", "compactRefText": "Brandon T. Sinn, 2018", "decision": "INCLUDED", "defaultSortOrder": 367, "name": "Sinn et al., 2018 Maximum Likelihood Concatenated (Brandon T. Sinn, 2018)", "ot:focalCladeOTTTaxonName": "Asarum", "ot:studyPublication": "http://dx.doi.org/10.1002/ajb2.1001", "ot:studyPublicationReference": "Brandon T. Sinn, Dylan D. Sedmak, Lawrence M. Kelly, John V. 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J., Sytsma, K. J., & Roalson, E. H. (2013). Phylogenetic relationships among the North American cleomoids (Cleomaceae): A test of Iltis\u2019s reduction series. American Journal of Botany, 100(10), 2102\u20132111. doi:10.3732/ajb.1300096\n", "compactRefText": "Riser, 2013", "decision": "INCLUDED", "defaultSortOrder": 425, "name": "TREE1 (Riser, 2013)", "ot:focalCladeOTTTaxonName": "Cleomella", "ot:studyPublication": "http://dx.doi.org/10.3732/ajb.1300096", "ot:studyPublicationReference": "Riser, J. P., Cardinal-McTeague, W. M., Hall, J. C., Hahn, W. J., Sytsma, K. J., & Roalson, E. H. (2013). Phylogenetic relationships among the North American cleomoids (Cleomaceae): A test of Iltis\u2019s reduction series. American Journal of Botany, 100(10), 2102\u20132111. doi:10.3732/ajb.1300096\n", "ot:studyYear": 2013, "studyID": "pg_2622", "treeID": "tree6137"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cardinal-McTeague, W. M., Sytsma, K. J., & Hall, J. C. (2016). 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Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyPublicationReference": "Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyYear": 2009, "studyID": "ot_2114", "treeID": "Tr6581"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. 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Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyYear": 2009, "studyID": "ot_2114", "treeID": "Tr6683"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "compactRefText": "Jung, 2009", "decision": "INCLUDED", "defaultSortOrder": 493, "name": "ITS BS (Jung, 2009)", "ot:focalCladeOTTTaxonName": "", "ot:studyPublication": "http://dx.doi.org/10.3767/003158509x442612", "ot:studyPublicationReferenc": "Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyPublicationReference": "Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyYear": 2009, "studyID": "ot_2114", "treeID": "Tr6096"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. 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Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyPublicationReference": "Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyYear": 2009, "studyID": "ot_2114", "treeID": "Tr6058"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. 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Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyPublicationReference": "Jung, T., & Burgess, T. I. (2009). Re-evaluation of <I>Phytophthora citricola</I> isolates from multiple woody hosts in Europe and North America reveals a new species, <I>Phytophthora plurivora</I> sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95\u2013110. https://doi.org/10.3767/003158509x442612\n", "ot:studyYear": 2009, "studyID": "ot_2114", "treeID": "Tr6474"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Scott, P. M., Burgess, T. I., Barber, P. A., Shearer, B. L., Stukely, M. J. C., Hardy, G. E. St. J., & Jung, T. 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Proceedings of the National Academy of Sciences, 115(48), 12253\u201312258. https://doi.org/10.1073/pnas.1719794115\n", "decision": "INCLUDED", "name": "RAxML_bipartitions.result.ladderized.dropped.tre", "studyID": "ot_2316", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ruth E Timme, Hugh Rand, Martin Shumway, Eija K Trees, Mustafa Simmons, Richa Agarwala, Steven Davis, Glen Tillman, Stephanie Defibaugh-Chavez, Heather A Carleton, William A Klimke, Lee S Katz, 2017, 'Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance'", "decision": "INCLUDED", "name": "Simulated-SalBareilly.tre", "studyID": "ot_301", "treeID": "tree4"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants\nMarek L. Borowiec, Y. Miles Zhang, Karen Neves, Manuela O. Ramalho, Brian L. Fisher, Andrea Lucky, Corrie S. 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(2022). Geographic range size and speciation in honeyeaters. BMC Ecology and Evolution, 22(1). https://doi.org/10.1186/s12862-022-02041-6\n", "decision": "INCLUDED", "name": "tree 1", "studyID": "ot_2320", "treeID": "tree5"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Pisanty, G., Richter, R., Martin, T., Dettman, J., & Cardinal, S. (2022). Molecular phylogeny, historical biogeography and revised classification of andrenine bees (Hymenoptera: Andrenidae). Molecular Phylogenetics and Evolution, 170, 107151. https://doi.org/10.1016/j.ympev.2021.107151\n", "decision": "INCLUDED", "name": "232T-F75,RAxML,rcluster.tree", "studyID": "ot_2321", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Henr\u00edquez-Piskulich, P., Hugall, A. F., & Stuart-Fox, D. (2024). A supermatrix phylogeny of the world\u2019s bees (Hymenoptera: Anthophila). 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Phylogenetic analysis of Blaberoidea reveals non\u2010monophyly of taxa and supports the creation of multiple new subfamilies. Cladistics, 39(3), 198\u2013214. Portico. https://doi.org/10.1111/cla.12535\n", "decision": "INCLUDED", "name": "Blaberoidea Fig. 2", "studyID": "ot_2329", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Djern\u00e6s, M., Varadinova, Z., Kotyl, M., Eulitz, U. and Klass, K., 2020. Phylogeny and life history evolution of Blaberoidea (Blattodea). Arthropod Systematics & Phylogeny, 78, pp.29-67.", "decision": "INCLUDED", "name": "bestREP1", "studyID": "ot_2330", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Beasley\u2010Hall, P. G., Rose, H. A., Walker, J., Kinjo, Y., Bourguignon, T., & Lo, N. (2021). Digging deep: a revised phylogeny of Australian burrowing cockroaches (Blaberidae: Panesthiinae, Geoscapheinae) confirms extensive nonmonophyly and provides insights into biogeography and evolution of burrowing. Systematic Entomology, 46(4), 767\u2013783. Portico. https://doi.org/10.1111/syen.12487\n", "decision": "INCLUDED", "name": "Geoscapheinae tree", "studyID": "ot_2331", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Djern\u00e6s, M., & Murienne, J. (2022). Phylogeny of Blattoidea (Dictyoptera: Blattodea) with a revised classification of Blattidae. Arthropod Systematics &amp; Phylogeny, 80, 209\u2013228. https://doi.org/10.3897/asp.80.e75819\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2333", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Deng, W., Luo, X., Ho, S. Y. W., Liao, S., Wang, Z., & Che, Y. (2023). Inclusion of rare taxa from Blattidae and Anaplectidae improves phylogenetic resolution in the cockroach superfamily Blattoidea. Systematic Entomology, 48(1), 23\u201339. Portico. https://doi.org/10.1111/syen.12560\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2334", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Rainford, J. L., Hofreiter, M., Nicholson, D. B., & Mayhew, P. J. (2014). Phylogenetic Distribution of Extant Richness Suggests Metamorphosis Is a Key Innovation Driving Diversification in Insects. PLoS ONE, 9(10), e109085. https://doi.org/10.1371/journal.pone.0109085\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2336", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Vasilikopoulos, A., Balke, M., Kukowka, S., Pflug, J. M., Martin, S., Meusemann, K., Hendrich, L., Mayer, C., Maddison, D. R., Niehuis, O., Beutel, R. G., & Misof, B. (2021). Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming. Systematic Entomology, 46(4), 991\u20131018. Portico. https://doi.org/10.1111/syen.12508\n", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "ot_2337", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Outomuro, D., Adams, D. C., & Johansson, F. (2013). Wing shape allometry and aerodynamics in calopterygid damselflies: a comparative approach. BMC Evolutionary Biology, 13(1), 118. https://doi.org/10.1186/1471-2148-13-118\n", "decision": "INCLUDED", "name": "Fig. 7", "studyID": "ot_2338", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Leoc\u00e1dio, M., Sim\u00f5es, M. V. P., Sekerka, L., Schrago, C. G., Mermudes, J. R. M., & Windsor, D. M. (2020). Molecular systematics reveals the origins of subsociality in tortoise beetles (Coleoptera, Chrysomelidae, Cassidinae). Systematic Entomology, 45(4), 894\u2013910. Portico. https://doi.org/10.1111/syen.12434\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2339", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Nelsen, M. P., Ree, R. H., & Moreau, C. S. (2018). Ant\u2013plant interactions evolved through increasing interdependence. Proceedings of the National Academy of Sciences, 115(48), 12253\u201312258. https://doi.org/10.1073/pnas.1719794115\n", "decision": "INCLUDED", "name": "Dryad_Supplementary_File_7_ML_TREE_treepl_185.tre", "studyID": "ot_2316", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Sless, T., & Rehan, S. (2023). Phylogeny of the carpenter bees (Apidae: Xylocopinae) highlights repeated evolution of sociality. Biology Letters, 19(8). https://doi.org/10.1098/rsbl.2023.0252\n", "decision": "INCLUDED", "name": "Tree 1", "studyID": "ot_2350", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Revely, L., Eggleton, P., Clement, R., Zhou, C., & Bishop, T. R. (2024). The diversity of social complexity in termites. Proceedings of the Royal Society B: Biological Sciences, 291(2024). https://doi.org/10.1098/rspb.2023.2791\n", "decision": "INCLUDED", "name": "Fig. 2", "studyID": "ot_2351", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from S\u00e1nchez-Guill\u00e9n, R. A., Ceccarelli, S., Villalobos, F., Neupane, S., Rivas-Torres, A., Sanmart\u00edn-Villar, I., ... & Cordero-Rivera, A. (2020). The evolutionary history of colour polymorphism in Ischnura damselflies (Odonata: Coenagrionidae). Odonatologica, 49(3-4), 333-370.", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "ot_2355", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ji, L., Jia, Z., & Bai, X. (2024). Comparative Analysis of the Mitochondrial Genomes of Three Species of Yangiella (Hemiptera: Aradidae) and the Phylogenetic Implications of Aradidae. Insects, 15(7), 533. https://doi.org/10.3390/insects15070533\n", "decision": "INCLUDED", "name": "Fig. 10", "studyID": "ot_2359", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gohli, J., Kirkendall, L. R., Smith, S. M., Cognato, A. I., Hulcr, J., & Jordal, B. H. (2017). Biological factors contributing to bark and ambrosia beetle species diversification. Evolution, 71(5), 1258\u20131272. Portico. https://doi.org/10.1111/evo.13219\n", "decision": "INCLUDED", "name": "Fig. 2", "studyID": "ot_2366", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from de Abreu-Jr, E. F., Pavan, S. E., Tsuchiya, M. T. N., Wilson, D. E., Percequillo, A. R., & Maldonado, J. E. (2020). Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul. BMC Evolutionary Biology, 20(1). https://doi.org/10.1186/s12862-020-01639-y\n", "decision": "INCLUDED", "name": "Dataset-5-43 OTUs", "studyID": "ot_2369", "treeID": "tree5"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhao, C., Zhang, H., Liu, G., Yang, X., & Zhang, J. (2016). The complete mitochondrial genome of the Tibetan fox (Vulpes ferrilata) and implications for the phylogeny of Canidae. Comptes Rendus. 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Phylogenetic tests reject Emery\u2019s rule in the evolution of social parasitism in yellowjackets and hornets (Hymenoptera: Vespidae, Vespinae). Royal Society Open Science, 2(9), 150159. https://doi.org/10.1098/rsos.150159\n", "decision": "INCLUDED", "name": "Figure 1c - con 50 majrule", "studyID": "ot_2377", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Piekarski, P. K., Carpenter, J. M., Lemmon, A. R., Moriarty Lemmon, E., & Sharanowski, B. J. (2018). Phylogenomic Evidence Overturns Current Conceptions of Social Evolution in Wasps (Vespidae). Molecular Biology and Evolution, 35(9), 2097\u20132109. https://doi.org/10.1093/molbev/msy124\n", "decision": "INCLUDED", "name": "Fig 2", "studyID": "ot_2380", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Menezes, R. S. T., Lloyd, M. W., & Brady, S. G. (2020). 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Ecological correlates of sociality in Pemphigus aphids, with a partial phylogeny of the genus. BMC Evolutionary Biology, 7(1), 185. https://doi.org/10.1186/1471-2148-7-185\n", "decision": "INCLUDED", "name": "Fig 3", "studyID": "ot_2393", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Uematsu, K., Kutsukake, M., Shigenobu, S., Yang, M.-M., Shibao, H., & Fukatsu, T. (2022). Seasonal polyphenism underlies the origin of a sterile caste in aphids. https://doi.org/10.1101/2022.08.19.501651\n", "decision": "INCLUDED", "name": "Fig S2", "studyID": "ot_2394", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lepeco, A., Branstetter, M. G., Melo, G. A. R., Freitas, F. V., Tobin, K. B., Gan, J., Jensen, J., & Almeida, E. A. B. (2024). Phylogenomic insights into the worldwide evolutionary relationships of the stingless bees (Apidae, Meliponini). Molecular Phylogenetics and Evolution, 201, 108219. https://doi.org/10.1016/j.ympev.2024.108219\n", "decision": "INCLUDED", "name": "Fig 2", "studyID": "ot_2397", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ACOSTA, R., & MORRONE, J. J. (2013). Phylogenetics of the tribe Phalacropsyllini (Siphonaptera: Ctenophthalmidae: Neopsyllinae) based on molecular and morphological evidence. Zootaxa, 3630(2). https://doi.org/10.11646/zootaxa.3630.2.8\n", "decision": "INCLUDED", "name": "Figure 3", "studyID": "ot_2400", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Robert S. 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Molecular Phylogenetics and Evolution, 31(3), 880\u2013893. https://doi.org/10.1016/j.ympev.2003.10.024\n", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "ot_2421", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Auger\u2010Rozenberg, M., Kerdelhu\u00e9, C., Magnoux, E., Turgeon, J., Rasplus, J., & Roques, A. (2005). Molecular phylogeny and evolution of host\u2010plant use in conifer seed chalcids in the genus Megastigmus (Hymenoptera: Torymidae). Systematic Entomology, 31(1), 47\u201364. Portico. https://doi.org/10.1111/j.1365-3113.2005.00310.x\n", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "ot_2422", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ayivi, S. P. G., Tong, Y., Storey, K. B., Yu, D.-N., & Zhang, J.-Y. (2021). The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae. Insects, 12(11), 1025. https://doi.org/10.3390/insects12111025\n", "decision": "INCLUDED", "name": "Fig. 3 Left", "studyID": "ot_2423", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Baca, S. M., & Short, A. E. Z. (2020). Molecular Phylogeny of the Notomicrine Water Beetles (Coleoptera: Noteridae) Reveals Signatures of Gondwanan Vicariance and Ecological Plasticity. Insect Systematics and Diversity, 4(6). https://doi.org/10.1093/isd/ixaa015\n", "decision": "INCLUDED", "name": "Fig. 2", "studyID": "ot_2424", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BADANO, D., ASP\u00d6CK, U., ASP\u00d6CK, H., & CERRETTI, P. (2016). Phylogeny of <scp>M</scp>yrmeleontiformia based on larval morphology (<scp>N</scp>europterida: <scp>N</scp>europtera). Systematic Entomology, 42(1), 94\u2013117. Portico. https://doi.org/10.1111/syen.12200\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2426", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Balke, M., Watts, C. H. S., Cooper, S. J. B., Humphreys, W. F., & Vogler, A. P. (2004). A highly modified stygobiont diving beetle of the genus Copelatus (Coleoptera, Dytiscidae): taxonomy and cladistic analysis based on mitochondrial DNA sequences. Systematic Entomology, 29(1), 59\u201367. Portico. https://doi.org/10.1111/j.1365-3113.2004.00229.x\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2428", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Balke, M., Ribera, I., & Vogler, A. P. (2004). MtDNA phylogeny and biogeography of Copelatinae, a highly diverse group of tropical diving beetles (Dytiscidae). Molecular Phylogenetics and Evolution, 32(3), 866\u2013880. https://doi.org/10.1016/j.ympev.2004.03.014\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2429", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bank, S., & Bradler, S. (2022). A second view on the evolution of flight in stick and leaf insects (Phasmatodea). BMC Ecology and Evolution, 22(1). https://doi.org/10.1186/s12862-022-02018-5\n", "decision": "INCLUDED", "name": "File.S3.nex.txt", "studyID": "ot_2430", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bank, S., Sann, M., Mayer, C., Meusemann, K., Donath, A., Podsiadlowski, L., Kozlov, A., Petersen, M., Krogmann, L., Meier, R., Rosa, P., Schmitt, T., Wurdack, M., Liu, S., Zhou, X., Misof, B., Peters, R. S., & Niehuis, O. (2017). Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae). Molecular Phylogenetics and Evolution, 116, 213\u2013226. https://doi.org/10.1016/j.ympev.2017.08.020\n", "decision": "INCLUDED", "name": "Fig. 2, 1-s2.0-S1055790317303305-mmc30.new", "studyID": "ot_2431", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bank, S., Cumming, R. T., Li, Y., Henze, K., Le Tirant, S., & Bradler, S. (2021). A tree of leaves: Phylogeny and historical biogeography of the leaf insects (Phasmatodea: Phylliidae). Communications Biology, 4(1). https://doi.org/10.1038/s42003-021-02436-z\n", "decision": "INCLUDED", "name": "42003_2021_2436_MOESM7_ESM.txt", "studyID": "ot_2432", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bank, S., Buckley, T. R., B\u00fcscher, T. H., Bresseel, J., Constant, J., de Haan, M., Dittmar, D., Dr\u00e4ger, H., Kahar, R. S., Kang, A., Kneub\u00fchler, B., Langton\u2010Myers, S. S., & Bradler, S. (2021). Reconstructing the nonadaptive radiation of an ancient lineage of ground\u2010dwelling stick insects (Phasmatodea: Heteropterygidae). Systematic Entomology, 46(3), 487\u2013507. Portico. https://doi.org/10.1111/syen.12472\n", "decision": "INCLUDED", "name": "syen12472-sup-0014-files3.nex", "studyID": "ot_2433", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Barber-James, H. M. (2009). A preliminary phylogeny of Prosopistomatidae (Ephemeroptera) based on morphological characters of the larvae, and an assessment of their distribution. Aquatic Insects, 31(sup1), 149\u2013166. https://doi.org/10.1080/01650420903020502\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2434", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Barker, S. C., Whiting, M., Johnson, K. P., & Murrell, A. (2003). Phylogeny of the lice (Insecta, Phthiraptera) inferred from small subunit rRNA. Zoologica Scripta, 32(5), 407\u2013414. Portico. https://doi.org/10.1046/j.1463-6409.2003.00120.x\n", "decision": "INCLUDED", "name": "Fig. 2", "studyID": "ot_2435", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bas\u00edlio, D. S., Cherman, M. A., Vaz-De-Mello, F. Z., & Almeida, L. M. (2023). Phylogenetic relationships in Hybosoridae (Coleoptera: Scarabaeoidea). Zoological Journal of the Linnean Society, 198(4), 1156\u20131170. https://doi.org/10.1093/zoolinnean/zlac095\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2436", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Basso, A., Negrisolo, E., Zilli, A., Battisti, A., & Cerretti, P. (2016). A total evidence phylogeny for the processionary moths of the genus Thaumetopoea (Lepidoptera: Notodontidae: Thaumetopoeinae). Cladistics, 33(6), 557\u2013573. Portico. https://doi.org/10.1111/cla.12181\n", "decision": "INCLUDED", "name": "Fig. S11", "studyID": "ot_2437", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bauer, F., St\u00fcbner, A., Neinhuis, C., & Nuss, M. (2012). Molecular phylogeny, larval case architecture, host\u2013plant associations and classification of European Coleophoridae (Lepidoptera). Zoologica Scripta, 41(3), 248\u2013265. Portico. https://doi.org/10.1111/j.1463-6409.2012.00532.x\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2438", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bayless, K. M., Trautwein, M. D., Meusemann, K., Shin, S., Petersen, M., Donath, A., Podsiadlowski, L., Mayer, C., Niehuis, O., Peters, R. S., Meier, R., Kutty, S. N., Liu, S., Zhou, X., Misof, B., Yeates, D. K., & Wiegmann, B. M. (2021). Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics. BMC Biology, 19(1). https://doi.org/10.1186/s12915-020-00944-8\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2439", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BELL, K. L., & PHILIPS, T. K. (2012). Molecular systematics and evolution of the Ptinidae (Coleoptera: Bostrichoidea) and related families. Zoological Journal of the Linnean Society, 165(1), 88\u2013108. https://doi.org/10.1111/j.1096-3642.2011.00792.x\n", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "ot_2440", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bell-Roberts, L., Douglas, A. E., & Werner, G. D. A. (2019). Match and mismatch between dietary switches and microbial partners in plant sap-feeding insects. Proceedings of the Royal Society B: Biological Sciences, 286(1902), 20190065. https://doi.org/10.1098/rspb.2019.0065\n", "decision": "INCLUDED", "name": "aucho_till_subfamily_boosterweb_dated.phy", "studyID": "ot_2441", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bellini, B. C., Zhang, F., de Souza, P. G. C., dos Santos-Costa, R. C., Medeiros, G. da S., & Godeiro, N. N. (2022). The Evolution of Collembola Higher Taxa (Arthropoda, Hexapoda) Based on Mitogenome Data. Diversity, 15(1), 7. https://doi.org/10.3390/d15010007\n", "decision": "INCLUDED", "name": "Fig. S1", "studyID": "ot_2442", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BELOKOBYLSKIJ, S. A., ZALDIVAR-RIVER\u00d3N, A., & QUICKE, D. L. J. (2004). Phylogeny of the genera of the parasitic wasps subfamily Doryctinae (Hymenoptera: Braconidae) based on morphological evidence. Zoological Journal of the Linnean Society, 142(3), 369\u2013404. https://doi.org/10.1111/j.1096-3642.2004.00133.x\n", "decision": "INCLUDED", "name": "Fig. 12", "studyID": "ot_2443", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Belshaw, R., & Quicke, D. L. J. (1997). A Molecular Phylogeny of the Aphidiinae (Hymenoptera: Braconidae). Molecular Phylogenetics and Evolution, 7(3), 281\u2013293. https://doi.org/10.1006/mpev.1996.0400\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2444", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bennett, A. M. R. (2001). Phylogeny of Agriotypinae (Hymenoptera: Ichneumonidae), with comments on the subfamily relationships of the basal Ichneumonidae. Systematic Entomology, 26(3), 329\u2013356. Portico. https://doi.org/10.1046/j.0307-6970.2001.00155.x\n", "decision": "INCLUDED", "name": "Fig. 17", "studyID": "ot_2445", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bennett, A. M. R., Cardinal, S., Gauld, I. D., & Wahl, D. B. (2019). Phylogeny of the subfamilies of Ichneumonidae (Hymenoptera). Journal of Hymenoptera Research, 71, 1\u2013156. https://doi.org/10.3897/jhr.71.32375\n", "decision": "INCLUDED", "name": "Fig. 124", "studyID": "ot_2446", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bernhard, D., Beutel, R., Komarek, A., & Ribera, I. (2009). Phylogenetic analysis of Hydrophiloidea (Coleoptera: Polyphaga) based on molecular data and morphological characters of adults and immature stages. Insect Systematics &amp; Evolution, 40(1), 3\u201341. https://doi.org/10.1163/187631209x416741\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2447", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from L\u00f3pez Berrizbeitia, M. F., Hastriter, M. W., Barquez, R. M., & D\u00edaz, M. M. (2019). Fleas of the genus Tetrapsyllus (Siphonaptera:Rhopalopsyllidae) associated with rodents from Northwestern Argentina. International Journal for Parasitology: Parasites and Wildlife, 9, 80\u201389. https://doi.org/10.1016/j.ijppaw.2019.03.001\n", "decision": "INCLUDED", "name": "Fig. 4a", "studyID": "ot_2448", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Deng, J., Stroi\u0144ski, A., Szwedo, J., Ghanavi, H. R., Yapar, E., Franco, D. C., Prus\u2010Frankowska, M., Michalik, A., Wahlberg, N., & \u0141ukasik, P. (2024). Phylogenomic insights into the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha). Systematic Entomology. Portico. https://doi.org/10.1111/syen.12666\n", "decision": "INCLUDED", "name": "fulgo_aa_285sp.contree", "studyID": "ot_2449", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from de Oliveira, J. V. L. C., & Zeppelini, D. (2024). A New Perspective to Oncopodura (Collembola: Oncopoduridae) Groups Based on Appendicular Morphology. Neotropical Entomology, 53(6), 1220\u20131259. https://doi.org/10.1007/s13744-024-01203-z\n", "decision": "INCLUDED", "name": "Fig. 31 left, MP", "studyID": "ot_2452", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Beutel, R. G., & H\u00f6rnschemeyer, T. (2002). Larval morphology and phylogenetic position of Micromalthus debilis LeConte (Coleoptera: Micromalthidae). Systematic Entomology, 27(2), 169\u2013190. Portico. https://doi.org/10.1046/j.1365-3113.2002.00172.x\n", "decision": "INCLUDED", "name": "Fig. 13", "studyID": "ot_2453", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Beutel, R. G., & Leschen, R. A. B. (2005). Phylogenetic analysis of Staphyliniformia (Coleoptera) based on characters of larvae and adults. Systematic Entomology, 30(4), 510\u2013548. Portico. https://doi.org/10.1111/j.1365-3113.2005.00293.x\n", "decision": "INCLUDED", "name": "Fig. 15", "studyID": "ot_2454", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BEUTEL, R. G., & \u015aLIPI\u0143SKI, S. A. (2001). Comparative study of head structures of larvae of Sphindidae and Protocucujidae (Coleoptera: Cucujoidea). European Journal of Entomology, 98(2), 219\u2013232. https://doi.org/10.14411/eje.2001.039\n", "decision": "INCLUDED", "name": "Fig. 19", "studyID": "ot_2455", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BEUTEL, R. G., FRIEDRICH, F., & ASP\u00d6CK, U. (2010). The larval head of Nevrorthidae and the phylogeny of Neuroptera (Insecta). Zoological Journal of the Linnean Society, 158(3), 533\u2013562. https://doi.org/10.1111/j.1096-3642.2009.00560.x\n", "decision": "INCLUDED", "name": "Fig. 11", "studyID": "ot_2457", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Beza-Beza CF, Jim\u00e9nez-Ferbans L, McKenna DD (2020) Phylogeny and Systematics of Wood-Degrading Neotro\u00adpical Bess Beetles (Coleoptera: Passalidae: Passalinae). Arthropod Systematics & Phylogeny, 78, 287-308.\n\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2458", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Blahnik, R. J. (2002). Systematics of Otarrha, a new Neotropical subgenus of Chimarra (Trichoptera: Philopotamidae). Systematic Entomology, 27(1), 65\u2013130. Portico. https://doi.org/10.1046/j.0307-6970.2001.00166.x\n", "decision": "INCLUDED", "name": "Fig. 59", "studyID": "ot_2460", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Blaimer, B. B., Brady, S. G., Schultz, T. R., Lloyd, M. W., Fisher, B. L., & Ward, P. S. (2015). Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants. BMC Evolutionary Biology, 15(1). https://doi.org/10.1186/s12862-015-0552-5\n", "decision": "INCLUDED", "name": "Addit. 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BMC Evolutionary Biology, 20(1). https://doi.org/10.1186/s12862-020-01716-2\n", "decision": "INCLUDED", "name": "125_70_unpart.tre", "studyID": "ot_2470", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BLASCHKE, J. D., STIREMAN, J. O., O\u2019HARA, J. E., CERRETTI, P., & MOULTON, J. K. (2018). Molecular phylogenetics and piercer evolution in the bug\u2010killing flies (Diptera: Tachinidae: Phasiinae). Systematic Entomology, 43(1), 218\u2013238. Portico. https://doi.org/10.1111/syen.12272\n", "decision": "INCLUDED", "name": "Fig. S1", "studyID": "ot_2472", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bocak, L., & Bocakova, M. (2008). Phylogeny and Classification of the Family Lycidae (Insecta: Coleoptera). Annales Zoologici, 58(4), 695\u2013720. https://doi.org/10.3161/000345408x396639\n", "decision": "INCLUDED", "name": "Fig. 2", "studyID": "ot_2473", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bocakova, M., Constantin, R., & Bocak, L. (2011). Molecular phylogenetics of the melyrid lineage (Coleoptera: Cleroidea). Cladistics, 28(2), 117\u2013129. Portico. https://doi.org/10.1111/j.1096-0031.2011.00368.x\n", "decision": "INCLUDED", "name": "Fig. 2", "studyID": "ot_2474", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BOCEK, M., FANCELLO, L., MOTYKA, M., BOCAKOVA, M., & BOCAK, L. (2017). The molecular phylogeny of Omalisidae (Coleoptera) defines the family limits and demonstrates low dispersal propensity and ancient vicariance patterns. Systematic Entomology, 43(2), 250\u2013261. Portico. https://doi.org/10.1111/syen.12271\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2475", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bologna, M. A., & Pinto, J. D. (2001). Phylogenetic studies of Meloidae (Coleoptera), with emphasis on the evolution of phoresy. Systematic Entomology, 26(1), 33\u201372. Portico. https://doi.org/10.1046/j.1365-3113.2001.00132.x\n", "decision": "INCLUDED", "name": "Fig. 10", "studyID": "ot_2476", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang F, Bellini BC, Soto-Adames FN (2019) New insights into the systematics of Entomobryoidea (Collembola: Entomobryomorpha): First instar chaetotaxy, homology and classification. Zoological Systematics, 44, 249-278. ", "decision": "INCLUDED", "name": "Fig. S25, ML", "studyID": "ot_2481", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bologna, M. A., Oliverio, M., Pitzalis, M., & Mariottini, P. (2008). Phylogeny and evolutionary history of the blister beetles (Coleoptera, Meloidae). Molecular Phylogenetics and Evolution, 48(2), 679\u2013693. https://doi.org/10.1016/j.ympev.2008.04.019\n", "decision": "INCLUDED", "name": "Fig. 5b", "studyID": "ot_2483", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Borissov, S. B., Heller, K., \u00c7\u0131plak, B., & Chobanov, D. P. (2023). Origin, evolution and systematics of the genusPoecilimon(Orthoptera: Tettigoniidae)\u2014An outburst of diversification in the Aegean area. Systematic Entomology, 48(1), 198\u2013220. Portico. https://doi.org/10.1111/syen.12580\n", "decision": "INCLUDED", "name": "Poecilimon_concatenation_phylogeny_BayesianInference.tre", "studyID": "ot_2484", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BORKENT, A. (2014). The Pupae of the Biting Midges of the World (Diptera: Ceratopogonidae), With a Generic Key and Analysis of the Phylogenetic Relationships Between Genera. Zootaxa, 3879(1). https://doi.org/10.11646/zootaxa.3879.1.1\n", "decision": "INCLUDED", "name": "Figs. 80,81", "studyID": "ot_2486", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Borkent, A. (2019). The Phylogenetic Relationships of Cretaceous Biting Midges, with a Key to All Known Genera (Diptera: Ceratopogonidae). American Museum Novitates, 2019(3921), 1. https://doi.org/10.1206/3921.1\n", "decision": "INCLUDED", "name": "Fig. 10", "studyID": "ot_2487", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Borowiec, M. L., Rabeling, C., Brady, S. G., Fisher, B. L., Schultz, T. R., & Ward, P. S. (2019). Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants. Molecular Phylogenetics and Evolution, 134, 111\u2013121. https://doi.org/10.1016/j.ympev.2019.01.024\n", "decision": "INCLUDED", "name": "Fig. S17", "studyID": "ot_2488", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bossert, S., Wood, T. J., Patiny, S., Michez, D., Almeida, E. A. B., Minckley, R. L., Packer, L., Neff, J. L., Copeland, R. S., Straka, J., Pauly, A., Griswold, T., Brady, S. G., Danforth, B. N., & Murray, E. A. (2021). Phylogeny, biogeography and diversification of the mining bee family Andrenidae. Systematic Entomology, 47(2), 283\u2013302. Portico. https://doi.org/10.1111/syen.12530\n", "decision": "INCLUDED", "name": "MB_100_most_informative_consensus.tre", "studyID": "ot_2489", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Boudinot, B. E., Borowiec, M. L., & Prebus, M. M. (2022). Phylogeny, evolution, and classification of the ant genus Lasius, the tribe Lasiini and the subfamily Formicinae (Hymenoptera: Formicidae). Systematic Entomology, 47(1), 113\u2013151. Portico. https://doi.org/10.1111/syen.12522\n", "decision": "INCLUDED", "name": "Fig. S6", "studyID": "ot_2490", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Viana, J. H., Roza, A. S., Vaz, S., Powell, G., & da Silveira, L. F. L. (2025). A new firefly genus from South America, with seven new species, a new combination, and notes on the phylogeny of Lampyrinae: Lucidotini (Coleoptera: Lampyridae). PeerJ, 13, e18967. Portico. https://doi.org/10.7717/peerj.18967\n", "decision": "INCLUDED", "name": "S6_Bayesian_Consensus_tree_file.tre", "studyID": "ot_2496", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BOYLE, J. H., KALISZEWSKA, Z. A., ESPELAND, M., SUDERMAN, T. R., FLEMING, J., HEATH, A., & PIERCE, N. E. (2014). Phylogeny of the <scp>A</scp>phnaeinae: myrmecophilous <scp>A</scp>frican butterflies with carnivorous and herbivorous life histories. Systematic Entomology, 40(1), 169\u2013182. Portico. https://doi.org/10.1111/syen.12098\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2497", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BRABY, M. F., & PIERCE, N. E. (2006). Systematics, biogeography and diversification of the Indo\u2010Australian genusDeliasH\u00fcbner (Lepidoptera: Pieridae): phylogenetic evidence supports an \u2018out\u2010of\u2010Australia\u2019 origin. Systematic Entomology, 32(1), 2\u201325. Portico. https://doi.org/10.1111/j.1365-3113.2006.00349.x\n", "decision": "INCLUDED", "name": "Fig. 4b", "studyID": "ot_2498", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BRABY, M. F., VILA, R., & PIERCE, N. E. (2006). Molecular phylogeny and systematics of the Pieridae (Lepidoptera: Papilionoidea): higher classification and biogeography. Zoological Journal of the Linnean Society, 147(2), 239\u2013275. https://doi.org/10.1111/j.1096-3642.2006.00218.x\n", "decision": "INCLUDED", "name": "Fig. 6, ML", "studyID": "ot_2499", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bradford, T. M., Ruta, R., Cooper, S. J. B., Libonatti, M. L., & Watts, C. H. S. (2022). Evolutionary history of the Australasian Scirtinae (Scirtidae; Coleoptera) inferred from ultraconserved elements. Invertebrate Systematics, 36(4), 291\u2013305. https://doi.org/10.1071/is21053\n", "decision": "INCLUDED", "name": "Fig. S3, BI", "studyID": "ot_2500", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BRADLER, S., ROBERTSON, J. A., & WHITING, M. F. (2014). A molecular phylogeny of <scp>P</scp>hasmatodea with emphasis on <scp>N</scp>ecrosciinae, the most species\u2010rich subfamily of stick insects. Systematic Entomology, 39(2), 205\u2013222. Portico. https://doi.org/10.1111/syen.12055\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2501", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bradler, S., Cliquennois, N., & Buckley, T. R. (2015). Single origin of the Mascarene stick insects: ancient radiation on sunken islands? BMC Evolutionary Biology, 15(1). https://doi.org/10.1186/s12862-015-0478-y\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2502", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zheng, Y.-N., Gu, J.-J., He, Z.-Q., Huang, H., & Ma, L.-B. (2023). On a taxonomic feature that has been overestimated in classification practice: an integrative taxonomic revision of Stephoblemmus Saussure, 1877 based on morphology and molecular phylogeny (Orthoptera: Grylloidea; Gryllidae; Gryllinae). Arthropod Systematics &amp; Phylogeny, 81, 761\u2013779. https://doi.org/10.3897/asp.81.e104772\n", "decision": "INCLUDED", "name": "Fig 2", "studyID": "ot_2503", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, F., Ma, Y., & Greenslade, P. (2017). New Australian Paronellidae (Collembola) reveal anomalies in existing tribal diagnoses. Invertebrate Systematics, 31(4), 375. https://doi.org/10.1071/is16073\n", "decision": "INCLUDED", "name": "Fig. A1 left, BI", "studyID": "ot_2506", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Brady, S. G., & Ward, P. S. (2005). Morphological phylogeny of army ants and other dorylomorphs (Hymenoptera: Formicidae). Systematic Entomology, 30(4), 593\u2013618. Portico. https://doi.org/10.1111/j.1365-3113.2005.00290.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2507", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BRAKE, I., & MATHIS, W. N. (2007). Revision of the genus Australimyza Harrison (Diptera: Australimyzidae). Systematic Entomology, 32(2), 252\u2013275. Portico. https://doi.org/10.1111/j.1365-3113.2006.00363.x\n", "decision": "INCLUDED", "name": "Fig. 17, MP", "studyID": "ot_2508", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Breitkreuz, L. C. V., Garz\u00f3n-Ordu\u00f1a, I. J., Winterton, S. L., & Engel, M. S. (2021). Phylogeny of Chrysopidae (Neuroptera), with emphasis on morphological trait evolution. Zoological Journal of the Linnean Society, 194(4), 1374\u20131395. https://doi.org/10.1093/zoolinnean/zlab024\n", "decision": "INCLUDED", "name": "Fig. 5, BI", "studyID": "ot_2510", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PACKER, L. (2007). Phylogeny and classification of the Xeromelissinae (Hymenoptera: Apoidea, Colletidae) with special emphasis on the genus Chilicola. Systematic Entomology, 33(1), 72\u201396. Portico. https://doi.org/10.1111/j.1365-3113.2007.00398.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2511", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Brower, A. V. Z., Freitas, A. V. L., Lee, M., Silva\u2010Brand\u00e3o, K. L., Whinnett, A., & Willmott, K. R. (2006). Phylogenetic relationships among the Ithomiini (Lepidoptera: Nymphalidae) inferred from one mitochondrial and two nuclear gene regions. Systematic Entomology, 31(2), 288\u2013301. Portico. https://doi.org/10.1111/j.1365-3113.2006.00321.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2512", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Brown, B., Dugdale, J. S., Emberson, R. M., & Paterson, A. M. (2000). Phylogeny of New Zealand hepialid moths (Lepidoptera: Hepialidae) inferred from a cladistic analysis of morphological data. Systematic Entomology, 25(1), 1\u201314. Portico. https://doi.org/10.1046/j.1365-3113.2000.00089.x\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_2513", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Br\u00fcstle, L., Alaruikka, D., Muona, J., & Ter\u00e4v\u00e4inen, M. (2010). The phylogeny of the Pantropical genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae). Cladistics, 26(1), 14\u201322. Portico. https://doi.org/10.1111/j.1096-0031.2009.00268.x\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_2514", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Tierney, S. M., Sanjur, O., Grajales, G. G., Santos, L. M., Bermingham, E., & Wcislo, W. T. (2011). Photic niche invasions: phylogenetic history of the dim-light foraging augochlorine bees (Halictidae). Proceedings of the Royal Society B: Biological Sciences, 279(1729), 794\u2013803. https://doi.org/10.1098/rspb.2011.1355\n", "decision": "INCLUDED", "name": "Fig 1a", "studyID": "ot_2515", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cosandey, V., Konvi\u010dka, O., & Toussaint, E. F. A. (2024). Legacy molecular phylogenetics suggests restricting the concept of Melandryidae and resurrecting Osphyidae (Coleoptera: Tenebrionoidea). Arthropod Systematics &amp; Phylogeny, 82, 621\u2013627. https://doi.org/10.3897/asp.82.e131738\n", "decision": "INCLUDED", "name": "Appendix+3+-+IQ-TREE+best+scoring+ML+topology.tre", "studyID": "ot_2518", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Almeida, E. A. B., Bossert, S., Danforth, B. N., Porto, D. S., Freitas, F. V., Davis, C. C., Murray, E. A., Blaimer, B. B., Spasojevic, T., Str\u00f6her, P. R., Orr, M. C., Packer, L., Brady, S. G., Kuhlmann, M., Branstetter, M. G., & Pie, M. R. (2023). The evolutionary history of bees in time and space. Current Biology, 33(16), 3409-3422.e6. https://doi.org/10.1016/j.cub.2023.07.005\n", "decision": "INCLUDED", "name": "MrBayes_20_MCL", "studyID": "ot_2517", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from MIC\u00d3, E., MOR\u00d3N, M. \u00c1., \u0160\u00cdPEK, P., & GALANTE, E. (2007). Larval morphology enhances phylogenetic reconstruction in Cetoniidae (Coleoptera: Scarabaeoidea) and allows the interpretation of the evolution of larval feeding habits. Systematic Entomology, 33(1), 128\u2013144. Portico. https://doi.org/10.1111/j.1365-3113.2007.00399.x\n", "decision": "INCLUDED", "name": "Fig. 15, MP", "studyID": "ot_2519", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bucek, A., \u0160obotn\u00edk, J., He, S., Shi, M., McMahon, D. P., Holmes, E. C., Roisin, Y., Lo, N., & Bourguignon, T. (2019). Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies. Current Biology, 29(21), 3728-3734.e4. https://doi.org/10.1016/j.cub.2019.08.076\n", "decision": "INCLUDED", "name": "Fig. S2F, ML", "studyID": "ot_2520", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bu\u010dek, A., Wang, M., \u0160obotn\u00edk, J., Hellemans, S., Sillam-Duss\u00e8s, D., Mizumoto, N., Stibl\u00edk, P., Clitheroe, C., Lu, T., Gonz\u00e1lez Plaza, J. J., Mohagan, A., Rafanomezantsoa, J.-J., Fisher, B., Engel, M. S., Roisin, Y., Evans, T. A., Scheffrahn, R., & Bourguignon, T. (2022). Molecular Phylogeny Reveals the Past Transoceanic Voyages of Drywood Termites (Isoptera, Kalotermitidae). Molecular Biology and Evolution, 39(5). https://doi.org/10.1093/molbev/msac093\n", "decision": "INCLUDED", "name": "IQTREE_REV2.nwk", "studyID": "ot_2521", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Buck, M. (2006). A new family and genus of acalypterate flies from the Neotropical region, with a phylogenetic analysis of Carnoidea family relationships (Diptera, Schizophora). Systematic Entomology, 31(3), 377\u2013404. Portico. https://doi.org/10.1111/j.1365-3113.2006.00328.x\n", "decision": "INCLUDED", "name": "Fig. 13a", "studyID": "ot_2522", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Buder, G., Grossmann, C., Hundsdoerfer, A., & Klass, K.-D. (2008). A contribution to the phylogeny of the Ciidae and its relationships with other cucujoid and tenebrionoid beetles (Coleoptera: Cucujiformia). Arthropod Systematics &amp; Phylogeny, 66(2), 165\u2013190. https://doi.org/10.3897/asp.66.e31683\n", "decision": "INCLUDED", "name": "Fig. 13", "studyID": "ot_2524", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Budrys, E., Orlovskyt\u0117, S., Lazauskait\u0117, M., & Budrien\u0117, A. (2023). Ancistroceruswasps (Hymenoptera, Vespidae) from the Centre of Europe: Phylogeny, cryptic species, neutral and non\u2010neutral markers. Zoologica Scripta, 52(5), 454\u2013474. Portico. https://doi.org/10.1111/zsc.12599\n", "decision": "INCLUDED", "name": "Fig. 4b", "studyID": "ot_2525", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Buenaventura, E. (2021). Museomics and phylogenomics with protein-encoding ultraconserved elements illuminate the evolution of life history and phallic morphology of flesh flies (Diptera: Sarcophagidae). BMC Ecology and Evolution, 21(1). https://doi.org/10.1186/s12862-021-01797-7\n", "decision": "INCLUDED", "name": "Fig. 1a", "studyID": "ot_2526", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Buenaventura, E., Lloyd, M. W., Perilla L\u00f3pez, J. M., Gonz\u00e1lez, V. L., Thomas\u2010Cabianca, A., & Dikow, T. (2020). Protein\u2010encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera: Calyptratae). Systematic Entomology, 46(1), 5\u201327. Portico. https://doi.org/10.1111/syen.12443\n", "decision": "INCLUDED", "name": "oest_50per_RAxML.tre", "studyID": "ot_2527", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ARNEDO, M. A., OROM\u00cd, P., MART\u00cdN DE ABREU, S., & RIBERA, C. (2007). Biogeographical and evolutionary patterns in the Macaronesian shield\u2010backed katydid genus Calliphona Krauss, 1892 (Orthoptera: Tettigoniidae) and allies as inferred from phylogenetic analyses of multiple mitochondrial genes. Systematic Entomology, 33(1), 145\u2013158. Portico. https://doi.org/10.1111/j.1365-3113.2007.00393.x\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_2528", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Buenaventura E., & Pape T. 2015. Phylogeny of the Peckia-genus group: evolution of male genitalia in the major necrophagous guild of Neotropical flesh flies (Diptera: Sarcophagidae). Organism, Diversity and Evolution, : 1-31.", "decision": "INCLUDED", "name": "Figs. 8 and S1  ", "studyID": "ot_1535", "treeID": "Tr85876"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bueter, C., Weckstein, J., Johnson, K. P., Bates, J. M., & Gordon, C. E. (2009). Comparative Phylogenetic Histories of Two Louse Genera Found on Catharus Thrushes and Other Birds. Journal of Parasitology, 95(2), 295\u2013307. https://doi.org/10.1645/ge-1642.1\n", "decision": "INCLUDED", "name": "Figs. 1,2", "studyID": "ot_2529", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bugrov, A., Novikova, O., Mayorov, V., Adkison, L., & Blinov, A. (2005). Molecular phylogeny of Palaearctic genera of Gomphocerinae grasshoppers (Orthoptera, Acrididae). Systematic Entomology, 31(2), 362\u2013368. Portico. https://doi.org/10.1111/j.1365-3113.2005.00317.x\n", "decision": "INCLUDED", "name": "Fig. 2, NJ", "studyID": "ot_2530", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BURCKHARDT, D., & OUVRARD, D. (2006). The taxonomy, biogeography and host plant relationships of jumping plant\u2010lice (Hemiptera: Psyllidae) associated with creosote bushes (Larrea spp., Zygophyllaceae). Systematic Entomology, 32(1), 136\u2013155. Portico. https://doi.org/10.1111/j.1365-3113.2006.00352.x\n", "decision": "INCLUDED", "name": "Fig. 9, MP", "studyID": "ot_2531", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Burks, R. A., Heraty, J. M., Gebiola, M., & Hansson, C. (2011). Combined molecular and morphological phylogeny of Eulophidae (Hymenoptera: Chalcidoidea), with focus on the subfamily Entedoninae. Cladistics, 27(6), 581\u2013605. https://doi.org/10.1111/j.1096-0031.2011.00358.x\n", "decision": "INCLUDED", "name": "Fig. 46, BI", "studyID": "ot_2532", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bybee, S. M., Taylor, S. D., Riley Nelson, C., & Whiting, M. F. (2004). A phylogeny of robber flies (Diptera: Asilidae) at the subfamilial level: molecular evidence. Molecular Phylogenetics and Evolution, 30(3), 789\u2013797. https://doi.org/10.1016/s1055-7903(03)00253-7\n", "decision": "INCLUDED", "name": "Fig. 4, ML", "studyID": "ot_2533", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bybee, S. M., Ogden, T. H., Branham, M. A., & Whiting, M. F. (2008). Molecules, morphology and fossils: a comprehensive approach to odonate phylogeny and the evolution of the odonate wing. Cladistics, 24(4), 477\u2013514. Portico. https://doi.org/10.1111/j.1096-0031.2007.00191.x\n", "decision": "INCLUDED", "name": "Fig. 4, MP", "studyID": "ot_2534", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bybee, S. M., Kalkman, V. J., Erickson, R. J., Frandsen, P. B., Breinholt, J. W., Suvorov, A., Dijkstra, K.-D. B., Cordero-Rivera, A., Skevington, J. H., Abbott, J. C., Sanchez Herrera, M., Lemmon, A. R., Moriarty Lemmon, E., & Ware, J. L. (2021). Phylogeny and classification of Odonata using targeted genomics. Molecular Phylogenetics and Evolution, 160, 107115. https://doi.org/10.1016/j.ympev.2021.107115\n", "decision": "INCLUDED", "name": "Fig. 2a, ML", "studyID": "ot_2535", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from REGIER, J. C., COOK, C. P., MITTER, C., & HUSSEY, A. (2008). A phylogenetic study of the \u2018bombycoid complex\u2019 (Lepidoptera) using five protein\u2010coding nuclear genes, with comments on the problem of macrolepidopteran phylogeny. Systematic Entomology, 33(1), 175\u2013189. Portico. https://doi.org/10.1111/j.1365-3113.2007.00409.x\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2536", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cabrero-Sa\u00f1udo, F.-J., & Zardoya, R. (2004). Phylogenetic relationships of Iberian Aphodiini (Coleoptera: Scarabaeidae) based on morphological and molecular data. Molecular Phylogenetics and Evolution, 31(3), 1084\u20131100. https://doi.org/10.1016/j.ympev.2003.10.019\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2537", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CAMERON, S. L., LAMBKIN, C. L., BARKER, S. C., & WHITING, M. F. (2006). A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Systematic Entomology, 32(1), 40\u201359. Portico. https://doi.org/10.1111/j.1365-3113.2006.00355.x\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2540", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cao, J., Wang, Y., Guo, X., Wang, G., Li, W., & Mur\u00e1nyi, D. (2021). Two Complete Mitochondrial Genomes From Leuctridae (Plecoptera: Nemouroidea): Implications for the Phylogenetic Relationships Among Stoneflies. Journal of Insect Science, 21(1). https://doi.org/10.1093/jisesa/ieab009\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2541", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Callahan, M. S., & McPeek, M. A. (2016). Multi-locus phylogeny and divergence time estimates of Enallagma damselflies (Odonata: Coenagrionidae). Molecular Phylogenetics and Evolution, 94, 182\u2013195. https://doi.org/10.1016/j.ympev.2015.08.013\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2544", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cardinal, S., Straka, J., & Danforth, B. N. (2010). Comprehensive phylogeny of apid bees reveals the evolutionary origins and antiquity of cleptoparasitism. Proceedings of the National Academy of Sciences, 107(37), 16207\u201316211. https://doi.org/10.1073/pnas.1006299107\n", "decision": "INCLUDED", "name": "Fig. S1, BI", "studyID": "ot_2545", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cardinal, S., Buchmann, S. L., & Russell, A. L. (2018). The evolution of floral sonication, a pollen foraging behavior used by bees (Anthophila). Evolution, 72(3), 590\u2013600. Portico. https://doi.org/10.1111/evo.13446\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2546", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ZWICK, A. (2008). Molecular phylogeny of Anthelidae and other bombycoid taxa (Lepidoptera: Bombycoidea). Systematic Entomology, 33(1), 190\u2013209. Portico. https://doi.org/10.1111/j.1365-3113.2007.00410.x\n", "decision": "INCLUDED", "name": "Fig. 4, ML", "studyID": "ot_2547", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CASTRO, L. R., & DOWTON, M. (2006). Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers. Systematic Entomology, 32(1), 60\u201369. Portico. https://doi.org/10.1111/j.1365-3113.2006.00356.x\n", "decision": "INCLUDED", "name": "Fig. 2C", "studyID": "ot_2548", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ceotto, P. C., & Mejdalani, G. (2004). Phylogenetic analysis of the Abana group of genera (Hemiptera: Cicadellidae: Cicadellinae: Proconiini). Systematic Entomology, 30(3), 480\u2013496. Portico. https://doi.org/10.1111/j.1365-3113.2004.00280.x\n", "decision": "INCLUDED", "name": "Fig. 44, MP", "studyID": "ot_2550", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CERRETTI, P., O\u2019HARA, J. E., WOOD, D. M., SHIMA, H., INCLAN, D. J., & STIREMAN, J. O. (2014). Signal through the noise? Phylogeny of the <scp>T</scp>achinidae (<scp>D</scp>iptera) as inferred from morphological evidence. Systematic Entomology, 39(2), 335\u2013353. Portico. https://doi.org/10.1111/syen.12062\n", "decision": "INCLUDED", "name": "File S4, MP", "studyID": "ot_2551", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chamorro, M. L., & Holzenthal, R. W. (2011). Phylogeny of Polycentropodidae Ulmer, 1903 (Trichoptera:Annulipalpia:Psychomyioidea) inferred from larval, pupal and adult characters. Invertebrate Systematics, 25(3), 219. https://doi.org/10.1071/is10024\n", "decision": "INCLUDED", "name": "Fig. 15, MP", "studyID": "ot_2552", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from HARDY, N. B., GULLAN, P. J., & HODGSON, C. J. (2008). A subfamily\u2010level classification of mealybugs (Hemiptera: Pseudococcidae) based on integrated molecular and morphological data. Systematic Entomology, 33(1), 51\u201371. Portico. https://doi.org/10.1111/j.1365-3113.2007.00408.x\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2553", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chang, H., & Huang, Y. (2016). The complete mitochondrial genome of the Hieroglyphus tonkinensis (Orthoptera: Acrididae). Mitochondrial DNA Part B, 1(1), 534\u2013535. https://doi.org/10.1080/23802359.2016.1197067\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2554", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chatzimanolis, S. (2005). Phylogeny of the neotropical rove beetle genus Nordus (Coleoptera: Staphylinidae) with a special reference to the evolution of coloration and secondary sexual characters. Systematic Entomology, 30(2), 267\u2013280. Portico. https://doi.org/10.1111/j.1365-3113.2004.00274.x\n", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "ot_2555", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Che, Y., Wang, D., Shi, Y., Du, X., Zhao, Y., Lo, N., & Wang, Z. (2016). A global molecular phylogeny and timescale of evolution for Cryptocercus woodroaches. Molecular Phylogenetics and Evolution, 98, 201\u2013209. https://doi.org/10.1016/j.ympev.2016.02.005\n", "decision": "INCLUDED", "name": "Fig. 3, ML", "studyID": "ot_2557", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Che, L., Zhang, P., Deng, S., Escalona, H. E., Wang, X., Li, Y., Pang, H., Vandenberg, N., \u015alipi\u0144ski, A., Tomaszewska, W., & Liang, D. (2021). New insights into the phylogeny and evolution of lady beetles (Coleoptera: Coccinellidae) by extensive sampling of genes and species. Molecular Phylogenetics and Evolution, 156, 107045. https://doi.org/10.1016/j.ympev.2020.107045\n", "decision": "INCLUDED", "name": "Fig. S2", "studyID": "ot_2558", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, Z.-T. (2022). \ufeffComparative mitogenomic analysis of two earwigs (Insecta, Dermaptera) and the preliminary phylogenetic implications. ZooKeys, 1087, 105\u2013122. https://doi.org/10.3897/zookeys.1087.78998\n", "decision": "INCLUDED", "name": "Fig. 10 left, BI", "studyID": "ot_2559", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, Y., Giles, K. L., & Greenstone, M. H. (2002). Molecular Evidence for a Species Complex in the Genus &lt;I&gt;Aphelinus&lt;/I&gt; (Hymenoptera: Aphelinidae), with Additional Data on Aphidiine Phylogeny (Hymenoptera: Braconidae). Annals of the Entomological Society of America, 95(1), 29\u201334. https://doi.org/10.1603/0013-8746(2002)095[0029:mefasc]2.0.co;2\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2560", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, B., Butlin, R. K., & Harbach, R. E. (2003). Molecular phylogenetics of the Oriental members of \u2028the Myzomyia Series of Anopheles subgenus Cellia (Diptera: Culicidae) inferred from nuclear and mitochondrial DNA sequences. Systematic Entomology, 28(1), 57\u201369. Portico. https://doi.org/10.1046/j.1365-3113.2003.00200.x\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2561", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, Y., Xiao, H., Fu, J., & Huang, D.-W. (2004). A molecular phylogeny of eurytomid wasps inferred from DNA sequence data of 28S, 18S, 16S, and COI genes. Molecular Phylogenetics and Evolution, 31(1), 300\u2013307. https://doi.org/10.1016/s1055-7903(03)00282-3\n", "decision": "INCLUDED", "name": "Fig. 1B, MP", "studyID": "ot_2562", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, Z., Zhou, S. Y., Ye, D., Chen, Y., & Lu, C. (2013). Molecular Phylogeny of the Ant Subfamily Formicinae (Hymenoptera, Formicidae) from China Based on Mitochondrial Genes. Sociobiology, 60(2), 135\u2013144. https://doi.org/10.13102/sociobiology.v60i2.135-144\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2563", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, S., Li, F.-H., Lan, X.-E., & You, P. (2016). The complete mitochondrial genome of Pycnarmon lactiferalis (Lepidoptera: Crambidae). Mitochondrial DNA Part B, 1(1), 638\u2013639. https://doi.org/10.1080/23802359.2016.1214551\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2564", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, Y., Shi, X., Li, D., Chen, B., Zhang, P., Wu, N., & Xu, Z. (2016). The complete nucleotide sequence of the mitochondrial genome of Calliphora chinghaiensis (Diptera: Calliphoridae). Mitochondrial DNA Part B, 1(1), 397\u2013398. https://doi.org/10.1080/23802359.2016.1174088\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2565", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, Z.-T., L\u00fc, L., Lu, M.-X., & Du, Y.-Z. (2017). Comparative mitogenomic analysis of Aposthonia borneensis and Aposthonia japonica (Embioptera: Oligotomidae) reveals divergent evolution of webspinners. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-09003-9\n", "decision": "INCLUDED", "name": "Fig. 7, BI", "studyID": "ot_2566", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from WEIRAUCH, C. (2008). Cladistic analysis of Reduviidae (Heteroptera: Cimicomorpha) based on morphological characters. Systematic Entomology, 33(2), 229\u2013274. Portico. https://doi.org/10.1111/j.1365-3113.2007.00417.x\n", "decision": "INCLUDED", "name": "Fig. 25, MP", "studyID": "ot_2567", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CHEN, Y.-Z., DENG, W.-A., WANG, J.-M., LIN, L.-L., & ZHOU, S.-Y. (2018). Phylogenetic relationships of Scelimeninae genera (Orthoptera: Tetrigoidea) based on COI, 16S rRNA and 18S rRNA gene sequences. Zootaxa, 4482(2). https://doi.org/10.11646/zootaxa.4482.2.11\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2568", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, Z.-T., Zhao, M.-Y., Xu, C., & Du, Y.-Z. (2018). Molecular phylogeny of Systellognatha (Plecoptera: Arctoperlaria) inferred from mitochondrial genome sequences. International Journal of Biological Macromolecules, 111, 542\u2013547. https://doi.org/10.1016/j.ijbiomac.2018.01.065\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2569", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chen, B., Liu, Y., Lu, X., Jiang, D., Wang, X., Zhang, Q., Yang, G., & Yang, X. (2023). Complete mitochondrial genome of Ctenophthalmus quadratus and Stenischia humilis in China provides insights into fleas phylogeny. Frontiers in Veterinary Science, 10. https://doi.org/10.3389/fvets.2023.1255017\n", "decision": "INCLUDED", "name": "Fig. 5", "studyID": "ot_2572", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chiotis, M., Jermiin, L. S., & Crozier, R. H. (2000). A Molecular Framework for the Phylogeny of the Ant Subfamily Dolichoderinae. Molecular Phylogenetics and Evolution, 17(1), 108\u2013116. https://doi.org/10.1006/mpev.2000.0821\n", "decision": "INCLUDED", "name": "Fig. 3c, ML", "studyID": "ot_2574", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chu, H., Wu, Z., Zhang, H., Li, C., Wang, G., Zhou, M., & Zhao, T. (2016). Sequencing and analysis of the complete mitochondrial genome of Culex tritaeniorhynchus (Dipera: Culicidae) in China. Mitochondrial DNA Part B, 1(1), 365\u2013366. https://doi.org/10.1080/23802359.2016.1168719\n", "decision": "INCLUDED", "name": "Fig. 1", "studyID": "ot_2575", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CIGLIANO, M. M. (2006). Review of the South American genus Eurotettix Bruner (Orthoptera, Acridoidea, Melanoplinae). Systematic Entomology, 32(1), 176\u2013195. Portico. https://doi.org/10.1111/j.1365-3113.2006.00353.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2576", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from \u00c7 \u0131plak, B. (2000). Systematics and phylogeny of Parapholidoptera (Orthoptera: Tettigoniidae: Tettigoniinae). Systematic Entomology, 25(4), 411\u2013436. Portico. https://doi.org/10.1111/j.1365-3113.2000.00112.x\n", "decision": "INCLUDED", "name": "Fig. 21, MP", "studyID": "ot_2577", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from \u010ckrki\u0107, J., Petrovi\u0107, A., Koci\u0107, K., Mitrovi\u0107, M., Kavallieratos, N. G., van Achterberg, C., Hebert, P. D. N., & Tomanovi\u0107, \u017d. (2020). Phylogeny of the Subtribe Monoctonina (Hymenoptera, Braconidae, Aphidiinae). Insects, 11(3), 160. https://doi.org/10.3390/insects11030160\n", "decision": "INCLUDED", "name": "Fig. 6, BI", "studyID": "ot_2578", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CLARKE, D. J., & GREBENNIKOV, V. V. (2009). Monophyly of Euaesthetinae (Coleoptera: Staphylinidae): phylogenetic evidence from adults and larvae, review of austral genera, and new larval descriptions. Systematic Entomology, 34(2), 346\u2013397. Portico. https://doi.org/10.1111/j.1365-3113.2009.00472.x\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_2579", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Clement, R. A., Saxton, N. A., Standring, S., Arnold, P. R., Johnson, K. K., Bybee, D. R., & Bybee, S. M. (2021). Phylogeny, migration and geographic range size evolution ofAnaxdragonflies (Anisoptera: Aeshnidae). Zoological Journal of the Linnean Society, 194(3), 858\u2013878. https://doi.org/10.1093/zoolinnean/zlab046\n", "decision": "INCLUDED", "name": "Fig. S1, BI", "studyID": "ot_2580", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CLINE, A. R., SMITH, T. R., MILLER, K., MOULTON, M., WHITING, M., & AUDISIO, P. (2014). Molecular phylogeny of <scp>N</scp>itidulidae: assessment of subfamilial and tribal classification and formalization of the family <scp>C</scp>ybocephalidae (<scp>C</scp>oleoptera: <scp>C</scp>ucujoidea). Systematic Entomology, 39(4), 758\u2013772. Portico. https://doi.org/10.1111/syen.12084\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2581", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Clouse, R. M., Janda, M., Blanchard, B., Sharma, P., Hoffmann, B. D., Andersen, A. N., Czekanski\u2010Moir, J. E., Krushelnycky, P., Rabeling, C., Wilson, E. O., Economo, E. P., Sarnat, E. M., General, D. M., Alpert, G. D., & Wheeler, W. C. (2014). Molecular phylogeny of<scp>I</scp>ndo\u2010<scp>P</scp>acific carpenter ants (<scp>H</scp>ymenoptera:<scp>F</scp>ormicidae,<scp>C</scp>amponotus) reveals waves of dispersal and colonization from diverse source areas. Cladistics, 31(4), 424\u2013437. Portico. https://doi.org/10.1111/cla.12099\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2582", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from HARUYAMA, N., MOCHIZUKI, A., DUELLI, P., NAKA, H., & NOMURA, M. (2008). Green lacewing phylogeny, based on three nuclear genes (Chrysopidae, Neuroptera). Systematic Entomology, 33(2), 275\u2013288. Portico. https://doi.org/10.1111/j.1365-3113.2008.00418.x\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2583", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Coelho, B. W. T. (2004). A review of the bee genus Augochlorella (Hymenoptera: Halictidae: Augochlorini). Systematic Entomology, 29(3), 282\u2013323. Portico. https://doi.org/10.1111/j.0307-6970.2004.00243.x\n", "decision": "INCLUDED", "name": "Fig. 14, MP", "studyID": "ot_2584", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Coeur d\u2019acier, A., Jousselin, E., Martin, J.-F., & Rasplus, J.-Y. (2007). Phylogeny of the Genus Aphis Linnaeus, 1758 (Homoptera: Aphididae) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 42(3), 598\u2013611. https://doi.org/10.1016/j.ympev.2006.10.006\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2585", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cognato, A. I., Taft, W., Osborn, R. K., & Rubinoff, D. (2022). Multi\u2010gene phylogeny of North American clear\u2010winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex. Cladistics, 39(1), 1\u201317. Portico. https://doi.org/10.1111/cla.12515\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_2586", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cohen, C. M., Noble, K., Jeffrey Cole, T., & Brewer, M. S. (2021). The phylogeny of robber flies (Asilidae) inferred from ultraconserved elements. Systematic Entomology, 46(4), 812\u2013826. Portico. https://doi.org/10.1111/syen.12490\n", "decision": "INCLUDED", "name": "10p_astral_results.txt", "studyID": "ot_2587", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Condamine, F. L., Silva-Brand\u00e3o, K. L., Kergoat, G. J., & Sperling, F. A. (2012). Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia. BMC Evolutionary Biology, 12(1), 82. https://doi.org/10.1186/1471-2148-12-82\n", "decision": "INCLUDED", "name": "12862_2012_2075_MOESM3_ESM.txt, Fig. 1, BI", "studyID": "ot_2588", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CONTRERAS-RAMOS, A. (2011). Phylogenetic review of dobsonflies of the subfamily Corydalinae and the genus Corydalus Latreille (Megaloptera: Corydalidae). Zootaxa, 2862(1). https://doi.org/10.11646/zootaxa.2862.1.1\n", "decision": "INCLUDED", "name": "Figs. 9,12, MP", "studyID": "ot_2589", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Couri, M. S., & Pont, A. C. (2000). Cladistic analysis of Coenosiini (Diptera: Muscidae: Coenosiinae). Systematic Entomology, 25(3), 373\u2013392. Portico. https://doi.org/10.1046/j.1365-3113.2000.00125.x\n", "decision": "INCLUDED", "name": "Fig. 75, MP", "studyID": "ot_2590", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Crampton-Platt, A., Timmermans, M. J. T. N., Gimmel, M. L., Kutty, S. N., Cockerill, T. D., Vun Khen, C., & Vogler, A. P. (2015). Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample. Molecular Biology and Evolution, 32(9), 2302\u20132316. https://doi.org/10.1093/molbev/msv111\n", "decision": "INCLUDED", "name": "Fig. S5", "studyID": "ot_2591", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CRANSTON, P. S., HARDY, N. B., MORSE, G. E., PUSLEDNIK, L., & McCLUEN, S. R. (2010). When molecules and morphology concur: the \u2018Gondwanan\u2019 midges (Diptera: Chironomidae). Systematic Entomology, 35(4), 636\u2013648. Portico. https://doi.org/10.1111/j.1365-3113.2010.00531.x\n", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "ot_2592", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from KERGOAT, G. J., & ALVAREZ, N. (2008). Assessing the phylogenetic usefulness of a previously neglected morphological structure through elliptic Fourier analyses: a case study in Bruchus seed\u2010beetles (Coleoptera: Chrysomelidae: Bruchinae). Systematic Entomology, 33(2), 289\u2013300. Portico. https://doi.org/10.1111/j.1365-3113.2007.00405.x\n", "decision": "INCLUDED", "name": "Fig. 7, BI", "studyID": "ot_2595", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cruaud, A., Jabbour\u2010Zahab, R., Genson, G., Cruaud, C., Couloux, A., Kjellberg, F., Van Noort, S., & Rasplus, J. (2010). Laying the foundations for a new classification of Agaonidae (Hymenoptera: Chalcidoidea), a multilocus phylogenetic approach. Cladistics, 26(4), 359\u2013387. Portico. https://doi.org/10.1111/j.1096-0031.2009.00291.x\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2597", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cruaud, A., Delvare, G., Nidelet, S., Saun\u00e9, L., Ratnasingham, S., Chartois, M., Blaimer, B. B., Gates, M., Brady, S. G., Faure, S., van Noort, S., Rossi, J., & Rasplus, J. (2020). Ultra\u2010Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics, 37(1), 1\u201335. Portico. https://doi.org/10.1111/cla.12416\n", "decision": "INCLUDED", "name": "trees_chalcididae_cladistics2020.nex", "studyID": "ot_2598", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cruaud, A., Rasplus, J., Zhang, J., Burks, R., Delvare, G., Fusu, L., Gumovsky, A., Huber, J. T., Jan\u0161ta, P., Mitroiu, M., Noyes, J. S., van Noort, S., Baker, A., B\u00f6hmov\u00e1, J., Baur, H., Blaimer, B. B., Brady, S. G., Buben\u00edkov\u00e1, K., Chartois, M., \u2026 Heraty, J. M. (2023). The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps. Cladistics, 40(1), 34\u201363. Portico. https://doi.org/10.1111/cla.12561\n", "decision": "INCLUDED", "name": "cla12561-sup-0001-appendixs1.nex", "studyID": "ot_2599", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cryan J. 2004. Molecular Phylogeny of Cicadomorpha (Insecta: Hemiptera: Cicadoidea, Cercopoidea, and Membracoidea): Adding Evidence to the Controversy. Systematic Entomology, null.", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "pg_1561", "treeID": "tree3123"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cryan, J., Wiegmann B., Deitz L., Dietrich C., & Whiting M. 2004. Treehopper trees: phylogeny of Membracidae (Hemiptera: Cicadomorpha: Membracoidea) based on molecules and morphology. Systematic Entomology 29 (4): 441-454.", "decision": "INCLUDED", "name": "Fig 3. MP strict consensus", "studyID": "pg_2581", "treeID": "tree5987"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cucini, C., Fanciulli, P. P., Frati, F., Convey, P., Nardi, F., & Carapelli, A. (2020). Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data. Genes, 12(1), 44. https://doi.org/10.3390/genes12010044\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2600", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cunha, R. L., Verd\u00fa, J. R., Lobo, J. M., & Zardoya, R. (2011). Ancient origin of endemic Iberian earth-boring dung beetles (Geotrupidae). Molecular Phylogenetics and Evolution, 59(3), 578\u2013586. https://doi.org/10.1016/j.ympev.2011.03.028\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2601", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Silva, F. L. da, & Ferrington, L. C. (2018). Systematics of the new world genus Pentaneura Phillip (Diptera: Chironomidae: Tanypodinae): Historical review, new species and phylogeny. Zoologischer Anzeiger, 274, 60\u201389. https://doi.org/10.1016/j.jcz.2017.11.010\n", "decision": "INCLUDED", "name": "Fig. 18, MP", "studyID": "ot_2602", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from da Silva, A. F., Machado, L. C., de Paula, M. B., da Silva Pessoa Vieira, C. J., de Morais Bronzoni, R. V., de Melo Santos, M. A. V., & Wallau, G. L. (2020). Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-74883-3\n", "decision": "INCLUDED", "name": "Fig. S4", "studyID": "ot_2603", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Silva, F. L. da, de Medeiros, B. A. S., & Farrell, B. D. (2024). Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification. Molecular Phylogenetics and Evolution, 194, 108025. https://doi.org/10.1016/j.ympev.2024.108025\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2604", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from FORSHAGE, M., NORDLANDER, G., & RONQUIST, F. (2008). Quasimodoana, a new Holarctic genus of eucoiline wasps (Hymenoptera, Cynipoidea, Figitidae), with a phylogenetic analysis of related genera. Systematic Entomology, 33(2), 301\u2013318. Portico. https://doi.org/10.1111/j.1365-3113.2007.00415.x\n", "decision": "INCLUDED", "name": "Fig. 12, MP", "studyID": "ot_2605", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dai, M., He, S.-L., Chen, B., & Li, T.-J. (2023). Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements. Insects, 14(9), 775. https://doi.org/10.3390/insects14090775\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2606", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Damgaard J. 2012. Phylogeny of the semiaquatic bugs (Hemiptera-Heteroptera, Gerromorpha). Insect Systematics & Evolution, 39(4): 431-460.", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "pg_1375", "treeID": "tree2746"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Damgaard, J., & Cognato, A. I. (2005). Phylogeny and reclassification of species groups in Aquarius Schellenberg, Limnoporus St\u00e5l and Gerris Fabricius (Insecta: Hemiptera\u2010Heteroptera, Gerridae). Systematic Entomology, 31(1), 93\u2013112. Portico. https://doi.org/10.1111/j.1365-3113.2005.00302.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2607", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Damgaard, J., & Sperling, F. A. H. (2001). Phylogeny of the water strider genus Gerris Fabricius (Heteroptera: Gerridae) based on COI mtDNA, EF\u20101\u03b1 nuclear DNA and morphology. Systematic Entomology, 26(2), 241\u2013254. Portico. https://doi.org/10.1046/j.1365-3113.2001.00141.x\n", "decision": "INCLUDED", "name": "Fig. 7, MP", "studyID": "ot_2608", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Damgaard, J., Andersen, N. M., & Meier, R. (2005). Combining molecular and morphological analyses of water strider phylogeny (Hemiptera\u2013Heteroptera, Gerromorpha): effects of alignment and taxon sampling. Systematic Entomology, 30(2), 289\u2013309. Portico. https://doi.org/10.1111/j.1365-3113.2004.00275.x\n", "decision": "INCLUDED", "name": "Fig. 4D, MP", "studyID": "ot_2609", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from HERMES, M. G., & MELO, G. A. R. (2008). Revision and cladistic analysis of the eumenine wasp genusPseudodynerusde Saussure (Hymenoptera, Vespidae, Eumeninae). Systematic Entomology, 33(2), 361\u2013394. Portico. https://doi.org/10.1111/j.1365-3113.2008.00421.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2614", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Danforth, B. N., Conway, L., & Ji, S. (2003). Phylogeny of Eusocial Lasioglossum Reveals Multiple Losses of Eusociality within a Primitively Eusocial Clade of Bees (Hymenoptera: Halictidae). Systematic Biology, 52(1), 23\u201336. https://doi.org/10.1080/10635150390132687\n", "decision": "INCLUDED", "name": "Fig. 4, ML", "studyID": "ot_2615", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dang, L., Wang, X., Xie, D., Gao, Y., & Zhao, L. (2021). Complete mitochondrial genome ofGynaikothrips ficorum(Thysanoptera: Phlaeothripidae). Mitochondrial DNA Part B, 6(7), 2033\u20132034. https://doi.org/10.1080/23802359.2021.1923412\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2616", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Daniel, G. M., Davis, A. L. V., Sole, C. L., & Scholtz, C. H. (2020). Evolutionary history and eco\u2010climatic diversification in southern African dung beetle Sisyphus. Journal of Biogeography, 47(12), 2698\u20132713. Portico. https://doi.org/10.1111/jbi.13974\n", "decision": "INCLUDED", "name": "RAXML_tree", "studyID": "ot_2617", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Daugeron, C., & Grootaert, P. (2003). Assessment of monophyly of species\u2010groups within Afrotropical Empidini (Diptera: Empididae: Empidinae), with a cladistic analysis of the Empis setitarsus\u2010group. Systematic Entomology, 28(3), 339\u2013360. Portico. https://doi.org/10.1046/j.1365-3113.2003.00214.x\n", "decision": "INCLUDED", "name": "Fig. 13, MP", "studyID": "ot_2619", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Deans, A. R., Gillespie, J. J., & Yoder, M. J. (2006). An evaluation of ensign wasp classification (Hymenoptera: Evaniidae) based on molecular data and insights from ribosomal RNA secondary structure. Systematic Entomology, 31(3), 517\u2013528. Portico. https://doi.org/10.1111/j.1365-3113.2006.00327.x\n", "decision": "INCLUDED", "name": "Fig. 5, BI", "studyID": "ot_2621", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Debevec A.H., Cardinal S., & Danforth B. 2012. Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea. Zoologica Scripta, 41, 527-535.", "decision": "INCLUDED", "name": "Fig. 2 / S1", "studyID": "pg_1774", "treeID": "tree3579"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dellicour, S., Lecocq, T., Kuhlmann, M., Mardulyn, P., & Michez, D. (2014). Molecular phylogeny, biogeography, and host plant shifts in the bee genus Melitta (Hymenoptera: Anthophila). Molecular Phylogenetics and Evolution, 70, 412\u2013419. https://doi.org/10.1016/j.ympev.2013.08.013\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2622", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Deng, Y.-P., Wang, W., Fu, Y.-T., Nie, Y., Xie, Y., & Liu, G.-H. (2023). Morphological and molecular evidence reveals a new species of chewing louse Pancola ailurus n. sp. (Phthiraptera: Trichodectidae) from the endangered Chinese red panda Ailurus styani. International Journal for Parasitology: Parasites and Wildlife, 20, 31\u201338. https://doi.org/10.1016/j.ijppaw.2022.12.004\n", "decision": "INCLUDED", "name": "Fig. 3, ML", "studyID": "ot_2623", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from De Jes\u00fas-Bonilla, V. S., Meza-L\u00e1zaro, R. N., & Zald\u00edvar-River\u00f3n, A. (2019). 3RAD-based systematics of the transitional Nearctic-Neotropical lubber grasshopper genus Taeniopoda (Orthoptera: Romaleidae). Molecular Phylogenetics and Evolution, 137, 64\u201375. https://doi.org/10.1016/j.ympev.2019.04.019\n", "decision": "INCLUDED", "name": "Fig. 5", "studyID": "ot_2624", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DE JONG, H., & CILIBERTI, P. (2014). How cold\u2010adapted flightless flies dispersed over the northern hemisphere: phylogeny and biogeography of the snow fly genus Chionea<scp>D</scp>alman (<scp>D</scp>iptera: <scp>L</scp>imoniidae). Systematic Entomology, 39(3), 563\u2013589. Portico. https://doi.org/10.1111/syen.12075\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_2625", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from de Moya, R. S. (2022). Phylogenomics and host-switching patterns of Philopteridae (Psocodea: Phthiraptera) feather lice. International Journal for Parasitology, 52(8), 525\u2013537. https://doi.org/10.1016/j.ijpara.2022.03.005\n", "decision": "INCLUDED", "name": "Fig. S1, BI", "studyID": "ot_2626", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Oliveira, L. A. de, Inez, T. G., Ferreira, W. D., & Hermes, M. G. (2019). A phylogenetic investigation of the Neotropical genus Alphamenes van der Vecht, 1977 (Hymenoptera, Vespidae, Eumeninae). Revista Brasileira de Entomologia, 63(1), 73\u201379. https://doi.org/10.1016/j.rbe.2018.11.006\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2628", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from JOHANSON, K. A., & KEIJSNER, M. (2008). Phylogeny of the Helicophidae (Trichoptera), with emphasis on the New Caledonian species of Helicopha. Systematic Entomology, 33(3), 451\u2013483. Portico. https://doi.org/10.1111/j.1365-3113.2008.00423.x\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_2629", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CEOTTO, P., & BOURGOIN, T. (2008). Insights into the phylogenetic relationships within Cixiidae (Hemiptera: Fulgoromorpha): cladistic analysis of a morphological dataset. Systematic Entomology, 33(3), 484\u2013500. Portico. https://doi.org/10.1111/j.1365-3113.2008.00426.x\n", "decision": "INCLUDED", "name": "Fig. 5, BI", "studyID": "ot_2630", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from de Paula, L. C. B., Dios, R. de V. P., Gudin, F. M., de Santis, M. D., Alvarez\u2010Garcia, D. M., Antunes J\u00fanior, M., Freire, B. V., Marques, F. P. de L., Lahr, D. J. G., & Nihei, S. S. (2023). Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships. Cladistics, 40(1), 64\u201381. Portico. https://doi.org/10.1111/cla.12562\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2631", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from de Santis, M. D., & Nihei, S. S. (2022). Phylogenetic analysis of the tribe Dufouriini (Diptera: Tachinidae) using a total evidence approach based on adult and immature stages. Arthropod Systematics &amp; Phylogeny, 80, 1\u201338. https://doi.org/10.3897/asp.80.e69618\n", "decision": "INCLUDED", "name": "Fig. 23, MP", "studyID": "ot_2632", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Desjardins, C. A., Regier, J. C., & Mitter, C. (2007). Phylogeny of pteromalid parasitic wasps (Hymenoptera: Pteromalidae): Initial evidence from four protein-coding nuclear genes. Molecular Phylogenetics and Evolution, 45(2), 454\u2013469. https://doi.org/10.1016/j.ympev.2007.08.004\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2633", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Desutter\u2010Grandcolas, L., & Robillard, T. (2005). Phylogenetic systematics and evolution of Agnotecous in New Caledonia (Orthoptera: Grylloidea, Eneopteridae). Systematic Entomology, 31(1), 65\u201392. Portico. https://doi.org/10.1111/j.1365-3113.2005.00299.x\n", "decision": "INCLUDED", "name": "Fig. 7, MP", "studyID": "ot_2634", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from D\u2019Haese, C. A. (2003). Morphological appraisal of Collembola phylogeny with special emphasis on Poduromorpha and a test of the aquatic origin hypothesis. Zoologica Scripta, 32(6), 563\u2013586. Portico. https://doi.org/10.1046/j.1463-6409.2003.00134.x\n", "decision": "INCLUDED", "name": "Fig. 8, MP", "studyID": "ot_2635", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dias, L. G., Molineri, C., Takiya, D., Benavides, P., & Bacca, T. (2019). Phylogeny of Tricorythodes Ulmer (Leptohyphidae: Ephemeroptera) based on molecular and morphological evidence. Zoologischer Anzeiger, 278, 38\u201345. https://doi.org/10.1016/j.jcz.2018.10.008\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2636", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dietrich, C. H. (2004). Phylogeny of the leafhopper subfamily Evacanthinae with a review of Neotropical species and notes on related groups (Hemiptera: Membracoidea: Cicadellidae). Systematic Entomology, 29(4), 455\u2013487. Portico. https://doi.org/10.1111/j.0307-6970.2004.00250.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2637", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dietrich, C. H., Mckamey, S. H., & Deitz, L. L. (2001). Morphology\u2010based phylogeny of the treehopper family Membracidae (Hemiptera: Cicadomorpha: Membracoidea). Systematic Entomology, 26(2), 213\u2013239. Portico. https://doi.org/10.1046/j.1365-3113.2001.00140.x\n", "decision": "INCLUDED", "name": "Fig. 10, MP", "studyID": "ot_2638", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ANG, Y., PUNIAMOORTHY, N., & MEIER, R. (2008). Secondarily reduced foreleg armature in Perochaeta dikowi sp.n. (Diptera: Cyclorrhapha: Sepsidae) due to a novel mounting technique. Systematic Entomology, 33(3), 552\u2013559. Portico. https://doi.org/10.1111/j.1365-3113.2008.00422.x\n", "decision": "INCLUDED", "name": "Fig. 4, MP", "studyID": "ot_2639", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Di Giulio, A., Fattorini, S., Kaupp, A., Taglianti, A. V., & Nagel, P. (2003). Review of competing hypotheses of phylogenetic relationships of Paussinae (Coleoptera: Carabidae) based on larval characters. Systematic Entomology, 28(4), 509\u2013537. Portico. https://doi.org/10.1046/j.1365-3113.2003.00227.x\n", "decision": "INCLUDED", "name": "Fig. 5, MP", "studyID": "ot_2640", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DIJKSTRA, K. B., KALKMAN, V. J., DOW, R. A., STOKVIS, F. R., & VAN TOL, J. (2013). Redefining the damselfly families: a comprehensive molecular phylogeny of <scp>Z</scp>ygoptera (<scp>O</scp>donata). Systematic Entomology, 39(1), 68\u201396. Portico. https://doi.org/10.1111/syen.12035\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2641", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dijkstra, E., Rubio, J. M., & Post, R. J. (2003). Resolving relationships over a wide taxonomic range in Delphacidae (Homoptera) using the COI gene. Systematic Entomology, 28(1), 89\u2013100. Portico. https://doi.org/10.1046/j.1365-3113.2003.00203.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2642", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ding, S., Li, W., Wang, Y., Cameron, S. L., Mur\u00e1nyi, D., & Yang, D. (2019). The phylogeny and evolutionary timescale of stoneflies (Insecta: Plecoptera) inferred from mitochondrial genomes. Molecular Phylogenetics and Evolution, 135, 123\u2013135. https://doi.org/10.1016/j.ympev.2019.03.005\n", "decision": "INCLUDED", "name": "Fig. 5 upper, BI", "studyID": "ot_2643", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dong, Y., Zhu, L.-X., Wang, C.-B., Zhang, M., & Ding, P.-P. (2016). The complete mitochondrial genome of Luehdorfia chinensis Leech (Lepidoptera: Papilionidae) from China. Mitochondrial DNA Part B, 1(1), 198\u2013199. https://doi.org/10.1080/23802359.2016.1155084\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2644", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LIU, X., HAYASHI, F., & YANG, D. (2008). Systematics and biogeography of the fishfly genus Parachauliodes (Megaloptera: Corydalidae) endemic to the east Asian islands. Systematic Entomology, 33(3), 560\u2013578. Portico. https://doi.org/10.1111/j.1365-3113.2008.00429.x\n", "decision": "INCLUDED", "name": "Fig. 8, MP", "studyID": "ot_2645", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dong, X., Wang, K., Tang, Z., Zhang, Y., Yi, W., Xue, H., Zheng, C., & Bu, W. (2022). Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae. Archives of Insect Biochemistry and Physiology, 110(1). Portico. https://doi.org/10.1002/arch.21878\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2646", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dong, Y., Zhao, M., & Shao, R. (2022). Fragmented mitochondrial genomes of seal lice (family Echinophthiriidae) and gorilla louse (family Pthiridae): frequent minichromosomal splits and a host switch of lice between seals. BMC Genomics, 23(1). https://doi.org/10.1186/s12864-022-08530-8\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2647", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dong, Z., Liu, X., Mao, C., He, J., & Li, X. (2022). \ufeffXenos yangi sp. nov.: A new twisted-wing parasite species (Strepsiptera, Xenidae) from Gaoligong Mountains, Southwest China. ZooKeys, 1085, 11\u201327. https://doi.org/10.3897/zookeys.1085.76484\n", "decision": "INCLUDED", "name": "Fig. 6, MP", "studyID": "ot_2648", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dong, Y., Jelocnik, M., Gillett, A., Valenza, L., Conroy, G., Potvin, D., & Shao, R. (2023). Mitochondrial Genome Fragmentation Occurred Multiple Times Independently in Bird Lice of the Families Menoponidae and Laemobothriidae. Animals, 13(12), 2046. https://doi.org/10.3390/ani13122046\n", "decision": "INCLUDED", "name": "Fig. 4, ML", "studyID": "ot_2650", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dom\u00ednguez, M. C., & Roig-Ju\u00f1ent, S. A. (2008). A phylogeny of the family Fanniidae Schnabl (Insecta:Diptera:Calyptratae) based on adult morphological characters, with special reference to the Austral species of the genus Fannia. Invertebrate Systematics, 22(5), 563. https://doi.org/10.1071/is08003\n", "decision": "INCLUDED", "name": "Figs. 4,5, MP", "studyID": "ot_2651", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CHO, S., MITCHELL, A., MITTER, C., REGIER, J., MATTHEWS, M., & ROBERTSON, R. (2008). Molecular phylogenetics of heliothine moths (Lepidoptera: Noctuidae: Heliothinae), with comments on the evolution of host range and pest status. Systematic Entomology, 33(4), 581\u2013594. Portico. https://doi.org/10.1111/j.1365-3113.2008.00427.x\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2652", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DOORENWEERD, C., VAN NIEUKERKEN, E. J., & HOARE, R. J. B. (2016). Phylogeny, classification and divergence times of pygmy leaf\u2010mining moths (<scp>L</scp>epidoptera: <scp>N</scp>epticulidae): the earliest lepidopteran radiation on <scp>A</scp>ngiosperms? Systematic Entomology, 42(1), 267\u2013287. Portico. https://doi.org/10.1111/syen.12212\n", "decision": "INCLUDED", "name": "Fig. S1, BI", "studyID": "ot_2653", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dorchin, N., Freidberg, A., & Mokady, O. (2004). Phylogeny of the Baldratiina (Diptera: Cecidomyiidae) inferred from morphological, ecological and molecular data sources, and evolutionary patterns in plant\u2013galler relationships. Molecular Phylogenetics and Evolution, 30(3), 503\u2013515. https://doi.org/10.1016/s1055-7903(03)00232-x\n", "decision": "INCLUDED", "name": "Fig. 2a, MP", "studyID": "ot_2654", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dorchin, N., Harris, K. M., & Stireman, J. O. (2019). Phylogeny of the gall midges (Diptera, Cecidomyiidae, Cecidomyiinae): Systematics, evolution of feeding modes and diversification rates. Molecular Phylogenetics and Evolution, 140, 106602. https://doi.org/10.1016/j.ympev.2019.106602\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2655", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dorchin, A., Shafir, A., Neumann, F. H., Langgut, D., Vereecken, N. J., & Mayrose, I. (2021). Bee flowers drive macroevolutionary diversification in long-horned bees. Proceedings of the Royal Society B: Biological Sciences, 288(1959). https://doi.org/10.1098/rspb.2021.0533\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2656", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Douglas, H. B., Kundrata, R., Brunke, A. J., Escalona, H. E., Chapados, J. T., Eyres, J., Richter, R., Savard, K., \u015alipi\u0144ski, A., McKenna, D., & Dettman, J. R. (2021). Anchored Phylogenomics, Evolution and Systematics of Elateridae: Are All Bioluminescent Elateroidea Derived Click Beetles? Biology, 10(6), 451. https://doi.org/10.3390/biology10060451\n", "decision": "INCLUDED", "name": "Figs. 2,3, ML", "studyID": "ot_2657", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Downie, D. A., & Gullan, P. J. (2004). Phylogenetic analysis of mealybugs (Hemiptera: Coccoidea: Pseudococcidae) based on DNA sequences from three nuclear genes, and a review of the higher classification. Systematic Entomology, 29(2), 238\u2013260. Portico. https://doi.org/10.1111/j.0307-6970.2004.00241.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2659", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LEE, S., & BROWN, R. L. (2008). Phylogenetic relationships of Holarctic Teleiodini (Lepidoptera: Gelechiidae) based on analysis of morphological and molecular data. Systematic Entomology, 33(4), 595\u2013612. Portico. https://doi.org/10.1111/j.1365-3113.2008.00430.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2661", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dowton, M., & Austin, A. D. (1998). Phylogenetic Relationships among the Microgastroid Wasps (Hymenoptera: Braconidae): Combined Analysis of 16S and 28S rDNA Genes and Morphological Data. Molecular Phylogenetics and Evolution, 10(3), 354\u2013366. https://doi.org/10.1006/mpev.1998.0533\n", "decision": "INCLUDED", "name": "Fig. 5b, MP", "studyID": "ot_2662", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Duan, J., Quan, G., Mittapalli, O., Cusson, M., Krell, P. J., & Doucet, D. (2017). The complete mitogenome of the Emerald Ash Borer (EAB), Agrilus planipennis (Insecta: Coleoptera: Buprestidae). Mitochondrial DNA Part B, 2(1), 134\u2013135. https://doi.org/10.1080/23802359.2017.1292476\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2663", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DUBITZKY, A. (2007). Phylogeny of the World Anthophorini (Hymenoptera: Apoidea: Apidae). Systematic Entomology, 32(4), 585\u2013600. Portico. https://doi.org/10.1111/j.1365-3113.2007.00397.x\n", "decision": "INCLUDED", "name": "Fig. 6, MP", "studyID": "ot_2664", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Duelli, P., Henry, C. S., Hayashi, M., Nomura, M., & Mochizuki, A. (2016). Molecular phylogeny and morphology of Pseudomallada (Neuroptera: Chrysopidae), one of the largest genera within Chrysopidae. Zoological Journal of the Linnean Society, 180(3), 556\u2013569. https://doi.org/10.1093/zoolinnean/zlw008\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2665", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dumans, A. T. N., Grimaldi, D. B., Furtado, C., Machado, E. de A., & Prosdocimi, F. (2017). The complete mitochondrial genome of the subsocial cockroachNauphoeta cinereaand phylogenomic analyses of Blattodea mitogenomes suggest reclassification of superfamilies. Mitochondrial DNA Part B, 2(1), 76\u201378. https://doi.org/10.1080/23802359.2017.1285207\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2666", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dumont, H. J., Vanfleteren, J. R., De Jonckheere, J. F., & Weekers, P. H. H. (2005). Phylogenetic Relationships, Divergence Time Estimation, and Global Biogeographic Patterns of Calopterygoid Damselflies (Odonata, Zygoptera) Inferred from Ribosomal DNA Sequences. Systematic Biology, 54(3), 347\u2013362. https://doi.org/10.1080/10635150590949869\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2667", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DUMONT, H. J., VIERSTRAETE, A., & VANFLETEREN, J. R. (2010). A molecular phylogeny of the Odonata (Insecta). Systematic Entomology, 35(1), 6\u201318. Portico. https://doi.org/10.1111/j.1365-3113.2009.00489.x\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2668", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DYER, N., LAWTON, S., RAVEL, S., CHOI, K., LEHANE, M., ROBINSON, A., OKEDI, L., HALL, M., SOLANO, P., & DONNELLY, M. (2008). Molecular phylogenetics of tsetse flies (Diptera: Glossinidae) based on mitochondrial (COI, 16S, ND2) and nuclear ribosomal DNA sequences, with an emphasis on the palpalis group. Molecular Phylogenetics and Evolution, 49(1), 227\u2013239. https://doi.org/10.1016/j.ympev.2008.07.011\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2669", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Edgerly, J. S., Sandel, B., Regoli, I., & Okolo, O. (2020). Silk Spinning Behavior Varies from Species-Specific to Individualistic in Embioptera: Do Environmental Correlates Account for this Diversity? Insect Systematics and Diversity, 4(2). https://doi.org/10.1093/isd/ixaa007\n", "decision": "INCLUDED", "name": "Fig. 5A, BI", "studyID": "ot_2670", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Eimanifar, A., Kimball, R. T., Braun, E. L., Fuchs, S., Gr\u00fcnewald, B., & Ellis, J. D. (2017). The complete mitochondrial genome and phylogenetic placement of Apis nigrocincta Smith (Insecta: Hymenoptera: Apidae), an Asian, cavity-nesting honey bee. Mitochondrial DNA Part B, 2(1), 249\u2013250. https://doi.org/10.1080/23802359.2017.1318683\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2671", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from SCHMIDT, B. C., & SPERLING, F. A. H. (2008). Widespread decoupling of mtDNA variation and species integrity in Grammia tiger moths (Lepidoptera: Noctuidae). Systematic Entomology, 33(4), 613\u2013634. Portico. https://doi.org/10.1111/j.1365-3113.2008.00433.x\n", "decision": "INCLUDED", "name": "Fig. 6A, MP", "studyID": "ot_2672", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ekrem T., Willassen E., & Stur E. 2010. Phylogenetic utility of five genes for dipteran phylogeny: a test case in the Chironomidae leads to generic synonymies. Molecular Phylogenetics and Evolution, 57: 561-571.", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "pg_1946", "treeID": "tree3964"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Elsayed, A. K. (2023). Integrative taxonomy reveals a new gall midge genus and species (Diptera: Cecidomyiidae) developing in the flower buds of Pongamia pinnata (Fabaceae) in Japan. Zoological Journal of the Linnean Society, 202(1). https://doi.org/10.1093/zoolinnean/zlad152\n", "decision": "INCLUDED", "name": "Fig. 8, ML", "studyID": "ot_2673", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ESCALONA, H. E., LAWRENCE, J. F., WANAT, M., & \u015aLIPI\u0143SKI, A. (2015). Phylogeny and placement of Boganiidae (Coleoptera, Cucujoidea) with a review of Australian and New Caledonian taxa. Systematic Entomology, 40(3), 628\u2013651. Portico. https://doi.org/10.1111/syen.12126\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2674", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Escalona, H. E., Zwick, A., Li, H.-S., Li, J., Wang, X., Pang, H., Hartley, D., Jermiin, L. S., Nedv\u011bd, O., Misof, B., Niehuis, O., \u015alipi\u0144ski, A., & Tomaszewska, W. (2017). Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini). BMC Evolutionary Biology, 17(1). https://doi.org/10.1186/s12862-017-1002-3\n", "decision": "INCLUDED", "name": "Fig. S2, BI", "studyID": "ot_2675", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Marianne Espeland, Jason P.W. Hall, Philip J. DeVries, David C. Lees, Mark Cornwall, Yu-Feng Hsu, Li-Wei Wu, Dana L. Campbell, Gerard Talavera, Roger Vila, Shayla Salzman, Sophie Ruehr, David J. Lohman, Naomi E. Pierce, 2015, 'Ancient Neotropical origin and recent recolonisation: Phylogeny, biogeography and diversification of the Riodinidae (Lepidoptera: Papilionoidea)', Molecular Phylogenetics and Evolution, vol. 93, pp. 296-306", "decision": "INCLUDED", "name": "Dated Bayesian", "studyID": "ot_524", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Espinasa, L., Flick, C., & Giribet, G. (2007). Phylogeny of the American silverfish Cubacubaninae (Hexapoda: Zygentoma: Nicoletiidae): a combined approach using morphology and five molecular loci. Cladistics, 23(1), 22\u201340. Portico. https://doi.org/10.1111/j.1096-0031.2006.00127.x\n", "decision": "INCLUDED", "name": "Fig. 1B, MP", "studyID": "ot_2676", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from EVANGELISTA, O., SAKAKIBARA, A. M., CRYAN, J. R., & URBAN, J. M. (2016). A phylogeny of the treehopper subfamily Heteronotinae reveals convergent pronotal traits (Hemiptera: Auchenorrhyncha: Membracidae). Systematic Entomology, 42(2), 410\u2013428. Portico. https://doi.org/10.1111/syen.12221\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2677", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from EVANS, A. M., MCKENNA, D. D., BELLAMY, C. L., & FARRELL, B. D. (2014). Large\u2010scale molecular phylogeny of metallic wood\u2010boring beetles (<scp>C</scp>oleoptera: <scp>B</scp>uprestoidea) provides new insights into relationships and reveals multiple evolutionary origins of the larval leaf\u2010mining habit. Systematic Entomology, 40(2), 385\u2013400. Portico. https://doi.org/10.1111/syen.12108\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2678", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Faille, A., Ribera, I., Deharveng, L., Bourdeau, C., Garnery, L., Qu\u00e9innec, E., & Deuve, T. (2010). A molecular phylogeny shows the single origin of the Pyrenean subterranean Trechini ground beetles (Coleoptera: Carabidae). Molecular Phylogenetics and Evolution, 54(1), 97\u2013106. https://doi.org/10.1016/j.ympev.2009.10.008\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2679", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ARCHANGELSKY, M. (2008). Phylogeny of Berosini (Coleoptera: Hydrophilidae, Hydrophilinae) based on larval and adult characters, and evolutionary scenarios related to habitat shift in larvae. Systematic Entomology, 33(4), 635\u2013650. Portico. https://doi.org/10.1111/j.1365-3113.2008.00425.x\n", "decision": "INCLUDED", "name": "Fig. 10, MP", "studyID": "ot_2680", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Faircloth, B. C., Branstetter, M. G., White, N. D., & Brady, S. G. (2014). Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among <scp>H</scp>ymenoptera. Molecular Ecology Resources, 15(3), 489\u2013501. Portico. https://doi.org/10.1111/1755-0998.12328\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2681", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Feindt, W., Osigus, H.-J., Herzog, R., Mason, C. E., & Hadrys, H. (2016). The complete mitochondrial genome of the neotropical helicopter damselflyMegaloprepus caerulatus(Odonata: Zygoptera) assembled from next generation sequencing data. Mitochondrial DNA Part B, 1(1), 497\u2013499. https://doi.org/10.1080/23802359.2016.1192504\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2683", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Feindt, W., Herzog, R., Osigus, H.-J., Schierwater, B., & Hadrys, H. (2016). Short read sequencing assembly revealed the complete mitochondrial genome of Ischnura elegans Vander Linden, 1820 (Odonata: Zygoptera). Mitochondrial DNA Part B, 1(1), 574\u2013576. https://doi.org/10.1080/23802359.2016.1192510\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2684", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ferreira, V. S., Keller, O., & Branham, M. A. (2020). Multilocus Phylogeny Support the Nonbioluminescent FireflyChespiritoas a New Subfamily in the Lampyridae (Coleoptera: Elateroidea). Insect Systematics and Diversity, 4(6). https://doi.org/10.1093/isd/ixaa014\n", "decision": "INCLUDED", "name": "Fig. 8, BI", "studyID": "ot_2686", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BERTONE, M. A., COURTNEY, G. W., & WIEGMANN, B. M. (2008). Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes. Systematic Entomology, 33(4), 668\u2013687. Portico. https://doi.org/10.1111/j.1365-3113.2008.00437.x\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2687", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CHENOWETH, L. B., FULLER, S., TIERNEY, S. M., PARK, Y. C., & SCHWARZ, M. P. (2008). Hasinamelissa: a new genus of allodapine bee from Madagascar revealed by larval morphology and DNA sequence data. Systematic Entomology, 33(4), 700\u2013710. Portico. https://doi.org/10.1111/j.1365-3113.2008.00432.x\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2688", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ferreira, V. S., Roza, A. S., Barbosa, F. F., Vega-Badillo, V., Zaragoza-Caballero, S., Mermudes, J. R. M., Ivie, M. A., Hansen, A. K., Brunke, A. J., Douglas, H. B., Solodovnikov, A., & Kundrata, R. (2024). Phylogenomics of Phengodidae (Coleoptera: Elateroidea): towards a natural classification of a bioluminescent and paedomorphic beetle lineage, with recognition of a new subfamily. Zoological Journal of the Linnean Society, 201(4). https://doi.org/10.1093/zoolinnean/zlae093\n", "decision": "INCLUDED", "name": "3-ML-45CPP-NT.txt", "studyID": "ot_2689", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Field J., Ohl M., & Kennedy M. 2011. A molecular phylogeny for digger wasps in the tribe Ammophilini (Hymenoptera, Apoidea, Sphecidae). Systematic Entomology, 36(4): 732-740.", "decision": "INCLUDED", "name": "Fig 1", "studyID": "pg_2325", "treeID": "tree4903"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Rocha Filho, L. C. D., & Packer, L. (2016). Phylogeny of the cleptoparasitic Megachilini generaCoelioxysandRadoszkowskiana, with the description of six new subgenera inCoelioxys(Hymenoptera: Megachilidae). Zoological Journal of the Linnean Society. Portico. https://doi.org/10.1111/zoj.12484\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2691", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Forgie, S. A., Philips, T. K., & Scholtz, C. H. (2004). Evolution of the Scarabaeini (Scarabaeidae: Scarabaeinae). Systematic Entomology, 30(1), 60\u201396. Portico. https://doi.org/10.1111/j.1365-3113.2004.00273.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2692", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Nico M. Franz, 2006, 'Towards a phylogenetic system of derelomine flower weevils (Coleoptera: Curculionidae)', Systematic Entomology, vol. 31, no. 2, pp. 220-287", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_605", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from FRESNEDA, J., SALGADO, J., & RIBERA, I. (2007). Phylogeny of western Mediterranean Leptodirini, with an emphasis on genital characters (Coleoptera: Leiodidae: Cholevinae). Systematic Entomology, 32(2), 332\u2013358. Portico. https://doi.org/10.1111/j.1365-3113.2006.00366.x\n", "decision": "INCLUDED", "name": "Fig. 15, MP", "studyID": "ot_2693", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from FRIC, Z., WAHLBERG, N., PECH, P., & ZRZAV\u00dd, J. (2007). Phylogeny and classification of the Phengaris\u2013Maculinea clade (Lepidoptera: Lycaenidae): total evidence and phylogenetic species concepts. Systematic Entomology, 32(3), 558\u2013567. Portico. https://doi.org/10.1111/j.1365-3113.2007.00387.x\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2694", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Fu, Y.-T., Xun, Y., Peng, Y.-Y., Zhang, Y., & Wu, X. (2024). The complete mitochondrial genome of the rodent flea Nosopsyllus laeviceps: genome description, comparative analysis, and phylogenetic implications. Parasites &amp; Vectors, 17(1). https://doi.org/10.1186/s13071-024-06329-y\n", "decision": "INCLUDED", "name": "Fig. 5, ML", "studyID": "ot_2695", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from KIM, H., & LEE, S. (2008). A molecular phylogeny of the tribe Aphidini (Insecta: Hemiptera: Aphididae) based on the mitochondrial tRNA/COII, 12S/16S and the nuclear EF1\u03b1 genes. Systematic Entomology, 33(4), 711\u2013721. Portico. https://doi.org/10.1111/j.1365-3113.2008.00440.x\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2696", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Finet, C., Kassner, V. A., Carvalho, A. B., Chung, H., Day, J. P., Day, S., Delaney, E. K., De R\u00e9, F. C., Dufour, H. D., Dupim, E., Izumitani, H. F., Gaut\u00e9rio, T. B., Justen, J., Katoh, T., Kopp, A., Koshikawa, S., Longdon, B., Loreto, E. L., Nunes, M. D. S., \u2026 Marl\u00e9taz, F. (2021). DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics. Genome Biology and Evolution, 13(8). https://doi.org/10.1093/gbe/evab179\n", "decision": "INCLUDED", "name": "All+taxa+and+other+genera_ML.contree_processed", "studyID": "ot_2174", "treeID": "tree9"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Flook, P. K., S. Klee, C. H. F. Rowell. 1999. Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics. Systematic Biology 48 (2): 233-253.", "decision": "INCLUDED", "name": "Untitled (tree566)", "studyID": "pg_445", "treeID": "tree566"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from FOLEY, I. A., & IVIE, M. A. (2008). A phylogenetic analysis of the tribe Zopherini with a review ofthe species and generic classification (Coleoptera: Zopheridae). Zootaxa, 1928(1). https://doi.org/10.11646/zootaxa.1928.1.1\n", "decision": "INCLUDED", "name": "Fig. 73, MP", "studyID": "ot_2698", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Frandsen, P. B., Holzenthal, R. W., Espeland, M., Breinholt, J., Thomas Thorpe, J. A., Simon, S., Kawahara, A. Y., Plotkin, D., Hotaling, S., Li, Y., Nelson, C. R., Niehuis, O., Mayer, C., Podsiadlowski, L., Donath, A., Misof, B., Moriarty Lemmon, E., Lemmon, A., Morse, J. C., \u2026 Zhou, X. (2024). Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature\u2019s underwater architects. Proceedings of the Royal Society B: Biological Sciences, 291(2026). https://doi.org/10.1098/rspb.2024.0514\n", "decision": "INCLUDED", "name": "ml_tree_01.dated.tre", "studyID": "ot_2701", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Freitas, A. V. L., & Brown, K. S. (2004). Phylogeny of the Nymphalidae (Lepidoptera). Systematic Biology, 53(3), 363\u2013383. https://doi.org/10.1080/10635150490445670\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2702", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Freidberg, A. (2002). Systematics of Schistopterini (Diptera: Tephritidae: Tephritinae), with descriptions of new genera and species. Systematic Entomology, 27(1), 1\u201329. Portico. https://doi.org/10.1046/j.0307-6970.2001.00162.x\n", "decision": "INCLUDED", "name": "Fig. 13, MP", "studyID": "ot_2703", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Friedlander, T. P., Horst, K. R., Regier, J. C., Mitter, C., Peigler, R. S., & Fang, Q. Q. (1998). Two Nuclear Genes Yield Concordant Relationships within Attacini (Lepidoptera: Saturniidae). Molecular Phylogenetics and Evolution, 9(1), 131\u2013140. https://doi.org/10.1006/mpev.1997.9999\n", "decision": "INCLUDED", "name": "Fig. 4a, MP", "studyID": "ot_2704", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Friedrich, F., & Beutel, R. G. (2010). The thoracic morphology ofNannochorista(Nannochoristidae) and its implications for the phylogeny of Mecoptera and Antliophora. Journal of Zoological Systematics and Evolutionary Research, 48(1), 50\u201374. https://doi.org/10.1111/j.1439-0469.2009.00535.x\n", "decision": "INCLUDED", "name": "Fig. 9, MP", "studyID": "ot_2705", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Friedrich, F., Pohl, H., Beckmann, F., & Beutel, R. G. (2013). The head of Merope tuber (Meropeidae) and the phylogeny of Mecoptera (Hexapoda). Arthropod Structure &amp; Development, 42(1), 69\u201388. https://doi.org/10.1016/j.asd.2012.09.006\n", "decision": "INCLUDED", "name": "Fig. 7, MP", "studyID": "ot_2706", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Froufe, E., Ferreira, S., Boudot, J.-P., Alves, P. C., & Harris, D. J. (2013). Molecular phylogeny of the Western PalaearcticCordulegastertaxa (Odonata: Anisoptera: Cordulegastridae). Biological Journal of the Linnean Society, 111(1), 49\u201357. https://doi.org/10.1111/bij.12190\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2707", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gaimari, S. D., & Tanasijtshuk, V. N. (2001). A new leucopine genus (Diptera: Chamaemyiidae) with species attacking Ceroplastes wax scales (Hemiptera: Coccidae) in South America. Systematic Entomology, 26(3), 311\u2013328. Portico. https://doi.org/10.1046/j.1365-3113.2001.00156.x\n", "decision": "INCLUDED", "name": "Fig. 12, MP", "studyID": "ot_2708", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Galinskaya, T. V., Astakhov, D. M., Propistsova, E. A., & Gorin, V. A. (2020). Phylogenetic Reconstruction of the Subfamilies Asilinae and Stichopogoninae (Diptera, Asilidae) Based on the Mitochondrial Genes 16S and 12S rDNA and Nuclear 18S rDNA. Russian Journal of Genetics, 56(8), 952\u2013971. https://doi.org/10.1134/s1022795420080049\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2709", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gao, X.-Y., Cai, Y.-Y., Yu, D.-N., Storey, K. B., & Zhang, J.-Y. (2018). Characteristics of the complete mitochondrial genome ofSuhpalacsa longialata(Neuroptera, Ascalaphidae) and its phylogenetic implications. PeerJ, 6, e5914. Portico. https://doi.org/10.7717/peerj.5914\n", "decision": "INCLUDED", "name": "Fig. 5 left, ML", "studyID": "ot_2710", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gao, Y., Ge, Y., Yan, L., Vikhrev, N. E., Wang, Q., Butterworth, N. J., & Zhang, D. (2022). Phylogenetic Analyses Support the Monophyly of the Genus Lispe Latreille (Diptera: Muscidae) with Insights into Intrageneric Relationships. Insects, 13(11), 1015. https://doi.org/10.3390/insects13111015\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2711", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Garz\u00f3n-Ordu\u00f1a, I. J., Menchaca-Armenta, I., Contreras-Ramos, A., Liu, X., & Winterton, S. L. (2016). The phylogeny of brown lacewings (Neuroptera: Hemerobiidae) reveals multiple reductions in wing venation. BMC Evolutionary Biology, 16(1). https://doi.org/10.1186/s12862-016-0746-5\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2712", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gauld, I. D., & Dubois, J. (2006). Phylogeny of thePolysphinctagroup of genera (Hymenoptera: Ichneumonidae; Pimplinae): a taxonomic revision of spider ectoparasitoids. Systematic Entomology, 31(3), 529\u2013564. Portico. https://doi.org/10.1111/j.1365-3113.2006.00334.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2714", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GAULD, I. D., WAHL, D. B., & BROAD, G. R. (2002). The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study. Zoological Journal of the Linnean Society, 136(3), 421\u2013485. https://doi.org/10.1046/j.1096-3642.2002.00031.x\n", "decision": "INCLUDED", "name": "Figs. 1-13, MP", "studyID": "ot_2715", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GREBENNIKOV, V. V. (2009). Discheramocephalini, a new pantropical tribe of featherwing beetles (Coleoptera: Ptiliidae): description of new taxa and phylogenetic analysis. Systematic Entomology, 34(1), 113\u2013136. Portico. https://doi.org/10.1111/j.1365-3113.2008.00444.x\n", "decision": "INCLUDED", "name": "Fig. 14, MP", "studyID": "ot_2716", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PRICE, D. L. (2009). Phylogeny and biogeography of the dung beetle genus Phanaeus (Coleoptera: Scarabaeidae). Systematic Entomology, 34(1), 137\u2013150. Portico. https://doi.org/10.1111/j.1365-3113.2008.00443.x\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2717", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GE, S., BEUTEL, R. G., & YANG, X. (2007). Thoracic morphology of adults of Derodontidae and Nosodendridae and its phylogenetic implications (Coleoptera). Systematic Entomology, 32(4), 635\u2013667. Portico. https://doi.org/10.1111/j.1365-3113.2007.00392.x\n", "decision": "INCLUDED", "name": "Fig. 28, MP", "studyID": "ot_2718", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ge, D., G\u00f3mez-Zurita, J., Chesters, D., Yang, X., & Vogler, A. P. (2012). Suprageneric systematics of flea beetles (Chrysomelidae: Alticinae) inferred from multilocus sequence data. Molecular Phylogenetics and Evolution, 62(3), 793\u2013805. https://doi.org/10.1016/j.ympev.2011.11.028\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2719", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ge, X., Zang, H., Ye, X., Peng, L., Wang, B., Lian, G., & Sun, C. (2022). Comparative Mitogenomic Analyses of Hydropsychidae Revealing the Novel Rearrangement of Protein-Coding Gene and tRNA (Trichoptera: Annulipalpia). Insects, 13(9), 759. https://doi.org/10.3390/insects13090759\n", "decision": "INCLUDED", "name": "Fig. 5b, BI", "studyID": "ot_2720", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ge, X., Peng, L., Vogler, A. P., Morse, J. C., Yang, L., Sun, C., & Wang, B. (2022). Massive gene rearrangements of mitochondrial genomes and implications for the phylogeny of Trichoptera (Insecta). Systematic Entomology, 48(2), 278\u2013295. Portico. https://doi.org/10.1111/syen.12575\n", "decision": "INCLUDED", "name": "Fig. 5, BI", "studyID": "ot_2721", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Geraci C (2007) Phylogeny and classification of Hydropsychidae subfamilies and genera of the World (Insecta: Trichoptera). All Dissertations, 160.\n", "decision": "INCLUDED", "name": "Fig. 1.3,  MP", "studyID": "ot_2722", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Germann, C., Wimmer, C., & Bernasconi, M. V. (2011). Molecular data sheds light on the classification of long-legged flies (Diptera:Dolichopodidae). Invertebrate Systematics, 25(4), 303. https://doi.org/10.1071/is11029\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2723", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ghanavi, H. R., Twort, V., Hartman, T. J., Zahiri, R., & Wahlberg, N. (2022). The (non) accuracy of mitochondrial genomes for family\u2010level phylogenetics in Erebidae (Lepidoptera). Zoologica Scripta, 51(6), 695\u2013707. Portico. https://doi.org/10.1111/zsc.12559\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2724", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gibbs, J., Brady, S. G., Kanda, K., & Danforth, B. N. (2012). Phylogeny of halictine bees supports a shared origin of eusociality for Halictus and Lasioglossum (Apoidea: Anthophila: Halictidae). Molecular Phylogenetics and Evolution, 65(3), 926\u2013939. https://doi.org/10.1016/j.ympev.2012.08.013\n", "decision": "INCLUDED", "name": "Fig. S1, BI", "studyID": "ot_2725", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GIBSON, J. F., & COURTNEY, G. W. (2007). Revision of the net\u2010winged midge genus Horaia Tonnoir and its phylogenetic relationship to other genera within the tribe Apistomyiini (Diptera: Blephariceridae). Systematic Entomology, 32(2), 276\u2013304. Portico. https://doi.org/10.1111/j.1365-3113.2006.00360.x\n", "decision": "INCLUDED", "name": "Fig. 85, MP", "studyID": "ot_2726", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gibson, J. F., Skevington, J. H., & Kelso, S. (2010). Placement of Conopidae (Diptera) within Schizophora based on mtDNA and nrDNA gene regions. Molecular Phylogenetics and Evolution, 56(1), 91\u2013103. https://doi.org/10.1016/j.ympev.2010.03.026\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2727", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gillespie, J. J., Tallamy, D. W., Riley, E. G., & Cognato, A. I. (2008). Molecular phylogeny of rootworms and related galerucine beetles (Coleoptera: Chrysomelidae). Zoologica Scripta, 37(2), 195\u2013222. Portico. https://doi.org/10.1111/j.1463-6409.2007.00320.x\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2729", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gimeno, C., Belshaw, R., & Quicke, D. L. J. (1997). Phylogenetic relationships of the Alysiinae/Opiinae (Hymenoptera: Braconidae) and the utility of cytochrome\u00a0b, 16S and 28S D2 rRNA. Insect Molecular Biology, 6(3), 273\u2013284. Portico. https://doi.org/10.1046/j.1365-2583.1997.00181.x\n", "decision": "INCLUDED", "name": "Fig. 4", "studyID": "ot_2730", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PEREYRA, V., & MOUND, L. A. (2009). Phylogenetic relationships within the genus Cranothrips (Thysanoptera, Melanthripidae) with consideration of host associations and disjunct distributions within the family. Systematic Entomology, 34(1), 151\u2013161. Portico. https://doi.org/10.1111/j.1365-3113.2008.00445.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2732", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gimmel, M. L., Bocakova, M., Gunter, N. L., & Leschen, R. A. B. (2019). Comprehensive phylogeny of the Cleroidea (Coleoptera: Cucujiformia). Systematic Entomology, 44(3), 527\u2013558. Portico. https://doi.org/10.1111/syen.12338\n", "decision": "INCLUDED", "name": "Fig. S1, ML", "studyID": "ot_2733", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Godeiro, N. N., Ding, Y., Cipola, N. G., Jantarit, S., Bellini, B. C., & Zhang, F. (2022). Phylogenomics and systematics of Entomobryoidea (Collembola): marker design, phylogeny and classification. Cladistics, 39(2), 101\u2013115. Portico. https://doi.org/10.1111/cla.12521\n", "decision": "INCLUDED", "name": "USCO_matrix90_abs75_bpcomp.con.tre", "studyID": "ot_2734", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gomes, L. R. P., Souza, D. de S., & de Carvalho, C. J. B. (2021). First insights into the evolution of neotropical anthomyiid flies (Diptera: Anthomyiidae). Systematics and Biodiversity, 19(7), 724\u2013737. https://doi.org/10.1080/14772000.2021.1914765\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2735", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from G\u00f3mez\u2010Zurita, J., & Cardoso, A. (2021). Molecular systematics, higher\u2010rank classification and Gondwanan origins of Cryptocephalinae leaf beetles. Zoologica Scripta, 50(5), 592\u2013615. Portico. https://doi.org/10.1111/zsc.12501\n", "decision": "INCLUDED", "name": "Fig. S6, ML", "studyID": "ot_2736", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from G\u00f3mez-Zurita, J., Jolivet, P., & Vogler, A. P. (2005). Molecular systematics of Eumolpinae and the relationships with Spilopyrinae (Coleoptera, Chrysomelidae). Molecular Phylogenetics and Evolution, 34(3), 584\u2013600. https://doi.org/10.1016/j.ympev.2004.11.022\n", "decision": "INCLUDED", "name": "Fig. 4, MP", "studyID": "ot_2738", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from G\u00f3mez-Zurita, J., Hunt, T., Kopliku, F., & Vogler, A. P. (2007). Recalibrated Tree of Leaf Beetles (Chrysomelidae) Indicates Independent Diversification of Angiosperms and Their Insect Herbivores. PLoS ONE, 2(4), e360. https://doi.org/10.1371/journal.pone.0000360\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2739", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GONZ\u00c1LEZ, J. A. C. (2006). Phylogenetic relationships of the genera of Epipsocetae (Psocoptera: Psocomorpha). Zootaxa, 1194(1). https://doi.org/10.11646/zootaxa.1194.1.1\n", "decision": "INCLUDED", "name": "Fig. 124, MP", "studyID": "ot_2740", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gonzalez V.H., & Griswold T.L. 2013. Wool carder bees of the genus Anthidium in the Western Hemisphere (Hymenoptera: Megachilidae): diversity, host plant associations, phylogeny, and biogeography. Zoological Journal of the Linnean Society, .", "decision": "INCLUDED", "name": "Untitled (tree6128)", "studyID": "pg_2617", "treeID": "tree6128"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gonz\u00e1lez-Obando, R., Garc\u00eda Aldrete, A. N., Carrejo-Gironza, N., & Mendivil, J. (2018). A new genus of Ptiloneuridae, its position within the family, and descriptions of five species (Psocodea, \u2018Psocoptera\u2019). ZooKeys, 780, 11\u201334. https://doi.org/10.3897/zookeys.780.26753\n", "decision": "INCLUDED", "name": "Fig. 47, MP", "studyID": "ot_2741", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from HOCHKIRCH, A., & G\u00d6RZIG, Y. (2009). Colonization and speciation on volcanic islands: phylogeography of the flightless grasshopper genus Arminda (Orthoptera, Acrididae) on the Canary Islands. Systematic Entomology, 34(1), 188\u2013197. Portico. https://doi.org/10.1111/j.1365-3113.2008.00449.x\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2742", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Goodman, K. R., & O\u2019Grady, P. (2013). Molecular Phylogeny and Biogeography of the Hawaiian Craneflies Dicranomyia (Diptera: Limoniidae). PLoS ONE, 8(9), e73019. https://doi.org/10.1371/journal.pone.0073019\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2743", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Stern, D. B., Breinholt, J., Pedraza\u2010Lara, C., L\u00f3pez\u2010Mej\u00eda, M., Owen, C. L., Bracken\u2010Grissom, H., Fetzner, J. W., & Crandall, K. A. (2017). Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead\u2010end. Evolution, 71(10), 2522\u20132532. Portico. https://doi.org/10.1111/evo.13326\n", "decision": "INCLUDED", "name": "Astacidea", "studyID": "ot_2745", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ghanavi, H. R., Rahimi, P., Tavana, M., Rezaei Tavabe, K., Jouladeh-Roudbar, A., & Doadrio, I. (2023). The evolutionary journey of freshwater crabs of the genus Potamon (Decapoda: Brachyura: Potamidae). Molecular Phylogenetics and Evolution, 180, 107690. https://doi.org/10.1016/j.ympev.2022.107690\n", "decision": "INCLUDED", "name": "Potamon", "studyID": "ot_2766", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Su, Z.-H., Sasaki, A., Minami, H., & Ozaki, K. (2024). Arthropod Phylotranscriptomics With a Special Focus on the Basal Phylogeny of the Myriapoda. Genome Biology and Evolution, 16(9). https://doi.org/10.1093/gbe/evae189\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_2768", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from JUNG, S., & LEE, S. (2011). Correlated evolution and Bayesian divergence time estimates of the Cimicoidea (Heteroptera: Cimicomorpha) reveal the evolutionary history. Systematic Entomology, 37(1), 22\u201331. Portico. https://doi.org/10.1111/j.1365-3113.2011.00596.x\n", "decision": "INCLUDED", "name": "Fig. S1, BI", "studyID": "ot_2772", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gough, H. M., Duran, D. P., Kawahara, A. Y., & Toussaint, E. F. A. (2018). A comprehensive molecular phylogeny of tiger beetles (Coleoptera, Carabidae, Cicindelinae). Systematic Entomology, 44(2), 305\u2013321. Portico. https://doi.org/10.1111/syen.12324\n", "decision": "INCLUDED", "name": "syen12324-sup-0002-appendixs2.tre", "studyID": "ot_2773", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BERNIKER, L., & WEIRAUCH, C. (2011). New World biogeography and the evolution of polychromatism: evidence from the bee assassin genus Apiomerus (Heteroptera: Reduviidae: Harpactorinae). Systematic Entomology, 37(1), 32\u201354. Portico. https://doi.org/10.1111/j.1365-3113.2011.00600.x\n", "decision": "INCLUDED", "name": "Fig. 10, MP", "studyID": "ot_2774", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DJERN\u00c6S, M., KLASS, K., PICKER, M. D., & DAMGAARD, J. (2011). Phylogeny of cockroaches (Insecta, Dictyoptera, Blattodea), with placement of aberrant taxa and exploration of out\u2010group sampling. Systematic Entomology, 37(1), 65\u201383. Portico. https://doi.org/10.1111/j.1365-3113.2011.00598.x\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2775", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GARZ\u00d3N\u2010ORDU\u00d1A, I. J. (2011). Phylogenetic evidence for loss of sound production and a shift in sexual recognition signals in Hamadryas butterflies (Nymphalidae: Biblidinae). Systematic Entomology, 37(1), 84\u2013101. Portico. https://doi.org/10.1111/j.1365-3113.2011.00599.x\n", "decision": "INCLUDED", "name": "Fig. 7B, MP", "studyID": "ot_2776", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ESCALONA, H. E., & \u015aLIPI\u0143SKI, A. (2011). Generic revision and phylogeny of Microweiseinae (Coleoptera: Coccinellidae). Systematic Entomology, 37(1), 125\u2013171. Portico. https://doi.org/10.1111/j.1365-3113.2011.00601.x\n", "decision": "INCLUDED", "name": "Fig. 1A, MP", "studyID": "ot_2777", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LAPOLLA, J. S., KALLAL, R. J., & BRADY, S. G. (2011). A new ant genus from the Greater Antilles and Central America, Zatania (Hymenoptera: Formicidae), exemplifies the utility of male and molecular character systems. Systematic Entomology, 37(1), 200\u2013214. Portico. https://doi.org/10.1111/j.1365-3113.2011.00605.x\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2778", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BLAIMER, B. B. (2011). Untangling complex morphological variation: taxonomic revision of the subgenus Crematogaster (Oxygyne) in Madagascar, with insight into the evolution and biogeography of this enigmatic ant clade (Hymenoptera: Formicidae). Systematic Entomology, 37(2), 240\u2013260. Portico. https://doi.org/10.1111/j.1365-3113.2011.00609.x\n", "decision": "INCLUDED", "name": "Fig. 16A, BI", "studyID": "ot_2779", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GRANDINETE, Y. C., HERMES, M. G., & NOLL, F. B. (2014). Systematics and phylogeny of the <scp>N</scp>eotropical Pachymenes de <scp>S</scp>aussure and Santamenes<scp>G</scp>iordani <scp>S</scp>oika (<scp>H</scp>ymenoptera, <scp>V</scp>espidae, <scp>E</scp>umeninae). Systematic Entomology, 40(2), 365\u2013384. Portico. https://doi.org/10.1111/syen.12105\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2780", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GRAY, D. A., WEISSMAN, D. B., COLE, J. A., LEMMON, E. M., & LEMMON, A. R. (2020). Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment. Zootaxa, 4750(3). https://doi.org/10.11646/zootaxa.4750.3.2\n", "decision": "INCLUDED", "name": "Gray_et_al_Gryllus_RAxML_tree.nex", "studyID": "ot_2781", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Stiller, J., Tilic, E., Rousset, V., Pleijel, F., & Rouse, G. W. (2020). Spaghetti to a Tree: A Robust Phylogeny for Terebelliformia (Annelida) Based on Transcriptomes, Molecular and Morphological Data. Biology, 9(4), 73. https://doi.org/10.3390/biology9040073\n", "decision": "INCLUDED", "name": "tree 1", "studyID": "ot_2783", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GONZALEZ, V. H., GRISWOLD, T., PRAZ, C. J., & DANFORTH, B. N. (2012). Phylogeny of the bee family Megachilidae (Hymenoptera: Apoidea) based on adult morphology. Systematic Entomology, 37(2), 261\u2013286. Portico. https://doi.org/10.1111/j.1365-3113.2012.00620.x\n", "decision": "INCLUDED", "name": "Fig. 23, MP", "studyID": "ot_2785", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Grebennikov, V. V., & Maddison, D. R. (2004). Phylogenetic analysis of Trechitae (Coleoptera: Carabidae) based on larval morphology, with a description of first\u2010instarPhrypeusand a key to genera. Systematic Entomology, 30(1), 38\u201359. Portico. https://doi.org/10.1111/j.1365-3113.2004.00259.x\n", "decision": "INCLUDED", "name": "Fig. 12, MP", "studyID": "ot_2786", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Grebennikov, V. V., Ballerio, A., Ocampo, F. C., & Scholtz, C. H. (2004). Larvae of Ceratocanthidae and Hybosoridae (Coleoptera: Scarabaeoidea): study of morphology, phylogenetic analysis and evidence of paraphyly of Hybosoridae. Systematic Entomology, 29(4), 524\u2013543. Portico. https://doi.org/10.1111/j.0307-6970.2004.00257.x\n", "decision": "INCLUDED", "name": "Fig.2, MP", "studyID": "ot_2787", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Glon, M. G., Broe, M. B., Crandall, K. A., Daly, M., Kong, S., Thoma, R. F., & Freudenstein, J. V. (2022). Anchored hybrid enrichment resolves the phylogeny ofLacunicambarusHobbs, 1969 (Decapoda: Astacidea: Cambaridae). Journal of Crustacean Biology, 42(1). https://doi.org/10.1093/jcbiol/ruab073\n", "decision": "INCLUDED", "name": "Lacunicambarus", "studyID": "ot_2790", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BUFFINGTON, M. L., BRADY, S. G., MORITA, S. I., & VAN NOORT, S. (2012). Divergence estimates and early evolutionary history of Figitidae (Hymenoptera: Cynipoidea). Systematic Entomology, 37(2), 287\u2013304. Portico. https://doi.org/10.1111/j.1365-3113.2012.00617.x\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2791", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CHENG, M., MUTUTANTRI, A., & CASSIS, G. (2012). Myrtlemiris, a new genus and new species of Australian plant bugs (Insecta: Heteroptera: Miridae): systematics, phylogeny and host associations. Systematic Entomology, 37(2), 305\u2013331. Portico. https://doi.org/10.1111/j.1365-3113.2012.00621.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2792", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Grzywacz, A., Trzeciak, P., Wiegmann, B. M., Cassel, B. K., Pape, T., Walczak, K., Bystrowski, C., Nelson, L., & Piwczy\u0144ski, M. (2021). Towards a new classification of Muscidae (Diptera): a comparison of hypotheses based on multiple molecular phylogenetic approaches. Systematic Entomology, 46(3), 508\u2013525. Portico. https://doi.org/10.1111/syen.12473\n", "decision": "INCLUDED", "name": "Fig. 3, ML", "studyID": "ot_2793", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Guan Z, Han B, Vierstraete A, Dumont HJ (2012) Additions and refinements to the molecular phylogeny of the Calopteryginae Sl (Zygoptera: Calopterygidae). Odonatologica, 41, 17-24.\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2797", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Guan, B., Guo, H., & Zhou, Z. (2016). Illumina next-generation sequencing reveals the mitochondrial genome of Ducetia japonica (Orthoptera: Tettigoniidae). Mitochondrial DNA Part B, 1(1), 361\u2013362. https://doi.org/10.1080/23802359.2016.1168717\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2798", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from HEMP, C., KEHL, S., HELLER, K., WOLFGANG W\u00c4GELE, J., & HEMP, A. (2012). Ecological adaptations of grassland\u2010inhabiting flightless Orthoptera: Fulvoscirtes and Acanthoscirtes, two new genera of African Karniellina (Orthoptera, Tettigoniidae, Conocephalinae, Conocephalini). Systematic Entomology, 37(2), 387\u2013407. Portico. https://doi.org/10.1111/j.1365-3113.2012.00622.x\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2801", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from FIK\u00c1\u010cEK, M., PROKIN, A., ANGUS, R. B., PONOMARENKO, A., YUE, Y., REN, D., & PROKOP, J. (2012). Phylogeny and the fossil record of the Helophoridae reveal Jurassic origin of extant hydrophiloid lineages (Coleoptera: Polyphaga). Systematic Entomology, 37(3), 420\u2013447. Portico. https://doi.org/10.1111/j.1365-3113.2012.00630.x\n", "decision": "INCLUDED", "name": "Fig. 10B, MP", "studyID": "ot_2802", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BRANSTETTER, M. G. (2012). Origin and diversification of the cryptic ant genus Stenamma Westwood (Hymenoptera: Formicidae), inferred from multilocus molecular data, biogeography and natural history. Systematic Entomology, 37(3), 478\u2013496. Portico. https://doi.org/10.1111/j.1365-3113.2012.00624.x\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2804", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CONFLITTI, I. M., SPIRONELLO, M., & CURRIE, D. C. (2012). Molecular phylogeny of the North American Simulium malyschevi\u2010group species (Diptera: Simuliidae). Systematic Entomology, 37(3), 571\u2013577. Portico. https://doi.org/10.1111/j.1365-3113.2012.00629.x\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2806", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from VUJI\u0106, A., RADENKOVI\u0106, S., ST\u00e5HLS, G., A\u010cANSKI, J., STEFANOVI\u0106, A., VESELI\u0106, S., ANDRI\u0106, A., & HAYAT, R. (2012). Systematics and taxonomy of theruficornisgroup of genusMerodonMeigen (Diptera: Syrphidae). Systematic Entomology, 37(3), 578\u2013602. Portico. https://doi.org/10.1111/j.1365-3113.2012.00631.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2807", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CURLER, G. R., & MOULTON, J. K. (2012). Phylogeny of psychodid subfamilies (Diptera: Psychodidae) inferred from nuclear DNA sequences with a review of morphological evidence for relationships. Systematic Entomology, 37(3), 603\u2013616. Portico. https://doi.org/10.1111/j.1365-3113.2012.00634.x\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2808", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LIU, X., HAYASHI, F., VIRAKTAMATH, C. A., & YANG, D. (2012). Systematics and biogeography of the dobsonfly genusNevromusRambur (Megaloptera: Corydalidae: Corydalinae) from the Oriental realm. Systematic Entomology, 37(4), 657\u2013669. Portico. https://doi.org/10.1111/j.1365-3113.2012.00635.x\n", "decision": "INCLUDED", "name": "Fig. 9, MP", "studyID": "ot_2809", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PENZ, C. M., DEVRIES, P. J., & WAHLBERG, N. (2012). Diversification of Morpho butterflies (Lepidoptera, Nymphalidae): a re\u2010evaluation of morphological characters and new insight from DNA sequence data. Systematic Entomology, 37(4), 670\u2013685. Portico. https://doi.org/10.1111/j.1365-3113.2012.00636.x\n", "decision": "INCLUDED", "name": "Fig. 2B, BI", "studyID": "ot_2810", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Guan, J.-Y., Zhang, Z.-Y., Cao, Y.-R., Xu, X.-D., Storey, K. B., Yu, D.-N., & Zhang, J.-Y. (2021). The complete mitochondrial genome of Choroterpes (Euthralus) yixingensis (Ephemeroptera: Leptophlebiidae) and its mitochondrial protein-coding gene expression under imidacloprid stress. Gene, 800, 145833. https://doi.org/10.1016/j.gene.2021.145833\n", "decision": "INCLUDED", "name": "Fig. 3", "studyID": "ot_2811", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PRADO, A., MCKENNA, D. D., & WINDSOR, D. (2012). Molecular evidence of cycad seed predation by immature Aulacoscelidinae (Coleoptera: Orsodacnidae). Systematic Entomology, 37(4), 747\u2013757. Portico. https://doi.org/10.1111/j.1365-3113.2012.00639.x\n", "decision": "INCLUDED", "name": "Fig. 4, ML", "studyID": "ot_2812", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from VEA, I. M., & GRIMALDI, D. A. (2012). Phylogeny of ensign scale insects (Hemiptera: Coccoidea: Ortheziidae) based on the morphology of Recent and fossil females. Systematic Entomology, 37(4), 758\u2013783. Portico. https://doi.org/10.1111/j.1365-3113.2012.00638.x\n", "decision": "INCLUDED", "name": "Fig. 13, MP", "studyID": "ot_2813", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from STAMPER, T., DAHLEM, G. A., COOKMAN, C., & DEBRY, R. W. (2012). Phylogenetic relationships of flesh flies in the subfamily Sarcophaginae based on three mtDNA fragments (Diptera: Sarcophagidae). Systematic Entomology, 38(1), 35\u201344. Portico. https://doi.org/10.1111/j.1365-3113.2012.00646.x\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2814", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LIU, L., HUANG, X., ZHANG, R., JIANG, L., & QIAO, G. (2012). Phylogenetic congruence between Mollitrichosiphum (Aphididae: Greenideinae) and Buchnera indicates insect\u2013bacteria parallel evolution. Systematic Entomology, 38(1), 81\u201392. Portico. https://doi.org/10.1111/j.1365-3113.2012.00647.x\n", "decision": "INCLUDED", "name": "Fig. 2A, MP", "studyID": "ot_2816", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jin, M., Zwick, A., \u015alipi\u0144ski, A., de Keyzer, R., & Pang, H. (2020). Museomics reveals extensive cryptic diversity of Australian prionine longhorn beetles with implications for their classification and conservation. Systematic Entomology, 45(4), 745\u2013770. Portico. https://doi.org/10.1111/syen.12424\n", "decision": "INCLUDED", "name": "syen12424-sup-0003-supinfos3.nex", "studyID": "ot_2823", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Thoma, R., Hurt, C., Williams, C., & Withers, D. (2023). Insights on the evolution and conservation of Appalachian burrowing crayfishes, with the description of a new species ofCambarusErichson, 1846 (Decapoda: Astacidea: Cambaridae). Journal of Crustacean Biology, 43(1). https://doi.org/10.1093/jcbiol/ruac066\n", "decision": "INCLUDED", "name": "Thoma et al. 2023", "studyID": "ot_2825", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Varela, C., Golightly, C., Timm, L. E., Wilkins, B., Frank, T., Fenolio, D., Collins, S. B., & Bracken-Grissom, H. D. (2021). DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters. Journal of Crustacean Biology, 41(1). https://doi.org/10.1093/jcbiol/ruab005\n", "decision": "INCLUDED", "name": "Lophogastrida", "studyID": "ot_2828", "treeID": "tree9"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Varela, C., Golightly, C., Timm, L. E., Wilkins, B., Frank, T., Fenolio, D., Collins, S. B., & Bracken-Grissom, H. D. (2021). DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters. Journal of Crustacean Biology, 41(1). https://doi.org/10.1093/jcbiol/ruab005\n", "decision": "INCLUDED", "name": "Amphipoda", "studyID": "ot_2828", "treeID": "tree7"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Varela, C., Golightly, C., Timm, L. E., Wilkins, B., Frank, T., Fenolio, D., Collins, S. B., & Bracken-Grissom, H. D. (2021). DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters. Journal of Crustacean Biology, 41(1). https://doi.org/10.1093/jcbiol/ruab005\n", "decision": "INCLUDED", "name": "Euphausiacea", "studyID": "ot_2828", "treeID": "tree6"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Patoka, J., Bl\u00e1ha, M., & Kouba, A. (2015). Cherax( Cherax) subterigneus, a new crayfish (Decapoda:\u00a0Parastacidae) from West Papua, Indonesia. Journal of Crustacean Biology, 35(6), 830\u2013838. https://doi.org/10.1163/1937240x-00002377\n", "decision": "INCLUDED", "name": "Cherax snowden", "studyID": "ot_2830", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lukhaup, C., Panteleit, J., & Schrimpf, A. (2015). Cherax snowden, a new species of crayfish (Crustacea, Decapoda, Parastacidae) from the Kepala Burung (Vogelkop) Peninsula in Irian Jaya (West Papua), Indonesia. ZooKeys, 518, 1\u201314. https://doi.org/10.3897/zookeys.518.6127\n", "decision": "INCLUDED", "name": "Cherax snowden", "studyID": "ot_2831", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lukhaup, C.; Eprilurahman, R.; von Rintelen, T. Two New Species of Crayfish of the Genus Cherax (Crustacea, Decapoda, Parastacidae) from Western and Eastern Indonesian New Guinea. Arthropoda 2024, 2, 264-293. https://doi.org/10.3390/arthropoda2040019", "decision": "INCLUDED", "name": "Lukhaup 2024", "studyID": "ot_2833", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lukhaup, C., & Eprilurahman, R. (2022). A new species of crayfish of the genus Cherax from Indonesian New Guinea (Crustacea, Decapoda, Parastacidae). Zoosystematics and Evolution, 98(2), 411\u2013425. https://doi.org/10.3897/zse.98.94753\n", "decision": "INCLUDED", "name": "Lukhaup 2022", "studyID": "ot_2834", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Wolfe, J. M., Breinholt, J. W., Crandall, K. A., Lemmon, A. R., Lemmon, E. M., Timm, L. E., Siddall, M. E., & Bracken-Grissom, H. D. (2019). A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans. Proceedings of the Royal Society B: Biological Sciences, 286(1901), 20190079. https://doi.org/10.1098/rspb.2019.0079\n", "decision": "INCLUDED", "name": "Pleocyemata", "studyID": "ot_2755", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Thoma, R. F., & Williams, B. W. (2025). Cambarus ocoeensis, a new species of crayfish (Decapoda: Cambaridae) from the Ocoee River Basin of Tennessee, USA. Zootaxa, 5618(1), 106\u2013118. https://doi.org/10.11646/zootaxa.5618.1.7\n", "decision": "INCLUDED", "name": "Thoma & Williams 2025", "studyID": "ot_2837", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Stringer, D. N., King, R. A., Austin, A. D., & Guzik, M. T. (2025). An Elusive New Genus and Species of Subterranean Amphipod (Hadzioidea: Eriopisidae) from Barrow Island, Western Australia. Diversity, 17(2), 84. https://doi.org/10.3390/d17020084\n", "decision": "INCLUDED", "name": "Stringer et al. 2025 (genus level)", "studyID": "ot_2841", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Stringer, D. N., King, R. A., Austin, A. D., & Guzik, M. T. (2025). An Elusive New Genus and Species of Subterranean Amphipod (Hadzioidea: Eriopisidae) from Barrow Island, Western Australia. Diversity, 17(2), 84. https://doi.org/10.3390/d17020084\n", "decision": "INCLUDED", "name": "Stringer et al. 2025 (species level)", "studyID": "ot_2841", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Pedraza-Lara, C., Guti\u00e9rrez-Yurrita, P. J., & Jesus-Bonilla, V. S. D. (2021). A new species of Procambarus (Decapoda, Cambaridae) from the State of Quer\u00e9taro, Mexico. ZooKeys, 1048, 1\u201321. https://doi.org/10.3897/zookeys.1048.57493\n", "decision": "INCLUDED", "name": "Pedraza-Lara et al. 2021", "studyID": "ot_2843", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Vojkovsk\u00e1, R., Hork\u00e1, I., & \u010euri\u0161, Z. (2020). Comparative morphology of crayfish mandibles, with insight into their evolution. Journal of Morphology, 281(3), 365\u2013376. Portico. https://doi.org/10.1002/jmor.21104\n", "decision": "INCLUDED", "name": "Vojkovsk\u00e1 et al. 2020", "studyID": "ot_2845", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bergsten, J., Nylander, J. A. A., Ospina, O. E., Lemmon, A. R., & Miller, K. B. (2025). Whole genome shotgun phylogenomics resolve the diving beetle tree of life. Systematic Entomology. Portico. https://doi.org/10.1111/syen.12685\n", "decision": "INCLUDED", "name": "Bergsten et al. 2025 (Figure 5)", "studyID": "ot_2846", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bergsten, J., Nylander, J. A. A., Ospina, O. E., Lemmon, A. R., & Miller, K. B. (2025). Whole genome shotgun phylogenomics resolve the diving beetle tree of life. Systematic Entomology. Portico. https://doi.org/10.1111/syen.12685\n", "decision": "INCLUDED", "name": "Bergsten et al. 2025 (Figure 5)", "studyID": "ot_2846", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Sato, S., Appeldorff, C., Wangensteen, O. S., Garc\u00e9s-Pastor, S., Laumer, C. E., Herranz, M., Giribet, G., Renault, D., Rask M\u00f8ller, P., & Worsaae, K. (2025). Phylogenomics of the rarest animals: a second species of Micrognathozoa identified by machine learning. Proceedings of the Royal Society B: Biological Sciences, 292(2041). https://doi.org/10.1098/rspb.2024.2867\n", "decision": "INCLUDED", "name": "Sato et al. 2025 (Figure 3)", "studyID": "ot_2847", "treeID": "tree4"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from TIHELKA, E., GIACOMELLI, M., HUANG, D.-Y., PISANI, D., DONOGHUE, P. C. J., & CAI, C.-Y. (2020). Fleas are parasitic scorpionfliest; Palaeoentomology, 3(6), 641\u2013653. https://doi.org/10.11646/palaeoentomology.3.6.16\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2852", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from WARE, J. L., LITMAN, J., KLASS, K., & SPEARMAN, L. A. (2008). Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology. Systematic Entomology, 33(3), 429\u2013450. Portico. https://doi.org/10.1111/j.1365-3113.2008.00424.x\n", "decision": "INCLUDED", "name": "Fig. 3A, BI", "studyID": "ot_2853", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, J., Zhou, C., Gai, Y., Song, D., & Zhou, K. (2008). The complete mitochondrial genome of Parafronurus youi (Insecta: Ephemeroptera) and phylogenetic position of the Ephemeroptera. Gene, 424(1\u20132), 18\u201324. https://doi.org/10.1016/j.gene.2008.07.037\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2854", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Whiting, M. F. (2002). Mecoptera is paraphyletic: multiple genes and phylogeny of Mecoptera and Siphonaptera. Zoologica Scripta, 31(1), 93\u2013104. Portico. https://doi.org/10.1046/j.0300-3256.2001.00095.x\n", "decision": "INCLUDED", "name": "Fig. 5, MP", "studyID": "ot_2855", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Meusemann, K., Trautwein, M., Friedrich, F., Beutel, R. G., Wiegmann, B. M., Donath, A., Podsiadlowski, L., Petersen, M., Niehuis, O., Mayer, C., Bayless, K. M., Shin, S., Liu, S., Hlinka, O., Minh, B. Q., Kozlov, A., Morel, B., Peters, R. S., Bartel, D., \u2026 Yeates, D. K. (2020). Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola). https://doi.org/10.1101/2020.11.19.390666\n", "decision": "INCLUDED", "name": "Fig. 2b, ML", "studyID": "ot_2856", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Schoville, S. D., Simon, S., Bai, M., Beethem, Z., Dudko, R. Y., Eberhard, M. J. B., Frandsen, P. B., K\u00fcpper, S. C., Machida, R., Verheij, M., Willadsen, P. C., Zhou, X., & Wipfler, B. (2020). Comparative transcriptomics of ice\u2010crawlers demonstrates cold specialization constrains niche evolution in a relict lineage. Evolutionary Applications, 14(2), 360\u2013382. Portico. https://doi.org/10.1111/eva.13120\n", "decision": "INCLUDED", "name": "Fig. 1a", "studyID": "ot_2857", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Shen, S.-Q., Cai, Y.-Y., Xu, K.-K., Chen, Q.-P., Cao, S.-S., Yu, D.-N., & Zhang, J.-Y. (2020). The complete mitochondrial genome of Pedetontus zhejiangensis (Microcoryphia: Machilidae) and its phylogeny. Mitochondrial DNA Part B, 5(3), 3143\u20133145. https://doi.org/10.1080/23802359.2020.1804472\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2861", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kaplin, V. G. (2018). A Survey of the Distribution and Phylogenetic Relationships of the Silvestrichilis Group of Genera and of the Species of the Genus Silvestrichilis Wygodz. (Archaeognatha, Machilidae) with Description of a New Species from South Ossetia. Entomological Review, 98(3), 329\u2013351. https://doi.org/10.1134/s0013873818030107\n", "decision": "INCLUDED", "name": "Fig. 2", "studyID": "ot_2862", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Wang, Z., Shi, Y., Qiu, Z., Che, Y., & Lo, N. (2017). Reconstructing the phylogeny of Blattodea: robust support for interfamilial relationships and major clades. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-04243-1\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2863", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Liu, J., Zhang, J., Han, W., Wang, Y., He, S., & Wang, Z. (2023). Advances in the understanding of Blattodea evolution: Insights from phylotranscriptomics and spermathecae. Molecular Phylogenetics and Evolution, 182, 107753. https://doi.org/10.1016/j.ympev.2023.107753\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2864", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Liu, G., Liu, M., Hui, W., Chen, C., & Zhang, Y. (2016). Complete mitochondrial genome of Polyphaga plancyi (Blattaria: Polyphagidae). Mitochondrial DNA Part B, 1(1), 625\u2013626. https://doi.org/10.1080/23802359.2016.1214545\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2866", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Wang, P., Zhu, J., Wang, M., Zhang, Y., Wang, J., Zhu, Y., & Zhang, P. (2016). The complete mitochondrial genome of Reticulitermes labralis and implications for Rhinotermitidae taxonomy. Mitochondrial DNA Part B, 1(1), 392\u2013393. https://doi.org/10.1080/23802359.2016.1174085\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2867", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lee, W., Han, T., Lee, J.-H., Hong, K.-J., & Park, J. (2017). The complete mitochondrial genome of the subterranean termite,Reticulitermes speratus kyushuensisMorimoto, 1968 (Isoptera: Rhinotermitidae). Mitochondrial DNA Part B, 2(1), 178\u2013179. https://doi.org/10.1080/23802359.2017.1303341\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2868", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Herv\u00e9, V., & Brune, A. (2017). The complete mitochondrial genomes of the higher termitesLabiotermes labralisandEmbiratermes neotenicus(Termitidae: Syntermitinae). Mitochondrial DNA Part B, 2(1), 109\u2013110. https://doi.org/10.1080/23802359.2017.1289349\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2869", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ROCHA, M. M., CANCELLO, E. M., & CARRIJO, T. F. (2012). Neotropical termites: revision ofArmitermesWasmann (Isoptera, Termitidae, Syntermitinae) and phylogeny of the Syntermitinae. Systematic Entomology, 37(4), 793\u2013827. Portico. https://doi.org/10.1111/j.1365-3113.2012.00645.x\n", "decision": "INCLUDED", "name": "Fig. 20, MP", "studyID": "ot_2870", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Davis, K. E., De\u00a0Grave, S., Delmer, C., Payne, A. R. D., Mitchell, S., & Wills, M. A. (2022). Ecological Transitions and the Shape of the Decapod Tree of Life. Integrative and Comparative Biology, 62(2), 332\u2013344. https://doi.org/10.1093/icb/icac052\n", "decision": "INCLUDED", "name": "Davis et al. 2022 (Figure 2)", "studyID": "ot_2876", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Shih HT, Rahayu DL, Pramono FA. 2025. Integrative taxonomy uncovers four new species and one new record of land hermit crabs Coenobita Latreille, 1829 (Crustacea: Decapoda: Anomura: Coenobitidae) from Indonesia. Zool Stud 64:11. doi:10.6620/ZS.2025.64-11.", "decision": "INCLUDED", "name": "Shih et al. 2025", "studyID": "ot_2877", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Wang, Z., Wang, Z., Chen, X., Jiang, W., Cui, C., & Cui, L. (2025). Based on Mitochondrial Genomes and Gene Order Rearrangements: Phylogenetic Relationships and Terrestrial Adaptability in Paguroidea (Crustacea: Decapoda). Ecology and Evolution, 15(8). Portico. https://doi.org/10.1002/ece3.71975\n", "decision": "INCLUDED", "name": "Wang et al. 2025", "studyID": "ot_2878", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Mota, T. A., De Grave, S., & Carvalho, F. L. (2025). Multigene analysis reveals that Pseudopalaemon Sollaud, 1911 is a junior synonym of the widespread genus Macrobrachium Spence Bate, 1868 (Decapoda: Caridea: Palaemonidae). Journal of Crustacean Biology, 45(3). https://doi.org/10.1093/jcbiol/ruaf048\n", "decision": "INCLUDED", "name": "Mota et al. 2025", "studyID": "ot_2880", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PIWCZY\u0143SKI, M., SZPILA, K., GRZYWACZ, A., & PAPE, T. (2014). A large\u2010scale molecular phylogeny of flesh flies (<scp>D</scp>iptera: <scp>S</scp>arcophagidae). Systematic Entomology, 39(4), 783\u2013799. Portico. https://doi.org/10.1111/syen.12086\n", "decision": "INCLUDED", "name": "Fig. 5, ML", "studyID": "ot_2881", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from HEMP, C., KEHL, S., SCHULTZ, O., W\u00c4GELE, J. W., & HEMP, A. (2014). Climatic fluctuations and orogenesis as motors for\u00a0speciation in <scp>E</scp>ast <scp>A</scp>frica: case study on Parepistaurus<scp>K</scp>arsch, 1896 (<scp>O</scp>rthoptera). Systematic Entomology, 40(1), 17\u201334. Portico. https://doi.org/10.1111/syen.12092\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2882", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from SONG, H., SHEFFIELD, N. C., CAMERON, S. L., MILLER, K. B., & WHITING, M. F. (2010). When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Systematic Entomology, 35(3), 429\u2013448. https://doi.org/10.1111/j.1365-3113.2009.00517.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2883", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DRESSLER, C., GE, S., & BEUTEL, R. G. (2011). Is Meru a specialized noterid (Coleoptera, Adephaga)? Systematic Entomology, 36(4), 705\u2013712. Portico. https://doi.org/10.1111/j.1365-3113.2011.00585.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2885", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LIEBHERR, J. K., MARRIS, J. W. M., EMBERSON, R. M., SYRETT, P., & ROIG\u2010JU\u00d1ENT, S. (2011). Orthoglymma wangapeka gen.n., sp.n. (Coleoptera: Carabidae: Broscini): a newly discovered relict from the Buller Terrane, north\u2010western South Island, New Zealand, corroborates a general pattern of Gondwanan endemism. Systematic Entomology, 36(3), 395\u2013414. Portico. https://doi.org/10.1111/j.1365-3113.2011.00569.x\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2886", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kavanaugh, D. H., Maddison, D. R., Simison, W. B., Schoville, S. D., Schmidt, J., Faille, A., Moore, W., Pflug, J. M., Archambeault, S. L., Hoang, T., & Chen, J.-Y. (2021). Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. ZooKeys, 1044, 41\u2013152. https://doi.org/10.3897/zookeys.1044.62245\n", "decision": "INCLUDED", "name": "NebriitaeMatricesAndTrees.nex", "studyID": "ot_2888", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Maddison, D. R., Kanda, K., Boyd, O. F., Faille, A., Porch, N., Erwin, T. L., & Roig-Ju\u00f1ent, S. (2019). Phylogeny of the beetle supertribe Trechitae (Coleoptera: Carabidae): Unexpected clades, isolated lineages, and morphological convergence. Molecular Phylogenetics and Evolution, 132, 151\u2013176. https://doi.org/10.1016/j.ympev.2018.11.006\n", "decision": "INCLUDED", "name": "TrechitesFinalMatricesAndAnalyses.nex", "studyID": "ot_2889", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Maddison, D. R., & Porch, N. (2021). A preliminary phylogeny and review of the genus Tasmanitachoides, with descriptions of two new species (Coleoptera, Carabidae, Bembidarenini). ZooKeys, 1044, 153\u2013196. https://doi.org/10.3897/zookeys.1044.62253\n", "decision": "INCLUDED", "name": "Fig. 5, ML", "studyID": "ot_2890", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PALADINI, A., TAKIYA, D. M., CAVICHIOLI, R. R., & CARVALHO, G. S. (2014). Phylogeny and biogeography of <scp>N</scp>eotropical spittlebugs (<scp>H</scp>emiptera: <scp>C</scp>ercopidae: <scp>I</scp>schnorhininae): revised tribal classification based on morphological data. Systematic Entomology, 40(1), 82\u2013108. Portico. https://doi.org/10.1111/syen.12091\n", "decision": "INCLUDED", "name": "Fig. 10, MP", "studyID": "ot_2892", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Hawlitschek, O., Hendrich, L., & Balke, M. (2012). Molecular phylogeny of the squeak beetles, a family with disjunct Palearctic-Australian range. Molecular Phylogenetics and Evolution, 62(1), 550\u2013554. https://doi.org/10.1016/j.ympev.2011.09.015\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2893", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from MICHAT, M. C., ALARIE, Y., & MILLER, K. B. (2017). Higher\u2010level phylogeny of diving beetles (<scp>C</scp>oleoptera: <scp>D</scp>ytiscidae) based on larval characters. Systematic Entomology, 42(4), 734\u2013767. Portico. https://doi.org/10.1111/syen.12243\n", "decision": "INCLUDED", "name": "Figs. 5,6", "studyID": "ot_2894", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Michat, M. C., & Alarie, Y. (2013). Phylogenetic relationships, larval morphology, and chaetotaxy of the subfamily Coptotominae (Coleoptera: Dytiscidae). The Canadian Entomologist, 145(3), 247\u2013264. https://doi.org/10.4039/tce.2012.100\n", "decision": "INCLUDED", "name": "Fig. 20, MP", "studyID": "ot_2895", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Miller, K. B., Bergsten, J., & Whiting, M. F. (2009). Phylogeny and classification of the tribe Hydaticini (Coleoptera: Dytiscidae): partition choice for Bayesian analysis with multiple nuclear and mitochondrial protein\u2010coding genes. Zoologica Scripta, 38(6), 591\u2013615. Portico. https://doi.org/10.1111/j.1463-6409.2009.00393.x\n", "decision": "INCLUDED", "name": "Fig. 23, BI", "studyID": "ot_2896", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Miller, K. B. (2001). Revision and phylogenetic analysis of the New World genus Neoclypeodytes Young (Coleoptera: Dytiscidae: Hydroporinae: Bidessini). Systematic Entomology, 26(1), 87\u2013123. Portico. https://doi.org/10.1046/j.1365-3113.2001.00144.x\n", "decision": "INCLUDED", "name": "Fig. 33", "studyID": "ot_2897", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ribera, I., Bilton, D. T., Balke, M., & Hendrich, L. (2003). Evolution, mitochondrial DNA phylogeny and systematic position of the Macaronesian endemic Hydrotarsus Falkenstr\u00f6m (Coleoptera: Dytiscidae). Systematic Entomology, 28(4), 493\u2013508. Portico. https://doi.org/10.1046/j.1365-3113.2003.00226.x\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_2898", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from MILLER, K. B., & BERGSTEN, J. (2012). Phylogeny and classification of whirligig beetles (Coleoptera: Gyrinidae): relaxed\u2010clock model outperforms parsimony and time\u2010free Bayesian analyses. Systematic Entomology, 37(4), 706\u2013746. Portico. https://doi.org/10.1111/j.1365-3113.2012.00640.x\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2900", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gustafson, G. T., Prokin, A. A., Bukontaite, R., Bergsten, J., & Miller, K. B. (2017). Tip-dated phylogeny of whirligig beetles reveals ancient lineage surviving on Madagascar. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-08403-1\n", "decision": "INCLUDED", "name": "Fig. S1, BI", "studyID": "ot_2901", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Li, Y., Liu, Z., Jarzembowski, E. A., Yin, Z., Huang, D., & Cai, C. (2019). Early evolution of Cupedidae revealed by a mid\u2010Cretaceous reticulated beetle from Myanmar (Coleoptera: Archostemata). Systematic Entomology, 44(4), 777\u2013786. Portico. https://doi.org/10.1111/syen.12355\n", "decision": "INCLUDED", "name": "Fig. 4, MP", "studyID": "ot_2902", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from H\u00d6RNSCHEMEYER, T. (2009). The species\u2010level phylogeny of archostematan beetles\u2014where doMicromalthus debilisandCrowsoniella relictabelong? Systematic Entomology, 34(3), 533\u2013558. Portico. https://doi.org/10.1111/j.1365-3113.2009.00476.x\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2903", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Yavorskaya, M. I., Anton, E., Ja\u0142oszy\u0144ski, P., Polilov, A., & Beutel, R. G. (2018). Cephalic anatomy of Sphaeriusidae and a morphology\u2010based phylogeny of the suborder Myxophaga (Coleoptera). Systematic Entomology, 43(4), 777\u2013797. Portico. https://doi.org/10.1111/syen.12304\n", "decision": "INCLUDED", "name": "Fig. 7, MP", "studyID": "ot_2904", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CATERINO, M. S., & TISHECHKIN, A. K. (2014). Phylogeny and generic limits in <scp>N</scp>ew <scp>W</scp>orld <scp>E</scp>xosternini (<scp>C</scp>oleoptera: <scp>H</scp>isteridae: <scp>H</scp>isterinae). Systematic Entomology, 40(1), 109\u2013142. Portico. https://doi.org/10.1111/syen.12095\n", "decision": "INCLUDED", "name": "Figs. 238-241, MP", "studyID": "ot_2905", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from SHORT, A. E. Z., JOLY, L. J., GARC\u00cdA, M., WILD, A. L., BLOOM, D. D., & MADDISON, D. R. (2015). Molecular phylogeny of the<scp>H</scp>ydroscaphidae (<scp>C</scp>oleoptera:<scp>M</scp>yxophaga) with description of a remarkable new lineage from the<scp>G</scp>uiana<scp>S</scp>hield. Systematic Entomology, 40(1), 214\u2013229. Portico. https://doi.org/10.1111/syen.12097\n", "decision": "INCLUDED", "name": "Fig. S1B, BI", "studyID": "ot_2906", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LESCHEN, R. A. B., & BUCKLEY, T. R. (2014). Revision and phylogeny of Syrphetodes (<scp>C</scp>oleoptera: <scp>U</scp>lodidae): implications for biogeography, alpinization and conservation. Systematic Entomology, 40(1), 143\u2013168. Portico. https://doi.org/10.1111/syen.12094\n", "decision": "INCLUDED", "name": "Fig. 11A, BI", "studyID": "ot_2908", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kiefer, J. S. T., Bauer, E., Okude, G., Fukatsu, T., Kaltenpoth, M., & Engl, T. (2023). Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles. The ISME Journal, 17(7), 1029\u20131039. https://doi.org/10.1038/s41396-023-01415-y\n", "decision": "INCLUDED", "name": "Fig. 1 Left, BI", "studyID": "ot_2911", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kiselyova, T., & Mchugh, J. V. (2006). A phylogenetic study of Dermestidae (Coleoptera) based on larval morphology. Systematic Entomology, 31(3), 469\u2013507. Portico. https://doi.org/10.1111/j.1365-3113.2006.00335.x\n", "decision": "INCLUDED", "name": "Fig. 27, MP", "studyID": "ot_2913", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LIU, Q., CHEN, J., HUANG, X., JIANG, L., & QIAO, G. (2014). Ancient association with <scp>F</scp>agaceae in the aphid tribe <scp>G</scp>reenideini (<scp>H</scp>emiptera: <scp>A</scp>phididae: <scp>G</scp>reenideinae). Systematic Entomology, 40(1), 230\u2013241. Portico. https://doi.org/10.1111/syen.12100\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2914", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Motyka, M., Kusy, D., H\u00e1va, J., Jahod\u00e1\u0159ov\u00e1, E., B\u00edlkov\u00e1, R., Vogler, A. P., & Bocak, L. (2021). Mitogenomic data elucidate the phylogeny and evolution of life strategies in Dermestidae (Coleoptera). Systematic Entomology, 47(1), 82\u201393. Portico. https://doi.org/10.1111/syen.12520\n", "decision": "INCLUDED", "name": "Fig. S2A", "studyID": "ot_2915", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ROBERTSON, J. A., \u015aLIPI\u0143SKI, A., MOULTON, M., SHOCKLEY, F. W., GIORGI, A., LORD, N. P., MCKENNA, D. D., TOMASZEWSKA, W., FORRESTER, J., MILLER, K. B., WHITING, M. F., & MCHUGH, J. V. (2015). Phylogeny and classification of<scp>C</scp>ucujoidea and the recognition of a new superfamily<scp>C</scp>occinelloidea (<scp>C</scp>oleoptera:<scp>C</scp>ucujiformia). Systematic Entomology, 40(4), 745\u2013778. Portico. https://doi.org/10.1111/syen.12138\n", "decision": "INCLUDED", "name": "Figs. 4-9, ML", "studyID": "ot_2917", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Robertson, J. A., Whiting, M. F., & McHugh, J. V. (2008). Searching for natural lineages within the Cerylonid Series (Coleoptera: Cucujoidea). Molecular Phylogenetics and Evolution, 46(1), 193\u2013205. https://doi.org/10.1016/j.ympev.2007.09.017\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2918", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Shin, N. R., Shin, S., Okamura, Y., Kirsch, R., Lombard, V., Svacha, P., Denux, O., Augustin, S., Henrissat, B., McKenna, D. D., & Pauchet, Y. (2021). Larvae of longhorned beetles (Coleoptera; Cerambycidae) have evolved a diverse and phylogenetically conserved array of plant cell wall degrading enzymes. Systematic Entomology, 46(4), 784\u2013797. Portico. https://doi.org/10.1111/syen.12488\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2919", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jin, M., Shin, S., Ashman, L. G., Leschen, R. A. B., Zwick, A., de Keyzer, R., McKenna, D. D., & \u015alipi\u0144ski, A. (2022). Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles. Molecular Phylogenetics and Evolution, 172, 107486. https://doi.org/10.1016/j.ympev.2022.107486\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2920", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Wang, J., Dai, X.-Y., Xu, X.-D., Zhang, Z.-Y., Yu, D.-N., Storey, K. B., & Zhang, J.-Y. (2019). The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae. PeerJ, 7, e7633. Portico. https://doi.org/10.7717/peerj.7633\n", "decision": "INCLUDED", "name": "Fig. 4 left, BI", "studyID": "ot_2921", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lee, S., & Lee, S. (2020). Multigene phylogeny uncovers oviposition-related evolutionary history of Cerambycinae (Coleoptera: Cerambycidae). Molecular Phylogenetics and Evolution, 145, 106707. https://doi.org/10.1016/j.ympev.2019.106707\n", "decision": "INCLUDED", "name": "Fig. 2", "studyID": "ot_2922", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Oberski, J. T. (2024). <scp>Ultraconserved element (UCE)</scp> phylogenomics illuminates the evolutionary history and biogeography of Dorymyrmex pyramid ants. Systematic Entomology, 50(2), 325\u2013348. Portico. https://doi.org/10.1111/syen.12658\n", "decision": "INCLUDED", "name": "IQtree-output_LFD-185t-870loci-122...", "studyID": "ot_2923", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Sutherland, L. N., Schnepp, K. E., Powell, G. S., & Bybee, S. M. (2021). Phylogenetic Placement of the Plesioclytini (Coleoptera: Cerambycidae: Cerambycinae). Diversity, 13(11), 597. https://doi.org/10.3390/d13110597\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2924", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, H., Song, N., & Yin, X. (2022). Higher-level phylogeny of Chrysomelidae based on expanded sampling of mitogenomes. PLOS ONE, 17(1), e0258587. https://doi.org/10.1371/journal.pone.0258587\n", "decision": "INCLUDED", "name": "Fig. S1, ML", "studyID": "ot_2925", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, Y. M., Delvare, G., Blaimer, B. B., Cruaud, A., Rasplus, J., Brady, S. G., & Gates, M. W. (2025). Phasing in and out of phytophagy: Phylogeny and evolution of the family Eurytomidae (Hymenoptera: Chalcidoidea) based on Ultraconserved Elements. Systematic Entomology. Portico. https://doi.org/10.1111/syen.12682\n", "decision": "INCLUDED", "name": "Eury70p_MCMCTree.tre", "studyID": "ot_2767", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, L.-J., Wu, L., Li, Y., Li, J.-G., Yang, X.-K., & Nie, R.-E. (2019). The complete mitochondrial genome of the seed-borer weevil, Bruchidius uberatus (Coleoptera: Chrysomelidae: Bruchinae). Mitochondrial DNA Part B, 5(1), 308\u2013309. https://doi.org/10.1080/23802359.2019.1698331\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2926", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cardoso, G. A., Cunha, V. A. S., Genevcius, B. C., Madeira\u2010Ott, T., Costa, B. M. de A., Rossoni, D. M., Thyssen, P. J., & Torres, T. T. (2025). Origins and Diversification of Myiasis Across Blowflies. Ecology and Evolution, 15(2). Portico. https://doi.org/10.1002/ece3.70993\n", "decision": "INCLUDED", "name": "Complete_tree.tre", "studyID": "ot_2927", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from WAICHERT, C., VON DOHLEN, C. D., & PITTS, J. P. (2014). Resurrection, revision and molecular phylogenetics of Eragenia<scp>B</scp>anks with implications for <scp>A</scp>geniellini systematics (<scp>H</scp>ymenoptera: <scp>P</scp>ompilidae). Systematic Entomology, 40(2), 291\u2013321. Portico. https://doi.org/10.1111/syen.12101\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2928", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Wu, M., Qian, X., Qin, M., Tu, T., & Zhang, R. (2020). Characterization of the complete mitochondrial genome ofCaryopemon giganteusPic (Coleoptera: Chrysomelidae: Bruchinae). Mitochondrial DNA Part B, 5(1), 929\u2013931. https://doi.org/10.1080/23802359.2020.1719927\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2929", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Song, N., Yin, X., Zhao, X., Chen, J., & Yin, J. (2017). Reconstruction of mitogenomes by NGS and phylogenetic implications for leaf beetles. Mitochondrial DNA Part A, 29(7), 1041\u20131050. https://doi.org/10.1080/24701394.2017.1404044\n", "decision": "INCLUDED", "name": "Fig. 3, ML", "studyID": "ot_2930", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PONCE, F. V., BREINHOLT, J. W., HOSSIE, T., BARBER, J. R., JANZEN, D. H., HALLWACHS, W., & KAWAHARA, A. Y. (2014). A molecular phylogeny of Eumorpha (<scp>L</scp>epidoptera: <scp>S</scp>phingidae) and the evolution of anti\u2010predator larval eyespots. Systematic Entomology, 40(2), 401\u2013408. Portico. https://doi.org/10.1111/syen.12111\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2931", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LEIVAS, F. W. T., BICHO, C. L., & ALMEIDA, L. M. (2014). Cladistic analysis of<scp>O</scp>malodini<scp>K</scp>ryzhanovskij (<scp>C</scp>oleoptera:<scp>H</scp>isteridae:<scp>H</scp>isterinae). Systematic Entomology, 40(2), 433\u2013455. Portico. https://doi.org/10.1111/syen.12112\n", "decision": "INCLUDED", "name": "Fig. 12, MP", "studyID": "ot_2932", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kirsch, R., Okamura, Y., Garc\u00eda-Lozano, M., Weiss, B., Keller, J., Vogel, H., Fukumori, K., Fukatsu, T., Konstantinov, A. S., Montagna, M., Moseyko, A. G., Riley, E. G., Slipinski, A., Vencl, F. V., Windsor, D. M., Salem, H., Kaltenpoth, M., & Pauchet, Y. (2025). Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles. Current Biology, 35(3), 640-654.e7. https://doi.org/10.1016/j.cub.2024.12.028\n", "decision": "INCLUDED", "name": "Fig. S3", "studyID": "ot_2933", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kergoat, G. J., Delobel, A., & Silvain, J.-F. (2004). Phylogeny and host-specificity of European seed beetles (Coleoptera, Bruchidae), new insights from molecular and ecological data. Molecular Phylogenetics and Evolution, 32(3), 855\u2013865. https://doi.org/10.1016/j.ympev.2004.02.019\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2934", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from WINTERTON, S. L., & WARE, J. L. (2015). Phylogeny, divergence times and biogeography of window flies (Scenopinidae) and the therevoid clade (Diptera: Asiloidea). Systematic Entomology, 40(3), 491\u2013519. Portico. https://doi.org/10.1111/syen.12117\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2935", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from L\u00d3PEZ\u2010P\u00c9REZ, S., ZARAGOZA\u2010CABALLERO, S., OCHOTERENA, H., & MORRONE, J. J. (2017). A phylogenetic study of the worldwide tribe Cassidini Gyllenhal, 1813 (Coleoptera: Chrysomelidae: Cassidinae) based on morphological data. Systematic Entomology, 43(2), 372\u2013386. Portico. https://doi.org/10.1111/syen.12280\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2936", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Matsumura, Y., Yao, I., Beutel, R., & Yoshizawa, K. (2014). Molecular phylogeny of the leaf beetle subfamily Criocerinae (Coleoptera: Chrysomelidae) and the correlated evolution of reproductive organs. Arthropod Systematics &amp; Phylogeny, 72(2), 95\u2013110. https://doi.org/10.3897/asp.72.e31887\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2937", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BILTON, D. T., TOUSSAINT, E. F. A., TURNER, C. R., & BALKE, M. (2015). Capelatus prykei gen. et sp.n. (Coleoptera: Dytiscidae: Copelatinae) \u2013 a phylogenetically isolated diving beetle from the Western Cape of South Africa. Systematic Entomology, 40(3), 520\u2013531. Portico. https://doi.org/10.1111/syen.12128\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2938", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from SIHVONEN, P., STAUDE, H. S., & MUTANEN, M. (2015). Systematic position of the enigmatic African cycad moths: an integrative approach to a nearly century old problem (Lepidoptera: Geometridae, Diptychini). Systematic Entomology, 40(3), 606\u2013627. Portico. https://doi.org/10.1111/syen.12125\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2939", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from K\u00f6lsch, G., & Pedersen, B. V. (2008). Molecular phylogeny of reed beetles (Col., Chrysomelidae, Donaciinae): The signature of ecological specialization and geographical isolation. Molecular Phylogenetics and Evolution, 48(3), 936\u2013952. https://doi.org/10.1016/j.ympev.2008.05.035\n", "decision": "INCLUDED", "name": "Fig. 3b, BI", "studyID": "ot_2941", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CRANSTON, P. S., & KROSCH, M. N. (2015). DNA sequences and austral taxa indicate generic synonymy of Paratrichocladius Santos\u2010Abreu with Cricotopus Wulp (Diptera: Chironomidae). Systematic Entomology, 40(4), 719\u2013732. Portico. https://doi.org/10.1111/syen.12130\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2942", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BALV\u00cdN, O., ROTH, S., & VIL\u00cdMOV\u00c1, J. (2015). Molecular evidence places the swallow bug genus Oeciacus St\u00e5l within the bat and bed bug genus Cimex Linnaeus (Heteroptera: Cimicidae). Systematic Entomology, 40(3), 652\u2013665. Portico. https://doi.org/10.1111/syen.12127\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2943", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Hayashi, M., & Sota, T. (2014). Quaternary donaciine beetles (Coleoptera, Chrysomelidae) in Japan: Colonization and divergence patterns inferred from fossil and molecular data. Quaternary International, 341, 255\u2013266. https://doi.org/10.1016/j.quaint.2013.08.022\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2944", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Reis, F., Kirsch, R., Pauchet, Y., Bauer, E., Bilz, L. C., Fukumori, K., Fukatsu, T., K\u00f6lsch, G., & Kaltenpoth, M. (2020). Bacterial symbionts support larval sap feeding and adult folivory in (semi-)aquatic reed beetles. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-16687-7\n", "decision": "INCLUDED", "name": "Fig. 4a, NJ", "studyID": "ot_2945", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from G\u00d3MEZ\u2010ZURITA, J., & CARDOSO, A. (2013). Systematics of the New <scp>C</scp>aledonian endemic genus Taophila<scp>H</scp>eller (<scp>C</scp>oleoptera: <scp>C</scp>hrysomelidae, <scp>E</scp>umolpinae) combining morphological, molecular and ecological data, with description of two new species. Systematic Entomology, 39(1), 111\u2013126. Portico. https://doi.org/10.1111/syen.12038\n", "decision": "INCLUDED", "name": "Fig. 5, ML", "studyID": "ot_2946", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CAI, C., LAWRENCE, J. F., \u015aLIPI\u0143SKI, A., & HUANG, D. (2015). Jurassic artematopodid beetles and their implications for the early evolution of <scp>A</scp>rtematopodidae (<scp>C</scp>oleoptera). Systematic Entomology, 40(4), 779\u2013788. Portico. https://doi.org/10.1111/syen.12131\n", "decision": "INCLUDED", "name": "Fig. 6, MP", "studyID": "ot_2948", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Nie, R., Breeschoten, T., Timmermans, M. J. T. N., Nadein, K., Xue, H., Bai, M., Huang, Y., Yang, X., & Vogler, A. P. (2017). The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear<scp>rRNA</scp>genes. Cladistics, 34(2), 113\u2013130. Portico. https://doi.org/10.1111/cla.12196\n", "decision": "INCLUDED", "name": "Fig. 5, BI", "studyID": "ot_2949", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Stapel, H., Misof, B., & Wagner, T. (2008). A Molecular and Morphological Phylogenetic Analysis of Afrotropical Monolepta Species and Related Galerucinae (Coleoptera: Chrysomelidae). Arthropod Systematics &amp; Phylogeny, 66(1), 3\u201317. https://doi.org/10.3897/asp.66.e31676\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2952", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Mckenna, Duane D., Alexander L. Wild, Kojun Kanda, Charles L. Bellamy, Rolf G. Beutel, Michael S. Caterino, Charles W. Farnum, David C. Hawks, Michael A. Ivie, Mary Liz Jameson, Richard A. B. Leschen, Adriana E. Marvaldi, Joseph V. Mchugh, Alfred F. Newton, James A. Robertson, Margaret K. Thayer, Michael F. Whiting, John F. Lawrence, Adam \u015alipi\u0144ski, David R. Maddison, Brian D. Farrell. 2015. The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversify during the Cretaceous terrestrial revolution. Systematic Entomology 40 (4): 835-880", "decision": "INCLUDED", "name": "Fig. 2 (BEAST MCC)", "studyID": "ot_772", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Yuan, L., Ge, X., Xie, G., Liu, H., & Yang, Y. (2021). First Complete Mitochondrial Genome of Melyridae(Coleoptera, Cleroidea): Genome Description and Phylogenetic Implications. Insects, 12(2), 87. https://doi.org/10.3390/insects12020087\n", "decision": "INCLUDED", "name": "Fig. 5a, ML", "studyID": "ot_2953", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Yuan, L., Liu, H., Ge, X., Yang, G., Xie, G., & Yang, Y. (2022). A Mitochondrial Genome Phylogeny of Cleridae (Coleoptera, Cleroidea). Insects, 13(2), 118. https://doi.org/10.3390/insects13020118\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2954", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from MOORE, M. R., BEZA\u2010BEZA, C. F., WICKELL, D. A., BECK, J. B., & JAMESON, M. L. (2015). Molecules, morphology and <scp>M</scp>imeoma scarabs: evolutionary and taxonomic implications for a palm\u2010associated scarab group. Systematic Entomology, 40(4), 891\u2013900. Portico. https://doi.org/10.1111/syen.12139\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2955", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from SOHN, J., REGIER, J. C., MITTER, C., ADAMSKI, D., LANDRY, J., HEIKKIL\u00c4, M., PARK, K., HARRISON, T., MITTER, K., ZWICK, A., KAWAHARA, A. Y., CHO, S., CUMMINGS, M. P., & SCHMITZ, P. (2015). Phylogeny and feeding trait evolution of the mega\u2010diverse Gelechioidea (Lepidoptera: Obtectomera): new insight from 19 nuclear genes. Systematic Entomology, 41(1), 112\u2013132. Portico. https://doi.org/10.1111/syen.12143\n", "decision": "INCLUDED", "name": "Fig. 3, ML", "studyID": "ot_2956", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GUNTER, N. L., LEAVENGOOD, J. M., BARTLETT, J. S., CHAPMAN, E. G., & CAMERON, S. L. (2013). A molecular phylogeny of the checkered beetles and a description of <scp>E</scp>piclininae a new subfamily (<scp>C</scp>oleoptera: <scp>C</scp>leroidea: <scp>C</scp>leridae). Systematic Entomology, 38(3), 626\u2013636. Portico. https://doi.org/10.1111/syen.12019\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2957", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LESCHEN, R. A. B., & LACKNER, T. (2013). Gondwanan Gymnochilini (Coleoptera: Trogossitidae): generic concepts, review of New Zealand species and long\u2010range Pacific dispersal. Systematic Entomology, 38(2), 278\u2013304. Portico. https://doi.org/10.1111/j.1365-3113.2012.00661.x\n", "decision": "INCLUDED", "name": "Fig. 7, MP", "studyID": "ot_2958", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Tomaszewska, W., Szawaryn, K., & Arriaga-Varela, E. (2023). \u2018Where is my family?\u2019 Molecular and morphological data reveal the phylogenetic position and diversity of the enigmatic handsome fungus beetle genus Anamycetaea Strohecker, 1975 (Coleoptera, Coccinelloidea). Invertebrate Systematics, 37(4), 231\u2013253. https://doi.org/10.1071/is22053\n", "decision": "INCLUDED", "name": "FileS4.contree", "studyID": "ot_2959", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BRATTSTR\u00d6M, O., ADUSE\u2010POKU, K., COLLINS, S. C., DI MICCO DE SANTO, T., & BRAKEFIELD, P. M. (2015). Revision of the Bicyclus sciathis species group (Lepidoptera: Nymphalidae) with descriptions of four new species and corrected distributional records. Systematic Entomology, 41(1), 207\u2013228. Portico. https://doi.org/10.1111/syen.12150\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2960", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Song, N., Li, X., Yin, X., Li, X., & Xi, Y. (2020). The mitochondrial genomes of ladybird beetles and implications for evolution and phylogeny. International Journal of Biological Macromolecules, 147, 1193\u20131203. https://doi.org/10.1016/j.ijbiomac.2019.10.089\n", "decision": "INCLUDED", "name": "Fig. 3, ML", "studyID": "ot_2961", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Magro, A., Lecompte, E., Magn\u00e9, F., Hemptinne, J.-L., & Crouau-Roy, B. (2010). Phylogeny of ladybirds (Coleoptera: Coccinellidae): Are the subfamilies monophyletic? Molecular Phylogenetics and Evolution, 54(3), 833\u2013848. https://doi.org/10.1016/j.ympev.2009.10.022\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_2962", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LIU, X., L\u00dc, Y., ASP\u00d6CK, H., YANG, D., & ASP\u00d6CK, U. (2015). Homology of the genital sclerites of<scp>M</scp>egaloptera (<scp>I</scp>nsecta:<scp>N</scp>europterida) and their phylogenetic relevance. Systematic Entomology, 41(1), 256\u2013286. Portico. https://doi.org/10.1111/syen.12154\n", "decision": "INCLUDED", "name": "Fig. 19, MP", "studyID": "ot_2963", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Seo, B. Y., Park, J., Kwon, W., & Park, J. (2019). The complete mitochondrial genome of Aiolocaria hexaspilota (Hope, 1831) (Coleoptera:Coccinellidae). Mitochondrial DNA Part B, 4(1), 1472\u20131474. https://doi.org/10.1080/23802359.2019.1598828\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_2964", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Tomaszewska, W., Escalona, H. E., Hartley, D., Li, J., Wang, X., Li, H., Pang, H., \u015alipi\u0144ski, A., & Zwick, A. (2021). Phylogeny of true ladybird beetles (Coccinellidae: Coccinellini) reveals pervasive convergent evolution and a rapid Cenozoic radiation. Systematic Entomology, 46(3), 611\u2013631. Portico. https://doi.org/10.1111/syen.12479\n", "decision": "INCLUDED", "name": "Fig. S2, ML", "studyID": "ot_2965", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from \u015aLIPI\u0143SKI, A., TOMASZEWSKA, W., & LAWRENCE, J. F. (2009). Phylogeny and classification of Corylophidae (Coleoptera: Cucujoidea) with descriptions of new genera and larvae. Systematic Entomology, 34(3), 409\u2013433. Portico. https://doi.org/10.1111/j.1365-3113.2009.00471.x\n", "decision": "INCLUDED", "name": "Fig. 1D, MP", "studyID": "ot_2966", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from POHL, H., & BEUTEL, R. G. (2016). \u2020<scp>K</scp>inzelbachilla ellenbergeri\u00a0\u2013\u00a0a new ancestral species, genus and family of <scp>S</scp>trepsiptera (<scp>I</scp>nsecta). Systematic Entomology, 41(1), 287\u2013297. Portico. https://doi.org/10.1111/syen.12158\n", "decision": "INCLUDED", "name": "Fig. S1, MP", "studyID": "ot_2967", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ROBERTSON, J. A., \u015aLIPI\u0143SKI, A., HIATT, K., MILLER, K. B., WHITING, M. F., & MCHUGH, J. V. (2012). Molecules, morphology and minute hooded beetles: a phylogenetic study with implications for the evolution and classification of Corylophidae (Coleoptera: Cucujoidea). Systematic Entomology, 38(1), 209\u2013232. Portico. https://doi.org/10.1111/j.1365-3113.2012.00655.x\n", "decision": "INCLUDED", "name": "Fig. 4A, BI", "studyID": "ot_2968", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from NATHAN PATRICK LORD, CHRISTOPHER S. HARTLEY, JOHN F. LAWRENCE, JOSEPH V. McHUGH, MICHAEL F. WHITING, KELLY B. MILLER, 2010, 'Phylogenetic analysis of the minute brown scavenger beetles (Coleoptera: Latridiidae), and recognition of a new beetle family, Akalyptoischiidae fam.n. (Coleoptera: Cucujoidea)', Systematic Entomology, vol. 35, no. 4, pp. 753-763", "decision": "INCLUDED", "name": "Fig. 6, BI", "studyID": "ot_1593", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Liu, J., Yang, Y., Yan, Z., Wang, H., Bai, M., Shi, C., & Li, J. (2023). Analysis of the Mitogenomes of Two Helotid Species Provides New Insights into the Phylogenetic Relationship of the Basal Cucujoidea (Insecta: Coleoptera). Biology, 12(1), 135. https://doi.org/10.3390/biology12010135\n", "decision": "INCLUDED", "name": "Fig. 10, BI", "studyID": "ot_2969", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from MCELRATH, T. C., ROBERTSON, J. A., THOMAS, M. C., OSBORNE, J., MILLER, K. B., MCHUGH, J. V., & WHITING, M. F. (2015). A molecular phylogenetic study of <scp>C</scp>ucujidae s.l. (<scp>C</scp>oleoptera: <scp>C</scp>ucujoidea). Systematic Entomology, 40(4), 705\u2013718. Portico. https://doi.org/10.1111/syen.12133\n", "decision": "INCLUDED", "name": "Fig. S1, ML", "studyID": "ot_2970", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jin, M., Zwick, A., \u015alipi\u0144ski, A., Marris, J. W. M., Thomas, M. C., & Pang, H. (2020). A comprehensive phylogeny of flat bark beetles (Coleoptera: Cucujidae) with a revised classification and a new South American genus. Systematic Entomology, 45(2), 248\u2013268. Portico. https://doi.org/10.1111/syen.12392\n", "decision": "INCLUDED", "name": "Fig. 3, ML", "studyID": "ot_2971", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Robertson, J. A., McHugh, J. V., & Whiting, M. F. (2004). A molecular phylogenetic analysis of the pleasing fungus beetles (Coleoptera: Erotylidae): evolution of colour patterns, gregariousness and mycophagy. Systematic Entomology, 29(2), 173\u2013187. Portico. https://doi.org/10.1111/j.0307-6970.2004.00242.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2972", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lee, M. H., Lee, S., Leschen, R. A. B., & Lee, S. (2020). Evolution of feeding habits of sap beetles (Coleoptera: Nitidulidae) and placement of Calonecrinae. Systematic Entomology, 45(4), 911\u2013923. Portico. https://doi.org/10.1111/syen.12441\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2973", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Powell, G. S., Cline, A. R., Duffy, A. G., & Zaspel, J. M. (2020). Phylogeny and reclassification of Carpophilinae (Coleoptera: Nitidulidae), with insights into the origins of anthophily. Zoological Journal of the Linnean Society, 189(4), 1359\u20131369. https://doi.org/10.1093/zoolinnean/zlaa001\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_2974", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Li, Y.-D., Engel, M. S., Tihelka, E., & Cai, C. (2023). Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity. Biology Letters, 19(9). https://doi.org/10.1098/rsbl.2023.0307\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2975", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from McKenna, D. D., A. S. Sequeira, A. E. Marvaldi, B. D. Farrell. 2009. Temporal lags and overlap in the diversification of weevils and flowering plants. Proceedings of the National Academy of Sciences 106 (17: 7083-7088", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_617", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Park, J., Kim, M. J., & Kim, I. (2019). Complete mitochondrial genome of the leaf-rolling-weevil, Apoderus jekelii Roelofs, 1874 (Coleoptera: Attelabidae). Mitochondrial DNA Part B, 4(1), 995\u2013997. https://doi.org/10.1080/23802359.2019.1580161\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2976", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GON\u00c7ALVES, R. B. (2016). A molecular and morphological phylogeny of the extant Augochlorini (Hymenoptera, Apoidea) with comments on implications for biogeography. Systematic Entomology, 41(2), 430\u2013440. Portico. https://doi.org/10.1111/syen.12166\n", "decision": "INCLUDED", "name": "Fig. 2, MP", "studyID": "ot_2977", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Song, N., Li, X., Yin, X., Li, X., Yin, S., & Yang, M. (2020). The mitochondrial genome ofApion squamigerum(Coleoptera, Curculionoidea, Brentidae) and the phylogenetic implications. PeerJ, 8, e8386. Portico. https://doi.org/10.7717/peerj.8386\n", "decision": "INCLUDED", "name": "Fig. 4, ML", "studyID": "ot_2978", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from SANTOS, A. P. M., NESSIMIAN, J. L., & TAKIYA, D. M. (2016). Revised classification and evolution of leucotrichiine microcaddisflies (Trichoptera: Hydroptilidae) based on morphological and molecular data. Systematic Entomology, 41(2), 458\u2013480. Portico. https://doi.org/10.1111/syen.12168\n", "decision": "INCLUDED", "name": "Fig. S1, BI", "studyID": "ot_2979", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, L., Li, Y., Ge, X., Li, X., Yang, Y., Bai, M., & Ge, S. (2022). Mitochondrial genomes of Sternochetus species (Coleoptera: Curculionidae) and the phylogenetic implications. Archives of Insect Biochemistry and Physiology, 111(1). Portico. https://doi.org/10.1002/arch.21898\n", "decision": "INCLUDED", "name": "Fig. 6, BI", "studyID": "ot_2980", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Adriana E. Marvaldi, 2005, 'Larval morphology and biology of oxycorynine weevils and the higher phylogeny of Belidae (Coleoptera, Curculionoidea)', Zoologica Scripta, vol. 34, no. 1, pp. 37-48", "decision": "INCLUDED", "name": "MP Morphology", "studyID": "ot_612", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Letsch, H., Balke, M., Toussaint, E. F. A., & Riedel, A. (2019). Historical biogeography of the hyperdiverse hidden snout weevils (Coleoptera, Curculionidae, Cryptorhynchinae). Systematic Entomology, 45(2), 312\u2013326. Portico. https://doi.org/10.1111/syen.12396\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2981", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Letsch, H., Balke, M., Kusy, D., McKenna, D. D., Pramesa Narakusumo, R., Sagata, K., Toussaint, E. F. A., White, L. T., & Riedel, A. (2023). Beetle evolution illuminates the geological history of the World\u2019s most diverse tropical archipelago. Ecography, 2023(12). Portico. https://doi.org/10.1111/ecog.06898\n", "decision": "INCLUDED", "name": "1K_iqtree.1021.bs.treefile", "studyID": "ot_2982", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LANTERI, A. A., & DEL RIO, M. G. (2016). Phylogeny of the tribe Naupactini (Coleoptera: Curculionidae) based on morphological characters. Systematic Entomology, 42(2), 429\u2013447. Portico. https://doi.org/10.1111/syen.12223\n", "decision": "INCLUDED", "name": "Fig. 10, MP", "studyID": "ot_2983", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Smith, S. M., & Cognato, A. I. (2022). New Non-native PseudocrypticCyclorhipidionSpecies (Coleoptera: Curculionidae: Scolytinae: Xyleborini) Found in the United States as Revealed in a Multigene Phylogeny. Insect Systematics and Diversity, 6(4). https://doi.org/10.1093/isd/ixac014\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_2985", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PISTONE, D., GOHLI, J., & JORDAL, B. H. (2017). Molecular phylogeny of bark and ambrosia beetles (Curculionidae: Scolytinae) based on 18 molecular markers. Systematic Entomology, 43(2), 387\u2013406. Portico. https://doi.org/10.1111/syen.12281\n", "decision": "INCLUDED", "name": "Fig. 6, BI", "studyID": "ot_2986", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, S., Shu, J., Wang, Y., Liu, Y., Peng, H., Zhang, W., & Wang, H. (2019). The complete mitochondrial genomes of two sibling species of camellia weevils (Coleoptera: Curculionidae) and patterns of Curculionini speciation. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-39895-8\n", "decision": "INCLUDED", "name": "Fig. 4, BI", "studyID": "ot_2987", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from RIEDEL, A., T\u00c4NZLER, R., PONS, J., SUHARDJONO, Y. R., & BALKE, M. (2016). Large\u2010scale molecular phylogeny of Cryptorhynchinae (Coleoptera, Curculionidae) from multiple genes suggests American origin and later Australian radiation. Systematic Entomology, 41(2), 492\u2013503. Portico. https://doi.org/10.1111/syen.12170\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2988", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from V\u00cdCTOR, J., & Z\u00da\u00d1IGA, G. (2015). Phylogeny ofDendroctonusbark beetles (Coleoptera: Curculionidae: Scolytinae) inferred from morphological and molecular data. Systematic Entomology, 41(1), 162\u2013177. Portico. https://doi.org/10.1111/syen.12149\n", "decision": "INCLUDED", "name": "Fig. 8b, MP", "studyID": "ot_2989", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gunter, N. L., Levkani\u010dov\u00e1, Z., Weir, T. H., \u015alipi\u0144ski, A., Cameron, S. L., & Bocak, L. (2014). Towards a phylogeny of the Tenebrionoidea (Coleoptera). Molecular Phylogenetics and Evolution, 79, 305\u2013312. https://doi.org/10.1016/j.ympev.2014.05.028\n", "decision": "INCLUDED", "name": "Fig. S4, ML", "studyID": "ot_2991", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from KERGOAT, G. J., SOLDATI, L., CLAMENS, A., JOURDAN, H., JABBOUR\u2010ZAHAB, R., GENSON, G., BOUCHARD, P., & CONDAMINE, F. L. (2014). Higher level molecular phylogeny of darkling beetles (<scp>C</scp>oleoptera:<scp>T</scp>enebrionidae). Systematic Entomology, 39(3), 486\u2013499. Portico. https://doi.org/10.1111/syen.12065\n", "decision": "INCLUDED", "name": "Fig. S1, ML", "studyID": "ot_2992", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CONDAMINE, F. L., SOLDATI, L., RASPLUS, J., & KERGOAT, G. J. (2011). New insights on systematics and phylogenetics of MediterraneanBlapsspecies (Coleoptera: Tenebrionidae: Blaptini), assessed through morphology and dense taxon sampling. Systematic Entomology, 36(2), 340\u2013361. Portico. https://doi.org/10.1111/j.1365-3113.2010.00567.x\n", "decision": "INCLUDED", "name": "Fig. 6, BI", "studyID": "ot_2993", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from SMITH, A. D. (2013). Phylogenetic revision of the<scp>N</scp>orth<scp>A</scp>merican<scp>A</scp>sidini (<scp>C</scp>oleoptera:<scp>T</scp>enebrionidae). Systematic Entomology, 38(3), 585\u2013614. Portico. https://doi.org/10.1111/syen.12017\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_2994", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kobayashi, T., & Sota, T. (2021). Evolution of host use in fungivorous ciid beetles (Coleoptera: Ciidae): Molecular phylogeny focusing on Japanese taxa. Molecular Phylogenetics and Evolution, 162, 107197. https://doi.org/10.1016/j.ympev.2021.107197\n", "decision": "INCLUDED", "name": "Fig. S2, BI", "studyID": "ot_2995", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PITZALIS, M., & BOLOGNA, M. A. (2010). Time of diversification in the Cape fauna endemisms, inferred by phylogenetic studies of the genusIselma(Coleoptera: Meloidae: Eleticinae). Systematic Entomology, 35(4), 739\u2013752. Portico. https://doi.org/10.1111/j.1365-3113.2010.00530.x\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_2996", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Riccieri, A., Mancini, E., Pitzalis, M., Salvi, D., & Bologna, M. A. (2022). Multigene phylogeny of blister beetles (Coleoptera, Meloidae) reveals extensive polyphyly of the tribe Lyttini and allows redefining its boundaries. Systematic Entomology, 47(4), 569\u2013580. Portico. https://doi.org/10.1111/syen.12547\n", "decision": "INCLUDED", "name": "Fig. S2a, ML", "studyID": "ot_2998", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BOLOGNA, M. A., DI GIULIO, A., & PITZALIS, M. (2008). Systematics and biogeography of the genusActenodia(Coleoptera: Meloidae: Mylabrini). Systematic Entomology, 33(2), 319\u2013360. Portico. https://doi.org/10.1111/j.1365-3113.2007.00402.x\n", "decision": "INCLUDED", "name": "Fig. 2B, MP", "studyID": "ot_2999", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Riccieri, A., Mancini, E., Salvi, D., & Bologna, M. A. (2020). Phylogeny, biogeography and systematics of the hyper-diverse blister beetle genus Hycleus (Coleoptera: Meloidae). Molecular Phylogenetics and Evolution, 144, 106706. https://doi.org/10.1016/j.ympev.2019.106706\n", "decision": "INCLUDED", "name": "Fig. S2", "studyID": "ot_3000", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Peris, D. (2016). Early Cretaceous origin of pollen\u2010feeding beetles (Insecta: Coleoptera: Oedemeridae). Cladistics, 33(3), 268\u2013278. Portico. https://doi.org/10.1111/cla.12168\n", "decision": "INCLUDED", "name": "Fig. 3, MP", "studyID": "ot_3001", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Wang, Y., Yang, X., Engel, M. S., Huo, Q., Du, Y.-Z., & Cai, C. (2025). Reconstructing the evolutionary history of stoneflies: phylogenetic insights and temporal dynamics. IScience, 113614. https://doi.org/10.1016/j.isci.2025.113614\n", "decision": "INCLUDED", "name": "bpcomp.con.tre", "studyID": "ot_3003", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from BARANOV, V. A., KVIFTE, G. M., & PERKOVSKY, E. E. (2016). Two new species of fossil Corethrella Coquillett from Late Eocene Rovno amber, with a species\u2010level phylogeny for the family based on morphological traits (Diptera: Corethrellidae). Systematic Entomology, 41(3), 531\u2013540. Portico. https://doi.org/10.1111/syen.12172\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_3004", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Pollock, D. (1995). Classification, reconstructed phylogeny and geographical history of genera of Pilipalpinae (Coleoptera\u202f: Tenebrionoidea\u202f: Pyrochroidae). Invertebrate Systematics, 9(4), 563. https://doi.org/10.1071/it9950563\n", "decision": "INCLUDED", "name": "Fig. 270, MP", "studyID": "ot_3005", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from KRISHNANKUTTY, S. M., DIETRICH, C. H., DAI, W., & SIDDAPPAJI, M. H. (2016). Phylogeny and historical biogeography of leafhopper subfamily Iassinae (Hemiptera: Cicadellidae) with a revised tribal classification based on morphological and molecular data. Systematic Entomology, 41(3), 580\u2013595. Portico. https://doi.org/10.1111/syen.12175\n", "decision": "INCLUDED", "name": "Fig. S2, ML", "studyID": "ot_3007", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PARKER, J. (2016). Emergence of a superradiation: pselaphine rove beetles in mid\u2010Cretaceous amber from Myanmar and their evolutionary implications. Systematic Entomology, 41(3), 541\u2013566. Portico. https://doi.org/10.1111/syen.12173\n", "decision": "INCLUDED", "name": "syen12173-sup-0003-supp-file-s1.nex", "studyID": "ot_3008", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from TOUSSAINT, E. F. A., HENDRICH, L., ESCALONA, H. E., PORCH, N., & BALKE, M. (2016). Evolutionary history of a secondary terrestrial Australian diving beetle (Coleoptera, Dytiscidae) reveals a lineage of high morphological and ecological plasticity. Systematic Entomology, 41(3), 650\u2013657. Portico. https://doi.org/10.1111/syen.12182\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_3009", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from DARWELL, C. T., RIVERS, D. M., & ALTHOFF, D. M. (2016). RAD\u2010seq phylogenomics recovers a well\u2010resolved phylogeny of a rapid radiation of mutualistic and antagonistic yucca moths. Systematic Entomology, 41(3), 672\u2013682. Portico. https://doi.org/10.1111/syen.12185\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_3010", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ADUSE\u2010POKU, K., LEES, D. C., BRATTSTR\u00d6M, O., KODANDARAMAIAH, U., COLLINS, S. C., WAHLBERG, N., & BRAKEFIELD, P. M. (2016). Molecular phylogeny and generic\u2010level taxonomy of the widespread palaeotropical \u2018Heteropsis clade\u2019 (Nymphalidae: Satyrinae: Mycalesina). Systematic Entomology, 41(4), 717\u2013731. Portico. https://doi.org/10.1111/syen.12183\n", "decision": "INCLUDED", "name": "Fig. 3, BI", "studyID": "ot_3011", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kami\u0144ski, M. J., Kanda, K., Lumen, R., Smith, A. D., & Iwan, D. (2018). Molecular phylogeny of Pedinini (Coleoptera, Tenebrionidae) and its implications for higher-level classification. Zoological Journal of the Linnean Society. https://doi.org/10.1093/zoolinnean/zly033\n", "decision": "INCLUDED", "name": "Fig. 3, ML", "studyID": "ot_3012", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from CHERMAN, M. A., MOR\u00d3N, M. A., & ALMEIDA, L. M. (2016). Phylogenetic relationships within <scp>D</scp>iplotaxini <scp>K</scp>irby (<scp>C</scp>oleoptera: <scp>M</scp>elolonthidae: <scp>M</scp>elolonthinae) with emphasis on <scp>L</scp>iogenys<scp>G</scp>u\u00e9rin\u2010<scp>M</scp>\u00e9neville. Systematic Entomology, 41(4), 744\u2013770. Portico. https://doi.org/10.1111/syen.12188\n", "decision": "INCLUDED", "name": "Fig. 8, MP", "studyID": "ot_3013", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Li, X., Bai, X., Kergoat, G. J., Pan, Z., & Ren, G. (2020). Phylogenetics, historical biogeography and molecular species delimitation of Gnaptorina Reitter (Coleoptera: Tenebrionidae: Blaptini). Systematic Entomology, 46(1), 239\u2013251. Portico. https://doi.org/10.1111/syen.12459\n", "decision": "INCLUDED", "name": "Fig. 2, BI", "studyID": "ot_3014", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ghanavi, H. R., Chazot, N., Sanmart\u00edn, I., Murillo\u2010Ramos, L., Duch\u00eane, S., Sihvonen, P., Brehm, G., & Wahlberg, N. (2024). Region\u2010specific diversification dynamics and biogeographic history of one of the most diverse families of insects. Systematic Entomology, 50(1), 206\u2013220. Portico. https://doi.org/10.1111/syen.12651\n", "decision": "INCLUDED", "name": "Tree70.tree", "studyID": "ot_3017", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Rodriguez, J., Frese, M., Dettmann, M., Chavoshi\u2010Jolfaei, M., & Macdonald, J. (2024). A new exceptionally preserved sawfly fossil (Hymenoptera: Pergidae) and an evaluation of its utility for divergence time estimation and biogeography. Systematic Entomology, 50(1), 237\u2013251. Portico. https://doi.org/10.1111/syen.12653\n", "decision": "INCLUDED", "name": "Matrix-3j-FBD.nex.con.tre", "studyID": "ot_3018", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Le Flanchec, T., Salazar, K., Malem, J., Vendanger, J., Poirier, E., Dutertre, V., Bonillo, C., Chifflet\u2010Belle, P., Legendre, F., Nattier, R., & Robillard, T. (2024). Early colonization of New Caledonia by ultrasonic crickets from New Guinea (Orthoptera: Gryllidae: Eneopterinae): Historical biogeography and description of a new genus. Systematic Entomology, 50(2), 269\u2013295. Portico. https://doi.org/10.1111/syen.12656\n", "decision": "INCLUDED", "name": "Dated_tree.newick", "studyID": "ot_3019", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Castillejos\u2010Lemus, D. E., Nieves\u2010Aldrey, J., Zhang, Y. M., Nicholls, J. A., Medianero, E., Rougon\u2010Cardoso, A., Stone, G. N., & Oyama, K. (2024). Phylogenomic insights and geographic distribution of the New World genus Amphibolips Reinhard (Hymenoptera: Cynipidae, Cynipini) using ultraconserved elements. Systematic Entomology, 50(2), 349\u2013368. Portico. https://doi.org/10.1111/syen.12659\n", "decision": "INCLUDED", "name": "FS8_Amphi_80p_SWSC.tree", "studyID": "ot_3020", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Li, X., Hash, J. M., Hartop, E., Yang, D., Smith, P. T., & Brown, B. V. (2024). A molecular phylogeny of scuttle flies (Diptera: Phoridae) unveils extensive concordance but intriguing divergences from morphological results. Systematic Entomology, 50(1), 68\u201381. Portico. https://doi.org/10.1111/syen.12644\n", "decision": "INCLUDED", "name": "NTDegen_PGM_ML.tre", "studyID": "ot_3022", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Souza, D. de S., French, R. L. K., J\u00fanior, J. O. S., Nearns, E. H., Marinoni, L., Swift, I. P., Miller, K. B., Sperling, F. A. H., & Monn\u00e9, M. L. (2024). Cutting the sap: First molecular phylogeny of twig\u2010girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviours contributed to morphological evolution. Systematic Entomology, 50(2), 369\u2013386. Portico. https://doi.org/10.1111/syen.12660\n", "decision": "INCLUDED", "name": "RAxML_bestTree.Onciderini_concat_matrix_ML", "studyID": "ot_3023", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Reboud, E. L., Nabholz, B., Chevalier, E., Lafon, B. J., Tilak, M., Mielke, C. G. C., Cotton, A. M., & Condamine, F. L. (2024). Clarifying the phylogeny and systematics of the recalcitrant tribe Leptocircini (Lepidoptera: Papilionidae) with whole\u2010genome data. Systematic Entomology, 50(2), 387\u2013414. Portico. https://doi.org/10.1111/syen.12661\n", "decision": "INCLUDED", "name": "Leptocircini_1402_genes_GTR_G.partitions", "studyID": "ot_3025", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Li, Z., Zhang, F., Zhang, W., Marathe, K., Maddison, W. P., & Zhang, J. (2025). Phylogeny of euophryine jumping spiders from ultra\u2010conserved elements, with evidence on the intersexual coevolution of genitalia (Araneae: Salticidae: Euophryini). Systematic Entomology, 50(3), 554\u2013567. Portico. https://doi.org/10.1111/syen.12669\n", "decision": "INCLUDED", "name": "3_117spp_2412loci_AncestralReconstruction", "studyID": "ot_3026", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Goodman, A., Abbott, J., Breinholt, J. W., Bybee, S., Frandsen, P. B., Guralnick, R., Kalkman, V. J., Kohli, M., Newton, L., & Ware, J. L. (2025). Systematics and biogeography of the Holarctic dragonfly genus Somatochlora (Anisoptera: Corduliidae). Systematic Entomology, 50(3), 585\u2013610. Portico. https://doi.org/10.1111/syen.12672\n", "decision": "INCLUDED", "name": "No_Coded_Bootstrap.tre", "studyID": "ot_3027", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, J., Lin, L., Mu, Y., Brelsford, A., & Purcell, J. (2025). A comparison of phylogenomic inference pipelines for low\u2010coverage whole\u2010genome sequencing in Formica ants. Systematic Entomology, 50(3), 611\u2013629. Portico. https://doi.org/10.1111/syen.12670\n", "decision": "INCLUDED", "name": "MCMCtree.Busco-nt.APL.run1.tre", "studyID": "ot_3029", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ward, P. S., Fisher, B. L., Wernegreen, J. J., & Blaimer, B. B. (2025). Evolutionary history, novel lineages and symbiont coevolution in the ant tribe Camponotini (Hymenoptera: Formicidae). Systematic Entomology, 50(3), 646\u2013676. Portico. https://doi.org/10.1111/syen.12678\n", "decision": "INCLUDED", "name": "Campo225-90-098.tre", "studyID": "ot_3030", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Batelka, J., Kundrata, R., & Straka, J. (2025). Phylogenomics and revised classification of Lymexyloidea and Tenebrionoidea (Coleoptera: Polyphaga: Cucujiformia). Systematic Entomology, 50(4), 794\u2013812. Portico. https://doi.org/10.1111/syen.12683\n", "decision": "INCLUDED", "name": "GhostLG_iqtree24a_cut.tre", "studyID": "ot_3031", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhang, R., Wang, L., Tian, S., Liu, Y., Jiang, Y., Zhou, X., Yang, D., Liu, X., & Wang, Y. (2025). Inconsistent performance of multi\u2010type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results. Systematic Entomology, 50(4), 855\u2013875. Portico. https://doi.org/10.1111/syen.12684\n", "decision": "INCLUDED", "name": "USCO_V-Dayhoff6.fas.treefile", "studyID": "ot_3032", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Wang, J., Zhou, X., Dietrich, C. H., Cao, Y., & Huang, M. (2025). Extensive hybridisation and complex evolutionary history in the leafhopper genus Agnesiella (Hemiptera: Cicadellidae: Typhlocybinae). Systematic Entomology, 50(4), 903\u2013919. Portico. https://doi.org/10.1111/syen.12686\n", "decision": "INCLUDED", "name": "SCOs_80_UCEs_100_NT_CID_800_filtergeneflow_ghost", "studyID": "ot_3033", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Plotkin, D., Breinholt, J. W., & Kawahara, A. Y. (2025). A target capture\u2010based phylogeny of emerald moths (Lepidoptera: Geometridae: Geometrinae) provides new insights into tribal\u2010level classification. Systematic Entomology, 50(4), 920\u2013939. Portico. https://doi.org/10.1111/syen.12689\n", "decision": "INCLUDED", "name": "FigS1_nt123.tre", "studyID": "ot_3034", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Rocha, I. C., Nessimian, J. L., & Santos, A. P. M. (2025). Systematics, divergence dating and historical biogeography of Ochrotrichiinae (Trichoptera: Hydroptilidae) based on morphological and molecular data. Systematic Entomology, 50(4), 1005\u20131024. Portico. https://doi.org/10.1111/syen.12695\n", "decision": "INCLUDED", "name": "Dated-tree-ochrotrichiinae-ingroup.newick", "studyID": "ot_3035", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Beasley\u2010Hall, P. G., Trewick, S. A., Eberhard, S. M., Zwick, A., Reed, E. H., Cooper, S. J. B., & Austin, A. D. (2025). Molecular phylogenetics illuminates the evolutionary history and hidden diversity of Australian cave crickets (Orthoptera: Rhaphidophoridae). Systematic Entomology, 50(4), 975\u2013987. Portico. https://doi.org/10.1111/syen.12690\n", "decision": "INCLUDED", "name": "IQTreephylogeny.tree", "studyID": "ot_3036", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Juv\u00e9, Y., Weyna, A., Lauroua, E., Nidelet, S., Khaldi, M., Barech, G., Lebas, C., Rasplus, J., Cruaud, A., Condamine, F. L., & Romiguier, J. (2025). Phylogenomics of Messor harvester ants (Hymenoptera: Formicidae: Stenammini) unravels their biogeographical origin and diversification patterns. Systematic Entomology, 50(4), 1025\u20131040. Portico. https://doi.org/10.1111/syen.12693\n", "decision": "INCLUDED", "name": "allseqs-gt05-sp8-pristine.fas.iqtree", "studyID": "ot_3037", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ortiz, D., Pek\u00e1r, S., Henrard, A., Jocqu\u00e9, R., Harvey, M. S., Haddad, C., & Van Bocxlaer, B. (2025). Phylogenomics unveils Afrotropical origin, trans\u2010oceanic global diversification and climatic niche conservatism in the sedentary Zodariidae ant spiders. Systematic Entomology, 50(4), 988\u20131004. Portico. https://doi.org/10.1111/syen.12694\n", "decision": "INCLUDED", "name": "Zodariidae_phylogeny_80_occup_IQTREE.tre", "studyID": "ot_3038", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from \u00d5unap, E., Nedumpally, V., Yapar, E., Lemmon, A. R., & Tammaru, T. (2024). Molecular phylogeny of north European Geometridae (Lepidoptera: Geometroidea). Systematic Entomology, 50(1), 32\u201367. Portico. https://doi.org/10.1111/syen.12638\n", "decision": "INCLUDED", "name": "file S4, ML", "studyID": "ot_3039", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Mahlerov\u00e1, K., Jakubec, P., Krak, K., & R\u016f\u017ei\u010dka, J. (2024). Resolving the intergeneric phylogeny of the large carrion beetles (<scp>Staphylinidae: Silphinae: Silphini</scp>). Systematic Entomology, 50(1), 168\u2013179. Portico. https://doi.org/10.1111/syen.12650\n", "decision": "INCLUDED", "name": "Fig. 1, ML", "studyID": "ot_3040", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cao, Y., Dietrich, C. H., Dmitriev, D. A., Kits, J. H., Xue, Q., & Zhang, Y. (2024). Phylogeny, biogeography and morphological evolution of the treehopper\u2010like leafhoppers (Hemiptera: Cicadellidae) Megophthalminae and Ulopinae. Systematic Entomology, 50(2), 296\u2013308. Portico. https://doi.org/10.1111/syen.12655\n", "decision": "INCLUDED", "name": "MLtree_nt.tre", "studyID": "ot_3042", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Luo, X., Deng, W., Han, W., Lo, N., Cai, J., Che, Y., & Wang, Z. (2025). Revision of the cockroach subfamily Blattinae based on morphological and molecular analyses. Systematic Entomology, 50(4), 836\u2013854. Portico. https://doi.org/10.1111/syen.12680\n", "decision": "INCLUDED", "name": "AUtest_IQ_partition.nex.iqtree", "studyID": "ot_3045", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ROBERTSON, J. A., & MOORE, W. (2016). Phylogeny of\n                    \n                      <scp>P</scp>\n                      aussus\n                    \n                    <scp>L</scp>\n                    . (\n                    <scp>C</scp>\n                    arabidae:\n                    <scp>P</scp>\n                    aussinae): unravelling morphological convergence associated with myrmecophilous life histories. Systematic Entomology, 42(1), 134\u2013170. Portico. https://doi.org/10.1111/syen.12205\n", "decision": "INCLUDED", "name": "Fig. 20, BI", "studyID": "ot_3046", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from HERREID, J. S., & HERATY, J. M. (2017). Hitchhikers at the dinner table: a revisionary study of a group of ant parasitoids (\n                    <scp>H</scp>\n                    ymenoptera:\n                    <scp>E</scp>\n                    ucharitidae) specializing in the use of extrafloral nectaries for host access. Systematic Entomology, 42(1), 204\u2013229. Portico. https://doi.org/10.1111/syen.12206\n", "decision": "INCLUDED", "name": "Fig. 1, BI", "studyID": "ot_3047", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LI, L., RASNITSYN, A. P., LABANDEIRA, C. C., SHIH, C., & REN, D. (2017). Phylogeny of\n                    <scp>S</scp>\n                    tephanidae (\n                    <scp>H</scp>\n                    ymenoptera:\n                    <scp>A</scp>\n                    pocrita) with a new genus from\n                    <scp>U</scp>\n                    pper\n                    <scp>C</scp>\n                    retaceous\n                    <scp>M</scp>\n                    yanmar amber. Systematic Entomology, 42(1), 194\u2013203. Portico. https://doi.org/10.1111/syen.12202\n", "decision": "INCLUDED", "name": "Fig. 1, MP", "studyID": "ot_3048", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lavrov, D. V., Diaz, M. C., Maldonado, M., Morrow, C. C., Perez, T., Pomponi, S. A., & Thacker, R. W. (2023). Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera). PLOS ONE, 18(12), e0287281. https://doi.org/10.1371/journal.pone.0287281\n", "decision": "INCLUDED", "name": "timing2_sample.chronogram (tree1)", "studyID": "ot_3049", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Rokas, A. (2021). Editor\u2019s evaluation: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record. https://doi.org/10.7554/elife.72460.sa0\n", "decision": "INCLUDED", "name": "clockCATGTR1_ln_sample (tree1)", "studyID": "ot_3050", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Frolov\u00e1, P., Hork\u00e1, I., & \u010euri\u0161, Z. (2022). Molecular phylogeny and historical biogeography of marine palaemonid shrimps (Palaemonidae: Palaemonella\u2013Cuapetes group). Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-19372-5\n", "decision": "INCLUDED", "name": "Molecular_clock_Tree", "studyID": "ot_3051", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Orr, R. J. S., Di Martino, E., Ramsfjell, M. H., Gordon, D. P., Berning, B., Chowdhury, I., Craig, S., Cumming, R. L., Figuerola, B., Florence, W., Harmelin, J.-G., Hirose, M., Huang, D., Jain, S. S., Jenkins, H. L., Kotenko, O. N., Kuklinski, P., Lee, H. E., Madurell, T., \u2026 Liow, L. H. (2022). Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny. Science Advances, 8(13). https://doi.org/10.1126/sciadv.abm7452\n", "decision": "INCLUDED", "name": "TRIMMED (Fig. 2)", "studyID": "ot_3052", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Qing, X., Zhang, Y. M., Sun, S., Ahmed, M., Lo, W.-S., Bert, W., Holovachov, O., & Li, H. (2024). Phylogenomic Insights into the Evolution and Origin of Nematoda. Systematic Biology, 74(3), 349\u2013358. https://doi.org/10.1093/sysbio/syae073\n", "decision": "INCLUDED", "name": "Nem_50p_aa_MCMCresult.tree", "studyID": "ot_3053", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Fusca, D. D., Dall\u2019Acqua, M. N., S\u00e1nchez-Ram\u00edrez, S., & Cutter, A. D. (2025). Phylogenomic timetree-calibrated speciation clocks for Caenorhabditis nematodes reveal slow but disproportionate accumulation of post-zygotic reproductive isolation. PLOS Genetics, 21(9), e1011852. https://doi.org/10.1371/journal.pgen.1011852\n", "decision": "INCLUDED", "name": "205_orthologs_gamma_priors_relaxed_clock_species_tree.tree", "studyID": "ot_3054", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Stein, R. W., Mull, C. G., Kuhn, T. S., Aschliman, N. C., Davidson, L. N. K., Joy, J. B., Smith, G. J., Dulvy, N. K., & Mooers, A. O. (2018). Global priorities for conserving the evolutionary history of sharks, rays and chimaeras. Nature Ecology &amp; Evolution, 2(2), 288\u2013298. https://doi.org/10.1038/s41559-017-0448-4\n", "decision": "INCLUDED", "name": "610.tree.10Cal.RAxML.BS.nex", "studyID": "ot_3055", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bucher, M., Condamine, F. L., Luo, Y., Wang, M., & Bourgoin, T. (2023). Phylogeny and diversification of planthoppers (Hemiptera: Fulgoromorpha) based on a comprehensive molecular dataset and large taxon sampling. Molecular Phylogenetics and Evolution, 186, 107862. https://doi.org/10.1016/j.ympev.2023.107862\n", "decision": "INCLUDED", "name": "Dated tree.tre", "studyID": "ot_3057", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bechteler, J., Pe\u00f1aloza\u2010Bojac\u00e1, G., Bell, D., Gordon Burleigh, J., McDaniel, S. F., Christine Davis, E., Sessa, E. B., Bippus, A., Christine Cargill, D., Chantanoarrapint, S., Draper, I., Endara, L., Forrest, L. L., Garilleti, R., Graham, S. W., Huttunen, S., Lazo, J. J., Lara, F., Larra\u00edn, J., \u2026 Villarreal A., J. C. (2023). Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. American Journal of Botany, 110(11). Portico. https://doi.org/10.1002/ajb2.16249\n", "decision": "INCLUDED", "name": "GoFlag_Bryo_July2021_treePL_config-v8.tre", "studyID": "ot_3059", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from RIGHETTI, N., NICOLINI, F., FORNI, G., & LUCHETTI, A. (2025). Towards a time-tree solution for Branchiopoda diversification: a jackknife assessment of fossil age priors. Palaeoentomology, 8(3), 316\u2013328. https://doi.org/10.11646/palaeoentomology.8.3.8\n", "decision": "INCLUDED", "name": "FINAL_calibrated_tree.nexus", "studyID": "ot_3061", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Colston, T. J., Kulkarni, P., Jetz, W., & Pyron, R. A. (2020). Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs). BMC Evolutionary Biology, 20(1). https://doi.org/10.1186/s12862-020-01642-3\n", "decision": "INCLUDED", "name": "archosauromorpha_ML_Phylogeny.tre (crocs)", "studyID": "ot_3062", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Colston, T. J., Kulkarni, P., Jetz, W., & Pyron, R. A. (2020). Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs). BMC Evolutionary Biology, 20(1). https://doi.org/10.1186/s12862-020-01642-3\n", "decision": "INCLUDED", "name": "archosauromorpha_ML_Phylogeny.tre (turtles)", "studyID": "ot_3062", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Thomson, R. C., Spinks, P. Q., & Shaffer, H. B. (2021). A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proceedings of the National Academy of Sciences, 118(7). https://doi.org/10.1073/pnas.2012215118\n", "decision": "INCLUDED", "name": "bd.mcc.median_heights.tre", "studyID": "ot_3063", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ahmed, M., Roberts, N. G., Adediran, F., Smythe, A. B., Kocot, K. M., & Holovachov, O. (2022). Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.769565\n", "decision": "INCLUDED", "name": "1_TRICHINELLIDA/12_ASTRAL/trichinellida_consensus_250221.tre", "studyID": "ot_3065", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ahmed, M., Roberts, N. G., Adediran, F., Smythe, A. B., Kocot, K. M., & Holovachov, O. (2022). Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.769565\n", "decision": "INCLUDED", "name": "3_TYLENCHINA/12_ASTRAL/Fullname_tylenchina_consensus.tre", "studyID": "ot_3065", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ahmed, M., Roberts, N. G., Adediran, F., Smythe, A. B., Kocot, K. M., & Holovachov, O. (2022). Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.769565\n", "decision": "INCLUDED", "name": "5_NEMATODA/12_ASTRAL/Fullname_nematoda_consensus.tre", "studyID": "ot_3065", "treeID": "tree5"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ahmed, M., Roberts, N. G., Adediran, F., Smythe, A. B., Kocot, K. M., & Holovachov, O. (2022). Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.769565\n", "decision": "INCLUDED", "name": "2_SPIRURINA/12_ASTRAL/Fullname_spirurina_consensus.tre", "studyID": "ot_3065", "treeID": "tree6"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ahmed, M., Roberts, N. G., Adediran, F., Smythe, A. B., Kocot, K. M., & Holovachov, O. (2022). Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.769565\n", "decision": "INCLUDED", "name": "4_RHABDITINA/12_ASTRAL/Fullname_rhabditina_consensus.tre", "studyID": "ot_3065", "treeID": "tree7"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Vaga, C. F., Quattrini, A. M., Galv\u00e3o de Lossio e Seiblitz, I., Huang, D., Quek, Z. B. R., Stolarski, J., Cairns, S. D., & Kitahara, M. V. (2025). A global coral phylogeny reveals resilience and vulnerability through deep time. Nature. https://doi.org/10.1038/s41586-025-09615-6\n", "decision": "INCLUDED", "name": "scle.mcc.mean.nex", "studyID": "ot_3066", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Tagliacollo, V. A., Tan, M., Reis, R. E., Gaia, R., Carrijo, V., Ranuzi, M., Craig, J. M., & Albert, J. S. (2024). Time-calibrated phylogeny of neotropical freshwater fishes. Frontiers in Bioinformatics, 4. https://doi.org/10.3389/fbinf.2024.1433995\n", "decision": "INCLUDED", "name": "time_tree_sp.tre", "studyID": "ot_3067", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jiao, B., Wei, M., Niu, G., Chen, X., Liu, Y., Huang, G., Chen, C., Zheng, J., Shen, J., Vitales, D., Vall\u00e8s, J., Verloove, F., Erst, A. S., Seregin, A. P., Soejima, A., Ge, X., Jabbour, F., Leostrin, A., Kokubugata, G., \u2026 Gao, T. (2025). Global phylogeny and taxonomy of Artemisia. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-64039-0\n", "decision": "INCLUDED", "name": "4_GM_dataset_gigamatrix-ML.tre", "studyID": "ot_3068", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dor\u00e9, M., Borowiec, M. L., Branstetter, M. G., Camacho, G. P., Fisher, B. L., Longino, J. T., Ward, P. S., & Blaimer, B. B. (2025). Evolutionary history of ponerine ants highlights how the timing of dispersal events shapes modern biodiversity. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-63709-3\n", "decision": "INCLUDED", "name": "SD_8.2_Time-calibrated_MCC_phylogeny_789t.tree", "studyID": "ot_3069", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Leslie, A. B., Beaulieu, J., Holman, G., Campbell, C. S., Mei, W., Raubeson, L. R., & Mathews, S. (2018). An overview of extant conifer evolution from the perspective of the fossil record. American Journal of Botany, 105(9), 1531\u20131544. Portico. https://doi.org/10.1002/ajb2.1143\n", "decision": "INCLUDED", "name": "Leslie et al_AJB 2018.tree", "studyID": "ot_3073", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Newton AF (1997) Review of Agyrtidae (coleoptera), with a New Genus and species from New Zealand. Annales Zoologici, 47(1):111-156.", "decision": "INCLUDED", "name": "Fig. 63", "studyID": "ot_3074", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Armis\u00e9n, D., Viala, S., Cordeiro, I. da R. S., Crumi\u00e8re, A. J. J., Hendaoui, E., Le Bouquin, A., Duchemin, W., Santos, E., Toubiana, W., Vargas-Lowman, A., Burguez Floriano, C. F., Polhemus, D. A., Wang, Y., Rowe, L., Moreira, F. F. F., & Khila, A. (2022). Transcriptome-based Phylogeny of the Semi-aquatic Bugs (Hemiptera: Heteroptera: Gerromorpha) Reveals Patterns of Lineage Expansion in a Series of New Adaptive Zones. Molecular Biology and Evolution, 39(11). https://doi.org/10.1093/molbev/msac229\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3079", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Mayer, C., Dietz, L., Call, E., Kukowka, S., Martin, S., & Espeland, M. (2021). Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens. Systematic Entomology, 46(3), 649\u2013671. Portico. https://doi.org/10.1111/syen.12481\n", "decision": "INCLUDED", "name": "AA_best_ML.tree", "studyID": "ot_3080", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kawahara, A. Y., Plotkin, D., Espeland, M., Meusemann, K., Toussaint, E. F. A., Donath, A., Gimnich, F., Frandsen, P. B., Zwick, A., dos Reis, M., Barber, J. R., Peters, R. S., Liu, S., Zhou, X., Mayer, C., Podsiadlowski, L., Storer, C., Yack, J. E., Misof, B., & Breinholt, J. W. (2019). Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths. Proceedings of the National Academy of Sciences, 116(45), 22657\u201322663. https://doi.org/10.1073/pnas.1907847116\n", "decision": "INCLUDED", "name": "Fig.S2.tre", "studyID": "ot_3081", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from K. L., V., Natesh, M., Mehta, P., Jayapal, R., Mukherjee, S., & Robin, V. V. (2022). Re\u2010assessing the phylogenetic status and evolutionary relationship of Forest Owlet (\n                    Athene blewitti\n                    (Hume\u20091873)) using genomic data. Ibis, 164(4), 1278\u20131284. Portico. https://doi.org/10.1111/ibi.13097\n", "decision": "INCLUDED", "name": "tree 1", "studyID": "ot_3089", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Sidlauskas, B. L., Assega, F. M., Melo, B. F., Oliveira, C., & Birindelli, J. L. O. (2021). Total evidence phylogenetic analysis reveals polyphyly ofAnostomoidesand uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes). Zoological Journal of the Linnean Society, 194(2), 626\u2013669. https://doi.org/10.1093/zoolinnean/zlab016\n", "decision": "INCLUDED", "name": "Maximum clade credibility tree morphology and molecules", "studyID": "ot_3093", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Sidlauskas, B. L., Assega, F. M., Melo, B. F., Oliveira, C., & Birindelli, J. L. O. (2021). Total evidence phylogenetic analysis reveals polyphyly ofAnostomoidesand uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes). Zoological Journal of the Linnean Society, 194(2), 626\u2013669. https://doi.org/10.1093/zoolinnean/zlab016\n", "decision": "INCLUDED", "name": "Maximum clade credibility molecules only", "studyID": "ot_3093", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Claramunt, S., Sheard, C., Brown, J. W., Cort\u00e9s-Ram\u00edrez, G., Cracraft, J., Su, M. M., Weeks, B. C., & Tobias, J. A. (2025). A new time tree of birds reveals the interplay between dispersal, geographic range size, and diversification. Current Biology, 35(16), 3883-3895.e4. https://doi.org/10.1016/j.cub.2025.07.004\n", "decision": "INCLUDED", "name": "BBtreeC2022.tre", "studyID": "ot_2879", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PETERS, M. J., & MARCUS, J. M. (2016). Taxonomy as a hypothesis: testing the status of the Bermuda buckeye butterfly\n                    Junonia coenia bergi\n                    (Lepidoptera: Nymphalidae). Systematic Entomology, 42(1), 288\u2013300. Portico. https://doi.org/10.1111/syen.12214\n", "decision": "INCLUDED", "name": "Fig. 2, ML", "studyID": "ot_3113", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ZHAO, T.-Y., HE, L., XU, X., CHEN, Z.-N., GAO, Y.-Y., & L\u00dc, L. (2022). The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications. Zootaxa, 5099(2), 179\u2013200. https://doi.org/10.11646/zootaxa.5099.2.2\n", "decision": "INCLUDED", "name": "AA_NP.tree", "studyID": "ot_3114", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Chang, J. J. M., Raupach, M. J., Cheng, L., Damgaard, J., Hongjamrassilp, W., Ip, Y. C. A., Ng, M. H.-C., Chan, W. W. R., Kunning, I., Liang, B. J. Y., Maggioni, D., Mana, R. R., Mishra, H., Mowe, M. A. D., Wainwright, B. J., Whitney, J. L., Wolfe, K., Yeo, D. C. J., & Huang, D. (2024). Skimming the skaters: genome skimming improves phylogenetic resolution of Halobatinae (Hemiptera: Gerridae). Insect Systematics and Diversity, 8(4). https://doi.org/10.1093/isd/ixae015\n", "decision": "INCLUDED", "name": "Gerromorpha_Chan_2024", "studyID": "ot_3115", "treeID": "tree5"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from WANG, R., LI, X., SZWEDO, J., STROI\u0143SKI, A., LIANG, A., & BOURGOIN, T. (2016). Testing Tropiduchini St\u00e5l 1866 (Hemiptera: Tropiduchidae) monophyly, a young inter\u2010tropical taxon of mainly insular species: taxonomy, distribution patterns and phylogeny, with the description of a new genus from Papua New Guinea. Systematic Entomology, 42(2), 359\u2013378. Portico. https://doi.org/10.1111/syen.12219\n", "decision": "INCLUDED", "name": "Fig. 12, MP", "studyID": "ot_3117", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ralph S. Peters, Lars Krogmann, Christoph Mayer, Alexander Donath, Simon Gunkel, Karen Meusemann, Alexey Kozlov, Lars Podsiadlowski, Malte Petersen, Robert Lanfear, Patricia A. Diez, John Heraty, Karl M. Kjer, Seraina Klopfstein, Rudolf Meier, Carlo Polidori, Thomas Schmitt, Shanlin Liu, Xin Zhou, Torsten Wappler, Jes Rust, Bernhard Misof, Oliver Niehuis, 2017, 'Evolutionary History of the Hymenoptera', Current Biology", "decision": "INCLUDED", "name": "Figure 1", "studyID": "ot_1053", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Sann, M., Niehuis, O., Peters, R. S., Mayer, C., Kozlov, A., Podsiadlowski, L., Bank, S., Meusemann, K., Misof, B., Bleidorn, C., & Ohl, M. (2018). Phylogenomic analysis of Apoidea sheds new light on the sister group of bees. BMC Evolutionary Biology, 18(1). https://doi.org/10.1186/s12862-018-1155-8\n", "decision": "INCLUDED", "name": "Time calibration run 1", "studyID": "ot_2466", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Johnson, K. P., Dietrich, C. H., Friedrich, F., Beutel, R. G., Wipfler, B., Peters, R. S., Allen, J. M., Petersen, M., Donath, A., Walden, K. K. O., Kozlov, A. M., Podsiadlowski, L., Mayer, C., Meusemann, K., Vasilikopoulos, A., Waterhouse, R. M., Cameron, S. L., Weirauch, C., Swanson, D. R., \u2026 Yoshizawa, K. (2018). Phylogenomics and the evolution of hemipteroid insects. Proceedings of the National Academy of Sciences, 115(50), 12775\u201312780. https://doi.org/10.1073/pnas.1815820115\n", "decision": "INCLUDED", "name": "Acer_FigTree_Long", "studyID": "ot_2611", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Orr, R. J. S., Di Martino, E., Ramsfjell, M. H., Gordon, D. P., Berning, B., Chowdhury, I., Craig, S., Cumming, R. L., Figuerola, B., Florence, W., Harmelin, J.-G., Hirose, M., Huang, D., Jain, S. S., Jenkins, H. L., Kotenko, O. N., Kuklinski, P., Lee, H. E., Madurell, T., \u2026 Liow, L. H. (2022). Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny. Science Advances, 8(13). https://doi.org/10.1126/sciadv.abm7452\n", "decision": "INCLUDED", "name": "TRIMMED (Fig. 2)", "studyID": "ot_3052", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Qing, X., Zhang, Y. M., Sun, S., Ahmed, M., Lo, W.-S., Bert, W., Holovachov, O., & Li, H. (2024). Phylogenomic Insights into the Evolution and Origin of Nematoda. Systematic Biology, 74(3), 349\u2013358. https://doi.org/10.1093/sysbio/syae073\n", "decision": "INCLUDED", "name": "Nem_50p_aa_MCMCresult.tree", "studyID": "ot_3053", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from RIGHETTI, N., NICOLINI, F., FORNI, G., & LUCHETTI, A. (2025). Towards a time-tree solution for Branchiopoda diversification: a jackknife assessment of fossil age priors. Palaeoentomology, 8(3), 316\u2013328. https://doi.org/10.11646/palaeoentomology.8.3.8\n", "decision": "INCLUDED", "name": "FINAL_calibrated_tree.nexus", "studyID": "ot_3061", "treeID": "tree4"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Thomas Thorpe, J. A. (2024). Phylogenomics supports a single origin of terrestriality in isopods. Proceedings of the Royal Society B: Biological Sciences, 291(2033). https://doi.org/10.1098/rspb.2024.1042\n", "decision": "INCLUDED", "name": "Isopoda.edit20.Oniscidates.SubM.LogNrml.mcc.tree", "studyID": "ot_3119", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Simion, Paul, Herv\u00e9 Philippe, Denis Baurain, Muriel Jager, Daniel J. Richter, Arnaud Di Franco, B\u00e9atrice Roure, Nori Satoh, \u00c9ric Qu\u00e9innec, Alexander Ereskovsky, Pascal Lap\u00e9bie, Erwan Corre, Fr\u00e9d\u00e9ric Delsuc, Nicole King, Gert W\u00f6rheide, Micha\u00ebl Manuel, 2017, 'A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals', Current Biology", "decision": "INCLUDED", "name": "Fig 3 (supermatrix of 401,632 Amino Acid Positions for 90 Species)", "studyID": "ot_1051", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gazave, E., Lap\u00e9bie, P., Renard, E., Vacelet, J., Rocher, C., Ereskovsky, A. V., Lavrov, D. V., & Borchiellini, C. (2010). Molecular Phylogeny Restores the Supra-Generic Subdivision of Homoscleromorph Sponges (Porifera, Homoscleromorpha). PLoS ONE, 5(12), e14290. https://doi.org/10.1371/journal.pone.0014290\n", "decision": "INCLUDED", "name": "tree1", "studyID": "ot_3126", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gazave, E., Lavrov, D. V., Cabrol, J., Renard, E., Rocher, C., Vacelet, J., Adamska, M., Borchiellini, C., & Ereskovsky, A. V. (2013). Systematics and Molecular Phylogeny of the Family Oscarellidae (Homoscleromorpha) with Description of Two New Oscarella Species. PLoS ONE, 8(5), e63976. https://doi.org/10.1371/journal.pone.0063976\n", "decision": "INCLUDED", "name": "Simplified Consensus Tree Based on tatC+atp6 Molecular Phylogenies", "studyID": "ot_3127", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Voigt, O., W\u00fclfing, E., & W\u00f6rheide, G. (2012). Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea). PLoS ONE, 7(3), e33417. https://doi.org/10.1371/journal.pone.0033417\n", "decision": "INCLUDED", "name": "Maximum-likelihood 16-state Doublet Substitution Model", "studyID": "ot_3128", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Burki, F., Roger, A. J., Brown, M. W., & Simpson, A. G. B. (2020). The New Tree of Eukaryotes. Trends in Ecology &amp; Evolution, 35(1), 43\u201355. https://doi.org/10.1016/j.tree.2019.08.008\n", "decision": "INCLUDED", "name": "Figure 1 - The New Tree of Eukaryotes", "studyID": "ot_3129", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Castelle, C. J., & Banfield, J. F. (2018). Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell, 172(6), 1181\u20131197. https://doi.org/10.1016/j.cell.2018.02.016\n", "decision": "INCLUDED", "name": "Maximum Likelihood Phylogenetic Tree for Three Domains of Life", "studyID": "ot_3130", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Thompson, J. B., Martinez, C., Avaria-Llautureo, J., Ram\u00edrez-Barahona, S., Manzanarez-Villasana, G., Culham, A., Gdaniec, A., Ryan, G., Venditti, C., Keeling, G., & Priest, N. K. (2026). CactEcoDB: Trait, spatial, environmental, phylogenetic and diversification data for the cactus family. Scientific Data. https://doi.org/10.1038/s41597-026-06936-7\n", "decision": "INCLUDED", "name": "CactEcoDB Phylogeny V2", "studyID": "ot_3131", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bolzoni, R., Monteil, C. L., Alonso, B., Bergot, M., Chevrier, D. 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Phylogeny of the Hexactinellida: phylogenetic reconstruction of the subclass Hexasterophora based on morphological characters. Journal of the Marine Biological Association of the United Kingdom, 95(7), 1365\u20131369. https://doi.org/10.1017/s0025315413000180\n", "decision": "INCLUDED", "name": "Fig. 2. Family Rossellidae: maximum parsimony tree", "studyID": "ot_3139", "treeID": "tree5"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Fan, P., He, K., Chen, X., Ortiz, A., Zhang, B., Zhao, C., Li, Y., Zhang, H., Kimock, C., Wang, W., Groves, C., Turvey, S. T., Roos, C., Helgen, K. M., & Jiang, X. (2017). Description of a new species of Hoolock gibbon (Primates: Hylobatidae) based on integrative taxonomy. American Journal of Primatology, 79(5). Portico. https://doi.org/10.1002/ajp.22631\n", "decision": "INCLUDED", "name": "Fig. 6", "studyID": "ot_3140", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Thinh, V.N., Mootnick, A.R., Thanh, V.N., Nadler, T., & Roos, C. (2010). A new species of crested gibbon, from the central Annamite mountain range.", "decision": "INCLUDED", "name": "Fig.19. Phylogenetic relationships among crested gibbon species", "studyID": "ot_3141", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Matsudaira, K., & Ishida, T. (2021). Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing. Heredity, 127(3), 312\u2013322. https://doi.org/10.1038/s41437-021-00452-7\n", "decision": "INCLUDED", "name": "Fig. 2. Gibbon mitogenome phylogenetic tree", "studyID": "ot_3142", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ereskovsky, A. V., Richter, D. J., Lavrov, D. V., Schippers, K. J., & Nichols, S. A. (2017). Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA. PLOS ONE, 12(9), e0183002. https://doi.org/10.1371/journal.pone.0183002\n", "decision": "INCLUDED", "name": "Fig 3. Homoscleromorph phylogenetic relationships from mtGenome", "studyID": "ot_3143", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Guiollot, E., Guillemain, D., Renard, E., Borchiellini, C., & Schenkelaars, Q. (2024). The Oscarella sponge genus: a hidden yet colorful diversity. https://doi.org/10.1101/2024.10.26.620226\n", "decision": "INCLUDED", "name": "Figure 2", "studyID": "ot_3144", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from PEREZ, T., & RUIZ, C. (2018). Description of the first Caribbean Oscarellidae (Porifera: Homoscleromorpha)\u00a0. Zootaxa, 4369(4). https://doi.org/10.11646/zootaxa.4369.4.3\n", "decision": "INCLUDED", "name": "FIGURE 8. ML Phylogenetic reconstruction of Oscarellidae", "studyID": "ot_3145", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cesar Ruiz, Guilherme Muricy, Anaira Lage, Celso Domingos, Sandrine Chenesseau, et al.. Descriptions of new sponge species and genus, including aspiculate Plakinidae, overturn the Homoscleromorpha classification. Zoological Journal of the Linnean Society, 2017, 179 (4), pp.707-724.\nff10.1111/zoj.12480ff. ffhal-01681524f", "decision": "INCLUDED", "name": "Figure 7. Phylogenetic reconstruction using ML values", "studyID": "ot_3146", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cabioch, C., Ruiz, C., Grenier, M., Ereskovsky, A., Moraes, F., Fauvelot, C., & P\u00e9rez, T. (2026). Cave-dwelling Homoscleromorpha (Porifera) from Cape Verde archipelago (Northeast Atlantic): one new genus of aspiculate Plakinidae and five new species. Zoological Journal of the Linnean Society, 206(3). https://doi.org/10.1093/zoolinnean/zlag040\n", "decision": "INCLUDED", "name": "Figure 12. Bayesian phylogenetic tree of concatenated COI + 28S data", "studyID": "ot_3147", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ereskovsky, A. V., Lavrov, D. V., & Willenz, P. (2013). Five new species of Homoscleromorpha (Porifera) from the Caribbean Sea and re-description ofPlakina jamaicensis. Journal of the Marine Biological Association of the United Kingdom, 94(2), 285\u2013307. https://doi.org/10.1017/s0025315413000295\n", "decision": "INCLUDED", "name": "Fig. 13. Phylogenetic analysis of homoscleromorph relationships using mitochondrial cob sequences", "studyID": "ot_3149", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from GRENIER, M., RUIZ, C., LAGE, A., & PEREZ, T. (2020). New cave-dwelling Plakina (Plakinidae, Homoscleromorpha, Porifera) from Martinique Island (French Antilles). Zootaxa, 4729(1). https://doi.org/10.11646/zootaxa.4729.1.6\n", "decision": "INCLUDED", "name": "FIGURE 5. Phylogenetic relationships of Homoscleromorpha using cytochrome oxidase 1", "studyID": "ot_3150", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from VICENTE, J., ZEA, S., & HILL, R. T. (2016). Sponge epizoism in the Caribbean and the discovery of new Plakortis and &lt;br /&gt;Haliclona species, and polymorphism of Xestospongia deweerdtae (Porifera). Zootaxa, 4178(2). https://doi.org/10.11646/zootaxa.4178.2.3\n", "decision": "INCLUDED", "name": "FIGURE 4 Maximum likelihood topology from cytochrome b oxidase ", "studyID": "ot_3148", "treeID": "tree4"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Manuel, M., Borchiellini, C., Alivon, E., Le Parco, Y., Vacelet, J., & Boury-Esnault, N. (2003). Phylogeny and Evolution of Calcareous Sponges: Monophyly of Calcinea and Calcaronea, High Level of Morphological Homoplasy, and the Primitive Nature of Axial Symmetry. Systematic Biology, 52(3), 311\u2013333. https://doi.org/10.1080/10635150390196966\n", "decision": "INCLUDED", "name": "FIGURE 2. B - Strict consensus of 81 shortest trees minus terminal taxa", "studyID": "ot_3151", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Manuel, M., Borchiellini, C., Alivon, E., Le Parco, Y., Vacelet, J., & Boury-Esnault, N. (2003). Phylogeny and Evolution of Calcareous Sponges: Monophyly of Calcinea and Calcaronea, High Level of Morphological Homoplasy, and the Primitive Nature of Axial Symmetry. Systematic Biology, 52(3), 311\u2013333. https://doi.org/10.1080/10635150390196966\n", "decision": "INCLUDED", "name": "FIGURE 4. Analyses of 18S rRNA data set in ML tree", "studyID": "ot_3151", "treeID": "tree5"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Voigt, O., & W\u00f6rheide, G. (2015). A short LSU rRNA fragment as a standard marker for integrative taxonomy in calcareous sponges (Porifera: Calcarea). Organisms Diversity &amp; Evolution, 16(1), 53\u201364. https://doi.org/10.1007/s13127-015-0247-1\n", "decision": "INCLUDED", "name": "Fig. 3 Bayesian phylogeny of LSU C-region", "studyID": "ot_3152", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Sanamyan, K. E., Sanamyan, N. P., Kukhlevskiy, A. D., & Shilov, V. A. (2023). New species of calcareous sponges of the family Leuconiidae (Porifera: Calcarea: Baeriida) from Kuril Islands, NW Pacific. Invertebrate Zoology, 20(2), 153\u2013179. https://doi.org/10.15298/invertzool.20.2.03\n", "decision": "INCLUDED", "name": "Fig. 13. ML tree from C-region of 28S rRNA sequences", "studyID": "ot_3153", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Voigt, O., Erpenbeck, D., & W\u00f6rheide, G. (2008). Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera. BMC Evolutionary Biology, 8(1). https://doi.org/10.1186/1471-2148-8-69\n", "decision": "INCLUDED", "name": "Figure 5. Phylogeny inferred with PHASE/MrBayes", "studyID": "ot_3154", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Schuster, A., Erpenbeck, D., Pisera, A., Hooper, J., Bryce, M., Fromont, J., & W\u00f6rheide, G. (2015). Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges. PLoS ONE, 10(1), e116038. https://doi.org/10.1371/journal.pone.0116038\n", "decision": "INCLUDED", "name": "Fig. 5. Bayesian Inference phylogeny of demosponge taxa based on CO1", "studyID": "ot_3155", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Alvizu, A., Eilertsen, M. H., Xavier, J. R., & Rapp, H. T. (2018). Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea). Organisms Diversity &amp; Evolution, 18(3), 279\u2013290. https://doi.org/10.1007/s13127-018-0368-4\n", "decision": "INCLUDED", "name": "Fig. 1. Phylogenetic reconstruction with Bayesian inference of 28S rDNA for Calcaronea", "studyID": "ot_3156", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from LOPES, M. V., PADUA, A., C\u00d3NDOR-LUJ\u00c1N, B., & KLAUTAU, M. (2018). Calcareous sponges (Porifera, Calcarea) from Florida: new species, new records and biogeographical affinities. Zootaxa, 4526(2). https://doi.org/10.11646/zootaxa.4526.2.2\n", "decision": "INCLUDED", "name": "FIGURE 6. ML tree reconstructed with ribosomal nuclear marker ITS", "studyID": "ot_3157", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Klautau, M., Ime\u0161ek, M., Azevedo, F., Ple\u0161e, B., Nikoli\u0107, V., & \u0106etkovi\u0107, H. (2016). Adriatic calcarean sponges (Porifera, Calcarea), with the description of six new species and a richness analysis. European Journal of Taxonomy, 178. https://doi.org/10.5852/ejt.2016.178\n", "decision": "INCLUDED", "name": "Fig. 16. ML tree based on ITS1-5.8S-ITS2 rDNA sequences of Calcinea", "studyID": "ot_3158", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Klautau, M., Ime\u0161ek, M., Azevedo, F., Ple\u0161e, B., Nikoli\u0107, V., & \u0106etkovi\u0107, H. (2016). Adriatic calcarean sponges (Porifera, Calcarea), with the description of six new species and a richness analysis. European Journal of Taxonomy, 178. https://doi.org/10.5852/ejt.2016.178\n", "decision": "INCLUDED", "name": "Fig. 17. ML tree based on partial 28S rDNA sequences of Calcinea", "studyID": "ot_3158", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Klautau, M., Ime\u0161ek, M., Azevedo, F., Ple\u0161e, B., Nikoli\u0107, V., & \u0106etkovi\u0107, H. (2016). Adriatic calcarean sponges (Porifera, Calcarea), with the description of six new species and a richness analysis. European Journal of Taxonomy, 178. https://doi.org/10.5852/ejt.2016.178\n", "decision": "INCLUDED", "name": "Fig. 19. ML tree based on partial 28S rDNA sequences of Calcaronea", "studyID": "ot_3158", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from KLAUTAU, M., LOPES, M. V., GUARABYRA, B., FOLCHER, E., EKINS, M., & DEBITUS, C. (2020). Calcareous sponges from the French Polynesia (Porifera: Calcarea). Zootaxa, 4748(2). https://doi.org/10.11646/zootaxa.4748.2.3\n", "decision": "INCLUDED", "name": "FIGURE 13. ML phylogenetic tree of the ITS from Calcinea", "studyID": "ot_3160", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from KLAUTAU, M., LOPES, M. V., GUARABYRA, B., FOLCHER, E., EKINS, M., & DEBITUS, C. (2020). Calcareous sponges from the French Polynesia (Porifera: Calcarea). Zootaxa, 4748(2). https://doi.org/10.11646/zootaxa.4748.2.3\n", "decision": "INCLUDED", "name": "FIGURE 15. ML phylogenetic tree of the LSU from Calcaronea", "studyID": "ot_3160", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from ALVIZU, A., XAVIER, J. R., & RAPP, H. T. (2019). Description of new chiactine-bearing sponges provides insights into the higher classification of Calcaronea (Porifera: Calcarea). Zootaxa, 4615(2). https://doi.org/10.11646/zootaxa.4615.2.1\n", "decision": "INCLUDED", "name": "FIGURE 21. Phylogenetic reconstruction using Bayesian inference of 18S + C-region rDNA for chiactine/pugiole-bearing sponges", "studyID": "ot_3161", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Van Soest, R., Hoeksema, B. W., Reimer, J. D., & De Voogd, N. J. (2015). New records of the rare calcareous sponge Paragrantia waguensis H\u00f4zawa, 1940. ZooKeys, 546, 1\u201320. https://doi.org/10.3897/zookeys.546.6122\n", "decision": "INCLUDED", "name": "Figure 8. ML phylogenetic tree of 28S partial sequences of Leucosolenida calcareous sponges", "studyID": "ot_3162", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Martin Dohrmann, Christopher Kelley, Michelle Kelly, Andrzej Pisera, John N. A. Hooper, Henry M. Reiswig, 2017, 'An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)', Frontiers in Zoology, vol. 14, no. 1", "decision": "INCLUDED", "name": "Fig. 8. Phylogeny of Amphidiscophora inferred with TNT", "studyID": "ot_1068", "treeID": "tree7"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Martin Dohrmann, Christopher Kelley, Michelle Kelly, Andrzej Pisera, John N. A. Hooper, Henry M. Reiswig, 2017, 'An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)', Frontiers in Zoology, vol. 14, no. 1", "decision": "INCLUDED", "name": "Fig. 9. Phylogeny of Sceptrulophora inferred with TNT", "studyID": "ot_1068", "treeID": "tree8"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Martin Dohrmann, Christopher Kelley, Michelle Kelly, Andrzej Pisera, John N. A. Hooper, Henry M. Reiswig, 2017, 'An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)', Frontiers in Zoology, vol. 14, no. 1", "decision": "INCLUDED", "name": "Fig. 10. Phylogeny of Anuncinataria inferred with TNT", "studyID": "ot_1068", "treeID": "tree12"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Hestetun, J. T., Rapp, H. T., & Pomponi, S. (2019). Deep-Sea Carnivorous Sponges From the Mariana Islands. Frontiers in Marine Science, 6. https://doi.org/10.3389/fmars.2019.00371\n", "decision": "INCLUDED", "name": "FIGURE 11. ML consensus tree of Cladorhizidae based on partial 28S rRNA, COI, and ALG11", "studyID": "ot_3163", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Rossi, M. E., Keating, J. N., Kenny, N. J., Giacomelli, M., \u00c1lvarez-Carretero, S., Schuster, A., C\u00e1rdenas, P., Taboada, S., Koutsouveli, V., Donoghue, P. C. J., Riesgo, A., & Pisani, D. (2026). Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history. Science Advances, 12(2). https://doi.org/10.1126/sciadv.adx1754\n", "decision": "INCLUDED", "name": "Fig. 1. Phylogeny of sponges", "studyID": "ot_3164", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Simion, P., Bekkouche, N., Jager, M., Qu\u00e9innec, E., & Manuel, M. (2015). Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora. Zoology, 118(2), 102\u2013114. https://doi.org/10.1016/j.zool.2014.06.004\n", "decision": "INCLUDED", "name": "Fig. 1A. Simplified 18S dataset tree at the metazoan level", "studyID": "ot_3165", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Simion, P., Bekkouche, N., Jager, M., Qu\u00e9innec, E., & Manuel, M. (2015). Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora. Zoology, 118(2), 102\u2013114. https://doi.org/10.1016/j.zool.2014.06.004\n", "decision": "INCLUDED", "name": "Fig. 3. Bayesian inference analysis using combined 18S-ITS dataset", "studyID": "ot_3165", "treeID": "tree4"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lu, T.-M., Kanda, M., Satoh, N., & Furuya, H. (2017). The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution. Zoological Letters, 3(1). https://doi.org/10.1186/s40851-017-0068-5\n", "decision": "INCLUDED", "name": "Fig. 3a. ML tree from dataset covering 29 taxa", "studyID": "ot_3166", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cannon, J. T., Rychel, A. L., Eccleston, H., Halanych, K. M., & Swalla, B. J. (2009). Molecular phylogeny of hemichordata, with updated status of deep-sea enteropneusts. Molecular Phylogenetics and Evolution, 52(1), 17\u201324. https://doi.org/10.1016/j.ympev.2009.03.027\n", "decision": "INCLUDED", "name": "Fig. 4. 18S rDNA topology in a Bayesian tree", "studyID": "ot_3168", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Koga, C., & Rouse, G. W. (2021). Mitogenomics and the Phylogeny of Mantis Shrimps (Crustacea: Stomatopoda). Diversity, 13(12), 647. https://doi.org/10.3390/d13120647\n", "decision": "INCLUDED", "name": "Figure 3B. ML tree from the mixed amino acid and nucleotide dataset of Stomatopoda", "studyID": "ot_3169", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Shane T. Ahyong, Phylogenetic Analysis of the Stomatopoda (Malacostraca), Journal of Crustacean Biology, Volume 17, Issue 4, 1 October 1997, Pages 695\u2013715, https://doi.org/10.1163/193724097X00134", "decision": "INCLUDED", "name": "Fig. 5. Single most parsimonious cladogram of the Stomatopoda", "studyID": "ot_3170", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cao, J., Poyarkov, N. A., Wei, P., Tie, M., Matsukoji, T., Suwannapoom, C., Ai, R., Lu, W., Sucharitakul, P., Wang, H., Chomdej, S., Yuan, Z., & Yan, F. (2026). Diversity, phylogeny, and biogeography of the subgenus Japonigekko (Gekkonidae: Gekko). Molecular Phylogenetics and Evolution, 217, 108530. https://doi.org/10.1016/j.ympev.2025.108530\n", "decision": "INCLUDED", "name": "ML tree for Japonigekko", "studyID": "ot_3171", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Zhou M, Cui Y, Vlas\u00e1k J, Wu Y, Li C, et al. 2026. Global phylogeny, divergence times and evolutionary history of Trichaptum s.l. (Hymenochaetales, Basidiomycota): two new families and six new species. Mycosphere 17: e004 doi: 10.48130/mycosphere-0026-0005", "decision": "INCLUDED", "name": "Figure 1. ML tree of Trichaptum s.l. based on five sequences (ITS, nLSU, TEF1, mt-SSU, and nuc-SSU)", "studyID": "ot_3172", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Xu, H., Shen, C., Huang, W., Cargill, D. C., Villarreal A., J. C., Chantanaorrapint, S., Promma, C., Wei, Y., Ho, B. C., Quandt, D., Peng, T., Xiang, Y., Zielman, H. R., Bakalin, V. A., Shu, L., & Zhu, R. (2025). Evolution and classification of hornworts: new insights from the first plastome\u2010based phylogeny. New Phytologist, 249(3), 1491\u20131508. Portico. https://doi.org/10.1111/nph.70672\n", "decision": "INCLUDED", "name": "Fig. 3. Joint consensus tree of hornworts from concatenated nucleotide sequences", "studyID": "ot_3173", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Huang, X., Sang, J., Yan, L., & Zhang, D. (2026). The phylogeny and evolution of blow flies (Diptera: Calliphoridae) from the perspective of mitogenomics. BMC Genomics, 27(1). https://doi.org/10.1186/s12864-026-12534-z\n", "decision": "INCLUDED", "name": "Fig. 5. ML and BI phylogenetic trees of Calliphoridae from mitogenomic data", "studyID": "ot_3174", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Obst, M., Faurby, S., Bussarawit, S., & Funch, P. (2012). Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species. Molecular Phylogenetics and Evolution, 62(1), 21\u201326. https://doi.org/10.1016/j.ympev.2011.08.025\n", "decision": "INCLUDED", "name": "Fig. 1. ML tree from combined analysis based on all molecular data from 100 independent runs", "studyID": "ot_3175", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cruz-Barraza, J. A., Vega, C., & Carballo, J. L. (2014). Taxonomy of family Plakinidae (Porifera: Homoscleromorpha) from eastern Pacific coral reefs, through morphology andcox1andcob\u2005mtDNA data. Zoological Journal of the Linnean Society, 171(2), 254\u2013276. https://doi.org/10.1111/zoj.12137\n", "decision": "INCLUDED", "name": "Figure 8. Phylogenetic reconstruction of cox1", "studyID": "ot_3177", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ime\u0161ek, M., Ple\u0161e, B., Pfannkuchen, M., Godrijan, J., Pfannkuchen, D. M., Klautau, M., & \u0106etkovi\u0107, H. (2013). Integrative taxonomy of four Clathrina species of the Adriatic Sea, with the first formal description of Clathrina rubra Sar\u00e0, 1958. Organisms Diversity &amp; Evolution, 14(1), 21\u201329. https://doi.org/10.1007/s13127-013-0156-0\n", "decision": "INCLUDED", "name": "Fig. 1. Bayesian tree based on concatenated ITS1-5.8S-ITS2 and partial 28S rDNA sequences", "studyID": "ot_3179", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from VOIGT, O., RUTHENSTEINER, B., LEIVA, L., FRADUSCO, B., & W\u00d6RHEIDE, G. (2018). A new species of the calcareous sponge genus Leuclathrina (Calcarea: Calcinea: Clathrinida) from the Maldives. Zootaxa, 4382(1). https://doi.org/10.11646/zootaxa.4382.1.5\n", "decision": "INCLUDED", "name": "FIGURE 4. Phylogenetic position of Leuclathrina translucida within Calcinea", "studyID": "ot_3178", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Azevedo, F., C\u00f3ndor-Luj\u00e1n, B., Willenz, P., Hajdu, E., Hooker, Y., & Klautau, M. (2015). Integrative taxonomy of calcareous sponges (subclass Calcinea) from the Peruvian coast: morphology, molecules, and biogeography. Zoological Journal of the Linnean Society, 173(4), 787\u2013817. https://doi.org/10.1111/zoj.12213\n", "decision": "INCLUDED", "name": "Figure 11. Bayesian 50% majority rule consensus tree from ITS rDNA alignment", "studyID": "ot_3180", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Riesgo A, Cavalcanti FF, Kenny NJ, R\u00edos P, Cristobo J, Lanna E. (2018) Integrative systematics of clathrinid sponges: morphological, reproductive and phylogenetic characterisation of a new species of Leucetta from Antarctica (Porifera, Calcarea, Calcinea) with notes on the occurrence of flagellated sperm. Invertebrate Systematics 32, 827\u2013841. https://doi.org/10.1071/IS17033\n\n", "decision": "INCLUDED", "name": "Fig. 7. ML phylogenetic inter-relationships within Clathrinida using 18S rRNA and 28S rRNA", "studyID": "ot_3181", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from C\u00d3NDOR-LUJ\u00c1N, B., & KLAUTAU, M. (2016). Nicola gen. nov. with redescription of Nicola tetela (Borojevic &amp;amp; Peixinho, 1976) (Porifera: Calcarea: Calcinea: Clathrinida)\u00a0. Zootaxa, 4103(3). https://doi.org/10.11646/zootaxa.4103.3.2\n", "decision": "INCLUDED", "name": "FIGURE 3. Bayesian 50% consensus tree from ITS rDNA", "studyID": "ot_3182", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Kober, K. M., & Nichols, S. A. (2007). On the phylogenetic relationships of hadromerid and poecilosclerid sponges. Journal of the Marine Biological Association of the United Kingdom, 87(6), 1585\u20131598. https://doi.org/10.1017/s0025315407058237\n", "decision": "INCLUDED", "name": "Figure 1. Bayesian inference tree based on SSU", "studyID": "ot_3183", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lopes, M. V., & Klautau, M. (2023). Phylogeny and revision ofLeucaltisandLeucettusa(Porifera: Calcarea), with new classification proposals and description of a new type of aquiferous system. Zoological Journal of the Linnean Society, 198(3), 691\u2013746. https://doi.org/10.1093/zoolinnean/zlad008\n", "decision": "INCLUDED", "name": "Figure 1. Phylogenetic ML tree for C-LSU marker of subclass Calcinea", "studyID": "ot_3184", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Lopes, M. V., & Klautau, M. (2023). Phylogeny and revision ofLeucaltisandLeucettusa(Porifera: Calcarea), with new classification proposals and description of a new type of aquiferous system. Zoological Journal of the Linnean Society, 198(3), 691\u2013746. https://doi.org/10.1093/zoolinnean/zlad008\n", "decision": "INCLUDED", "name": "Figure 2. Phylogenetic ML tree for ITS marker of subclass Calcinea", "studyID": "ot_3184", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Borchiellini, C., Chombard, C., Manuel, M., Alivon, E., Vacelet, J., & Boury-Esnault, N. (2004). Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution. Molecular Phylogenetics and Evolution, 32(3), 823\u2013837. https://doi.org/10.1016/j.ympev.2004.02.021\n", "decision": "INCLUDED", "name": "Fig. 2. ML Tree from 18S rRNA dataset", "studyID": "ot_3185", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Borchiellini, C., Chombard, C., Manuel, M., Alivon, E., Vacelet, J., & Boury-Esnault, N. (2004). Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution. Molecular Phylogenetics and Evolution, 32(3), 823\u2013837. https://doi.org/10.1016/j.ympev.2004.02.021\n", "decision": "INCLUDED", "name": "Fig. 3. ML trees from analyses of 28S rRNA dataset", "studyID": "ot_3185", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jo\u00e3o Filipe Riva Tonini, Karen H. Beard, Rodrigo Barbosa Ferreira, Walter Jetz, R. Alexander Pyron, 2016, 'Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status', Biological Conservation, vol. 204, pp. 23-31", "decision": "INCLUDED", "name": "Tonini et al. (2016) Squamate Phylogeny", "studyID": "ot_1332", "treeID": "tree4"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Agarwal, I., Bauer, A. M., Gamble, T., Giri, V. B., Jablonski, D., Khandekar, A., Mohapatra, P. P., Masroor, R., Mishra, A., & Ramakrishnan, U. (2022). The evolutionary history of an accidental model organism, the leopard gecko Eublepharis macularius (Squamata: Eublepharidae). Molecular Phylogenetics and Evolution, 168, 107414. https://doi.org/10.1016/j.ympev.2022.107414\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_2274", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Barber, J. R., Plotkin, D., Rubin, J. J., Homziak, N. T., Leavell, B. C., Houlihan, P. R., Miner, K. A., Breinholt, J. W., Quirk-Royal, B., Padr\u00f3n, P. S., Nunez, M., & Kawahara, A. Y. (2022). Anti-bat ultrasound production in moths is globally and phylogenetically widespread. Proceedings of the National Academy of Sciences, 119(25). https://doi.org/10.1073/pnas.2117485119\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_2275", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Barbosa, E. P., Seraphim, N., Valencia, G., Azeredo-Espin, A. M. L., & Freitas, A. V. L. (2022). Phylogenetic systematics of Yphthimoides Forster, 1964 and related taxa, with notes on the biogeographical history of Yphthimoides species. Molecular Phylogenetics and Evolution, 168, 107390. https://doi.org/10.1016/j.ympev.2022.107390\n", "decision": "INCLUDED", "name": "Untitled (tree2)", "studyID": "ot_2276", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Bitencourt, J. A., Affonso, P. R. A. M., Ramos, R. T. C., Schneider, H., & Sampaio, I. (2023). Phylogenetic relationships and the origin of New World soles (Teleostei: Pleuronectiformes: Achiridae): The role of estuarine habitats. Molecular Phylogenetics and Evolution, 178, 107631. https://doi.org/10.1016/j.ympev.2022.107631\n", "decision": "INCLUDED", "name": "ML Achiridae Tree", "studyID": "ot_3186", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Breslin, P. B., Wojciechowski, M. F., & Majure, L. C. (2022). Remarkably rapid, recent diversification of Cochemiea and Mammillaria in the Baja California, Mexico region. American Journal of Botany, 109(9), 1472\u20131487. Portico. https://doi.org/10.1002/ajb2.16048\n", "decision": "INCLUDED", "name": "Bayesian Mammilloid Tree", "studyID": "ot_3187", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Brownstein, C. D., & Near, T. J. (2023). Phylogenetics and the Cenozoic radiation of lampreys. Current Biology, 33(2), 397-404.e3. https://doi.org/10.1016/j.cub.2022.12.018\n", "decision": "INCLUDED", "name": "Phylogeny of lampreys using BEAST", "studyID": "ot_3188", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cai, C., Tihelka, E., Giacomelli, M., Lawrence, J. F., \u015alipi\u0144ski, A., Kundrata, R., Yamamoto, S., Thayer, M. K., Newton, A. F., Leschen, R. A. B., Gimmel, M. L., L\u00fc, L., Engel, M. S., Bouchard, P., Huang, D., Pisani, D., & Donoghue, P. C. J. (2022). Integrated phylogenomics and fossil data illuminate the evolution of beetles. Royal Society Open Science, 9(3). https://doi.org/10.1098/rsos.211771\n", "decision": "INCLUDED", "name": "bpcomp.con.tre", "studyID": "ot_2539", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cali\u00f3, M. F., Thode, V. A., Bacon, C. D., Silvestro, D., Antonelli, A., & Lohmann, L. G. (2022). Spatio\u2010temporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions. Journal of Biogeography, 49(6), 1086\u20131098. Portico. https://doi.org/10.1111/jbi.14368\n", "decision": "INCLUDED", "name": "Bayesian Tree for Anemopaegma Based on Uncorrelated Lognormal Relaxed Clock", "studyID": "ot_3189", "treeID": "tree5"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Calonje, M., Meerow, A. W., Griffith, M. P., Salas-Leiva, D., Vovides, A. P., Coiro, M., & Francisco-Ortega, J. (2019). A Time-Calibrated Species Tree Phylogeny of the New World Cycad Genus Zamia L. (Zamiaceae, Cycadales). International Journal of Plant Sciences, 180(4), 286\u2013314. https://doi.org/10.1086/702642\n", "decision": "INCLUDED", "name": "Fifty Percent Majority-rule Consensus Tree of 1820 Parsimonious Trees for Zamia", "studyID": "ot_3190", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Cannizzaro, A. G., & Berg, D. J. (2022). Gone with Gondwana: Amphipod diversification in freshwaters followed the breakup of the supercontinent. Molecular Phylogenetics and Evolution, 171, 107464. https://doi.org/10.1016/j.ympev.2022.107464\n", "decision": "INCLUDED", "name": "Amphipoda ML Tree", "studyID": "ot_3191", "treeID": "tree3"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dogantzis, K. A., Tiwari, T., Conflitti, I. M., Dey, A., Patch, H. M., Muli, E. M., Garnery, L., Whitfield, C. W., Stolle, E., Alqarni, A. S., Allsopp, M. H., & Zayed, A. (2021). Thrice out of Asia and the adaptive radiation of the western honey bee. Science Advances, 7(49). https://doi.org/10.1126/sciadv.abj2151\n", "decision": "INCLUDED", "name": "Phylogeny of A. mellifera Subspecies for Biographic Range Reconstruction", "studyID": "ot_3192", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Dupin, J., Hong-Wa, C., Pillon, Y., & Besnard, G. (2022). From the Mediterranean to the Pacific: re-circumscription towardsNotelaea s.l.and historical biogeography of a generic complex in Oleinae (Oleaceae). Botanical Journal of the Linnean Society, 200(3), 360\u2013377. https://doi.org/10.1093/botlinnean/boac024\n", "decision": "INCLUDED", "name": "ML Cladogram Representing Relationships Between Species in MMP + Eurasian Osmanthus Clade", "studyID": "ot_3193", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Fouquet, A., R\u00e9jaud, A., Rodrigues, M. T., Ron, S. R., Chaparro, J. C., Osorno, M., Werneck, F. P., Hrbek, T., Lima, A. P., Camacho-Badani, T., Jaramillo-Martinez, A. F., & Chave, J. (2022). Diversification of the Pristimantis conspicillatus group (Anura: Craugastoridae) within distinct neotropical areas throughout the Neogene. Systematics and Biodiversity, 20(1), 1\u201316. https://doi.org/10.1080/14772000.2022.2130464\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3194", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Fouquet, A., Cornuault, J., Rodrigues, M. T., Werneck, F. P., Hrbek, T., Acosta-Galvis, A. R., Massemin, D., Kok, P. J. R., & Ernst, R. (2022). Diversity, biogeography, and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae). Molecular Phylogenetics and Evolution, 170, 107442. https://doi.org/10.1016/j.ympev.2022.107442\n", "decision": "INCLUDED", "name": "Bayesian Tree Based on nuDNA for ", "studyID": "ot_3195", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Frable, B. W., Melo, B. F., Fontenelle, J. P., Oliveira, C., & Sidlauskas, B. L. (2022). Biogeographic reconstruction of the migratory Neotropical fish family Prochilodontidae (Teleostei: Characiformes). Zoologica Scripta, 51(3), 348\u2013364. Portico. https://doi.org/10.1111/zsc.12531\n", "decision": "INCLUDED", "name": "Time-calibrated PHylogeny of Prochilodontidae Estimated by BEAST", "studyID": "ot_3196", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Frankel, L., Mur\u00faa, M., & Esp\u00edndola, A. (2022). Biogeography and ecological drivers of evolution in the Andes: resolving the phylogenetic backbone forCalceolaria(Calceolariaceae). Botanical Journal of the Linnean Society, 199(1), 76\u201392. https://doi.org/10.1093/botlinnean/boab079\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3197", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Freitas, F. V., Branstetter, M. G., Casali, D. M., Aguiar, A. J. C., Griswold, T., & Almeida, E. A. B. (2022). Phylogenomic dating and Bayesian biogeography illuminate an antitropical pattern for eucerine bees. Journal of Biogeography, 49(6), 1034\u20131047. Portico. https://doi.org/10.1111/jbi.14359\n", "decision": "INCLUDED", "name": "Fig 2", "studyID": "ot_2479", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Fumia, N., Rubinoff, D., Zenil-Ferguson, R., Khoury, C. K., Pironon, S., Gore, M. A., & Kantar, M. B. (2022). Interactions between breeding system and ploidy affect niche breadth in\n            Solanum. Royal Society Open Science, 9(1). https://doi.org/10.1098/rsos.211862\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3198", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Ghezelayagh, A., Harrington, R. C., Burress, E. D., Campbell, M. A., Buckner, J. C., Chakrabarty, P., Glass, J. R., McCraney, W. T., Unmack, P. J., Thacker, C. E., Alfaro, M. E., Friedman, S. T., Ludt, W. B., Cowman, P. F., Friedman, M., Price, S. A., Dornburg, A., Faircloth, B. C., Wainwright, P. C., & Near, T. J. (2022). Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous. Nature Ecology &amp; Evolution, 6(8), 1211\u20131220. https://doi.org/10.1038/s41559-022-01801-3\n", "decision": "INCLUDED", "name": "Acanthomorph_GhezelayaghEtAl2022", "studyID": "ot_2824", "treeID": "tree4"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gorneau, J. A., Rheims, C. A., Moreau, C. S., & Rayor, L. S. (2022). Huntsman spider phylogeny informs evolution of life history, egg sacs, and morphology. Molecular Phylogenetics and Evolution, 174, 107530. https://doi.org/10.1016/j.ympev.2022.107530\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3199", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gostel, M. R., Sancho, G., Roque, N., Donato, M., & Funk, V. A. (2022). Phylogenomic loci define the generic boundaries of Gochnatieae and improve resolution at the species level in Moquiniastrum (Compositae). Molecular Phylogenetics and Evolution, 175, 107558. https://doi.org/10.1016/j.ympev.2022.107558\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3200", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Graboski, R., Grazziotin, F. G., Mott, T., & Trefaut Rodrigues, M. (2022). The phylogenetic position of ridley\u2019s worm lizard reveals the complex biogeographic history of New World insular amphisbaenids. Molecular Phylogenetics and Evolution, 173, 107518. https://doi.org/10.1016/j.ympev.2022.107518\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3201", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Hawlitschek, O., Ortiz, E. M., Noori, S., Webster, K. C., Husemann, M., & Pereira, R. J. (2022). Transcriptomic data reveals nuclear-mitochondrial discordance in Gomphocerinae grasshoppers (Insecta: Orthoptera: Acrididae). Molecular Phylogenetics and Evolution, 170, 107439. https://doi.org/10.1016/j.ympev.2022.107439\n", "decision": "INCLUDED", "name": "Untitled (tree2)", "studyID": "ot_3202", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Heritage, S., & Seiffert, E. R. (2022). Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria). PeerJ, 10, e13886. Portico. https://doi.org/10.7717/peerj.13886\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3203", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Hughes, L. C., Nash, C. M., White, W. T., & Westneat, M. W. (2022). Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae). Systematic Biology, 72(3), 530\u2013543. https://doi.org/10.1093/sysbio/syac072\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3204", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Janiak, M. C., Silva, F. E., Beck, R. M. D., de Vries, D., Kuderna, L. F. K., Torosin, N. S., Melin, A. D., Marqu\u00e8s\u2010Bonet, T., Goodhead, I. B., Messias, M., da Silva, M. N. F., Sampaio, I., Farias, I. P., Rossi, R., de Melo, F. R., Valsecchi, J., Hrbek, T., & Boubli, J. P. (2022). Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Molecular Ecology, 31(14), 3888\u20133902. Portico. https://doi.org/10.1111/mec.16554\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3205", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Johnson, K. P., Matthee, C., & Do\u00f1a, J. (2022). Phylogenomics reveals the origin of mammal lice out of Afrotheria. Nature Ecology &amp; Evolution, 6(8), 1205\u20131210. https://doi.org/10.1038/s41559-022-01803-1\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3206", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Jovanovska, E., Hauffe, T., Stelbrink, B., Cvetkoska, A., Levkov, Z., Wagner, B., Lacey, J. H., Ognjanova\u2010Rumenova, N., Hamilton, P. B., Brandenburg, K. M., Albrecht, C., & Wilke, T. (2022). Environmental filtering drives assembly of diatom communities over evolutionary time\u2010scales. Global Ecology and Biogeography, 31(5), 954\u2013967. Portico. https://doi.org/10.1111/geb.13471\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3207", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Laurin, M., Lapauze, O., & Marjanovi\u0107, D. (2022). What do ossification sequences tell us about the origin of extant amphibians? Peer Community Journal, 2. https://doi.org/10.24072/pcjournal.89\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3208", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Li, X.-R. (2022). \ufeffPhylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift, 69(1), 1\u201318. https://doi.org/10.3897/dez.69.68373\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3209", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from L\u00f3pez\u2010Estrada, E. K., Sanmart\u00edn, I., Uribe, J. E., Abalde, S., Jim\u00e9nez\u2010Ruiz, Y., & Garc\u00eda\u2010Par\u00eds, M. (2022). Mitogenomics and hidden\u2010trait models reveal the role of phoresy and host shifts in the diversification of parasitoid blister beetles (Coleoptera: Meloidae). Molecular Ecology, 31(8), 2453\u20132474. Portico. https://doi.org/10.1111/mec.16390\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3210", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Mittan, C. S., Zamudio, K. R., Thom\u00e9, M. T. C., Camurugi, F., Colli, G. R., Garda, A. A., Haddad, C. F. B., & Prado, C. P. A. (2022). Temporal and spatial diversification along the Amazonia-Cerrado transition in Neotropical treefrogs of the Boana albopunctata species group. Molecular Phylogenetics and Evolution, 175, 107579. https://doi.org/10.1016/j.ympev.2022.107579\n", "decision": "INCLUDED", "name": "Untitled (tree1)", "studyID": "ot_3212", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Vacelet J. et al. 2000. \u2014 Morphological,  chemical and  biochemical characterization  of anew species of sponge without skeleton (Porifera, Demospongiae) from the MediterraneanSea. Zoosystema 22 (2) : 313-326.", "decision": "INCLUDED", "name": "Fig. 4. Phylogenetic tree based on comparison of 28S rRNA sequences from 22 species", "studyID": "ot_3213", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Erpenbeck, D., Sutcliffe, P., Cook, S. de C., Dietzel, A., Maldonado, M., van Soest, R. W. M., Hooper, J. N. A., & W\u00f6rheide, G. (2012). Horny sponges and their affairs: On the phylogenetic relationships of keratose sponges. Molecular Phylogenetics and Evolution, 63(3), 809\u2013816. https://doi.org/10.1016/j.ympev.2012.02.024\n", "decision": "INCLUDED", "name": "Fig. 1. Phylogenetic relationships for Keratosa and Verongimorpha from 28S and CO1 fragments", "studyID": "ot_3214", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Erpenbeck, D., Ekins, M., Enghuber, N., Hooper, J. N. A., Lehnert, H., Poliseno, A., Schuster, A., Setiawan, E., De Voogd, N. J., W\u00f6rheide, G., & Van Soest, R. W. M. (2015). Nothing in (sponge) biology makes sense \u2013 except when based on holotypes. Journal of the Marine Biological Association of the United Kingdom, 96(2), 305\u2013311. https://doi.org/10.1017/s0025315415000521\n", "decision": "INCLUDED", "name": "Fig. 1. ML phylogram of 28S fragments", "studyID": "ot_3215", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from D\u00cdAZ, M. C., THACKER, R. W., REDMOND, N. E., PEREZ, T., & COLLINS, A. G. (2015). Vansoestia caribensis gen. nov., sp. nov.: first report of the family Ianthellidae (Verongida, Demospongiae) in the Caribbean\u00a0. Zootaxa, 3956(3). https://doi.org/10.11646/zootaxa.3956.3.5\n", "decision": "INCLUDED", "name": "FIGURE 5. Phylogenetic relationships of genera of Verongida, summarizing four previously published phylogenies", "studyID": "ot_3216", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Erpenbeck, D., Galitz, A., Ekins, M., Cook, S. de C., Soest, R. W. M., Hooper, J. N. A., & W\u00f6rheide, G. (2020). Soft sponges with tricky tree: On the phylogeny of dictyoceratid sponges. Journal of Zoological Systematics and Evolutionary Research, 58(1), 27\u201340. Portico. https://doi.org/10.1111/jzs.12351\n", "decision": "INCLUDED", "name": "FIGURE 1. Phylogenetic hypothesis from current ITS and 28S data ", "studyID": "ot_3217", "treeID": "tree2"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Galitz, A., Cook, S. de C., Ekins, M., Hooper, J. N. A., Naumann, P. T., de Voogd, N. J., Abdul Wahab, M., W\u00f6rheide, G., & Erpenbeck, D. (2018). Identification of an aquaculture poriferan \u201cPest with Potential\u201d and its phylogenetic implications. PeerJ, 6, e5586. Portico. https://doi.org/10.7717/peerj.5586\n", "decision": "INCLUDED", "name": "Figure 4. Bayesian inference phylogram of ITS2 of Phyllospongiinae", "studyID": "ot_3218", "treeID": "tree1"}, {"SHA": "", "comments": "Added via API (include_tree_in_synth) from Gao, B., & Gupta, R. S. (2007). Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. 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