{"sha": "2aa180baef3c5e313da1e7f09c83ce2c0467b457", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-03-13T03:28:44.210Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": true, "searchContext": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-03-13T03:28:44.210Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-03-13T03:28:44.210Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "FailleRibera2010Trechini.nwk", "@size": 851, "@type": "newick", "@url": "/curator/download/supporting_files.doc.a45da83fdc1dc81f.4661696c6c65526962657261323031305472656368696e692e6e776b.nwk", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "image.png", "@size": 685, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.acc3578454cbde51.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 638, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.85f167d3d3424ff9.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 1308, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.828af7b7ccf444cd.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 1862, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.96c10ce04b5f2939.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 6034, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.aba1b7a27314da21.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": "otu31", "@otusID": "otus1", "@otuID": "otu31"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["highestMintedElementIDs"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["dchesters"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 804605, "^ot:focalCladeOTTTaxonName": "Trechini", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_2679", "^ot:studyPublication": {"@href": "https://doi.org/10.1016/j.ympev.2009.10.008"}, "^ot:studyPublicationReference": "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", "^ot:studyYear": 2010, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 72, "message": 0, "node": 73, "otu": 37, "otus": 2, "tree": 1, "trees": 2}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Trechus quadristriatus", "^ot:ottId": 866920, "^ot:ottTaxonName": "Trechus quadristriatus"}, "otu10": {"^ot:originalLabel": "Hydraphaenops galani", "^ot:ottId": 1031403, "^ot:ottTaxonName": "Hydraphaenops galani"}, "otu11": {"^ot:originalLabel": "Aphaenops leschenaulti", "^ot:ottId": 404721, "^ot:ottTaxonName": "Aphaenops leschenaulti"}, "otu12": {"^ot:originalLabel": "Aphaenops catalonicus", "^ot:ottId": 85180, "^ot:ottTaxonName": "Aphaenops catalonicus"}, "otu13": {"^ot:originalLabel": "Aphaenops cabidochei", "^ot:ottId": 930540, "^ot:ottTaxonName": "Aphaenops cabidochei"}, "otu14": {"^ot:originalLabel": "Aphaenops ochsi", "^ot:ottId": 1082062, "^ot:ottTaxonName": "Aphaenops ochsi"}, "otu15": {"^ot:originalLabel": "Aphaenops ludovici", "^ot:ottId": 1082058, "^ot:ottTaxonName": "Aphaenops ludovici"}, "otu16": {"^ot:originalLabel": "Aphaenops rhadamanthus", "^ot:ottId": 1082054, "^ot:ottTaxonName": "Aphaenops rhadamanthus"}, "otu17": {"^ot:originalLabel": "Aphaenops alberti", "^ot:ottId": 930533, "^ot:ottTaxonName": "Aphaenops alberti"}, "otu18": {"^ot:originalLabel": "Aphaenops jeanneli", "^ot:ottId": 404731, "^ot:ottTaxonName": "Aphaenops jeanneli"}, "otu19": {"^ot:originalLabel": "Aphaenops loubensi", "^ot:ottId": 404724, "^ot:ottTaxonName": "Aphaenops loubensi"}, "otu2": {"^ot:originalLabel": "Geotrechus orpheus", "^ot:ottId": 555575, "^ot:ottTaxonName": "Geotrechus orpheus"}, "otu20": {"^ot:originalLabel": "Aphaenops abodiensis", "^ot:ottId": 930536, "^ot:ottTaxonName": "Aphaenops abodiensis"}, "otu21": {"^ot:originalLabel": "Hydraphaenops elegans", "^ot:ottId": 1031405, "^ot:ottTaxonName": "Hydraphaenops elegans"}, "otu22": {"^ot:originalLabel": "Hydraphaenops penacollaradensis", "^ot:ottId": 505519, "^ot:ottTaxonName": "Hydraphaenops penacollaradensis"}, "otu23": {"^ot:originalLabel": "Hydraphaenops bourgoini", "^ot:ottId": 455037, "^ot:ottTaxonName": "Hydraphaenops coiffaiti"}, "otu24": {"^ot:originalLabel": "Hydraphaenops ehlersi", "^ot:ottId": 1031407, "^ot:ottTaxonName": "Hydraphaenops ehlersi"}, "otu25": {"^ot:originalLabel": "Hydraphaenops pecoudi", "^ot:ottId": 1031424, "^ot:ottTaxonName": "Hydraphaenops pecoudi"}, "otu26": {"^ot:originalLabel": "Aphaenops tiresias", "^ot:ottId": 1082044, "^ot:ottTaxonName": "Aphaenops tiresias"}, "otu27": {"^ot:originalLabel": "Aphaenops hustachei", "^ot:ottId": 404726, "^ot:ottTaxonName": "Aphaenops hustachei"}, "otu28": {"^ot:originalLabel": "Aphaenops bucephalus", "^ot:ottId": 930542, "^ot:ottTaxonName": "Aphaenops bucephalus"}, "otu29": {"^ot:originalLabel": "Aphaenops cerberus", "^ot:ottId": 404736, "^ot:ottTaxonName": "Aphaenops cerberus"}, "otu3": {"^ot:originalLabel": "Geotrechus vulcanus", "^ot:ottId": 1031409, "^ot:ottTaxonName": "Geotrechus vulcanus"}, "otu30": {"^ot:originalLabel": "Aphaenops jauzioni", "^ot:ottId": 404728, "^ot:ottTaxonName": "Aphaenops jauzioni"}, "otu31": {"^ot:originalLabel": "Aphaenops delbreili"}, "otu32": {"^ot:originalLabel": "Aphaenops laurenti", "^ot:ottId": 404734, "^ot:ottTaxonName": "Aphaenops laurenti"}, "otu33": {"^ot:originalLabel": "Aphaenops pluto", "^ot:ottId": 1082048, "^ot:ottTaxonName": "Aphaenops pluto"}, "otu34": {"^ot:originalLabel": "Aphaenops mariaerosae", "^ot:ottId": 455035, "^ot:ottTaxonName": "Aphaenops mariaerosae"}, "otu35": {"^ot:originalLabel": "Aphaenops vandeli", "^ot:ottId": 455025, "^ot:ottTaxonName": "Aphaenops vandeli"}, "otu36": {"^ot:originalLabel": "Aphaenops crypticola", "^ot:ottId": 388806, "^ot:ottTaxonName": "Aphaenops crypticola"}, "otu37": {"^ot:originalLabel": "Aphaenops parallelus", "^ot:ottId": 1082050, "^ot:ottTaxonName": "Aphaenops parallelus"}, "otu4": {"^ot:originalLabel": "Geotrechus saulcyi", "^ot:ottId": 1031417, "^ot:ottTaxonName": "Geotrechus saulcyi"}, "otu5": {"^ot:originalLabel": "Geotrechus trophonius", "^ot:ottId": 1031413, "^ot:ottTaxonName": "Geotrechus trophonius"}, "otu6": {"^ot:originalLabel": "Hydraphaenops pandellei", "^ot:ottId": 1031426, "^ot:ottTaxonName": "Hydraphaenops pandellei"}, "otu7": {"^ot:originalLabel": "Geotrechus gallicus", "^ot:ottId": 555577, "^ot:ottTaxonName": "Geotrechus gallicus"}, "otu8": {"^ot:originalLabel": "Hydraphaenops delicatulus", "^ot:ottId": 455022, "^ot:ottTaxonName": "Hydraphaenops vasconicus delicatulus"}, "otu9": {"^ot:originalLabel": "Hydraphaenops vasconicus", "^ot:ottId": 455027, "^ot:ottTaxonName": "Hydraphaenops vasconicus"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 4, BI", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node3", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@source": "node1", "@target": "node2"}, "edge2": {"@source": "node1", "@target": "node3"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge17": {"@source": "node10", "@target": "node18"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge14": {"@source": "node11", "@target": "node15"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge13": {"@source": "node12", "@target": "node14"}}, "node15": {"edge15": {"@source": "node15", "@target": "node16"}, "edge16": {"@source": "node15", "@target": "node17"}}, "node18": {"edge18": {"@source": "node18", "@target": "node19"}, "edge21": {"@source": "node18", "@target": "node22"}}, "node19": {"edge19": {"@source": "node19", "@target": "node20"}, "edge20": {"@source": "node19", "@target": "node21"}}, "node22": {"edge22": {"@source": "node22", "@target": "node23"}, "edge25": {"@source": "node22", "@target": "node26"}}, "node23": {"edge23": {"@source": "node23", "@target": "node24"}, "edge24": {"@source": "node23", "@target": "node25"}}, "node26": {"edge26": {"@source": "node26", "@target": "node27"}, "edge33": {"@source": "node26", "@target": "node34"}}, "node27": {"edge27": {"@source": "node27", "@target": "node28"}, "edge30": {"@source": "node27", "@target": "node31"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge29": {"@source": "node28", "@target": "node30"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge8": {"@source": "node3", "@target": "node9"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge32": {"@source": "node31", "@target": "node33"}}, "node34": {"edge34": {"@source": "node34", "@target": "node35"}, "edge37": {"@source": "node34", "@target": "node38"}}, "node35": {"edge35": {"@source": "node35", "@target": "node36"}, "edge36": {"@source": "node35", "@target": "node37"}}, "node38": {"edge38": {"@source": "node38", "@target": "node39"}, "edge39": {"@source": "node38", "@target": "node40"}}, "node4": {"edge4": {"@source": "node4", "@target": "node5"}, "edge5": {"@source": "node4", "@target": "node6"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge44": {"@source": "node41", "@target": "node45"}}, "node42": {"edge42": {"@source": "node42", "@target": "node43"}, "edge43": {"@source": "node42", "@target": "node44"}}, "node45": {"edge45": {"@source": "node45", "@target": "node46"}, "edge50": {"@source": "node45", "@target": "node51"}}, "node46": {"edge46": {"@source": "node46", "@target": "node47"}, "edge47": {"@source": "node46", "@target": "node48"}}, "node48": {"edge48": {"@source": "node48", "@target": "node49"}, "edge49": {"@source": "node48", "@target": "node50"}}, "node51": {"edge51": {"@source": "node51", "@target": "node52"}, "edge52": {"@source": "node51", "@target": "node53"}}, "node53": {"edge53": {"@source": "node53", "@target": "node54"}, "edge54": {"@source": "node53", "@target": "node55"}}, "node55": {"edge55": {"@source": "node55", "@target": "node56"}, "edge60": {"@source": "node55", "@target": "node61"}}, "node56": {"edge56": {"@source": "node56", "@target": "node57"}, "edge57": {"@source": "node56", "@target": "node58"}}, "node58": {"edge58": {"@source": "node58", "@target": "node59"}, "edge59": {"@source": "node58", "@target": "node60"}}, "node6": {"edge6": {"@source": "node6", "@target": "node7"}, "edge7": {"@source": "node6", "@target": "node8"}}, "node61": {"edge61": {"@source": "node61", "@target": "node62"}, "edge64": {"@source": "node61", "@target": "node65"}}, "node62": {"edge62": {"@source": "node62", "@target": "node63"}, "edge63": {"@source": "node62", "@target": "node64"}}, "node65": {"edge65": {"@source": "node65", "@target": "node66"}, "edge66": {"@source": "node65", "@target": "node67"}}, "node67": {"edge67": {"@source": "node67", "@target": "node68"}, "edge68": {"@source": "node67", "@target": "node69"}}, "node69": {"edge69": {"@source": "node69", "@target": "node70"}, "edge70": {"@source": "node69", "@target": "node71"}}, "node71": {"edge71": {"@source": "node71", "@target": "node72"}, "edge72": {"@source": "node71", "@target": "node73"}}, "node9": {"edge40": {"@source": "node9", "@target": "node41"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {}, "node12": {}, "node13": {"@otu": "otu5"}, "node14": {"@otu": "otu6"}, "node15": {}, "node16": {"@otu": "otu7"}, "node17": {"@otu": "otu8"}, "node18": {}, "node19": {}, "node2": {"@otu": "otu1"}, "node20": {"@otu": "otu9"}, "node21": {"@otu": "otu10"}, "node22": {}, "node23": {}, "node24": {"@otu": "otu11"}, "node25": {"@otu": "otu12"}, "node26": {}, "node27": {}, "node28": {}, "node29": {"@otu": "otu13"}, "node3": {}, "node30": {"@otu": "otu14"}, "node31": {}, "node32": {"@otu": "otu15"}, "node33": {"@otu": "otu16"}, "node34": {}, "node35": {}, "node36": {"@otu": "otu17"}, "node37": {"@otu": "otu18"}, "node38": {}, "node39": {"@otu": "otu19"}, "node4": {}, "node40": {"@otu": "otu20"}, "node41": {}, "node42": {}, "node43": {"@otu": "otu21"}, "node44": {"@otu": "otu22"}, "node45": {}, "node46": {}, "node47": {"@otu": "otu23"}, "node48": {}, "node49": {"@otu": "otu24"}, "node5": {"@otu": "otu2"}, "node50": {"@otu": "otu25"}, "node51": {}, "node52": {"@otu": "otu26"}, "node53": {}, "node54": {"@otu": "otu27"}, "node55": {}, "node56": {}, "node57": {"@otu": "otu28"}, "node58": {}, "node59": {"@otu": "otu29"}, "node6": {}, "node60": {"@otu": "otu30"}, "node61": {}, "node62": {}, "node63": {"@otu": "otu31"}, "node64": {"@otu": "otu32"}, "node65": {}, "node66": {"@otu": "otu33"}, "node67": {}, "node68": {"@otu": "otu34"}, "node69": {}, "node7": {"@otu": "otu3"}, "node70": {"@otu": "otu35"}, "node71": {}, "node72": {"@otu": "otu36"}, "node73": {"@otu": "otu37"}, "node8": {"@otu": "otu4"}, "node9": {}}}}}}}}, "branch2sha": {"master": "2aa180baef3c5e313da1e7f09c83ce2c0467b457"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "fc3655e7025db0a92e4a12aa7c4da1fe78b41b6f", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Thu, 13 Mar 2025 03:31:52 +0000", "date_ISO_8601": "2025-03-13 03:31:52 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Initial commit Faille et al. (2010)", "message_body": "FailleRibera2010Trechini.nwk\nConfusing taxonomy partly due to use of ambiguated (abbreviated) names, e.g. there is both a G. vandeli and A. vandeli used in the figures, text and sample table. Figure 4 seems to be a subset of Figure 2, but not specified in the legends (both stated as Trechini).\n\n(Update document 'ot_2679' via OpenTree API)"}, {"id": "cb7b7d00d76ccba8478e430e1df621eaec9a176d", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Thu, 13 Mar 2025 03:28:37 +0000", "date_ISO_8601": "2025-03-13 03:28:37 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Update document 'ot_2679' via OpenTree API"}]}