{"sha": "c33806c9ee11db205ee8c02a42e31b1c3128e299", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-10-11T01:33:52.353Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": true, "searchContext": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-10-11T01:33:52.353Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-10-11T01:33:52.353Z", "@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": "CastillejosLemus2025Amphibolips.nwk", "@size": 1210, "@type": "newick", "@url": "/curator/download/supporting_files.doc.b11f3da188e28a30.43617374696c6c656a6f734c656d757332303235416d706869626f6c6970732e6e776b.nwk", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu10", "otu11", "otu13", "otu14", "otu15", "otu17", "otu18", "otu19", "otu2", "otu21", "otu22", "otu23", "otu4", "otu9"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@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"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu10", "otu11", "otu13", "otu14", "otu15", "otu17", "otu18", "otu19", "otu2", "otu21", "otu22", "otu23", "otu4", "otu9"], "@otusID": "otus1", "@otuID": ["otu10", "otu11", "otu13", "otu14", "otu15", "otu17", "otu18", "otu19", "otu2", "otu21", "otu22", "otu23", "otu4", "otu9"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["dchesters"], "^ot:dataDeposit": {"@href": "https://doi.org/10.5061/dryad.3ffbg79tk"}, "^ot:focalClade": 4540489, "^ot:focalCladeOTTTaxonName": "Amphibolips", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_3020", "^ot:studyPublication": {"@href": "https://doi.org/10.1111/syen.12659"}, "^ot:studyPublicationReference": "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", "^ot:studyYear": 2025, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "^xhtml:license": {"@href": "", "@name": ""}, "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 46, "message": 0, "node": 47, "otu": 24, "otus": 2, "tree": 1, "trees": 2}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Dryocosmus minusculus", "^ot:ottId": 7862792, "^ot:ottTaxonName": "Dryocosmus minusculus"}, "otu10": {"^ot:originalLabel": "Amphibolips cookii"}, "otu11": {"^ot:originalLabel": "Amphibolips quercusinanis"}, "otu12": {"^ot:originalLabel": "Amphibolips castroviejoi", "^ot:ottId": 6284697, "^ot:ottTaxonName": "Amphibolips castroviejoi"}, "otu13": {"^ot:originalLabel": "Amphibolips magnigalla"}, "otu14": {"^ot:originalLabel": "Amphibolips kinseyi"}, "otu15": {"^ot:originalLabel": "Amphibolips fusus"}, "otu16": {"^ot:originalLabel": "Amphibolips trizonata", "^ot:ottId": 7862600, "^ot:ottTaxonName": "Amphibolips trizonata"}, "otu17": {"^ot:originalLabel": "Amphibolips dampfi"}, "otu18": {"^ot:originalLabel": "Amphibolips durangensis"}, "otu19": {"^ot:originalLabel": "Amphibolips malinche"}, "otu2": {"^ot:originalLabel": "Amphibolips quercusostensackenii"}, "otu20": {"^ot:originalLabel": "Amphibolips hidalgoensis", "^ot:ottId": 6284698, "^ot:ottTaxonName": "Amphibolips hidalgoensis"}, "otu21": {"^ot:originalLabel": "Amphibolips michoacaensis"}, "otu22": {"^ot:originalLabel": "Amphibolips jaliscensis"}, "otu23": {"^ot:originalLabel": "Amphibolips nevadensis"}, "otu24": {"^ot:originalLabel": "Amphibolips zacatecaensis", "^ot:ottId": 6284701, "^ot:ottTaxonName": "Amphibolips zacatecaensis"}, "otu3": {"^ot:originalLabel": "Amphibolips salicifoliae", "^ot:ottId": 6284700, "^ot:ottTaxonName": "Amphibolips salicifoliae"}, "otu4": {"^ot:originalLabel": "Amphibolips nubilipennis"}, "otu5": {"^ot:originalLabel": "Amphibolips quercusjuglans", "^ot:ottId": 7409422, "^ot:ottTaxonName": "Amphibolips quercusjuglans"}, "otu6": {"^ot:originalLabel": "Amphibolips quercusracemaria", "^ot:ottId": 7409424, "^ot:ottTaxonName": "Amphibolips quercusracemaria"}, "otu7": {"^ot:originalLabel": "Amphibolips aliciae", "^ot:ottId": 6284696, "^ot:ottTaxonName": "Amphibolips aliciae"}, "otu8": {"^ot:originalLabel": "Amphibolips globulus", "^ot:ottId": 7862592, "^ot:ottTaxonName": "Amphibolips globulus"}, "otu9": {"^ot:originalLabel": "Amphibolips confluenta"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "FS8_Amphi_80p_SWSC.tree", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum likelihood ", "^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": {"@length": 0.250594, "@source": "node1", "@target": "node2"}, "edge2": {"@length": 0.030534, "@source": "node1", "@target": "node3"}}, "node10": {"edge10": {"@length": 0.069716, "@source": "node10", "@target": "node11"}, "edge11": {"@length": 0.022132, "@source": "node10", "@target": "node12"}}, "node13": {"edge13": {"@length": 0.029628, "@source": "node13", "@target": "node14"}, "edge22": {"@length": 0.046598, "@source": "node13", "@target": "node23"}}, "node14": {"edge14": {"@length": 0.005438, "@source": "node14", "@target": "node15"}, "edge17": {"@length": 0.024659, "@source": "node14", "@target": "node18"}}, "node15": {"edge15": {"@length": 0.046755, "@source": "node15", "@target": "node16"}, "edge16": {"@length": 0.036001, "@source": "node15", "@target": "node17"}}, "node18": {"edge18": {"@length": 0.065936, "@source": "node18", "@target": "node19"}, "edge19": {"@length": 0.007809, "@source": "node18", "@target": "node20"}}, "node20": {"edge20": {"@length": 0.017769, "@source": "node20", "@target": "node21"}, "edge21": {"@length": 0.057581, "@source": "node20", "@target": "node22"}}, "node23": {"edge23": {"@length": 0.122972, "@source": "node23", "@target": "node24"}, "edge24": {"@length": 0.002364, "@source": "node23", "@target": "node25"}}, "node25": {"edge25": {"@length": 0.004368, "@source": "node25", "@target": "node26"}, "edge28": {"@length": 0.000469, "@source": "node25", "@target": "node29"}}, "node26": {"edge26": {"@length": 0.01642, "@source": "node26", "@target": "node27"}, "edge27": {"@length": 0.014618, "@source": "node26", "@target": "node28"}}, "node29": {"edge29": {"@length": 0.041835, "@source": "node29", "@target": "node30"}, "edge30": {"@length": 0.000508, "@source": "node29", "@target": "node31"}}, "node3": {"edge3": {"@length": 0.089314, "@source": "node3", "@target": "node4"}, "edge6": {"@length": 0.066915, "@source": "node3", "@target": "node7"}}, "node31": {"edge31": {"@length": 0.00326, "@source": "node31", "@target": "node32"}, "edge36": {"@length": 0.004647, "@source": "node31", "@target": "node37"}}, "node32": {"edge32": {"@length": 0.032112, "@source": "node32", "@target": "node33"}, "edge33": {"@length": 0.005454, "@source": "node32", "@target": "node34"}}, "node34": {"edge34": {"@length": 0.016053, "@source": "node34", "@target": "node35"}, "edge35": {"@length": 0.030755, "@source": "node34", "@target": "node36"}}, "node37": {"edge37": {"@length": 0.003399, "@source": "node37", "@target": "node38"}, "edge40": {"@length": 0.001061, "@source": "node37", "@target": "node41"}}, "node38": {"edge38": {"@length": 0.017935, "@source": "node38", "@target": "node39"}, "edge39": {"@length": 0.073686, "@source": "node38", "@target": "node40"}}, "node4": {"edge4": {"@length": 0.066358, "@source": "node4", "@target": "node5"}, "edge5": {"@length": 0.069734, "@source": "node4", "@target": "node6"}}, "node41": {"edge41": {"@length": 0.000921, "@source": "node41", "@target": "node42"}, "edge44": {"@length": 0.001291, "@source": "node41", "@target": "node45"}}, "node42": {"edge42": {"@length": 0.021755, "@source": "node42", "@target": "node43"}, "edge43": {"@length": 0.024065, "@source": "node42", "@target": "node44"}}, "node45": {"edge45": {"@length": 0.020459, "@source": "node45", "@target": "node46"}, "edge46": {"@length": 0.012616, "@source": "node45", "@target": "node47"}}, "node7": {"edge12": {"@length": 0.01336, "@source": "node7", "@target": "node13"}, "edge7": {"@length": 0.038652, "@source": "node7", "@target": "node8"}}, "node8": {"edge8": {"@length": 0.036518, "@source": "node8", "@target": "node9"}, "edge9": {"@length": 0.005889, "@source": "node8", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {"@otu": "otu5"}, "node12": {"@otu": "otu6"}, "node13": {}, "node14": {}, "node15": {}, "node16": {"@otu": "otu7"}, "node17": {"@otu": "otu8"}, "node18": {}, "node19": {"@otu": "otu9"}, "node2": {"@otu": "otu1"}, "node20": {}, "node21": {"@otu": "otu10"}, "node22": {"@otu": "otu11"}, "node23": {}, "node24": {"@otu": "otu12"}, "node25": {}, "node26": {}, "node27": {"@otu": "otu13"}, "node28": {"@otu": "otu14"}, "node29": {}, "node3": {}, "node30": {"@otu": "otu15"}, "node31": {}, "node32": {}, "node33": {"@otu": "otu16"}, "node34": {}, "node35": {"@otu": "otu17"}, "node36": {"@otu": "otu18"}, "node37": {}, "node38": {}, "node39": {"@otu": "otu19"}, "node4": {}, "node40": {"@otu": "otu20"}, "node41": {}, "node42": {}, "node43": {"@otu": "otu21"}, "node44": {"@otu": "otu22"}, "node45": {}, "node46": {"@otu": "otu23"}, "node47": {"@otu": "otu24"}, "node5": {"@otu": "otu2"}, "node6": {"@otu": "otu3"}, "node7": {}, "node8": {}, "node9": {"@otu": "otu4"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "48e622f56ac57aba0f74427f49304f8c16f9f630", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Sat, 11 Oct 2025 01:36:50 +0000", "date_ISO_8601": "2025-10-11 01:36:50 +0000", "relative_date": "7 months ago", "message_subject": "Init Castillejos-Lemus et al 2025", "message_body": "CastillejosLemus2025Amphibolips.nwk\nAuthors plot (Fig 5) 'SWSC-EN partitioning scheme with the 80% matrix'; Assuming file named FS8_Amphi_80p_SWSC.tree is authors preferred out of 13 file. Rooted as per figure, removed all but one of outgroup. Pruned a lot of uninformative terminal, e.g. 50 species repeats.\n\n(Update document 'ot_3020' via OpenTree API)"}, {"id": "064317fd1237d14ea914116bd1a93d3d134210bf", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Sat, 11 Oct 2025 01:33:48 +0000", "date_ISO_8601": "2025-10-11 01:33:48 +0000", "relative_date": "7 months ago", "message_subject": "Update document 'ot_3020' via OpenTree API"}]}