{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-02-19T00:52:06.535Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": true, "searchContext": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-02-19T00:52:06.535Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-02-19T00:52:06.535Z", "@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": "Blaimer2016Acropyga.nwk", "@size": 461, "@type": "newick", "@url": "/curator/download/supporting_files.doc.9d76ea4bf36f8dbc.426c61696d6572323031364163726f707967612e6e776b.nwk", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "image.png", "@size": 574, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.a9fd45da19f9b759.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 659, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.b1c51db61b7a2135.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 992, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.8992000c10e545a2.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 1683, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.bbba5ef75ef66b4a.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 2222, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.8132b59002a44a08.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 2650, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.9b51dcc93d86de04.696d6167652e706e67.png", "description": {"$": ""}, "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": "otu23", "@otusID": "otus1", "@otuID": "otu23"}, "@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": 301896, "^ot:focalCladeOTTTaxonName": "Acropyga", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_2469", "^ot:studyPublication": {"@href": "https://doi.org/10.1016/j.ympev.2016.05.030"}, "^ot:studyPublicationReference": "Blaimer, B. B., LaPolla, J. S., Branstetter, M. G., Lloyd, M. W., & Brady, S. G. (2016). Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga. Molecular Phylogenetics and Evolution, 102, 20\u201329. https://doi.org/10.1016/j.ympev.2016.05.030\n", "^ot:studyYear": 2016, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 44, "message": 0, "node": 45, "otu": 23, "otus": 2, "tree": 1, "trees": 2}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Acropyga epedana", "^ot:ottId": 301913, "^ot:ottTaxonName": "Acropyga epedana"}, "otu10": {"^ot:originalLabel": "Acropyga donisthorpei", "^ot:ottId": 269489, "^ot:ottTaxonName": "Acropyga donisthorpei"}, "otu11": {"^ot:originalLabel": "Acropyga panamensis", "^ot:ottId": 3260672, "^ot:ottTaxonName": "Acropyga panamensis"}, "otu12": {"^ot:originalLabel": "Acropyga ayanganna", "^ot:ottId": 5961602, "^ot:ottTaxonName": "Acropyga ayanganna"}, "otu13": {"^ot:originalLabel": "Acropyga acutiventris", "^ot:ottId": 301894, "^ot:ottTaxonName": "Acropyga acutiventris"}, "otu14": {"^ot:originalLabel": "Acropyga pallida", "^ot:ottId": 3260643, "^ot:ottTaxonName": "Acropyga pallida"}, "otu15": {"^ot:originalLabel": "Acropyga ambigua", "^ot:ottId": 3260650, "^ot:ottTaxonName": "Acropyga ambigua"}, "otu16": {"^ot:originalLabel": "Acropyga myops", "^ot:ottId": 3260628, "^ot:ottTaxonName": "Acropyga myops"}, "otu17": {"^ot:originalLabel": "Acropyga butteli", "^ot:ottId": 3260668, "^ot:ottTaxonName": "Acropyga butteli"}, "otu18": {"^ot:originalLabel": "Acropyga sauteri", "^ot:ottId": 3260670, "^ot:ottTaxonName": "Acropyga sauteri"}, "otu19": {"^ot:originalLabel": "Acropyga lauta", "^ot:ottId": 3260647, "^ot:ottTaxonName": "Acropyga lauta"}, "otu2": {"^ot:originalLabel": "Acropyga decedens", "^ot:ottId": 3260630, "^ot:ottTaxonName": "Acropyga decedens"}, "otu20": {"^ot:originalLabel": "Acropyga kinomurai", "^ot:ottId": 5961604, "^ot:ottTaxonName": "Acropyga kinomurai"}, "otu21": {"^ot:originalLabel": "Acropyga arnoldi", "^ot:ottId": 301892, "^ot:ottTaxonName": "Acropyga arnoldi"}, "otu22": {"^ot:originalLabel": "Acropyga silvestrii", "^ot:ottId": 3260642, "^ot:ottTaxonName": "Acropyga silvestrii"}, "otu23": {"^ot:originalLabel": "Agraulomyrmex sp"}, "otu3": {"^ot:originalLabel": "Acropyga dubitata", "^ot:ottId": 3260634, "^ot:ottTaxonName": "Acropyga dubitata"}, "otu4": {"^ot:originalLabel": "Acropyga hirsutula", "^ot:ottId": 5961603, "^ot:ottTaxonName": "Acropyga hirsutula"}, "otu5": {"^ot:originalLabel": "Acropyga romeo", "^ot:ottId": 5961605, "^ot:ottTaxonName": "Acropyga romeo"}, "otu6": {"^ot:originalLabel": "Acropyga fuhrmanni", "^ot:ottId": 3260655, "^ot:ottTaxonName": "Acropyga fuhrmanni"}, "otu7": {"^ot:originalLabel": "Acropyga smithii", "^ot:ottId": 3260627, "^ot:ottTaxonName": "Acropyga smithii"}, "otu8": {"^ot:originalLabel": "Acropyga guianensis", "^ot:ottId": 3260624, "^ot:ottTaxonName": "Acropyga guianensis"}, "otu9": {"^ot:originalLabel": "Acropyga stenotes", "^ot:ottId": 5961607, "^ot:ottTaxonName": "Acropyga stenotes"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 2, RAxML_Besttree_Acropyga_UCE-944.tre", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node2", "^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"}, "edge44": {"@source": "node1", "@target": "node45"}}, "node15": {"edge15": {"@source": "node15", "@target": "node16"}, "edge16": {"@source": "node15", "@target": "node17"}}, "node18": {"edge18": {"@source": "node18", "@target": "node19"}, "edge19": {"@source": "node18", "@target": "node20"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge25": {"@source": "node2", "@target": "node26"}}, "node21": {"edge21": {"@source": "node21", "@target": "node22"}, "edge24": {"@source": "node21", "@target": "node25"}}, "node22": {"edge22": {"@source": "node22", "@target": "node23"}, "edge23": {"@source": "node22", "@target": "node24"}}, "node26": {"edge26": {"@source": "node26", "@target": "node27"}, "edge41": {"@source": "node26", "@target": "node42"}}, "node27": {"edge27": {"@source": "node27", "@target": "node28"}, "edge38": {"@source": "node27", "@target": "node39"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge37": {"@source": "node28", "@target": "node38"}}, "node29": {"edge29": {"@source": "node29", "@target": "node30"}, "edge30": {"@source": "node29", "@target": "node31"}}, "node3": {"edge20": {"@source": "node3", "@target": "node21"}, "edge3": {"@source": "node3", "@target": "node4"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge36": {"@source": "node31", "@target": "node37"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge35": {"@source": "node32", "@target": "node36"}}, "node33": {"edge33": {"@source": "node33", "@target": "node34"}, "edge34": {"@source": "node33", "@target": "node35"}}, "node39": {"edge39": {"@source": "node39", "@target": "node40"}, "edge40": {"@source": "node39", "@target": "node41"}}, "node4": {"edge17": {"@source": "node4", "@target": "node18"}, "edge4": {"@source": "node4", "@target": "node5"}}, "node42": {"edge42": {"@source": "node42", "@target": "node43"}, "edge43": {"@source": "node42", "@target": "node44"}}, "node5": {"edge14": {"@source": "node5", "@target": "node15"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node6": {"edge13": {"@source": "node6", "@target": "node14"}, "edge6": {"@source": "node6", "@target": "node7"}}, "node7": {"edge12": {"@source": "node7", "@target": "node13"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node8": {"edge11": {"@source": "node8", "@target": "node12"}, "edge8": {"@source": "node8", "@target": "node9"}}, "node9": {"edge10": {"@source": "node9", "@target": "node11"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu1"}, "node11": {"@otu": "otu2"}, "node12": {"@otu": "otu3"}, "node13": {"@otu": "otu4"}, "node14": {"@otu": "otu5"}, "node15": {}, "node16": {"@otu": "otu6"}, "node17": {"@otu": "otu7"}, "node18": {}, "node19": {"@otu": "otu8"}, "node2": {}, "node20": {"@otu": "otu9"}, "node21": {}, "node22": {}, "node23": {"@otu": "otu10"}, "node24": {"@otu": "otu11"}, "node25": {"@otu": "otu12"}, "node26": {}, "node27": {}, "node28": {}, "node29": {}, "node3": {}, "node30": {"@otu": "otu13"}, "node31": {}, "node32": {}, "node33": {}, "node34": {"@otu": "otu14"}, "node35": {"@otu": "otu15"}, "node36": {"@otu": "otu16"}, "node37": {"@otu": "otu17"}, "node38": {"@otu": "otu18"}, "node39": {}, "node4": {}, "node40": {"@otu": "otu19"}, "node41": {"@otu": "otu20"}, "node42": {}, "node43": {"@otu": "otu21"}, "node44": {"@otu": "otu22"}, "node45": {"@otu": "otu23"}, "node5": {}, "node6": {}, "node7": {}, "node8": {}, "node9": {}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "c214e0a63fbbcfcc61c327a63797ab0fc1bc5bc3", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Wed, 19 Feb 2025 00:55:01 +0000", "date_ISO_8601": "2025-02-19 00:55:01 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Initial commit Blaimer et al. (2016)", "message_body": "Blaimer2016Acropyga.nwk\nRemoved species repeats and codes appended to terminal IDs.\n\n(Update document 'ot_2469' via OpenTree API)"}, {"id": "58f166fe4b4141e62f1d36ba6a8f78d67b86e657", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Wed, 19 Feb 2025 00:52:02 +0000", "date_ISO_8601": "2025-02-19 00:52:02 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Update document 'ot_2469' via OpenTree API"}]}