{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-03-03T10:37:58.978Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": true, "searchContext": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-03-03T10:37:58.978Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-03-03T10:37:58.978Z", "@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": "Coeurdacier2007Aphis.nwk", "@size": 588, "@type": "newick", "@url": "/curator/download/supporting_files.doc.b9970a5a0ee69cec.436f6575726461636965723230303741706869732e6e776b.nwk", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "image.png", "@size": 597, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.b89de4b8a7a8cc3e.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 666, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.a3ec1d66d5223dce.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 1893, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.b312084ca9b8453f.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 2155, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.b7900abfed14c765.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 2224, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.99b1a4fa9bf22fd1.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu13", "otu2", "otu29"], "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": ["otu13", "otu2", "otu29"], "@otusID": "otus1", "@otuID": ["otu13", "otu2", "otu29"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["dchesters"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 1026470, "^ot:focalCladeOTTTaxonName": "Aphis", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_2585", "^ot:studyPublication": {"@href": "https://doi.org/10.1016/j.ympev.2006.10.006"}, "^ot:studyPublicationReference": "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", "^ot:studyYear": 2007, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 64, "message": 0, "node": 65, "otu": 33, "otus": 2, "tree": 1, "trees": 2}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Hyperomyzus lactucae", "^ot:ottId": 203054, "^ot:ottTaxonName": "Hyperomyzus lactucae"}, "otu10": {"^ot:originalLabel": "Aphis affinis", "^ot:ottId": 565195, "^ot:ottTaxonName": "Aphis affinis"}, "otu11": {"^ot:originalLabel": "Aphis taraxacicola", "^ot:ottId": 514534, "^ot:ottTaxonName": "Aphis taraxacicola"}, "otu12": {"^ot:originalLabel": "Aphis chloris", "^ot:ottId": 565198, "^ot:ottTaxonName": "Aphis chloris"}, "otu13": {"^ot:originalLabel": "Aphis hypochoeridis"}, "otu14": {"^ot:originalLabel": "Aphis oenotherae", "^ot:ottId": 44142, "^ot:ottTaxonName": "Aphis oenotherae"}, "otu15": {"^ot:originalLabel": "Aphis schneideri", "^ot:ottId": 514519, "^ot:ottTaxonName": "Aphis schneideri"}, "otu16": {"^ot:originalLabel": "Aphis epilobii", "^ot:ottId": 44124, "^ot:ottTaxonName": "Aphis epilobii"}, "otu17": {"^ot:originalLabel": "Aphis grossulariae", "^ot:ottId": 44133, "^ot:ottTaxonName": "Aphis grossulariae"}, "otu18": {"^ot:originalLabel": "Aphis cytisorum", "^ot:ottId": 44121, "^ot:ottTaxonName": "Aphis cytisorum"}, "otu19": {"^ot:originalLabel": "Aphis acetosae", "^ot:ottId": 565188, "^ot:ottTaxonName": "Aphis acetosae"}, "otu2": {"^ot:originalLabel": "Rhopalosiphum insertum"}, "otu20": {"^ot:originalLabel": "Aphis salviae", "^ot:ottId": 514522, "^ot:ottTaxonName": "Aphis salviae"}, "otu21": {"^ot:originalLabel": "Aphis craccae", "^ot:ottId": 565204, "^ot:ottTaxonName": "Aphis craccae"}, "otu22": {"^ot:originalLabel": "Aphis intybi", "^ot:ottId": 44130, "^ot:ottTaxonName": "Aphis intybi"}, "otu23": {"^ot:originalLabel": "Aphis craccivora", "^ot:ottId": 805075, "^ot:ottTaxonName": "Aphis craccivora"}, "otu24": {"^ot:originalLabel": "Aphis coronillae", "^ot:ottId": 565207, "^ot:ottTaxonName": "Aphis coronillae"}, "otu25": {"^ot:originalLabel": "Aphis rumicis", "^ot:ottId": 902674, "^ot:ottTaxonName": "Aphis rumicis"}, "otu26": {"^ot:originalLabel": "Aphis arbuti", "^ot:ottId": 565192, "^ot:ottTaxonName": "Aphis arbuti"}, "otu27": {"^ot:originalLabel": "Aphis fabae", "^ot:ottId": 54045, "^ot:ottTaxonName": "Aphis fabae"}, "otu28": {"^ot:originalLabel": "Aphis armata", "^ot:ottId": 565201, "^ot:ottTaxonName": "Aphis armata"}, "otu29": {"^ot:originalLabel": "Aphis viburni"}, "otu3": {"^ot:originalLabel": "Melanaphis luzulella", "^ot:ottId": 1054835, "^ot:ottTaxonName": "Melanaphis luzulella"}, "otu30": {"^ot:originalLabel": "Aphis spiraecola", "^ot:ottId": 115901, "^ot:ottTaxonName": "Aphis spiraecola"}, "otu31": {"^ot:originalLabel": "Aphis jacobaeae", "^ot:ottId": 44139, "^ot:ottTaxonName": "Aphis jacobaeae"}, "otu32": {"^ot:originalLabel": "Aphis vandergooti", "^ot:ottId": 902671, "^ot:ottTaxonName": "Toxopterina vandergooti"}, "otu33": {"^ot:originalLabel": "Aphis veratri", "^ot:ottId": 910568, "^ot:ottTaxonName": "Aphis veratri"}, "otu4": {"^ot:originalLabel": "Aphis terricola", "^ot:ottId": 514529, "^ot:ottTaxonName": "Protaphis terricola"}, "otu5": {"^ot:originalLabel": "Aphis nerii", "^ot:ottId": 948809, "^ot:ottTaxonName": "Aphis nerii"}, "otu6": {"^ot:originalLabel": "Aphis idaei", "^ot:ottId": 44127, "^ot:ottTaxonName": "Aphis idaei"}, "otu7": {"^ot:originalLabel": "Aphis ulmariae", "^ot:ottId": 441488, "^ot:ottTaxonName": "Aphis ulmariae"}, "otu8": {"^ot:originalLabel": "Aphis frangulae", "^ot:ottId": 263605, "^ot:ottTaxonName": "Aphis frangulae"}, "otu9": {"^ot:originalLabel": "Aphis teucrii", "^ot:ottId": 902677, "^ot:ottTaxonName": "Aphis teucrii"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 2, BI", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node9", "^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"}, "edge11": {"@source": "node10", "@target": "node12"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge13": {"@source": "node12", "@target": "node14"}}, "node14": {"edge14": {"@source": "node14", "@target": "node15"}, "edge15": {"@source": "node14", "@target": "node16"}}, "node16": {"edge16": {"@source": "node16", "@target": "node17"}, "edge19": {"@source": "node16", "@target": "node20"}}, "node17": {"edge17": {"@source": "node17", "@target": "node18"}, "edge18": {"@source": "node17", "@target": "node19"}}, "node20": {"edge20": {"@source": "node20", "@target": "node21"}, "edge21": {"@source": "node20", "@target": "node22"}}, "node22": {"edge22": {"@source": "node22", "@target": "node23"}, "edge23": {"@source": "node22", "@target": "node24"}}, "node24": {"edge24": {"@source": "node24", "@target": "node25"}, "edge25": {"@source": "node24", "@target": "node26"}}, "node27": {"edge27": {"@source": "node27", "@target": "node28"}, "edge34": {"@source": "node27", "@target": "node35"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge29": {"@source": "node28", "@target": "node30"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge6": {"@source": "node3", "@target": "node7"}}, "node30": {"edge30": {"@source": "node30", "@target": "node31"}, "edge31": {"@source": "node30", "@target": "node32"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge33": {"@source": "node32", "@target": "node34"}}, "node35": {"edge35": {"@source": "node35", "@target": "node36"}, "edge48": {"@source": "node35", "@target": "node49"}}, "node36": {"edge36": {"@source": "node36", "@target": "node37"}, "edge37": {"@source": "node36", "@target": "node38"}}, "node38": {"edge38": {"@source": "node38", "@target": "node39"}, "edge41": {"@source": "node38", "@target": "node42"}}, "node39": {"edge39": {"@source": "node39", "@target": "node40"}, "edge40": {"@source": "node39", "@target": "node41"}}, "node4": {"edge4": {"@source": "node4", "@target": "node5"}, "edge5": {"@source": "node4", "@target": "node6"}}, "node42": {"edge42": {"@source": "node42", "@target": "node43"}, "edge43": {"@source": "node42", "@target": "node44"}}, "node44": {"edge44": {"@source": "node44", "@target": "node45"}, "edge45": {"@source": "node44", "@target": "node46"}}, "node46": {"edge46": {"@source": "node46", "@target": "node47"}, "edge47": {"@source": "node46", "@target": "node48"}}, "node49": {"edge49": {"@source": "node49", "@target": "node50"}, "edge58": {"@source": "node49", "@target": "node59"}}, "node50": {"edge50": {"@source": "node50", "@target": "node51"}, "edge51": {"@source": "node50", "@target": "node52"}}, "node52": {"edge52": {"@source": "node52", "@target": "node53"}, "edge53": {"@source": "node52", "@target": "node54"}}, "node54": {"edge54": {"@source": "node54", "@target": "node55"}, "edge55": {"@source": "node54", "@target": "node56"}}, "node56": {"edge56": {"@source": "node56", "@target": "node57"}, "edge57": {"@source": "node56", "@target": "node58"}}, "node59": {"edge59": {"@source": "node59", "@target": "node60"}, "edge60": {"@source": "node59", "@target": "node61"}}, "node61": {"edge61": {"@source": "node61", "@target": "node62"}, "edge62": {"@source": "node61", "@target": "node63"}}, "node63": {"edge63": {"@source": "node63", "@target": "node64"}, "edge64": {"@source": "node63", "@target": "node65"}}, "node7": {"edge7": {"@source": "node7", "@target": "node8"}, "edge8": {"@source": "node7", "@target": "node9"}}, "node9": {"edge26": {"@source": "node9", "@target": "node27"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {"@otu": "otu5"}, "node12": {}, "node13": {"@otu": "otu6"}, "node14": {}, "node15": {"@otu": "otu7"}, "node16": {}, "node17": {}, "node18": {"@otu": "otu8"}, "node19": {"@otu": "otu9"}, "node2": {"@otu": "otu1"}, "node20": {}, "node21": {"@otu": "otu10"}, "node22": {}, "node23": {"@otu": "otu11"}, "node24": {}, "node25": {"@otu": "otu12"}, "node26": {"@otu": "otu13"}, "node27": {}, "node28": {}, "node29": {"@otu": "otu14"}, "node3": {}, "node30": {}, "node31": {"@otu": "otu15"}, "node32": {}, "node33": {"@otu": "otu16"}, "node34": {"@otu": "otu17"}, "node35": {}, "node36": {}, "node37": {"@otu": "otu18"}, "node38": {}, "node39": {}, "node4": {}, "node40": {"@otu": "otu19"}, "node41": {"@otu": "otu20"}, "node42": {}, "node43": {"@otu": "otu21"}, "node44": {}, "node45": {"@otu": "otu22"}, "node46": {}, "node47": {"@otu": "otu23"}, "node48": {"@otu": "otu24"}, "node49": {}, "node5": {"@otu": "otu2"}, "node50": {}, "node51": {"@otu": "otu25"}, "node52": {}, "node53": {"@otu": "otu26"}, "node54": {}, "node55": {"@otu": "otu27"}, "node56": {}, "node57": {"@otu": "otu28"}, "node58": {"@otu": "otu29"}, "node59": {}, "node6": {"@otu": "otu3"}, "node60": {"@otu": "otu30"}, "node61": {}, "node62": {"@otu": "otu31"}, "node63": {}, "node64": {"@otu": "otu32"}, "node65": {"@otu": "otu33"}, "node7": {}, "node8": {"@otu": "otu4"}, "node9": {}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "9faf378d19135a2dbbbfe301203f58f98661be06", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Mon, 3 Mar 2025 10:40:06 +0000", "date_ISO_8601": "2025-03-03 10:40:06 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Initial commit Coeur d'acier et al. (2007)", "message_body": "Coeurdacier2007Aphis.nwk\nIgnored polyphyletic Aphis_gossypii.\n\n(Update document 'ot_2585' via OpenTree API)"}, {"id": "8e556f0719e603fd70c7935633e192141884d708", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Mon, 3 Mar 2025 10:37:54 +0000", "date_ISO_8601": "2025-03-03 10:37:54 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Update document 'ot_2585' via OpenTree API"}]}