{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-05-04T00:52:30.899Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": true, "searchContext": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-05-04T00:52:30.899Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-05-04T00:52:30.899Z", "@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": "GarzonOrduna2012Hamadryas.nwk", "@size": 409, "@type": "newick", "@url": "/curator/download/supporting_files.doc.ab60ae1c706aace0.4761727a6f6e4f7264756e613230313248616d6164727961732e6e776b.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": ["otu19", "otu3"], "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": ["otu19", "otu3"], "@otusID": "otus1", "@otuID": ["otu19", "otu3"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["dchesters"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 977966, "^ot:focalCladeOTTTaxonName": "Hamadryas (genus in Opisthokonta)", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_2776", "^ot:studyPublication": {"@href": "https://doi.org/10.1111/j.1365-3113.2011.00599.x"}, "^ot:studyPublicationReference": "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", "^ot:studyYear": 2012, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 38, "message": 0, "node": 39, "otu": 20, "otus": 2, "tree": 1, "trees": 2}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Ectima iona", "^ot:ottId": 3116343, "^ot:ottTaxonName": "Ectima iona"}, "otu10": {"^ot:originalLabel": "Hamadryas iphthime", "^ot:ottId": 512297, "^ot:ottTaxonName": "Hamadryas iphthime"}, "otu11": {"^ot:originalLabel": "Hamadryas epinome", "^ot:ottId": 3116359, "^ot:ottTaxonName": "Hamadryas epinome"}, "otu12": {"^ot:originalLabel": "Hamadryas feronia", "^ot:ottId": 356613, "^ot:ottTaxonName": "Hamadryas feronia"}, "otu13": {"^ot:originalLabel": "Hamadryas guatemalena", "^ot:ottId": 675087, "^ot:ottTaxonName": "Hamadryas guatemalena"}, "otu14": {"^ot:originalLabel": "Hamadryas fornax", "^ot:ottId": 3116382, "^ot:ottTaxonName": "Hamadryas fornax"}, "otu15": {"^ot:originalLabel": "Hamadryas belladonna", "^ot:ottId": 3116418, "^ot:ottTaxonName": "Hamadryas belladonna"}, "otu16": {"^ot:originalLabel": "Hamadryas amphinome", "^ot:ottId": 433295, "^ot:ottTaxonName": "Hamadryas amphinome"}, "otu17": {"^ot:originalLabel": "Hamadryas arinome", "^ot:ottId": 1041208, "^ot:ottTaxonName": "Hamadryas arinome"}, "otu18": {"^ot:originalLabel": "Hamadryas velutina", "^ot:ottId": 3116393, "^ot:ottTaxonName": "Hamadryas velutina"}, "otu19": {"^ot:originalLabel": "Hamadryas arete"}, "otu2": {"^ot:originalLabel": "Hamadryas atlantis", "^ot:ottId": 3116365, "^ot:ottTaxonName": "Hamadryas atlantis"}, "otu20": {"^ot:originalLabel": "Hamadryas laodamia", "^ot:ottId": 433306, "^ot:ottTaxonName": "Hamadryas laodamia"}, "otu3": {"^ot:originalLabel": "Hamadryas albicornis"}, "otu4": {"^ot:originalLabel": "Hamadryas chloe", "^ot:ottId": 552638, "^ot:ottTaxonName": "Hamadryas chloe"}, "otu5": {"^ot:originalLabel": "Hamadryas alicia", "^ot:ottId": 3116369, "^ot:ottTaxonName": "Hamadryas alicia"}, "otu6": {"^ot:originalLabel": "Hamadryas februa", "^ot:ottId": 858548, "^ot:ottTaxonName": "Hamadryas februa"}, "otu7": {"^ot:originalLabel": "Hamadryas amphichloe", "^ot:ottId": 3116389, "^ot:ottTaxonName": "Hamadryas amphichloe"}, "otu8": {"^ot:originalLabel": "Hamadryas glauconome", "^ot:ottId": 758652, "^ot:ottTaxonName": "Hamadryas glauconome"}, "otu9": {"^ot:originalLabel": "Hamadryas julitta", "^ot:ottId": 834395, "^ot:ottTaxonName": "Hamadryas julitta"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 7B, MP", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum parsimony ", "^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"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge18": {"@source": "node11", "@target": "node19"}}, "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"}, "edge17": {"@source": "node16", "@target": "node18"}}, "node19": {"edge19": {"@source": "node19", "@target": "node20"}, "edge20": {"@source": "node19", "@target": "node21"}}, "node21": {"edge21": {"@source": "node21", "@target": "node22"}, "edge22": {"@source": "node21", "@target": "node23"}}, "node23": {"edge23": {"@source": "node23", "@target": "node24"}, "edge26": {"@source": "node23", "@target": "node27"}}, "node24": {"edge24": {"@source": "node24", "@target": "node25"}, "edge25": {"@source": "node24", "@target": "node26"}}, "node27": {"edge27": {"@source": "node27", "@target": "node28"}, "edge28": {"@source": "node27", "@target": "node29"}}, "node29": {"edge29": {"@source": "node29", "@target": "node30"}, "edge30": {"@source": "node29", "@target": "node31"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge4": {"@source": "node3", "@target": "node5"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge32": {"@source": "node31", "@target": "node33"}}, "node33": {"edge33": {"@source": "node33", "@target": "node34"}, "edge34": {"@source": "node33", "@target": "node35"}}, "node35": {"edge35": {"@source": "node35", "@target": "node36"}, "edge36": {"@source": "node35", "@target": "node37"}}, "node37": {"edge37": {"@source": "node37", "@target": "node38"}, "edge38": {"@source": "node37", "@target": "node39"}}, "node5": {"edge5": {"@source": "node5", "@target": "node6"}, "edge8": {"@source": "node5", "@target": "node9"}}, "node6": {"edge6": {"@source": "node6", "@target": "node7"}, "edge7": {"@source": "node6", "@target": "node8"}}, "node9": {"edge10": {"@source": "node9", "@target": "node11"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu5"}, "node11": {}, "node12": {}, "node13": {"@otu": "otu6"}, "node14": {}, "node15": {"@otu": "otu7"}, "node16": {}, "node17": {"@otu": "otu8"}, "node18": {"@otu": "otu9"}, "node19": {}, "node2": {"@otu": "otu1"}, "node20": {"@otu": "otu10"}, "node21": {}, "node22": {"@otu": "otu11"}, "node23": {}, "node24": {}, "node25": {"@otu": "otu12"}, "node26": {"@otu": "otu13"}, "node27": {}, "node28": {"@otu": "otu14"}, "node29": {}, "node3": {}, "node30": {"@otu": "otu15"}, "node31": {}, "node32": {"@otu": "otu16"}, "node33": {}, "node34": {"@otu": "otu17"}, "node35": {}, "node36": {"@otu": "otu18"}, "node37": {}, "node38": {"@otu": "otu19"}, "node39": {"@otu": "otu20"}, "node4": {"@otu": "otu2"}, "node5": {}, "node6": {}, "node7": {"@otu": "otu3"}, "node8": {"@otu": "otu4"}, "node9": {}}}}}}}}, "branch2sha": {"master": "2aa180baef3c5e313da1e7f09c83ce2c0467b457"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "71daff53911425b783a195a84fe62332b5503f3b", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Sun, 4 May 2025 00:54:53 +0000", "date_ISO_8601": "2025-05-04 00:54:53 +0000", "relative_date": "1 year ago", "message_subject": "Initial commit GARZ\u00d3N-ORDU\u00d1A 2012", "message_body": "GarzonOrduna2012Hamadryas.nwk\nReduced outgroup to single terminal.\n\n(Update document 'ot_2776' via OpenTree API)"}, {"id": "6dde2a9cd488f3c14340e651e369df69b3d8ddfa", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Sun, 4 May 2025 00:52:28 +0000", "date_ISO_8601": "2025-05-04 00:52:28 +0000", "relative_date": "1 year ago", "message_subject": "Update document 'ot_2776' via OpenTree API"}]}