{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-08-09T03:47:05.444Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": false, "searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-08-09T03:47:05.444Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "<content provided as a string in a \"content\" rather than a file upload>", "@size": 626, "@type": "newick", "@url": "/curator/default/to_nexson?output=input&uploadid=u6567af59-6b54-4a35-86fe-672af3fb21d2", "description": {"$": "Source data for tree 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2023-03-30T22:51:22.502Z", "@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"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node10", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node10"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node13", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node13"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node14", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node14"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node15", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node15"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node18", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node18"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node19", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node19"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node35", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node35"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node36", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node36"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node37", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node37"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node48", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node48"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node49", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node49"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node50", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node50"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node8", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node8"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node9", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node9"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu1", "otu2", "otu3", "otu4", "otu5", "otu6"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu12", "otu13"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu14", "otu15", "otu16"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu23", "otu24", "otu25"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu7", "otu8"], "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": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1"], "^ot:comment": "", "^ot:curatorName": ["Joseph W. Brown", "Emily Jane McTavish"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 5860997, "^ot:focalCladeOTTTaxonName": "Cardinalidae", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_169", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1111/jbi.12218"}, "^ot:studyPublicationReference": "Robert W. Bryson, Jaime Chaves, Brian Tilston Smith, Matthew J. Miller, Kevin Winker, Jorge L. P\u00e9rez-Em\u00e1n, John Klicka, 2014, 'Diversification across the New World within the \u2018blue\u2019 cardinalids (Aves: Cardinalidae)', Journal of Biogeography, vol. 41, no. 3, pp. 587-599", "^ot:studyYear": 2014, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Cyanocompsa cyanoides A", "^ot:ottId": 486842, "^ot:ottTaxonName": "Cyanocompsa cyanoides"}, "otu10": {"^ot:originalLabel": "Amaurospiza carrizalensis", "^ot:ottId": 3597356, "^ot:ottTaxonName": "Amaurospiza carrizalensis"}, "otu11": {"^ot:originalLabel": "Amaurospiza moesta", "^ot:ottId": 1044598, "^ot:ottTaxonName": "Amaurospiza moesta"}, "otu12": {"^ot:originalLabel": "Amaurospiza concolor B", "^ot:ottId": 596726, "^ot:ottTaxonName": "Amaurospiza concolor"}, "otu13": {"^ot:originalLabel": "Amaurospiza concolor A", "^ot:ottId": 596726, "^ot:ottTaxonName": "Amaurospiza concolor"}, "otu14": {"^ot:originalLabel": "Passerina versicolor C", "^ot:ottId": 887258, "^ot:ottTaxonName": "Passerina versicolor"}, "otu15": {"^ot:originalLabel": "Passerina versicolor B", "^ot:ottId": 887258, "^ot:ottTaxonName": "Passerina versicolor"}, "otu16": {"^ot:originalLabel": "Passerina versicolor A", "^ot:ottId": 887258, "^ot:ottTaxonName": "Passerina versicolor"}, "otu17": {"^ot:originalLabel": "Passerina ciris", "^ot:ottId": 887250, "^ot:ottTaxonName": "Passerina ciris"}, "otu18": {"^ot:originalLabel": "Passerina leclancherii", "^ot:ottId": 887253, "^ot:ottTaxonName": "Passerina leclancherii"}, "otu19": {"^ot:originalLabel": "Passerina rositae", "^ot:ottId": 724916, "^ot:ottTaxonName": "Passerina rositae"}, "otu2": {"^ot:originalLabel": "Cyanocompsa cyanoides C", "^ot:ottId": 486842, "^ot:ottTaxonName": "Cyanocompsa cyanoides"}, "otu20": {"^ot:originalLabel": "Passerina amoena", "^ot:ottId": 119888, "^ot:ottTaxonName": "Passerina amoena"}, "otu21": {"^ot:originalLabel": "Passerina caerulea", "^ot:ottId": 486840, "^ot:ottTaxonName": "Passerina caerulea"}, "otu22": {"^ot:originalLabel": "Passerina cyanea", "^ot:ottId": 939942, "^ot:ottTaxonName": "Passerina cyanea"}, "otu23": {"^ot:originalLabel": "Cyanocompsa parellina B", "^ot:ottId": 772205, "^ot:ottTaxonName": "Cyanocompsa parellina"}, "otu24": {"^ot:originalLabel": "Cyanocompsa parellina C", "^ot:ottId": 772205, "^ot:ottTaxonName": "Cyanocompsa parellina"}, "otu25": {"^ot:originalLabel": "Cyanocompsa parellina A", "^ot:ottId": 772205, "^ot:ottTaxonName": "Cyanocompsa parellina"}, "otu26": {"^ot:originalLabel": "Spiza americana", "^ot:ottId": 364334, "^ot:ottTaxonName": "Spiza americana"}, "otu3": {"^ot:originalLabel": "Cyanocompsa cyanoides B", "^ot:ottId": 486842, "^ot:ottTaxonName": "Cyanocompsa cyanoides"}, "otu4": {"^ot:originalLabel": "Cyanocompsa cyanoides D", "^ot:ottId": 486842, "^ot:ottTaxonName": "Cyanocompsa cyanoides"}, "otu5": {"^ot:originalLabel": "Cyanocompsa cyanoides F", "^ot:ottId": 486842, "^ot:ottTaxonName": "Cyanocompsa cyanoides"}, "otu6": {"^ot:originalLabel": "Cyanocompsa cyanoides E", "^ot:ottId": 486842, "^ot:ottTaxonName": "Cyanocompsa cyanoides"}, "otu7": {"^ot:originalLabel": "Cyanocompsa brissonii A", "^ot:ottId": 7661234, "^ot:ottTaxonName": "Cyanoloxia brissonii"}, "otu8": {"^ot:originalLabel": "Cyanocompsa brissonii B", "^ot:ottId": 7661234, "^ot:ottTaxonName": "Cyanoloxia brissonii"}, "otu9": {"^ot:originalLabel": "Cyanoloxia glaucocaerulea", "^ot:ottId": 75499, "^ot:ottTaxonName": "Cyanoloxia glaucocaerulea"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 3 (multilocus)", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node1", "^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"}, "edge50": {"@source": "node1", "@target": "node51"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge14": {"@source": "node11", "@target": "node15"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge13": {"@source": "node12", "@target": "node14"}}, "node16": {"edge16": {"@source": "node16", "@target": "node17"}, "edge19": {"@source": "node16", "@target": "node20"}}, "node17": {"edge17": {"@source": "node17", "@target": "node18"}, "edge18": {"@source": "node17", "@target": "node19"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge27": {"@source": "node2", "@target": "node28"}}, "node21": {"edge21": {"@source": "node21", "@target": "node22"}, "edge26": {"@source": "node21", "@target": "node27"}}, "node22": {"edge22": {"@source": "node22", "@target": "node23"}, "edge25": {"@source": "node22", "@target": "node26"}}, "node23": {"edge23": {"@source": "node23", "@target": "node24"}, "edge24": {"@source": "node23", "@target": "node25"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge45": {"@source": "node28", "@target": "node46"}}, "node29": {"edge29": {"@source": "node29", "@target": "node30"}, "edge40": {"@source": "node29", "@target": "node41"}}, "node3": {"edge20": {"@source": "node3", "@target": "node21"}, "edge3": {"@source": "node3", "@target": "node4"}}, "node30": {"edge30": {"@source": "node30", "@target": "node31"}, "edge39": {"@source": "node30", "@target": "node40"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge38": {"@source": "node31", "@target": "node39"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge37": {"@source": "node32", "@target": "node38"}}, "node33": {"edge33": {"@source": "node33", "@target": "node34"}, "edge36": {"@source": "node33", "@target": "node37"}}, "node34": {"edge34": {"@source": "node34", "@target": "node35"}, "edge35": {"@source": "node34", "@target": "node36"}}, "node4": {"edge15": {"@source": "node4", "@target": "node16"}, "edge4": {"@source": "node4", "@target": "node5"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge44": {"@source": "node41", "@target": "node45"}}, "node42": {"edge42": {"@source": "node42", "@target": "node43"}, "edge43": {"@source": "node42", "@target": "node44"}}, "node46": {"edge46": {"@source": "node46", "@target": "node47"}, "edge49": {"@source": "node46", "@target": "node50"}}, "node47": {"edge47": {"@source": "node47", "@target": "node48"}, "edge48": {"@source": "node47", "@target": "node49"}}, "node5": {"edge10": {"@source": "node5", "@target": "node11"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node6": {"edge6": {"@source": "node6", "@target": "node7"}, "edge9": {"@source": "node6", "@target": "node10"}}, "node7": {"edge7": {"@source": "node7", "@target": "node8"}, "edge8": {"@source": "node7", "@target": "node9"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu3", "^ot:isTaxonExemplar": false}, "node11": {}, "node12": {}, "node13": {"@otu": "otu4", "^ot:isTaxonExemplar": true}, "node14": {"@otu": "otu5", "^ot:isTaxonExemplar": false}, "node15": {"@otu": "otu6", "^ot:isTaxonExemplar": false}, "node16": {}, "node17": {}, "node18": {"@otu": "otu7", "^ot:isTaxonExemplar": true}, "node19": {"@otu": "otu8", "^ot:isTaxonExemplar": false}, "node2": {}, "node20": {"@otu": "otu9"}, "node21": {}, "node22": {}, "node23": {}, "node24": {"@otu": "otu10"}, "node25": {"@otu": "otu11"}, "node26": {"@otu": "otu12"}, "node27": {"@otu": "otu13"}, "node28": {}, "node29": {}, "node3": {}, "node30": {}, "node31": {}, "node32": {}, "node33": {}, "node34": {}, "node35": {"@otu": "otu14", "^ot:isTaxonExemplar": true}, "node36": {"@otu": "otu15", "^ot:isTaxonExemplar": false}, "node37": {"@otu": "otu16", "^ot:isTaxonExemplar": false}, "node38": {"@otu": "otu17"}, "node39": {"@otu": "otu18"}, "node4": {}, "node40": {"@otu": "otu19"}, "node41": {}, "node42": {}, "node43": {"@otu": "otu20"}, "node44": {"@otu": "otu21"}, "node45": {"@otu": "otu22"}, "node46": {}, "node47": {}, "node48": {"@otu": "otu23", "^ot:isTaxonExemplar": true}, "node49": {"@otu": "otu24", "^ot:isTaxonExemplar": false}, "node5": {}, "node50": {"@otu": "otu25", "^ot:isTaxonExemplar": false}, "node51": {"@otu": "otu26"}, "node6": {}, "node7": {}, "node8": {"@otu": "otu1", "^ot:isTaxonExemplar": false}, "node9": {"@otu": "otu2", "^ot:isTaxonExemplar": false}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "5d07557524a0b8918f3ba7984d08bb2ee23d3d78", "author_name": "Emily Jane McTavish", "author_email": "ejmctavish@ucmerced.edu", "date": "Thu, 30 Mar 2023 22:54:23 +0000", "date_ISO_8601": "2023-03-30 22:54:23 +0000", "relative_date": "3 years ago", "message_subject": "Update mappings to align with eBird", "message_body": "(Update document 'ot_169' via OpenTree API)"}, {"id": "89680537b79d5841daed0e31d3dd59d55ca56b6b", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Mon, 19 Sep 2016 00:38:30 +0000", "date_ISO_8601": "2016-09-19 00:38:30 +0000", "relative_date": "10 years ago", "message_subject": "focal clade", "message_body": "(Update document 'ot_169' via OpenTree API)"}, {"id": "c22c52a5eacb0e4c822f8630b7c9d86aef33b923", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Sat, 9 Aug 2014 03:48:49 +0000", "date_ISO_8601": "2014-08-09 03:48:49 +0000", "relative_date": "12 years ago", "message_subject": "blue cardinalids", "message_body": "(Update Study #ot_169 via OpenTree API)"}, {"id": "38c6a356c4e9c8edc92a67bd4225848ec4209f02", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Sat, 9 Aug 2014 03:29:49 +0000", "date_ISO_8601": "2014-08-09 03:29:49 +0000", "relative_date": "12 years ago", "message_subject": "Update Study #ot_169 via OpenTree API"}]}