{"sha": "142b59402741da4f1e137c40ebdffe63d66a5e08", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2016-12-20T15:30:17.645Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2016-12-20T15:30:17.645Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "PASTED.tre", "@size": 866, "@type": "newick", "@url": "/curator/download/supporting_files.doc.aeccc1e215056641.5041535445442e747265.tre", "description": {"$": "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": "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": [], "^ot:comment": "trivial test commit.", "^ot:curatorName": ["Joseph W. Brown"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 765193, "^ot:focalCladeOTTTaxonName": "Anatidae", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_1022", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/s1055-7903(02)00019-2"}, "^ot:studyPublicationReference": "Donne-Gouss\u00e9, Carole, Vincent Laudet, Catherine H\u00e4nni. 2002. A molecular phylogeny of anseriformes based on mitochondrial DNA analysis. Molecular Phylogenetics and Evolution 23 (3): 339-356", "^ot:studyYear": 2002, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Anas strepera", "^ot:ottId": 30856, "^ot:ottTaxonName": "Mareca strepera"}, "otu10": {"^ot:originalLabel": "Aythya marila", "^ot:ottId": 1044561, "^ot:ottTaxonName": "Aythya marila"}, "otu11": {"^ot:originalLabel": "Aythya nyroca", "^ot:ottId": 789865, "^ot:ottTaxonName": "Aythya nyroca"}, "otu12": {"^ot:originalLabel": "Netta rufina", "^ot:ottId": 693335, "^ot:ottTaxonName": "Netta rufina"}, "otu13": {"^ot:originalLabel": "Marmaronetta angustirostris", "^ot:ottId": 552052, "^ot:ottTaxonName": "Marmaronetta angustirostris"}, "otu14": {"^ot:originalLabel": "Chenonetta jubata", "^ot:ottId": 436829, "^ot:ottTaxonName": "Chenonetta jubata"}, "otu15": {"^ot:originalLabel": "Cairina moschata", "^ot:ottId": 714469, "^ot:ottTaxonName": "Cairina moschata"}, "otu16": {"^ot:originalLabel": "Aix galericulata", "^ot:ottId": 765197, "^ot:ottTaxonName": "Aix galericulata"}, "otu17": {"^ot:originalLabel": "Mergus cucullatus", "^ot:ottId": 809009, "^ot:ottTaxonName": "Lophodytes cucullatus"}, "otu18": {"^ot:originalLabel": "Mergus albellus", "^ot:ottId": 166692, "^ot:ottTaxonName": "Mergellus albellus"}, "otu19": {"^ot:originalLabel": "Mergus serrator", "^ot:ottId": 662625, "^ot:ottTaxonName": "Mergus serrator"}, "otu2": {"^ot:originalLabel": "Anas sibilatrix", "^ot:ottId": 604188, "^ot:ottTaxonName": "Mareca sibilatrix"}, "otu20": {"^ot:originalLabel": "Bucephala clangula", "^ot:ottId": 166683, "^ot:ottTaxonName": "Bucephala clangula"}, "otu21": {"^ot:originalLabel": "Melanitta nigra", "^ot:ottId": 948668, "^ot:ottTaxonName": "Melanitta nigra"}, "otu22": {"^ot:originalLabel": "Callonetta leucophrys", "^ot:ottId": 552044, "^ot:ottTaxonName": "Callonetta leucophrys"}, "otu23": {"^ot:originalLabel": "Somateria mollissima", "^ot:ottId": 785961, "^ot:ottTaxonName": "Somateria mollissima"}, "otu24": {"^ot:originalLabel": "Clangula hyemalis", "^ot:ottId": 316879, "^ot:ottTaxonName": "Clangula hyemalis"}, "otu25": {"^ot:originalLabel": "Tadorna tadornoides", "^ot:ottId": 282327, "^ot:ottTaxonName": "Tadorna tadornoides"}, "otu26": {"^ot:originalLabel": "Tadorna tadorna", "^ot:ottId": 30847, "^ot:ottTaxonName": "Tadorna tadorna"}, "otu27": {"^ot:originalLabel": "Alopochen aegyptiacus", "^ot:ottId": 693339, "^ot:ottTaxonName": "Alopochen aegyptiacus"}, "otu28": {"^ot:originalLabel": "Chloephaga picta", "^ot:ottId": 140309, "^ot:ottTaxonName": "Chloephaga picta"}, "otu29": {"^ot:originalLabel": "Anser rossii", "^ot:ottId": 767830, "^ot:ottTaxonName": "Anser rossii"}, "otu3": {"^ot:originalLabel": "Anas bahamensis", "^ot:ottId": 656778, "^ot:ottTaxonName": "Anas bahamensis"}, "otu30": {"^ot:originalLabel": "Anser anser", "^ot:ottId": 190887, "^ot:ottTaxonName": "Anser anser"}, "otu31": {"^ot:originalLabel": "Anser indicus", "^ot:ottId": 190897, "^ot:ottTaxonName": "Anser indicus"}, "otu32": {"^ot:originalLabel": "Anser erythropus", "^ot:ottId": 691333, "^ot:ottTaxonName": "Anser erythropus"}, "otu33": {"^ot:originalLabel": "Anser caerulescens", "^ot:ottId": 190878, "^ot:ottTaxonName": "Anser caerulescens"}, "otu34": {"^ot:originalLabel": "Anser albifrons", "^ot:ottId": 430239, "^ot:ottTaxonName": "Anser albifrons"}, "otu35": {"^ot:originalLabel": "Anser canagicus", "^ot:ottId": 166688, "^ot:ottTaxonName": "Anser canagica"}, "otu36": {"^ot:originalLabel": "Branta leucopsis", "^ot:ottId": 799124, "^ot:ottTaxonName": "Branta leucopsis"}, "otu37": {"^ot:originalLabel": "Branta canadensis", "^ot:ottId": 714461, "^ot:ottTaxonName": "Branta canadensis"}, "otu38": {"^ot:originalLabel": "Branta bernicla", "^ot:ottId": 135287, "^ot:ottTaxonName": "Branta bernicla"}, "otu39": {"^ot:originalLabel": "Branta ruficollis", "^ot:ottId": 799106, "^ot:ottTaxonName": "Branta ruficollis"}, "otu4": {"^ot:originalLabel": "Anas acuta", "^ot:ottId": 855474, "^ot:ottTaxonName": "Anas acuta"}, "otu40": {"^ot:originalLabel": "Coscoroba coscoroba", "^ot:ottId": 140305, "^ot:ottTaxonName": "Coscoroba coscoroba"}, "otu41": {"^ot:originalLabel": "Cereopsis novaehollandiae", "^ot:ottId": 714459, "^ot:ottTaxonName": "Cereopsis novaehollandiae"}, "otu42": {"^ot:originalLabel": "Cygnus atratus", "^ot:ottId": 140312, "^ot:ottTaxonName": "Cygnus atratus"}, "otu43": {"^ot:originalLabel": "Dendrocygna eytoni", "^ot:ottId": 662615, "^ot:ottTaxonName": "Dendrocygna eytoni"}, "otu44": {"^ot:originalLabel": "Dendrocygna bicolor", "^ot:ottId": 662618, "^ot:ottTaxonName": "Dendrocygna bicolor"}, "otu45": {"^ot:originalLabel": "Chauna torquata", "^ot:ottId": 860132, "^ot:ottTaxonName": "Chauna torquata"}, "otu5": {"^ot:originalLabel": "Anas platyrhynchos", "^ot:ottId": 765167, "^ot:ottTaxonName": "Anas platyrhynchos"}, "otu6": {"^ot:originalLabel": "Lophonetta specularoides", "^ot:ottId": 552046, "^ot:ottTaxonName": "Lophonetta specularioides"}, "otu7": {"^ot:originalLabel": "Anas crecca", "^ot:ottId": 656799, "^ot:ottTaxonName": "Anas crecca"}, "otu8": {"^ot:originalLabel": "Anas clypeata", "^ot:ottId": 656794, "^ot:ottTaxonName": "Anas clypeata"}, "otu9": {"^ot:originalLabel": "Aythya americana", "^ot:ottId": 693332, "^ot:ottTaxonName": "Aythya americana"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 5a (topology only)", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Neighbor-joining ", "^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"}, "edge88": {"@source": "node1", "@target": "node89"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge19": {"@source": "node10", "@target": "node20"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge18": {"@source": "node11", "@target": "node19"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge15": {"@source": "node12", "@target": "node16"}}, "node13": {"edge13": {"@source": "node13", "@target": "node14"}, "edge14": {"@source": "node13", "@target": "node15"}}, "node16": {"edge16": {"@source": "node16", "@target": "node17"}, "edge17": {"@source": "node16", "@target": "node18"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge85": {"@source": "node2", "@target": "node86"}}, "node21": {"edge21": {"@source": "node21", "@target": "node22"}, "edge22": {"@source": "node21", "@target": "node23"}}, "node24": {"edge24": {"@source": "node24", "@target": "node25"}, "edge27": {"@source": "node24", "@target": "node28"}}, "node25": {"edge25": {"@source": "node25", "@target": "node26"}, "edge26": {"@source": "node25", "@target": "node27"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge29": {"@source": "node28", "@target": "node30"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge58": {"@source": "node3", "@target": "node59"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge32": {"@source": "node31", "@target": "node33"}}, "node34": {"edge34": {"@source": "node34", "@target": "node35"}, "edge35": {"@source": "node34", "@target": "node36"}}, "node37": {"edge37": {"@source": "node37", "@target": "node38"}, "edge48": {"@source": "node37", "@target": "node49"}}, "node38": {"edge38": {"@source": "node38", "@target": "node39"}, "edge45": {"@source": "node38", "@target": "node46"}}, "node39": {"edge39": {"@source": "node39", "@target": "node40"}, "edge44": {"@source": "node39", "@target": "node45"}}, "node4": {"edge4": {"@source": "node4", "@target": "node5"}, "edge51": {"@source": "node4", "@target": "node52"}}, "node40": {"edge40": {"@source": "node40", "@target": "node41"}, "edge43": {"@source": "node40", "@target": "node44"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge42": {"@source": "node41", "@target": "node43"}}, "node46": {"edge46": {"@source": "node46", "@target": "node47"}, "edge47": {"@source": "node46", "@target": "node48"}}, "node49": {"edge49": {"@source": "node49", "@target": "node50"}, "edge50": {"@source": "node49", "@target": "node51"}}, "node5": {"edge36": {"@source": "node5", "@target": "node37"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node52": {"edge52": {"@source": "node52", "@target": "node53"}, "edge57": {"@source": "node52", "@target": "node58"}}, "node53": {"edge53": {"@source": "node53", "@target": "node54"}, "edge56": {"@source": "node53", "@target": "node57"}}, "node54": {"edge54": {"@source": "node54", "@target": "node55"}, "edge55": {"@source": "node54", "@target": "node56"}}, "node59": {"edge59": {"@source": "node59", "@target": "node60"}, "edge80": {"@source": "node59", "@target": "node81"}}, "node6": {"edge33": {"@source": "node6", "@target": "node34"}, "edge6": {"@source": "node6", "@target": "node7"}}, "node60": {"edge60": {"@source": "node60", "@target": "node61"}, "edge73": {"@source": "node60", "@target": "node74"}}, "node61": {"edge61": {"@source": "node61", "@target": "node62"}, "edge72": {"@source": "node61", "@target": "node73"}}, "node62": {"edge62": {"@source": "node62", "@target": "node63"}, "edge71": {"@source": "node62", "@target": "node72"}}, "node63": {"edge63": {"@source": "node63", "@target": "node64"}, "edge70": {"@source": "node63", "@target": "node71"}}, "node64": {"edge64": {"@source": "node64", "@target": "node65"}, "edge69": {"@source": "node64", "@target": "node70"}}, "node65": {"edge65": {"@source": "node65", "@target": "node66"}, "edge68": {"@source": "node65", "@target": "node69"}}, "node66": {"edge66": {"@source": "node66", "@target": "node67"}, "edge67": {"@source": "node66", "@target": "node68"}}, "node7": {"edge30": {"@source": "node7", "@target": "node31"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node74": {"edge74": {"@source": "node74", "@target": "node75"}, "edge79": {"@source": "node74", "@target": "node80"}}, "node75": {"edge75": {"@source": "node75", "@target": "node76"}, "edge78": {"@source": "node75", "@target": "node79"}}, "node76": {"edge76": {"@source": "node76", "@target": "node77"}, "edge77": {"@source": "node76", "@target": "node78"}}, "node8": {"edge23": {"@source": "node8", "@target": "node24"}, "edge8": {"@source": "node8", "@target": "node9"}}, "node81": {"edge81": {"@source": "node81", "@target": "node82"}, "edge84": {"@source": "node81", "@target": "node85"}}, "node82": {"edge82": {"@source": "node82", "@target": "node83"}, "edge83": {"@source": "node82", "@target": "node84"}}, "node86": {"edge86": {"@source": "node86", "@target": "node87"}, "edge87": {"@source": "node86", "@target": "node88"}}, "node9": {"edge20": {"@source": "node9", "@target": "node21"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {}, "node12": {}, "node13": {}, "node14": {"@otu": "otu1"}, "node15": {"@otu": "otu2"}, "node16": {}, "node17": {"@otu": "otu3"}, "node18": {"@otu": "otu4"}, "node19": {"@otu": "otu5"}, "node2": {}, "node20": {"@otu": "otu6"}, "node21": {}, "node22": {"@otu": "otu7"}, "node23": {"@otu": "otu8"}, "node24": {}, "node25": {}, "node26": {"@otu": "otu9"}, "node27": {"@otu": "otu10"}, "node28": {}, "node29": {"@otu": "otu11"}, "node3": {}, "node30": {"@otu": "otu12"}, "node31": {}, "node32": {"@otu": "otu13"}, "node33": {"@otu": "otu14"}, "node34": {}, "node35": {"@otu": "otu15"}, "node36": {"@otu": "otu16"}, "node37": {}, "node38": {}, "node39": {}, "node4": {}, "node40": {}, "node41": {}, "node42": {"@otu": "otu17"}, "node43": {"@otu": "otu18"}, "node44": {"@otu": "otu19"}, "node45": {"@otu": "otu20"}, "node46": {}, "node47": {"@otu": "otu21"}, "node48": {"@otu": "otu22"}, "node49": {}, "node5": {}, "node50": {"@otu": "otu23"}, "node51": {"@otu": "otu24"}, "node52": {}, "node53": {}, "node54": {}, "node55": {"@otu": "otu25"}, "node56": {"@otu": "otu26"}, "node57": {"@otu": "otu27"}, "node58": {"@otu": "otu28"}, "node59": {}, "node6": {}, "node60": {}, "node61": {}, "node62": {}, "node63": {}, "node64": {}, "node65": {}, "node66": {}, "node67": {"@otu": "otu29"}, "node68": {"@otu": "otu30"}, "node69": {"@otu": "otu31"}, "node7": {}, "node70": {"@otu": "otu32"}, "node71": {"@otu": "otu33"}, "node72": {"@otu": "otu34"}, "node73": {"@otu": "otu35"}, "node74": {}, "node75": {}, "node76": {}, "node77": {"@otu": "otu36"}, "node78": {"@otu": "otu37"}, "node79": {"@otu": "otu38"}, "node8": {}, "node80": {"@otu": "otu39"}, "node81": {}, "node82": {}, "node83": {"@otu": "otu40"}, "node84": {"@otu": "otu41"}, "node85": {"@otu": "otu42"}, "node86": {}, "node87": {"@otu": "otu43"}, "node88": {"@otu": "otu44"}, "node89": {"@otu": "otu45"}, "node9": {}}}}}}}}, "branch2sha": {"master": "142b59402741da4f1e137c40ebdffe63d66a5e08"}, "commentHTML": "
trivial test commit.
", "duplicateStudyIDs": [], "shardName": "phylesystem-0", "versionHistory": [{"id": "1929954972dff01726db98ce7593a584d51d81ef", "author_name": "Benjamin Redelings", "author_email": "benjamin.redelings@gmail.com", "date": "Tue, 16 Jan 2018 10:42:59 -0500", "date_ISO_8601": "2018-01-16 10:42:59 -0500", "relative_date": "6 years ago", "message_subject": "Sync from phylesystem-1 using 'cp'."}]}