{"sha": "02befbde630ec4faf8171b08c2571e92a6b342e8", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2016-02-23T11:54:53.987Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Mammals"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2016-02-23T11:54:53.987Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "PASTED.tre", "@size": 1258, "@type": "newick", "@url": "/curator/download/supporting_files.doc.850d00a2dbb5e09f.5041535445442e747265.tre", "description": {"$": "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": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu17", "otu21"], "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"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1"], "^ot:comment": "", "^ot:curatorName": ["Joseph W. Brown"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 495017, "^ot:focalCladeOTTTaxonName": "Cingulata (order in Deuterostomia)", "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_642", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.cub.2016.01.039"}, "^ot:studyPublicationReference": "Delsuc, Fr\u00e9d\u00e9ric, Gillian C. Gibb, Melanie Kuch, Guillaume Billet, Lionel Hautier, John Southon, Jean-Marie Rouillard, Juan Carlos Fernicola, Sergio F. Vizca\u00edno, Ross D.E. MacPhee, Hendrik N. Poinar. 2016. The phylogenetic affinities of the extinct glyptodonts. Current Biology 26 (4): R155-R156", "^ot:studyYear": 2016, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Orycteropus afer", "^ot:ottId": 561087, "^ot:ottTaxonName": "Orycteropus afer"}, "otu10": {"^ot:originalLabel": "Bradypus torquatus", "^ot:ottId": 759319, "^ot:ottTaxonName": "Bradypus torquatus"}, "otu11": {"^ot:originalLabel": "Bradypus pygmaeus", "^ot:ottId": 736497, "^ot:ottTaxonName": "Bradypus pygmaeus"}, "otu12": {"^ot:originalLabel": "Bradypus variegatus", "^ot:ottId": 273233, "^ot:ottTaxonName": "Bradypus variegatus"}, "otu13": {"^ot:originalLabel": "Bradypus tridactylus", "^ot:ottId": 527342, "^ot:ottTaxonName": "Bradypus tridactylus"}, "otu14": {"^ot:originalLabel": "Dasypus kappleri", "^ot:ottId": 905104, "^ot:ottTaxonName": "Dasypus kappleri"}, "otu15": {"^ot:originalLabel": "Dasypus septemcinctus", "^ot:ottId": 4119195, "^ot:ottTaxonName": "Dasypus septemcinctus"}, "otu16": {"^ot:originalLabel": "Dasypus hybridus", "^ot:ottId": 4119193, "^ot:ottTaxonName": "Dasypus hybridus"}, "otu17": {"^ot:originalLabel": "Dasypus novemcinctus FG", "^ot:ottId": 796672, "^ot:ottTaxonName": "Dasypus novemcinctus"}, "otu18": {"^ot:originalLabel": "Dasypus yepesi", "^ot:ottId": 4119192, "^ot:ottTaxonName": "Dasypus yepesi"}, "otu19": {"^ot:originalLabel": "Dasypus sabanicola", "^ot:ottId": 4119191, "^ot:ottTaxonName": "Dasypus sabanicola"}, "otu2": {"^ot:originalLabel": "Loxodonta africana", "^ot:ottId": 541936, "^ot:ottTaxonName": "Loxodonta africana"}, "otu20": {"^ot:originalLabel": "Dasypus pilosus", "^ot:ottId": 4119194, "^ot:ottTaxonName": "Dasypus pilosus"}, "otu21": {"^ot:originalLabel": "Dasypus novemcinctus US", "^ot:ottId": 796672, "^ot:ottTaxonName": "Dasypus novemcinctus"}, "otu22": {"^ot:originalLabel": "Euphractus sexcinctus", "^ot:ottId": 292508, "^ot:ottTaxonName": "Euphractus sexcinctus"}, "otu23": {"^ot:originalLabel": "Chaetophractus villosus", "^ot:ottId": 180375, "^ot:ottTaxonName": "Chaetophractus villosus"}, "otu24": {"^ot:originalLabel": "Zaedyus pichiy", "^ot:ottId": 1002419, "^ot:ottTaxonName": "Zaedyus pichiy"}, "otu25": {"^ot:originalLabel": "Chaetophractus vellerosus", "^ot:ottId": 627609, "^ot:ottTaxonName": "Chaetophractus vellerosus"}, "otu26": {"^ot:originalLabel": "Doedicurus sp", "^ot:ottId": 4943308, "^ot:ottTaxonName": "Doedicurus"}, "otu27": {"^ot:originalLabel": "Chlamyphorus truncatus", "^ot:ottId": 552069, "^ot:ottTaxonName": "Chlamyphorus truncatus"}, "otu28": {"^ot:originalLabel": "Calyptophractus retusus", "^ot:ottId": 390325, "^ot:ottTaxonName": "Calyptophractus retusus"}, "otu29": {"^ot:originalLabel": "Priodontes maximus", "^ot:ottId": 476113, "^ot:ottTaxonName": "Priodontes maximus"}, "otu3": {"^ot:originalLabel": "Dugong dugon", "^ot:ottId": 835324, "^ot:ottTaxonName": "Dugong dugon"}, "otu30": {"^ot:originalLabel": "Tolypeutes tricinctus", "^ot:ottId": 476111, "^ot:ottTaxonName": "Tolypeutes tricinctus"}, "otu31": {"^ot:originalLabel": "Tolypeutes matacus", "^ot:ottId": 515354, "^ot:ottTaxonName": "Tolypeutes matacus"}, "otu32": {"^ot:originalLabel": "Cabassous tatouay", "^ot:ottId": 4119202, "^ot:ottTaxonName": "Cabassous tatouay"}, "otu33": {"^ot:originalLabel": "Cabassous chacoensis", "^ot:ottId": 4119201, "^ot:ottTaxonName": "Cabassous chacoensis"}, "otu34": {"^ot:originalLabel": "Cabassous unicinctus", "^ot:ottId": 1014321, "^ot:ottTaxonName": "Cabassous unicinctus"}, "otu35": {"^ot:originalLabel": "Cabassous centralis", "^ot:ottId": 4119200, "^ot:ottTaxonName": "Cabassous centralis"}, "otu4": {"^ot:originalLabel": "Cyclopes didactylus", "^ot:ottId": 675099, "^ot:ottTaxonName": "Cyclopes didactylus"}, "otu5": {"^ot:originalLabel": "Myrmecophaga tridactyla", "^ot:ottId": 490538, "^ot:ottTaxonName": "Myrmecophaga tridactyla"}, "otu6": {"^ot:originalLabel": "Tamandua tetradactyla", "^ot:ottId": 1014324, "^ot:ottTaxonName": "Tamandua tetradactyla"}, "otu7": {"^ot:originalLabel": "Tamandua mexicana", "^ot:ottId": 273227, "^ot:ottTaxonName": "Tamandua mexicana"}, "otu8": {"^ot:originalLabel": "Choloepus hoffmanni", "^ot:ottId": 273247, "^ot:ottTaxonName": "Choloepus hoffmanni"}, "otu9": {"^ot:originalLabel": "Choloepus didactylus", "^ot:ottId": 977390, "^ot:ottTaxonName": "Choloepus didactylus"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 1 PhyloBayes CAT-GTR-G", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:time", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node7", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@length": 4.5706, "@source": "node1", "@target": "node2"}, "edge6": {"@length": 37.1925, "@source": "node1", "@target": "node7"}}, "node11": {"edge11": {"@length": 11.3813, "@source": "node11", "@target": "node12"}, "edge12": {"@length": 10.491, "@source": "node11", "@target": "node13"}}, "node13": {"edge13": {"@length": 0.8903, "@source": "node13", "@target": "node14"}, "edge14": {"@length": 0.8903, "@source": "node13", "@target": "node15"}}, "node16": {"edge16": {"@length": 20.9018, "@source": "node16", "@target": "node17"}, "edge19": {"@length": 11.6343, "@source": "node16", "@target": "node20"}}, "node17": {"edge17": {"@length": 9.023, "@source": "node17", "@target": "node18"}, "edge18": {"@length": 9.023, "@source": "node17", "@target": "node19"}}, "node2": {"edge2": {"@length": 100.421, "@source": "node2", "@target": "node3"}, "edge3": {"@length": 39.1376, "@source": "node2", "@target": "node4"}}, "node20": {"edge20": {"@length": 18.2905, "@source": "node20", "@target": "node21"}, "edge21": {"@length": 10.9971, "@source": "node20", "@target": "node22"}}, "node22": {"edge22": {"@length": 7.2934, "@source": "node22", "@target": "node23"}, "edge23": {"@length": 1.8898, "@source": "node22", "@target": "node24"}}, "node24": {"edge24": {"@length": 5.4035, "@source": "node24", "@target": "node25"}, "edge25": {"@length": 5.4035, "@source": "node24", "@target": "node26"}}, "node27": {"edge27": {"@length": 33.352, "@source": "node27", "@target": "node28"}, "edge42": {"@length": 7.9409, "@source": "node27", "@target": "node43"}}, "node28": {"edge28": {"@length": 12.0962, "@source": "node28", "@target": "node29"}, "edge29": {"@length": 7.2273, "@source": "node28", "@target": "node30"}}, "node30": {"edge30": {"@length": 4.8028, "@source": "node30", "@target": "node31"}, "edge33": {"@length": 1.3287, "@source": "node30", "@target": "node34"}}, "node31": {"edge31": {"@length": 0.066, "@source": "node31", "@target": "node32"}, "edge32": {"@length": 0.066, "@source": "node31", "@target": "node33"}}, "node34": {"edge34": {"@length": 3.5401, "@source": "node34", "@target": "node35"}, "edge35": {"@length": 0.7736, "@source": "node34", "@target": "node36"}}, "node36": {"edge36": {"@length": 2.1506, "@source": "node36", "@target": "node37"}, "edge39": {"@length": 0.1161, "@source": "node36", "@target": "node40"}}, "node37": {"edge37": {"@length": 0.6158, "@source": "node37", "@target": "node38"}, "edge38": {"@length": 0.6158, "@source": "node37", "@target": "node39"}}, "node4": {"edge4": {"@length": 61.2838, "@source": "node4", "@target": "node5"}, "edge5": {"@length": 61.2838, "@source": "node4", "@target": "node6"}}, "node40": {"edge40": {"@length": 2.6503, "@source": "node40", "@target": "node41"}, "edge41": {"@length": 2.6503, "@source": "node40", "@target": "node42"}}, "node43": {"edge43": {"@length": 27.1026, "@source": "node43", "@target": "node44"}, "edge50": {"@length": 2.8114, "@source": "node43", "@target": "node51"}}, "node44": {"edge44": {"@length": 10.4047, "@source": "node44", "@target": "node45"}, "edge45": {"@length": 1.9364, "@source": "node44", "@target": "node46"}}, "node46": {"edge46": {"@length": 8.4682, "@source": "node46", "@target": "node47"}, "edge47": {"@length": 0.8825, "@source": "node46", "@target": "node48"}}, "node48": {"edge48": {"@length": 7.5857, "@source": "node48", "@target": "node49"}, "edge49": {"@length": 7.5857, "@source": "node48", "@target": "node50"}}, "node51": {"edge51": {"@length": 34.6959, "@source": "node51", "@target": "node52"}, "edge52": {"@length": 2.2798, "@source": "node51", "@target": "node53"}}, "node53": {"edge53": {"@length": 13.0867, "@source": "node53", "@target": "node54"}, "edge56": {"@length": 7.3486, "@source": "node53", "@target": "node57"}}, "node54": {"edge54": {"@length": 19.3293, "@source": "node54", "@target": "node55"}, "edge55": {"@length": 19.3293, "@source": "node54", "@target": "node56"}}, "node57": {"edge57": {"@length": 25.0674, "@source": "node57", "@target": "node58"}, "edge58": {"@length": 3.2951, "@source": "node57", "@target": "node59"}}, "node59": {"edge59": {"@length": 8.6166, "@source": "node59", "@target": "node60"}, "edge62": {"@length": 11.3741, "@source": "node59", "@target": "node63"}}, "node60": {"edge60": {"@length": 13.1556, "@source": "node60", "@target": "node61"}, "edge61": {"@length": 13.1556, "@source": "node60", "@target": "node62"}}, "node63": {"edge63": {"@length": 10.398, "@source": "node63", "@target": "node64"}, "edge64": {"@length": 2.3113, "@source": "node63", "@target": "node65"}}, "node65": {"edge65": {"@length": 8.0867, "@source": "node65", "@target": "node66"}, "edge66": {"@length": 6.942, "@source": "node65", "@target": "node67"}}, "node67": {"edge67": {"@length": 1.1446, "@source": "node67", "@target": "node68"}, "edge68": {"@length": 1.1446, "@source": "node67", "@target": "node69"}}, "node7": {"edge26": {"@length": 22.3511, "@source": "node7", "@target": "node27"}, "edge7": {"@length": 9.2798, "@source": "node7", "@target": "node8"}}, "node8": {"edge15": {"@length": 28.5947, "@source": "node8", "@target": "node16"}, "edge8": {"@length": 20.6935, "@source": "node8", "@target": "node9"}}, "node9": {"edge10": {"@length": 26.4446, "@source": "node9", "@target": "node11"}, "edge9": {"@length": 37.826, "@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu4"}, "node11": {}, "node12": {"@otu": "otu5"}, "node13": {}, "node14": {"@otu": "otu6"}, "node15": {"@otu": "otu7"}, "node16": {}, "node17": {}, "node18": {"@otu": "otu8"}, "node19": {"@otu": "otu9"}, "node2": {}, "node20": {}, "node21": {"@otu": "otu10"}, "node22": {}, "node23": {"@otu": "otu11"}, "node24": {}, "node25": {"@otu": "otu12"}, "node26": {"@otu": "otu13"}, "node27": {}, "node28": {}, "node29": {"@otu": "otu14"}, "node3": {"@otu": "otu1"}, "node30": {}, "node31": {}, "node32": {"@otu": "otu15"}, "node33": {"@otu": "otu16"}, "node34": {}, "node35": {"@otu": "otu17"}, "node36": {}, "node37": {}, "node38": {"@otu": "otu18"}, "node39": {"@otu": "otu19"}, "node4": {}, "node40": {}, "node41": {"@otu": "otu20"}, "node42": {"@otu": "otu21"}, "node43": {}, "node44": {}, "node45": {"@otu": "otu22"}, "node46": {}, "node47": {"@otu": "otu23"}, "node48": {}, "node49": {"@otu": "otu24"}, "node5": {"@otu": "otu2"}, "node50": {"@otu": "otu25"}, "node51": {}, "node52": {"@otu": "otu26"}, "node53": {}, "node54": {}, "node55": {"@otu": "otu27"}, "node56": {"@otu": "otu28"}, "node57": {}, "node58": {"@otu": "otu29"}, "node59": {}, "node6": {"@otu": "otu3"}, "node60": {}, "node61": {"@otu": "otu30"}, "node62": {"@otu": "otu31"}, "node63": {}, "node64": {"@otu": "otu32"}, "node65": {}, "node66": {"@otu": "otu33"}, "node67": {}, "node68": {"@otu": "otu34"}, "node69": {"@otu": "otu35"}, "node7": {}, "node8": {}, "node9": {}}}}}}}}, "branch2sha": {"master": "02befbde630ec4faf8171b08c2571e92a6b342e8"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "27bc520c17f52b15fec6bd0f0b402399bca828c7", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Tue, 23 Feb 2016 12:13:46 +0000", "date_ISO_8601": "2016-02-23 12:13:46 +0000", "relative_date": "10 years ago", "message_subject": "Cingulata tree", "message_body": "(Update document 'ot_642' via OpenTree API)"}, {"id": "1b4b850a52d4e6a96f9d32929470d0d37d663d7e", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Tue, 23 Feb 2016 12:09:32 +0000", "date_ISO_8601": "2016-02-23 12:09:32 +0000", "relative_date": "10 years ago", "message_subject": "init", "message_body": "(Update document 'ot_642' via OpenTree API)"}, {"id": "6d2689e853bb14d540f59ccaafa2fc600f5d5ded", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Tue, 23 Feb 2016 11:54:25 +0000", "date_ISO_8601": "2016-02-23 11:54:25 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_642' via OpenTree API"}]}