{"sha": "c33806c9ee11db205ee8c02a42e31b1c3128e299", "data": {"nexml": {"@generator": "Phylografter nexml-json exporter", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-06-27T14:53:20.563Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Animals"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-06-27T14:53:20.563Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "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"}]}]}, "^ot:candidateTreeForSynthesis": ["tree6550"], "^ot:comment": "", "^ot:curatorName": ["Joseph Brown", "Joseph W. Brown"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 816442, "^ot:focalCladeOTTTaxonName": "Panarthropoda", "^ot:messages": {"message": []}, "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus2813"], "^ot:studyId": "pg_2813", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1098/rspb.2010.0590"}, "^ot:studyPublicationReference": "Rota-Stabelli, O., L. Campbell, H. Brinkmann, G. D. Edgecombe, S. J. Longhorn, K. J. Peterson, D. Pisani, H. Philippe, M. J. Telford. 2011. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proceedings of the Royal Society B: Biological Sciences 278 (1703): 298-306.", "^ot:studyYear": 2011, "^ot:tag": [], "^ot:treesElementOrder": ["trees2813"], "otusById": {"otus2813": {"otuById": {"otu417714": {"^ot:originalLabel": "Tribolium castaneum", "^ot:ottId": 148904, "^ot:ottTaxonName": "Tribolium castaneum"}, "otu417715": {"^ot:originalLabel": "Nasonia vitripennis", "^ot:ottId": 729593, "^ot:ottTaxonName": "Nasonia vitripennis"}, "otu417716": {"^ot:originalLabel": "Gryllus bimaculatus", "^ot:ottId": 1077624, "^ot:ottTaxonName": "Gryllus bimaculatus"}, "otu417717": {"^ot:originalLabel": "Onychiurus arcticus", "^ot:ottId": 799602, "^ot:ottTaxonName": "Megaphorura arctica"}, "otu417718": {"^ot:originalLabel": "Folsomia candida", "^ot:ottId": 861693, "^ot:ottTaxonName": "Folsomia candida"}, "otu417719": {"^ot:originalLabel": "Daphnia pulex", "^ot:ottId": 59086, "^ot:ottTaxonName": "Daphnia pulex"}, "otu417720": {"^ot:originalLabel": "Artemia franciscana", "^ot:ottId": 59094, "^ot:ottTaxonName": "Artemia franciscana"}, "otu417721": {"^ot:originalLabel": "Petrolisthes cinctipes", "^ot:ottId": 892510, "^ot:ottTaxonName": "Petrolisthes cinctipes"}, "otu417722": {"^ot:originalLabel": "Litopenaeus vannamei", "^ot:ottId": 169168, "^ot:ottTaxonName": "Litopenaeus vannamei"}, "otu417723": {"^ot:originalLabel": "Strigamia maritima", "^ot:ottId": 274999, "^ot:ottTaxonName": "Strigamia maritima"}, "otu417724": {"^ot:originalLabel": "Scutigera coleoptrata", "^ot:ottId": 431229, "^ot:ottTaxonName": "Scutigera coleoptrata"}, "otu417725": {"^ot:originalLabel": "Ixodes scapularis", "^ot:ottId": 621065, "^ot:ottTaxonName": "Ixodes scapularis"}, "otu417726": {"^ot:originalLabel": "Boophilus microplus", "^ot:ottId": 621053, "^ot:ottTaxonName": "Rhipicephalus microplus"}, "otu417727": {"^ot:originalLabel": "Acanthoscurria gomesiana", "^ot:ottId": 26968, "^ot:ottTaxonName": "Acanthoscurria gomesiana"}, "otu417728": {"^ot:originalLabel": "Anoplodactylus eroticus", "^ot:ottId": 1046338, "^ot:ottTaxonName": "Anoplodactylus eroticus"}, "otu417729": {"^ot:originalLabel": "Richtersius coronifer", "^ot:ottId": 176559, "^ot:ottTaxonName": "Richtersius coronifer"}, "otu417730": {"^ot:originalLabel": "Hypsibius dujardini", "^ot:ottId": 977540, "^ot:ottTaxonName": "Hypsibius dujardini"}, "otu417731": {"^ot:originalLabel": "Euperipatoides kanangrensis", "^ot:ottId": 1046340, "^ot:ottTaxonName": "Euperipatoides kanangrensis"}, "otu417732": {"^ot:originalLabel": "Pristionchus pacificus", "^ot:ottId": 197875, "^ot:ottTaxonName": "Pristionchus pacificus"}, "otu417733": {"^ot:originalLabel": "Caenorhabditis elegans", "^ot:ottId": 395048, "^ot:ottTaxonName": "Caenorhabditis elegans"}, "otu417734": {"^ot:originalLabel": "Brugia malayi", "^ot:ottId": 295367, "^ot:ottTaxonName": "Brugia malayi"}, "otu417735": {"^ot:originalLabel": "Ascaris suum", "^ot:ottId": 345758, "^ot:ottTaxonName": "Ascaris suum"}, "otu417736": {"^ot:originalLabel": "Xiphinema index", "^ot:ottId": 165364, "^ot:ottTaxonName": "Xiphinema index"}, "otu417737": {"^ot:originalLabel": "Trichinella spiralis", "^ot:ottId": 567340, "^ot:ottTaxonName": "Trichinella spiralis"}, "otu417738": {"^ot:originalLabel": "Priapulus caudatus", "^ot:ottId": 1033111, "^ot:ottTaxonName": "Priapulus caudatus"}, "otu417739": {"^ot:originalLabel": "Echinoderes horni", "^ot:ottId": 1046342, "^ot:ottTaxonName": "Echinoderes horni"}, "otu417740": {"^ot:originalLabel": "Helobdella robusta", "^ot:ottId": 870792, "^ot:ottTaxonName": "Helobdella robusta"}, "otu417741": {"^ot:originalLabel": "Capitella sp.", "^ot:ottId": 966426, "^ot:ottTaxonName": "Capitella"}, "otu417742": {"^ot:originalLabel": "Crassostrea gigas", "^ot:ottId": 987409, "^ot:ottTaxonName": "Crassostrea gigas"}, "otu417743": {"^ot:originalLabel": "Aplysia californica", "^ot:ottId": 51009, "^ot:ottTaxonName": "Aplysia californica"}}}}, "treesById": {"trees2813": {"@otus": "otus2813", "^ot:treeElementOrder": ["tree6550"], "treeById": {"tree6550": {"@label": "Fig. 1 Bayesian CAT + Gamma", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:substitutionCount", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node1136811", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1136808", "^ot:specifiedRoot": "node1136808", "^ot:tag": ["ingroup added;"], "^ot:unrootedTree": false, "edgeBySourceId": {"node1136808": {"edge1136809": {"@length": 0.0341085, "@source": "node1136808", "@target": "node1136809"}, "edge1136860": {"@length": 0.06821699999999997, "@source": "node1136808", "@target": "node1136860"}}, "node1136809": {"edge1136810": {"@length": 0.025311000000000083, "@source": "node1136809", "@target": "node1136810"}, "edge1136857": {"@length": 0.026451000000000002, "@source": "node1136809", "@target": "node1136857"}}, "node1136810": {"edge1136811": {"@length": 0.022204, "@source": "node1136810", "@target": "node1136811"}, "edge1136846": {"@length": 0.3578300000000001, "@source": "node1136810", "@target": "node1136846"}}, "node1136811": {"edge1136812": {"@length": 0.030424000000000007, "@source": "node1136811", "@target": "node1136812"}, "edge1136841": {"@length": 0.019214999999999982, "@source": "node1136811", "@target": "node1136841"}}, "node1136812": {"edge1136813": {"@length": 0.011638999999999955, "@source": "node1136812", "@target": "node1136813"}, "edge1136834": {"@length": 0.01843600000000012, "@source": "node1136812", "@target": "node1136834"}}, "node1136813": {"edge1136814": {"@length": 0.05529600000000001, "@source": "node1136813", "@target": "node1136814"}, "edge1136831": {"@length": 0.062251999999999974, "@source": "node1136813", "@target": "node1136831"}}, "node1136814": {"edge1136815": {"@length": 0.022737999999999925, "@source": "node1136814", "@target": "node1136815"}, "edge1136828": {"@length": 0.2954220000000001, "@source": "node1136814", "@target": "node1136828"}}, "node1136815": {"edge1136816": {"@length": 0.025713000000000097, "@source": "node1136815", "@target": "node1136816"}, "edge1136825": {"@length": 0.09013899999999997, "@source": "node1136815", "@target": "node1136825"}}, "node1136816": {"edge1136817": {"@length": 0.06700499999999998, "@source": "node1136816", "@target": "node1136817"}, "edge1136822": {"@length": 0.19293300000000002, "@source": "node1136816", "@target": "node1136822"}}, "node1136817": {"edge1136818": {"@length": 0.02845399999999998, "@source": "node1136817", "@target": "node1136818"}, "edge1136821": {"@length": 0.12923099999999998, "@source": "node1136817", "@target": "node1136821"}}, "node1136818": {"edge1136819": {"@length": 0.14258499999999996, "@source": "node1136818", "@target": "node1136819"}, "edge1136820": {"@length": 0.176184, "@source": "node1136818", "@target": "node1136820"}}, "node1136822": {"edge1136823": {"@length": 0.16999699999999995, "@source": "node1136822", "@target": "node1136823"}, "edge1136824": {"@length": 0.12969699999999995, "@source": "node1136822", "@target": "node1136824"}}, "node1136825": {"edge1136826": {"@length": 0.17570200000000014, "@source": "node1136825", "@target": "node1136826"}, "edge1136827": {"@length": 0.30329000000000006, "@source": "node1136825", "@target": "node1136827"}}, "node1136828": {"edge1136829": {"@length": 0.12657499999999988, "@source": "node1136828", "@target": "node1136829"}, "edge1136830": {"@length": 0.09889099999999995, "@source": "node1136828", "@target": "node1136830"}}, "node1136831": {"edge1136832": {"@length": 0.188396, "@source": "node1136831", "@target": "node1136832"}, "edge1136833": {"@length": 0.09141600000000016, "@source": "node1136831", "@target": "node1136833"}}, "node1136834": {"edge1136835": {"@length": 0.06436599999999992, "@source": "node1136834", "@target": "node1136835"}, "edge1136840": {"@length": 0.27619700000000014, "@source": "node1136834", "@target": "node1136840"}}, "node1136835": {"edge1136836": {"@length": 0.1449800000000001, "@source": "node1136835", "@target": "node1136836"}, "edge1136839": {"@length": 0.20048599999999994, "@source": "node1136835", "@target": "node1136839"}}, "node1136836": {"edge1136837": {"@length": 0.06089699999999998, "@source": "node1136836", "@target": "node1136837"}, "edge1136838": {"@length": 0.07095499999999988, "@source": "node1136836", "@target": "node1136838"}}, "node1136841": {"edge1136842": {"@length": 0.595845, "@source": "node1136841", "@target": "node1136842"}, "edge1136845": {"@length": 0.19827700000000004, "@source": "node1136841", "@target": "node1136845"}}, "node1136842": {"edge1136843": {"@length": 0.132548, "@source": "node1136842", "@target": "node1136843"}, "edge1136844": {"@length": 0.10800200000000004, "@source": "node1136842", "@target": "node1136844"}}, "node1136846": {"edge1136847": {"@length": 0.440635, "@source": "node1136846", "@target": "node1136847"}, "edge1136854": {"@length": 0.06349399999999994, "@source": "node1136846", "@target": "node1136854"}}, "node1136847": {"edge1136848": {"@length": 0.1232129999999999, "@source": "node1136847", "@target": "node1136848"}, "edge1136851": {"@length": 0.05304900000000001, "@source": "node1136847", "@target": "node1136851"}}, "node1136848": {"edge1136849": {"@length": 0.19419500000000012, "@source": "node1136848", "@target": "node1136849"}, "edge1136850": {"@length": 0.25320999999999994, "@source": "node1136848", "@target": "node1136850"}}, "node1136851": {"edge1136852": {"@length": 0.2166490000000001, "@source": "node1136851", "@target": "node1136852"}, "edge1136853": {"@length": 0.08931800000000001, "@source": "node1136851", "@target": "node1136853"}}, "node1136854": {"edge1136855": {"@length": 0.27584699999999995, "@source": "node1136854", "@target": "node1136855"}, "edge1136856": {"@length": 0.6692449999999999, "@source": "node1136854", "@target": "node1136856"}}, "node1136857": {"edge1136858": {"@length": 0.317828, "@source": "node1136857", "@target": "node1136858"}, "edge1136859": {"@length": 0.37067800000000006, "@source": "node1136857", "@target": "node1136859"}}, "node1136860": {"edge1136861": {"@length": 0.06605100000000008, "@source": "node1136860", "@target": "node1136861"}, "edge1136864": {"@length": 0.06750499999999993, "@source": "node1136860", "@target": "node1136864"}}, "node1136861": {"edge1136862": {"@length": 0.30728999999999995, "@source": "node1136861", "@target": "node1136862"}, "edge1136863": {"@length": 0.2519039999999999, "@source": "node1136861", "@target": "node1136863"}}, "node1136864": {"edge1136865": {"@length": 0.2513170000000001, "@source": "node1136864", "@target": "node1136865"}, "edge1136866": {"@length": 0.2528950000000001, "@source": "node1136864", "@target": "node1136866"}}}, "nodeById": {"node1136808": {"@root": true}, "node1136809": {}, "node1136810": {}, "node1136811": {}, "node1136812": {}, "node1136813": {}, "node1136814": {}, "node1136815": {}, "node1136816": {}, "node1136817": {}, "node1136818": {}, "node1136819": {"@otu": "otu417714"}, "node1136820": {"@otu": "otu417715"}, "node1136821": {"@otu": "otu417716"}, "node1136822": {}, "node1136823": {"@otu": "otu417717"}, "node1136824": {"@otu": "otu417718"}, "node1136825": {}, "node1136826": {"@otu": "otu417719"}, "node1136827": {"@otu": "otu417720"}, "node1136828": {}, "node1136829": {"@otu": "otu417721"}, "node1136830": {"@otu": "otu417722"}, "node1136831": {}, "node1136832": {"@otu": "otu417723"}, "node1136833": {"@otu": "otu417724"}, "node1136834": {}, "node1136835": {}, "node1136836": {}, "node1136837": {"@otu": "otu417725"}, "node1136838": {"@otu": "otu417726"}, "node1136839": {"@otu": "otu417727"}, "node1136840": {"@otu": "otu417728"}, "node1136841": {}, "node1136842": {}, "node1136843": {"@otu": "otu417729"}, "node1136844": {"@otu": "otu417730"}, "node1136845": {"@otu": "otu417731"}, "node1136846": {}, "node1136847": {}, "node1136848": {}, "node1136849": {"@otu": "otu417732"}, "node1136850": {"@otu": "otu417733"}, "node1136851": {}, "node1136852": {"@otu": "otu417734"}, "node1136853": {"@otu": "otu417735"}, "node1136854": {}, "node1136855": {"@otu": "otu417736"}, "node1136856": {"@otu": "otu417737"}, "node1136857": {}, "node1136858": {"@otu": "otu417738"}, "node1136859": {"@otu": "otu417739"}, "node1136860": {}, "node1136861": {}, "node1136862": {"@otu": "otu417740"}, "node1136863": {"@otu": "otu417741"}, "node1136864": {}, "node1136865": {"@otu": "otu417742"}, "node1136866": {"@otu": "otu417743"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "9cf7569612a0120be828f115882f12bacfba912e", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Fri, 27 Jun 2014 15:55:05 +0100", "date_ISO_8601": "2014-06-27 15:55:05 +0100", "relative_date": "12 years ago", "message_subject": "fix", "message_body": "(Update Study #pg_2813 via OpenTree API)"}, {"id": "565d1accd737f44fe53bb4a11e77f6743fa716ce", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Fri, 27 Jun 2014 15:53:54 +0100", "date_ISO_8601": "2014-06-27 15:53:54 +0100", "relative_date": "12 years ago", "message_subject": "fix", "message_body": "(Update Study #pg_2813 via OpenTree API)"}, {"id": "d33fb39501605772a074dffc82affa5344ea9a94", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Wed, 11 Jun 2014 22:18:34 -0500", "date_ISO_8601": "2014-06-11 22:18:34 -0500", "relative_date": "12 years ago", "message_subject": "corrected study ids"}, {"id": "593d6fbab385716dc0a12f3fc95133e8b7479b37", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Tue, 29 Apr 2014 20:05:19 -0500", "date_ISO_8601": "2014-04-29 20:05:19 -0500", "relative_date": "12 years ago", "message_subject": "initial commit with phylografter files from 29 Apr, 2014"}]}