{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-07-28T21:33:32.653Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Arthropods"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-07-28T21:33:32.653Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "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"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree6749", "@treesID": "trees2921", "@treeID": "tree6749"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree6749"], "^ot:comment": "", "^ot:curatorName": ["Christine Ewers", "Joseph W. Brown", "Christine Ewers-Saucedo"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 2958818, "^ot:focalCladeOTTTaxonName": "Coronuloidea", "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus2921"], "^ot:studyId": "pg_2921", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2012.12.018"}, "^ot:studyPublicationReference": "Ryota Hayashi, Benny K.K. Chan, Noa Simon-Blecher, Hiromi Watanabe, Tamar Guy-Haim, Takahiro Yonezawa, Yaniv Levy, Takuho Shuto, Yair Achituv. 2013. Phylogenetic position and evolutionary history of the turtle and whale barnacles (Cirripedia: Balanomorpha: Coronuloidea). Molecular Phylogenetics and Evolution 67(1):9-14.", "^ot:studyYear": 2013, "^ot:tag": [], "^ot:treesElementOrder": ["trees2921"], "^xhtml:license": {"@href": "http://creativecommons.org/publicdomain/zero/1.0/", "@name": "CC0"}, "otusById": {"otus2921": {"otuById": {"otu432364": {"^ot:originalLabel": "Chthamalus stellatus", "^ot:ottId": 165470, "^ot:ottTaxonName": "Chthamalus stellatus"}, "otu432365": {"^ot:originalLabel": "Chamaesipho tasmanica", "^ot:ottId": 898714, "^ot:ottTaxonName": "Chamaesipho tasmanica"}, "otu432366": {"^ot:originalLabel": "Pachylasma japonicum", "^ot:ottId": 553792, "^ot:ottTaxonName": "Pachylasma japonicum"}, "otu432367": {"^ot:originalLabel": "Catomerus polymerus", "^ot:ottId": 1096023, "^ot:ottTaxonName": "Catomerus polymerus"}, "otu432368": {"^ot:originalLabel": "Tetraclita japonica", "^ot:ottId": 221273, "^ot:ottTaxonName": "Tetraclita japonica"}, "otu432369": {"^ot:originalLabel": "Tetraclitella purpurasens", "^ot:ottId": 324421, "^ot:ottTaxonName": "Tetraclitella purpurascens"}, "otu432370": {"^ot:originalLabel": "Austrobalanus imperator", "^ot:ottId": 1026336, "^ot:ottTaxonName": "Austrobalanus imperator"}, "otu432371": {"^ot:originalLabel": "Cylindrolepas sinica", "^ot:ottId": 499778, "^ot:ottTaxonName": "Cylindrolepas sinica"}, "otu432372": {"^ot:originalLabel": "Coronula diadema", "^ot:ottId": 499772, "^ot:ottTaxonName": "Coronula diadema"}, "otu432373": {"^ot:originalLabel": "Cryptolepas rhachianecti", "^ot:ottId": 499784, "^ot:ottTaxonName": "Cryptolepas rhachianecti"}, "otu432374": {"^ot:originalLabel": "Xenobalanus globicipites", "^ot:ottId": 499775, "^ot:ottTaxonName": "Xenobalanus globicipitis"}, "otu432375": {"^ot:originalLabel": "Cylindrolepas darwiniana", "^ot:ottId": 206723, "^ot:ottTaxonName": "Cylindrolepas darwiniana"}, "otu432376": {"^ot:originalLabel": "Platylepas hexastylos", "^ot:ottId": 206746, "^ot:ottTaxonName": "Platylepas hexastylos"}, "otu432377": {"^ot:originalLabel": "Tubicinella cheloniae", "^ot:ottId": 845546, "^ot:ottTaxonName": "Tubicinella cheloniae"}, "otu432378": {"^ot:originalLabel": "Platylepas decorata", "^ot:ottId": 874478, "^ot:ottTaxonName": "Platylepas decorata"}, "otu432379": {"^ot:originalLabel": "Stomatolepas transversa", "^ot:ottId": 874473, "^ot:ottTaxonName": "Stomatolepas transversa"}, "otu432380": {"^ot:originalLabel": "Stomatolepas praegustator", "^ot:ottId": 874467, "^ot:ottTaxonName": "Stomatolepas praegustator"}, "otu432381": {"^ot:originalLabel": "Stomatolepas elegans", "^ot:ottId": 2958413, "^ot:ottTaxonName": "Stomatolepas elegans"}, "otu432382": {"^ot:originalLabel": "Stephanolepas muricata", "^ot:ottId": 845540, "^ot:ottTaxonName": "Stephanolepas muricata"}, "otu432383": {"^ot:originalLabel": "Chelonibia caretta", "^ot:ottId": 968069, "^ot:ottTaxonName": "Chelonibia caretta"}, "otu432384": {"^ot:originalLabel": "Chelonibia manati", "^ot:ottId": 349828, "^ot:ottTaxonName": "Chelonibia manati"}, "otu432385": {"^ot:originalLabel": "Chelonibia patula", "^ot:ottId": 6741, "^ot:ottTaxonName": "Chelonibia patula"}, "otu432386": {"^ot:originalLabel": "Chelonibia testudinaria", "^ot:ottId": 968070, "^ot:ottTaxonName": "Chelonibia testudinaria"}, "otu432387": {"^ot:originalLabel": "Semibalanus cariosus", "^ot:ottId": 949511, "^ot:ottTaxonName": "Semibalanus cariosus"}, "otu432388": {"^ot:originalLabel": "Megabalanus tintinnbullum", "^ot:ottId": 203266, "^ot:ottTaxonName": "Megabalanus tintinnabulum"}, "otu432389": {"^ot:originalLabel": "Megabalanus occator", "^ot:ottId": 1023077, "^ot:ottTaxonName": "Megabalanus occator"}, "otu432390": {"^ot:originalLabel": "Austromegabalanus psittacus", "^ot:ottId": 324426, "^ot:ottTaxonName": "Austromegabalanus psittacus"}, "otu432391": {"^ot:originalLabel": "Verruca stroemia", "^ot:ottId": 259513, "^ot:ottTaxonName": "Verruca stroemia"}}}}, "treesById": {"trees2921": {"@otus": "otus2921", "^ot:treeElementOrder": ["tree6749"], "treeById": {"tree6749": {"@label": "Fig. 1a", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:substitutionCount", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Bayesian", "^ot:inGroupClade": "node1174441", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1174425", "^ot:specifiedRoot": "node1174425", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1174425": {"edge1174426": {"@length": 0.1800817316223667, "@source": "node1174425", "@target": "node1174426"}, "edge1174479": {"@length": 0.18008173162236665, "@source": "node1174425", "@target": "node1174479"}}, "node1174426": {"edge1174427": {"@length": 0.021091359367331808, "@source": "node1174426", "@target": "node1174427"}, "edge1174434": {"@length": 0.01564441832244301, "@source": "node1174426", "@target": "node1174434"}}, "node1174427": {"edge1174428": {"@length": 0.010263027095102628, "@source": "node1174427", "@target": "node1174428"}, "edge1174433": {"@length": 0.10013928635197583, "@source": "node1174427", "@target": "node1174433"}}, "node1174428": {"edge1174429": {"@length": 0.14562909760127324, "@source": "node1174428", "@target": "node1174429"}, "edge1174430": {"@length": 0.01225745163194597, "@source": "node1174428", "@target": "node1174430"}}, "node1174430": {"edge1174431": {"@length": 0.13302040343363197, "@source": "node1174430", "@target": "node1174431"}, "edge1174432": {"@length": 0.09311852138541943, "@source": "node1174430", "@target": "node1174432"}}, "node1174434": {"edge1174435": {"@length": 0.012244795658123975, "@source": "node1174434", "@target": "node1174435"}, "edge1174472": {"@length": 0.050067988747801384, "@source": "node1174434", "@target": "node1174472"}}, "node1174435": {"edge1174436": {"@length": 0.019955452133321727, "@source": "node1174435", "@target": "node1174436"}, "edge1174439": {"@length": 0.012401393715702536, "@source": "node1174435", "@target": "node1174439"}}, "node1174436": {"edge1174437": {"@length": 0.06271520804988273, "@source": "node1174436", "@target": "node1174437"}, "edge1174438": {"@length": 0.05047580532046936, "@source": "node1174436", "@target": "node1174438"}}, "node1174439": {"edge1174440": {"@length": 0.06447718537784053, "@source": "node1174439", "@target": "node1174440"}, "edge1174441": {"@length": 0.0365676180278367, "@source": "node1174439", "@target": "node1174441"}}, "node1174441": {"edge1174442": {"@length": 0.02900511536980116, "@source": "node1174441", "@target": "node1174442"}, "edge1174463": {"@length": 0.11228997637255256, "@source": "node1174441", "@target": "node1174463"}}, "node1174442": {"edge1174443": {"@length": 0.02524899742221337, "@source": "node1174442", "@target": "node1174443"}, "edge1174458": {"@length": 0.058750136076595905, "@source": "node1174442", "@target": "node1174458"}}, "node1174443": {"edge1174444": {"@length": 0.023953633621698833, "@source": "node1174443", "@target": "node1174444"}, "edge1174451": {"@length": 0.012507157699936572, "@source": "node1174443", "@target": "node1174451"}}, "node1174444": {"edge1174445": {"@length": 0.03288410017639398, "@source": "node1174444", "@target": "node1174445"}, "edge1174446": {"@length": 0.016085617109417194, "@source": "node1174444", "@target": "node1174446"}}, "node1174446": {"edge1174447": {"@length": 0.021665582355957558, "@source": "node1174446", "@target": "node1174447"}, "edge1174450": {"@length": 0.033113441686318856, "@source": "node1174446", "@target": "node1174450"}}, "node1174447": {"edge1174448": {"@length": 0.035554766574405594, "@source": "node1174447", "@target": "node1174448"}, "edge1174449": {"@length": 0.013645590195895119, "@source": "node1174447", "@target": "node1174449"}}, "node1174451": {"edge1174452": {"@length": 0.0436446558962891, "@source": "node1174451", "@target": "node1174452"}, "edge1174455": {"@length": 0.006598309073023251, "@source": "node1174451", "@target": "node1174455"}}, "node1174452": {"edge1174453": {"@length": 0.026079768048921592, "@source": "node1174452", "@target": "node1174453"}, "edge1174454": {"@length": 0.017940704011962683, "@source": "node1174452", "@target": "node1174454"}}, "node1174455": {"edge1174456": {"@length": 0.05790717958994002, "@source": "node1174455", "@target": "node1174456"}, "edge1174457": {"@length": 0.03098710299920615, "@source": "node1174455", "@target": "node1174457"}}, "node1174458": {"edge1174459": {"@length": 0.04863581319931792, "@source": "node1174458", "@target": "node1174459"}, "edge1174460": {"@length": 0.03532243946496233, "@source": "node1174458", "@target": "node1174460"}}, "node1174460": {"edge1174461": {"@length": 0.03785366507508636, "@source": "node1174460", "@target": "node1174461"}, "edge1174462": {"@length": 0.022100584095712472, "@source": "node1174460", "@target": "node1174462"}}, "node1174463": {"edge1174464": {"@length": 0.01978644706239352, "@source": "node1174463", "@target": "node1174464"}, "edge1174465": {"@length": 0.03655361112085492, "@source": "node1174463", "@target": "node1174465"}}, "node1174465": {"edge1174466": {"@length": 0.11280640899848204, "@source": "node1174465", "@target": "node1174466"}, "edge1174467": {"@length": 0.009303663554889485, "@source": "node1174465", "@target": "node1174467"}}, "node1174467": {"edge1174468": {"@length": 0.02468864537917398, "@source": "node1174467", "@target": "node1174468"}, "edge1174471": {"@length": 0.0015537041274981123, "@source": "node1174467", "@target": "node1174471"}}, "node1174468": {"edge1174469": {"@length": 0.016071228855344344, "@source": "node1174468", "@target": "node1174469"}, "edge1174470": {"@length": 0.002635596295655185, "@source": "node1174468", "@target": "node1174470"}}, "node1174472": {"edge1174473": {"@length": 0.09935658148268306, "@source": "node1174472", "@target": "node1174473"}, "edge1174474": {"@length": 0.06467160739148348, "@source": "node1174472", "@target": "node1174474"}}, "node1174474": {"edge1174475": {"@length": 0.0559044639374594, "@source": "node1174474", "@target": "node1174475"}, "edge1174478": {"@length": 0.020041738149430055, "@source": "node1174474", "@target": "node1174478"}}, "node1174475": {"edge1174476": {"@length": 0.017195417279992853, "@source": "node1174475", "@target": "node1174476"}, "edge1174477": {"@length": 0.035731566575957996, "@source": "node1174475", "@target": "node1174477"}}}, "nodeById": {"node1174425": {"@root": true}, "node1174426": {}, "node1174427": {}, "node1174428": {}, "node1174429": {"@otu": "otu432364"}, "node1174430": {}, "node1174431": {"@otu": "otu432365"}, "node1174432": {"@otu": "otu432366"}, "node1174433": {"@otu": "otu432367"}, "node1174434": {}, "node1174435": {}, "node1174436": {}, "node1174437": {"@otu": "otu432368"}, "node1174438": {"@otu": "otu432369"}, "node1174439": {}, "node1174440": {"@otu": "otu432370"}, "node1174441": {}, "node1174442": {}, "node1174443": {}, "node1174444": {}, "node1174445": {"@otu": "otu432371"}, "node1174446": {}, "node1174447": {}, "node1174448": {"@otu": "otu432372"}, "node1174449": {"@otu": "otu432373"}, "node1174450": {"@otu": "otu432374"}, "node1174451": {}, "node1174452": {}, "node1174453": {"@otu": "otu432375"}, "node1174454": {"@otu": "otu432376"}, "node1174455": {}, "node1174456": {"@otu": "otu432377"}, "node1174457": {"@otu": "otu432378"}, "node1174458": {}, "node1174459": {"@otu": "otu432379"}, "node1174460": {}, "node1174461": {"@otu": "otu432380"}, "node1174462": {"@otu": "otu432381"}, "node1174463": {}, "node1174464": {"@otu": "otu432382"}, "node1174465": {}, "node1174466": {"@otu": "otu432383"}, "node1174467": {}, "node1174468": {}, "node1174469": {"@otu": "otu432384"}, "node1174470": {"@otu": "otu432385"}, "node1174471": {"@otu": "otu432386"}, "node1174472": {}, "node1174473": {"@otu": "otu432387"}, "node1174474": {}, "node1174475": {}, "node1174476": {"@otu": "otu432388"}, "node1174477": {"@otu": "otu432389"}, "node1174478": {"@otu": "otu432390"}, "node1174479": {"@otu": "otu432391"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "54fe8011ed28fa607d418b275d17bd8f5d921e91", "author_name": "Christine Ewers-Saucedo", "author_email": "ANONYMOUS", "date": "Sat, 26 Mar 2016 15:11:06 +0000", "date_ISO_8601": "2016-03-26 15:11:06 +0000", "relative_date": "10 years ago", "message_subject": "Approved study", "message_body": "(Update document 'pg_2921' via OpenTree API)"}, {"id": "ce1a9f1424a3da9bdf0c89475d592ef3cd1a6f6e", "author_name": "Christine Ewers-Saucedo", "author_email": "ANONYMOUS", "date": "Sat, 26 Mar 2016 15:10:17 +0000", "date_ISO_8601": "2016-03-26 15:10:17 +0000", "relative_date": "10 years ago", "message_subject": "Approved study", "message_body": "(Update document 'pg_2921' via OpenTree API)"}, {"id": "b7d067cb291b81190ada417cb662ec3e675f5600", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Mon, 28 Jul 2014 21:35:27 +0000", "date_ISO_8601": "2014-07-28 21:35:27 +0000", "relative_date": "12 years ago", "message_subject": "update mrca", "message_body": "(Update Study #pg_2921 via OpenTree API)"}, {"id": "d7f3f00345c7c0e8f9b6d22c7c75f039bd8e21d5", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Mon, 28 Jul 2014 21:35:06 +0000", "date_ISO_8601": "2014-07-28 21:35:06 +0000", "relative_date": "12 years ago", "message_subject": "tree name, confirm rooting", "message_body": "(Update Study #pg_2921 via OpenTree API)"}, {"id": "fb9410bc19523ea9ec208a35959e8a4cab0030d5", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Thu, 29 May 2014 11:33:49 -0500", "date_ISO_8601": "2014-05-29 11:33:49 -0500", "relative_date": "12 years ago", "message_subject": "otu labels to the new system.", "message_body": "Ran peyotl/dev/phylografter_workaround.py to\nfix this.\nNoted (in phylografter issue 119), that study\n2918 is not valid."}, {"id": "7a347d6429bf00b437f010b84909c39d0332caa4", "author_name": "Mark T. Holder", "author_email": "None", "date": "Thu, 29 May 2014 15:31:00 +0000", "date_ISO_8601": "2014-05-29 15:31:00 +0000", "relative_date": "12 years ago", "message_subject": "Update Study #pg_2921 via OpenTree API"}]}