{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2017-02-25T18:44:45.077Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Arthropods"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": true}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2017-02-25T18:44:45.077Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "Tung_etal_2014_fig5.trees.nex", "@size": 1450, "@type": "nexus", "@url": "/curator/download/supporting_files.doc.817045650f9b0c00.54756e675f6574616c5f323031345f666967352e74726565732e6e6578.nex", "description": {"$": "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": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@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": "", "^ot:curatorName": ["jbernot"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalCladeOTTTaxonName": "", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_1048", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1086/bblv226n1p69"}, "^ot:studyPublicationReference": "Che-Huang Tung, Yu-Rong Cheng, Ching-Yi Lin, Ju-Shey Ho, Chih-Horng Kuo, Jr-Kai Yu, Yi-Hsien Su, 2014, 'A New Copepod With Transformed Body Plan and Unique Phylogenetic Position Parasitic in the Acorn Worm Ptychodera flava', The Biological Bulletin, vol. 226, no. 1, pp. 69-80", "^ot:studyYear": 2014, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Squilla empusa", "^ot:ottId": 552485, "^ot:ottTaxonName": "Squilla empusa"}, "otu10": {"^ot:originalLabel": "Irodes sauridi", "^ot:ottId": 92633, "^ot:ottTaxonName": "Irodes sauridi"}, "otu11": {"^ot:originalLabel": "Homobomolochus ", "^ot:ottId": 924251, "^ot:ottTaxonName": "Holobomolochus"}, "otu12": {"^ot:originalLabel": "Umazuracola elongatus", "^ot:ottId": 834287, "^ot:ottTaxonName": "Umazuracola elongatus"}, "otu13": {"^ot:originalLabel": "Taeniacanthus zeugopteri", "^ot:ottId": 877908, "^ot:ottTaxonName": "Taeniacanthus zeugopteri"}, "otu14": {"^ot:originalLabel": "Taeniacanthus kitamakura", "^ot:ottId": 877981, "^ot:ottTaxonName": "Taeniacanthus kitamakura"}, "otu15": {"^ot:originalLabel": "Clavisodalis abbreviatus", "^ot:ottId": 992890, "^ot:ottTaxonName": "Clavisodalis abbreviatus"}, "otu16": {"^ot:originalLabel": "Bradya", "^ot:ottId": 296854, "^ot:ottTaxonName": "Bradya"}, "otu17": {"^ot:originalLabel": "Dactylopusia", "^ot:ottId": 2951756, "^ot:ottTaxonName": "Dactylopusia"}, "otu18": {"^ot:originalLabel": "Bryocamptus pygmaeus", "^ot:ottId": 296843, "^ot:ottTaxonName": "Bryocamptus pygmaeus"}, "otu19": {"^ot:originalLabel": "Paramphiascella fulvofasciata", "^ot:ottId": 879905, "^ot:ottTaxonName": "Paramphiascella fulvofasciata"}, "otu2": {"^ot:originalLabel": "Berndtia purpurea", "^ot:ottId": 6739, "^ot:ottTaxonName": "Berndtia purpurea"}, "otu20": {"^ot:originalLabel": "Misophriopsis okinawensis", "^ot:ottId": 92620, "^ot:ottTaxonName": "Misophriopsis okinawensis"}, "otu21": {"^ot:originalLabel": "Misophria", "^ot:ottId": 46461, "^ot:ottTaxonName": "Misophria"}, "otu22": {"^ot:originalLabel": "Misophriopsis", "^ot:ottId": 46459, "^ot:ottTaxonName": "Misophriopsis"}, "otu23": {"^ot:originalLabel": "Ecbathyrion prolixicauda", "^ot:ottId": 246561, "^ot:ottTaxonName": "Ecbathyrion prolixicauda"}, "otu24": {"^ot:originalLabel": "Parabrachiella bispinosa", "^ot:ottId": 821336, "^ot:ottTaxonName": "Parabrachiella bispinosa"}, "otu25": {"^ot:originalLabel": "Gloiopotes watsoni", "^ot:ottId": 871952, "^ot:ottTaxonName": "Gloiopotes watsoni"}, "otu26": {"^ot:originalLabel": "Hatschekia pagrosomi", "^ot:ottId": 821341, "^ot:ottTaxonName": "Hatschekia pagrosomi"}, "otu27": {"^ot:originalLabel": "Notodelphys prasina", "^ot:ottId": 920581, "^ot:ottTaxonName": "Notodelphys prasina"}, "otu28": {"^ot:originalLabel": "Cyclopina gracilis", "^ot:ottId": 398353, "^ot:ottTaxonName": "Cyclopina gracilis"}, "otu29": {"^ot:originalLabel": "Oithona", "^ot:ottId": 840664, "^ot:ottTaxonName": "Oithona"}, "otu3": {"^ot:originalLabel": "Ulophysema oeresundense", "^ot:ottId": 579396, "^ot:ottTaxonName": "Ulophysema oeresundense"}, "otu30": {"^ot:originalLabel": "Euryte", "^ot:ottId": 1023222, "^ot:ottTaxonName": "Euryte"}, "otu31": {"^ot:originalLabel": "Apocyclops royi", "^ot:ottId": 396577, "^ot:ottTaxonName": "Apocyclops royi"}, "otu32": {"^ot:originalLabel": "Cyclops", "^ot:ottId": 850514, "^ot:ottTaxonName": "Cyclops"}, "otu33": {"^ot:originalLabel": "Acanthocyclops viridis", "^ot:ottId": 396575, "^ot:ottTaxonName": "Acanthocyclops viridis"}, "otu34": {"^ot:originalLabel": "Ive ptychoderae", "^ot:ottId": 5756396, "^ot:ottTaxonName": "Ive ptychoderae"}, "otu35": {"^ot:originalLabel": "Scambicornus", "^ot:ottId": 922502, "^ot:ottTaxonName": "Scambicornus"}, "otu36": {"^ot:originalLabel": "Mecomerinx heterocentroti", "^ot:ottId": 92628, "^ot:ottTaxonName": "Mecomerinx heterocentroti"}, "otu37": {"^ot:originalLabel": "Pseudanthessius", "^ot:ottId": 347470, "^ot:ottTaxonName": "Pseudanthessius"}, "otu38": {"^ot:originalLabel": "Lernentoma asellina", "^ot:ottId": 972838, "^ot:ottTaxonName": "Lernentoma asellina"}, "otu39": {"^ot:originalLabel": "Chondracanthus lophii", "^ot:ottId": 102494, "^ot:ottTaxonName": "Chondracanthus lophii"}, "otu4": {"^ot:originalLabel": "Pseudocyclops", "^ot:ottId": 1023223, "^ot:ottTaxonName": "Pseudocyclops"}, "otu40": {"^ot:originalLabel": "Vahinius", "^ot:ottId": 922505, "^ot:ottTaxonName": "Vahinius"}, "otu41": {"^ot:originalLabel": "Lichomolgus canui", "^ot:ottId": 92623, "^ot:ottTaxonName": "Lichomolgus canui"}, "otu42": {"^ot:originalLabel": "Stellicola", "^ot:ottId": 972840, "^ot:ottTaxonName": "Stellicola"}, "otu43": {"^ot:originalLabel": "Astericola clausi", "^ot:ottId": 438159, "^ot:ottTaxonName": "Astericola clausii"}, "otu44": {"^ot:originalLabel": "Sabelliphilus elongatus", "^ot:ottId": 922504, "^ot:ottTaxonName": "Sabelliphilus elongatus"}, "otu45": {"^ot:originalLabel": "Xarifia", "^ot:ottId": 5517446, "^ot:ottTaxonName": "Xarifia"}, "otu46": {"^ot:originalLabel": "Anchimolgidae", "^ot:ottId": 396574, "^ot:ottTaxonName": "Anchimolgidae"}, "otu47": {"^ot:originalLabel": "Anchimolgus", "^ot:ottId": 396573, "^ot:ottTaxonName": "Anchimolgus"}, "otu48": {"^ot:originalLabel": "Critomolgus", "^ot:ottId": 347475, "^ot:ottTaxonName": "Critomolgus"}, "otu49": {"^ot:originalLabel": "Doridicola agilis", "^ot:ottId": 2946490, "^ot:ottTaxonName": "Doridicola agilis"}, "otu5": {"^ot:originalLabel": "Exumella mediterranea", "^ot:ottId": 99192, "^ot:ottTaxonName": "Exumella mediterranea"}, "otu6": {"^ot:originalLabel": "Hemicyclops thalassius", "^ot:ottId": 92630, "^ot:ottTaxonName": "Hemicyclops thalassius"}, "otu7": {"^ot:originalLabel": "Clausidium vancouverense", "^ot:ottId": 5520867, "^ot:ottTaxonName": "Clausidium vancouverense"}, "otu8": {"^ot:originalLabel": "Catinidae", "^ot:ottId": 924252, "^ot:ottTaxonName": "Catiniidae (family in subphylum Crustacea)"}, "otu9": {"^ot:originalLabel": "Catinia", "^ot:ottId": 992896, "^ot:ottTaxonName": "Catinia"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 5", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Bayesian inference ", "^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"}, "edge90": {"@source": "node1", "@target": "node91"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge11": {"@source": "node10", "@target": "node12"}}, "node13": {"edge13": {"@source": "node13", "@target": "node14"}, "edge18": {"@source": "node13", "@target": "node19"}}, "node14": {"edge14": {"@source": "node14", "@target": "node15"}, "edge15": {"@source": "node14", "@target": "node16"}}, "node16": {"edge16": {"@source": "node16", "@target": "node17"}, "edge17": {"@source": "node16", "@target": "node18"}}, "node19": {"edge19": {"@source": "node19", "@target": "node20"}, "edge20": {"@source": "node19", "@target": "node21"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge87": {"@source": "node2", "@target": "node88"}}, "node21": {"edge21": {"@source": "node21", "@target": "node22"}, "edge22": {"@source": "node21", "@target": "node23"}}, "node23": {"edge23": {"@source": "node23", "@target": "node24"}, "edge24": {"@source": "node23", "@target": "node25"}}, "node26": {"edge26": {"@source": "node26", "@target": "node27"}, "edge38": {"@source": "node26", "@target": "node39"}}, "node27": {"edge27": {"@source": "node27", "@target": "node28"}, "edge31": {"@source": "node27", "@target": "node32"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge29": {"@source": "node28", "@target": "node30"}, "edge30": {"@source": "node28", "@target": "node31"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge69": {"@source": "node3", "@target": "node70"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge33": {"@source": "node32", "@target": "node34"}}, "node34": {"edge34": {"@source": "node34", "@target": "node35"}, "edge35": {"@source": "node34", "@target": "node36"}}, "node36": {"edge36": {"@source": "node36", "@target": "node37"}, "edge37": {"@source": "node36", "@target": "node38"}}, "node39": {"edge39": {"@source": "node39", "@target": "node40"}, "edge40": {"@source": "node39", "@target": "node41"}}, "node4": {"edge25": {"@source": "node4", "@target": "node26"}, "edge4": {"@source": "node4", "@target": "node5"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge50": {"@source": "node41", "@target": "node51"}}, "node42": {"edge42": {"@source": "node42", "@target": "node43"}, "edge49": {"@source": "node42", "@target": "node50"}}, "node43": {"edge43": {"@source": "node43", "@target": "node44"}, "edge48": {"@source": "node43", "@target": "node49"}}, "node44": {"edge44": {"@source": "node44", "@target": "node45"}, "edge45": {"@source": "node44", "@target": "node46"}}, "node46": {"edge46": {"@source": "node46", "@target": "node47"}, "edge47": {"@source": "node46", "@target": "node48"}}, "node5": {"edge12": {"@source": "node5", "@target": "node13"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node51": {"edge51": {"@source": "node51", "@target": "node52"}, "edge58": {"@source": "node51", "@target": "node59"}}, "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"}, "edge60": {"@source": "node59", "@target": "node61"}}, "node6": {"edge6": {"@source": "node6", "@target": "node7"}, "edge7": {"@source": "node6", "@target": "node8"}}, "node61": {"edge61": {"@source": "node61", "@target": "node62"}, "edge66": {"@source": "node61", "@target": "node67"}}, "node62": {"edge62": {"@source": "node62", "@target": "node63"}, "edge65": {"@source": "node62", "@target": "node66"}}, "node63": {"edge63": {"@source": "node63", "@target": "node64"}, "edge64": {"@source": "node63", "@target": "node65"}}, "node67": {"edge67": {"@source": "node67", "@target": "node68"}, "edge68": {"@source": "node67", "@target": "node69"}}, "node70": {"edge70": {"@source": "node70", "@target": "node71"}, "edge77": {"@source": "node70", "@target": "node78"}}, "node71": {"edge71": {"@source": "node71", "@target": "node72"}, "edge74": {"@source": "node71", "@target": "node75"}}, "node72": {"edge72": {"@source": "node72", "@target": "node73"}, "edge73": {"@source": "node72", "@target": "node74"}}, "node75": {"edge75": {"@source": "node75", "@target": "node76"}, "edge76": {"@source": "node75", "@target": "node77"}}, "node78": {"edge78": {"@source": "node78", "@target": "node79"}, "edge79": {"@source": "node78", "@target": "node80"}}, "node8": {"edge8": {"@source": "node8", "@target": "node9"}, "edge9": {"@source": "node8", "@target": "node10"}}, "node80": {"edge80": {"@source": "node80", "@target": "node81"}, "edge81": {"@source": "node80", "@target": "node82"}}, "node82": {"edge82": {"@source": "node82", "@target": "node83"}, "edge83": {"@source": "node82", "@target": "node84"}, "edge86": {"@source": "node82", "@target": "node87"}}, "node84": {"edge84": {"@source": "node84", "@target": "node85"}, "edge85": {"@source": "node84", "@target": "node86"}}, "node88": {"edge88": {"@source": "node88", "@target": "node89"}, "edge89": {"@source": "node88", "@target": "node90"}}, "node91": {"edge91": {"@source": "node91", "@target": "node92"}, "edge92": {"@source": "node91", "@target": "node93"}}, "node93": {"edge93": {"@source": "node93", "@target": "node94"}, "edge94": {"@source": "node93", "@target": "node95"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {"@otu": "otu18"}, "node12": {"@otu": "otu19"}, "node13": {}, "node14": {}, "node15": {"@otu": "otu20"}, "node16": {}, "node17": {"@otu": "otu21"}, "node18": {"@otu": "otu22"}, "node19": {}, "node2": {}, "node20": {"@otu": "otu23"}, "node21": {}, "node22": {"@otu": "otu24"}, "node23": {}, "node24": {"@otu": "otu25"}, "node25": {"@otu": "otu26"}, "node26": {}, "node27": {}, "node28": {}, "node29": {"@otu": "otu27"}, "node3": {}, "node30": {"@otu": "otu28"}, "node31": {"@otu": "otu29"}, "node32": {}, "node33": {"@otu": "otu30"}, "node34": {}, "node35": {"@otu": "otu31"}, "node36": {}, "node37": {"@otu": "otu32"}, "node38": {"@otu": "otu33"}, "node39": {}, "node4": {}, "node40": {"@otu": "otu34"}, "node41": {}, "node42": {}, "node43": {}, "node44": {}, "node45": {"@otu": "otu37"}, "node46": {}, "node47": {"@otu": "otu38"}, "node48": {"@otu": "otu39"}, "node49": {"@otu": "otu36"}, "node5": {}, "node50": {"@otu": "otu35"}, "node51": {}, "node52": {}, "node53": {}, "node54": {}, "node55": {"@otu": "otu43"}, "node56": {"@otu": "otu42"}, "node57": {"@otu": "otu41"}, "node58": {"@otu": "otu40"}, "node59": {}, "node6": {}, "node60": {"@otu": "otu44"}, "node61": {}, "node62": {}, "node63": {}, "node64": {"@otu": "otu46"}, "node65": {"@otu": "otu47"}, "node66": {"@otu": "otu45"}, "node67": {}, "node68": {"@otu": "otu48"}, "node69": {"@otu": "otu49"}, "node7": {"@otu": "otu16"}, "node70": {}, "node71": {}, "node72": {}, "node73": {"@otu": "otu7"}, "node74": {"@otu": "otu6"}, "node75": {}, "node76": {"@otu": "otu8"}, "node77": {"@otu": "otu9"}, "node78": {}, "node79": {"@otu": "otu10"}, "node8": {}, "node80": {}, "node81": {"@otu": "otu11"}, "node82": {}, "node83": {"@otu": "otu13"}, "node84": {}, "node85": {"@otu": "otu14"}, "node86": {"@otu": "otu15"}, "node87": {"@otu": "otu12"}, "node88": {}, "node89": {"@otu": "otu4"}, "node9": {"@otu": "otu17"}, "node90": {"@otu": "otu5"}, "node91": {}, "node92": {"@otu": "otu1"}, "node93": {}, "node94": {"@otu": "otu2"}, "node95": {"@otu": "otu3"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "d3c78b97b16927cbeb7962334b976c8030b6ad8f", "author_name": "jbernot", "author_email": "ANONYMOUS", "date": "Sat, 25 Feb 2017 18:48:02 +0000", "date_ISO_8601": "2017-02-25 18:48:02 +0000", "relative_date": "9 years ago", "message_subject": "added tree data", "message_body": "(Update document 'ot_1048' via OpenTree API)"}, {"id": "3d79e30c3add785f039a82a082d720579dec3b6a", "author_name": "jbernot", "author_email": "ANONYMOUS", "date": "Sat, 25 Feb 2017 18:46:10 +0000", "date_ISO_8601": "2017-02-25 18:46:10 +0000", "relative_date": "9 years ago", "message_subject": "mapped OTUs", "message_body": "(Update document 'ot_1048' via OpenTree API)"}, {"id": "04ba6af671db79a480cbf56302bb27c7995c5949", "author_name": "jbernot", "author_email": "ANONYMOUS", "date": "Sat, 25 Feb 2017 00:28:25 +0000", "date_ISO_8601": "2017-02-25 00:28:25 +0000", "relative_date": "9 years ago", "message_subject": "Update document 'ot_1048' via OpenTree API"}]}