{"sha": "19ec8a2da4b35c55075f155f9fb4d01281774fe5", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2017-01-02T23:35:44.192Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Arthropods"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": true}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2017-01-02T23:35:44.192Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "Huys_etal_2009_Fig1.trees.nex", "@size": 943, "@type": "nexus", "@url": "/curator/download/supporting_files.doc.b95efd1333eda3f9.487579735f6574616c5f323030395f466967312e74726565732e6e6578.nex", "description": {"$": "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_1039", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2008.12.007"}, "^ot:studyPublicationReference": "Rony Huys, Jacqueline Mackenzie-Dodds, Julia Llewellyn-Hughes, 2009, 'Cancrincolidae (Copepoda, Harpacticoida) associated with land crabs: A semiterrestrial leaf of the ameirid tree', Molecular Phylogenetics and Evolution, vol. 51, no. 2, pp. 143-156", "^ot:studyYear": 2009, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Squilla empusa", "^ot:ottId": 552485, "^ot:ottTaxonName": "Squilla empusa"}, "otu10": {"^ot:originalLabel": "Diathrodes sp.", "^ot:ottId": 2951740, "^ot:ottTaxonName": "Diarthrodes"}, "otu11": {"^ot:originalLabel": "Itunella muelleri", "^ot:ottId": 879873, "^ot:ottTaxonName": "Itunella muelleri"}, "otu12": {"^ot:originalLabel": "Mesochra rapiens", "^ot:ottId": 1061763, "^ot:ottTaxonName": "Mesochra rapiens"}, "otu13": {"^ot:originalLabel": "Attheyella crassa", "^ot:ottId": 1011615, "^ot:ottTaxonName": "Attheyella crassa"}, "otu14": {"^ot:originalLabel": "Bryocamptus pygmaeus", "^ot:ottId": 296843, "^ot:ottTaxonName": "Bryocamptus pygmaeus"}, "otu15": {"^ot:originalLabel": "Eurycletodes laticauda", "^ot:ottId": 535409, "^ot:ottTaxonName": "Eurycletodes laticauda"}, "otu16": {"^ot:originalLabel": "Argestigens sp.", "^ot:ottId": 1011609, "^ot:ottTaxonName": "Argestigens"}, "otu17": {"^ot:originalLabel": "Sarsameira sp.", "^ot:ottId": 586976, "^ot:ottTaxonName": "Sarsameira"}, "otu18": {"^ot:originalLabel": "Ameira scotti", "^ot:ottId": 1011610, "^ot:ottTaxonName": "Ameira scotti"}, "otu19": {"^ot:originalLabel": "Nitocra hibernica", "^ot:ottId": 879887, "^ot:ottTaxonName": "Nitokra hibernica"}, "otu2": {"^ot:originalLabel": "Berndtia purpurea", "^ot:ottId": 6739, "^ot:ottTaxonName": "Berndtia purpurea"}, "otu20": {"^ot:originalLabel": "Cancrincola plumipes", "^ot:ottId": 977892, "^ot:ottTaxonName": "Cancrincola plumipes"}, "otu21": {"^ot:originalLabel": "Tegastes sp.", "^ot:ottId": 14262, "^ot:ottTaxonName": "Tegastes"}, "otu22": {"^ot:originalLabel": "Peltidium sp.", "^ot:ottId": 586972, "^ot:ottTaxonName": "Peltidium (genus in Opisthokonta)"}, "otu23": {"^ot:originalLabel": "Alteuthellopsis sp.", "^ot:ottId": 485316, "^ot:ottTaxonName": "Alteuthellopsis"}, "otu24": {"^ot:originalLabel": "Stenhelia sp.", "^ot:ottId": 586970, "^ot:ottTaxonName": "Stenhelia"}, "otu25": {"^ot:originalLabel": "Diosaccus sp.", "^ot:ottId": 2950859, "^ot:ottTaxonName": "Diosaccus"}, "otu26": {"^ot:originalLabel": "Miracia efferata", "^ot:ottId": 429741, "^ot:ottTaxonName": "Miracia efferata"}, "otu27": {"^ot:originalLabel": "Typhlamphiascus typhlops", "^ot:ottId": 14257, "^ot:ottTaxonName": "Typhlamphiascus typhlops"}, "otu28": {"^ot:originalLabel": "Paramphiascella fluvofasciata", "^ot:ottId": 879905, "^ot:ottTaxonName": "Paramphiascella fulvofasciata"}, "otu29": {"^ot:originalLabel": "Paramenophia sp.", "^ot:ottId": 879883, "^ot:ottTaxonName": "Paramenophia"}, "otu3": {"^ot:originalLabel": "Pseudocyclops sp.", "^ot:ottId": 1023223, "^ot:ottTaxonName": "Pseudocyclops"}, "otu30": {"^ot:originalLabel": "Eudactylopus sp.", "^ot:ottId": 535406, "^ot:ottTaxonName": "Eudactylopus"}, "otu31": {"^ot:originalLabel": "Parastenhelia sp.", "^ot:ottId": 1061770, "^ot:ottTaxonName": "Parastenhelia"}, "otu4": {"^ot:originalLabel": "Exumella mediterranea", "^ot:ottId": 99192, "^ot:ottTaxonName": "Exumella mediterranea"}, "otu5": {"^ot:originalLabel": "Phyllothalestris sp.", "^ot:ottId": 586974, "^ot:ottTaxonName": "Phyllothalestris"}, "otu6": {"^ot:originalLabel": "Zaus caeruleus", "^ot:ottId": 2951569, "^ot:ottTaxonName": "Zaus caeruleus"}, "otu7": {"^ot:originalLabel": "Harpacticus sp.", "^ot:ottId": 1031465, "^ot:ottTaxonName": "Harpacticus"}, "otu8": {"^ot:originalLabel": "Dactylopusia sp.", "^ot:ottId": 2951756, "^ot:ottTaxonName": "Dactylopusia"}, "otu9": {"^ot:originalLabel": "Sewellia tropica", "^ot:ottId": 586969, "^ot:ottTaxonName": "Sewellia tropica"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 1", "@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"}, "edge58": {"@source": "node1", "@target": "node59"}}, "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"}, "edge55": {"@source": "node2", "@target": "node56"}}, "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"}, "edge27": {"@source": "node26", "@target": "node28"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge29": {"@source": "node28", "@target": "node30"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge50": {"@source": "node3", "@target": "node51"}}, "node30": {"edge30": {"@source": "node30", "@target": "node31"}, "edge31": {"@source": "node30", "@target": "node32"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge33": {"@source": "node32", "@target": "node34"}}, "node34": {"edge34": {"@source": "node34", "@target": "node35"}, "edge35": {"@source": "node34", "@target": "node36"}}, "node37": {"edge37": {"@source": "node37", "@target": "node38"}, "edge38": {"@source": "node37", "@target": "node39"}}, "node39": {"edge39": {"@source": "node39", "@target": "node40"}, "edge40": {"@source": "node39", "@target": "node41"}}, "node4": {"edge4": {"@source": "node4", "@target": "node5"}, "edge41": {"@source": "node4", "@target": "node42"}}, "node42": {"edge42": {"@source": "node42", "@target": "node43"}, "edge47": {"@source": "node42", "@target": "node48"}}, "node43": {"edge43": {"@source": "node43", "@target": "node44"}, "edge46": {"@source": "node43", "@target": "node47"}}, "node44": {"edge44": {"@source": "node44", "@target": "node45"}, "edge45": {"@source": "node44", "@target": "node46"}}, "node48": {"edge48": {"@source": "node48", "@target": "node49"}, "edge49": {"@source": "node48", "@target": "node50"}}, "node5": {"edge36": {"@source": "node5", "@target": "node37"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node51": {"edge51": {"@source": "node51", "@target": "node52"}, "edge52": {"@source": "node51", "@target": "node53"}}, "node53": {"edge53": {"@source": "node53", "@target": "node54"}, "edge54": {"@source": "node53", "@target": "node55"}}, "node56": {"edge56": {"@source": "node56", "@target": "node57"}, "edge57": {"@source": "node56", "@target": "node58"}}, "node59": {"edge59": {"@source": "node59", "@target": "node60"}, "edge60": {"@source": "node59", "@target": "node61"}}, "node6": {"edge25": {"@source": "node6", "@target": "node26"}, "edge6": {"@source": "node6", "@target": "node7"}}, "node7": {"edge12": {"@source": "node7", "@target": "node13"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node8": {"edge8": {"@source": "node8", "@target": "node9"}, "edge9": {"@source": "node8", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {"@otu": "otu6"}, "node12": {"@otu": "otu7"}, "node13": {}, "node14": {}, "node15": {"@otu": "otu8"}, "node16": {}, "node17": {"@otu": "otu10"}, "node18": {"@otu": "otu9"}, "node19": {}, "node2": {}, "node20": {"@otu": "otu11"}, "node21": {}, "node22": {"@otu": "otu12"}, "node23": {}, "node24": {"@otu": "otu13"}, "node25": {"@otu": "otu14"}, "node26": {}, "node27": {"@otu": "otu15"}, "node28": {}, "node29": {"@otu": "otu16"}, "node3": {}, "node30": {}, "node31": {"@otu": "otu17"}, "node32": {}, "node33": {"@otu": "otu18"}, "node34": {}, "node35": {"@otu": "otu19"}, "node36": {"@otu": "otu20"}, "node37": {}, "node38": {"@otu": "otu21"}, "node39": {}, "node4": {}, "node40": {"@otu": "otu22"}, "node41": {"@otu": "otu23"}, "node42": {}, "node43": {}, "node44": {}, "node45": {"@otu": "otu25"}, "node46": {"@otu": "otu26"}, "node47": {"@otu": "otu24"}, "node48": {}, "node49": {"@otu": "otu27"}, "node5": {}, "node50": {"@otu": "otu28"}, "node51": {}, "node52": {"@otu": "otu29"}, "node53": {}, "node54": {"@otu": "otu30"}, "node55": {"@otu": "otu31"}, "node56": {}, "node57": {"@otu": "otu4"}, "node58": {"@otu": "otu3"}, "node59": {}, "node6": {}, "node60": {"@otu": "otu1"}, "node61": {"@otu": "otu2"}, "node7": {}, "node8": {}, "node9": {"@otu": "otu5"}}}}}}}}, "branch2sha": {"master": "19ec8a2da4b35c55075f155f9fb4d01281774fe5"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "c36be0bc17f1177f5762e3859f790e2c5c890f72", "author_name": "jbernot", "author_email": "ANONYMOUS", "date": "Mon, 2 Jan 2017 23:48:05 +0000", "date_ISO_8601": "2017-01-02 23:48:05 +0000", "relative_date": "9 years ago", "message_subject": "mapped OTU, designated outgroups", "message_body": "(Update document 'ot_1039' via OpenTree API)"}, {"id": "e69355d2c0047992fc21f0c2b4870507ffd53a41", "author_name": "jbernot", "author_email": "ANONYMOUS", "date": "Mon, 2 Jan 2017 23:42:20 +0000", "date_ISO_8601": "2017-01-02 23:42:20 +0000", "relative_date": "9 years ago", "message_subject": "mapped OTUs", "message_body": "(Update document 'ot_1039' via OpenTree API)"}, {"id": "1faea8f8c672c42d1d10cc4c928cdc2b97be5695", "author_name": "jbernot", "author_email": "ANONYMOUS", "date": "Mon, 2 Jan 2017 23:35:41 +0000", "date_ISO_8601": "2017-01-02 23:35:41 +0000", "relative_date": "9 years ago", "message_subject": "Update document 'ot_1039' via OpenTree API"}]}