{"sha": "6bed60428352c04d00341ad513a8efb9442e4d8a", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-08-06T03:43:45.937Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-08-06T03:43:45.936Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "<content provided as a string in a \"content\" rather than a file upload>", "@size": "", "@type": "newick", "@url": "", "description": {"$": ""}, "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": ["otu20", "otu7"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthMode"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:messages", "^ot:nearestTaxonMRCAName", "^ot:nearestTaxonMRCAOttId"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu20", "otu7"], "@otusID": "otus1", "@otuID": ["otu20", "otu7"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1"], "^ot:comment": "Aethia psittacula not mapped. Proposed synonym Cyclorrhynchus psittacula is not generally accepted (http://avibase.bsc-eoc.org/species.jsp?lang=EN&avibaseid=2B46719DC058D033). Pinguinus impennis in taxonomy as Laridae instead of Alcidae (unmapped here).", "^ot:curatorName": ["Joseph W. Brown"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 855478, "^ot:focalCladeOTTTaxonName": "Alcidae", "^ot:messages": {"message": []}, "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_144", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2007.11.020"}, "^ot:studyPublicationReference": "Pereira, Sergio L., Allan J. Baker. 2008. DNA evidence for a Paleocene origin of the Alcidae (Aves: Charadriiformes) in the Pacific and multiple dispersals across northern oceans. Molecular Phylogenetics and Evolution 46 (2): 430-445.", "^ot:studyYear": 2008, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Uria aalge aalge", "^ot:ottId": 1097995, "^ot:ottTaxonName": "Uria aalge aalge"}, "otu10": {"^ot:originalLabel": "Synthliboramphus craveri", "^ot:ottId": 454492, "^ot:ottTaxonName": "Synthliboramphus craveri"}, "otu11": {"^ot:originalLabel": "Synthliboramphus hypoleucus", "^ot:ottId": 1078413, "^ot:ottTaxonName": "Synthliboramphus hypoleucus"}, "otu12": {"^ot:originalLabel": "Cepphus carbo", "^ot:ottId": 536766, "^ot:ottTaxonName": "Cepphus carbo"}, "otu13": {"^ot:originalLabel": "Cepphus columba", "^ot:ottId": 280900, "^ot:ottTaxonName": "Cepphus columba"}, "otu14": {"^ot:originalLabel": "Cepphus grylle", "^ot:ottId": 280901, "^ot:ottTaxonName": "Cepphus grylle"}, "otu15": {"^ot:originalLabel": "Brachyramphus brevirostris", "^ot:ottId": 280897, "^ot:ottTaxonName": "Brachyramphus brevirostris"}, "otu16": {"^ot:originalLabel": "Brachyramphus marmoratus", "^ot:ottId": 280902, "^ot:ottTaxonName": "Brachyramphus marmoratus"}, "otu17": {"^ot:originalLabel": "Brachyramphus perdix", "^ot:ottId": 1097991, "^ot:ottTaxonName": "Brachyramphus perdix"}, "otu18": {"^ot:originalLabel": "Aethia pusilla", "^ot:ottId": 855484, "^ot:ottTaxonName": "Aethia pusilla"}, "otu19": {"^ot:originalLabel": "Aethia cristatella", "^ot:ottId": 855480, "^ot:ottTaxonName": "Aethia cristatella"}, "otu2": {"^ot:originalLabel": "Uria aalge inornata", "^ot:ottId": 1097994, "^ot:ottTaxonName": "Uria aalge inornata"}, "otu20": {"^ot:originalLabel": "Aethia psittacula"}, "otu21": {"^ot:originalLabel": "Aethia pygmaea", "^ot:ottId": 855482, "^ot:ottTaxonName": "Aethia pygmaea"}, "otu22": {"^ot:originalLabel": "Ptychoramphus aleuticus", "^ot:ottId": 979353, "^ot:ottTaxonName": "Ptychoramphus aleuticus"}, "otu23": {"^ot:originalLabel": "Fratercula arctica", "^ot:ottId": 864865, "^ot:ottTaxonName": "Fratercula arctica"}, "otu24": {"^ot:originalLabel": "Fratercula corniculata", "^ot:ottId": 1078400, "^ot:ottTaxonName": "Fratercula corniculata"}, "otu25": {"^ot:originalLabel": "Fratercula cirrhata", "^ot:ottId": 385981, "^ot:ottTaxonName": "Fratercula cirrhata"}, "otu26": {"^ot:originalLabel": "Cerorhinca monocerata", "^ot:ottId": 989958, "^ot:ottTaxonName": "Cerorhinca monocerata"}, "otu3": {"^ot:originalLabel": "Uria lomvia", "^ot:ottId": 551817, "^ot:ottTaxonName": "Uria lomvia"}, "otu4": {"^ot:originalLabel": "Alle alle alle", "^ot:ottId": 571570, "^ot:ottTaxonName": "Alle alle alle"}, "otu5": {"^ot:originalLabel": "Alle alle polaris", "^ot:ottId": 147723, "^ot:ottTaxonName": "Alle alle polaris"}, "otu6": {"^ot:originalLabel": "Alca torda", "^ot:ottId": 855485, "^ot:ottTaxonName": "Alca torda"}, "otu7": {"^ot:originalLabel": "Pinguinus impennis"}, "otu8": {"^ot:originalLabel": "Synthliboramphus antiquus", "^ot:ottId": 1078411, "^ot:ottTaxonName": "Synthliboramphus antiquus"}, "otu9": {"^ot:originalLabel": "Synthliboramphus wumizusume", "^ot:ottId": 551819, "^ot:ottTaxonName": "Synthliboramphus wumizusume"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 3", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node1", "^ot:messages": {"message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@id": "messageu252925aa-4dee-4768-bccf-16e8e86b2bfa", "@severity": "INFO", "@wasGeneratedBy": "opentree.2nexml", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "<content provided as a string in a \"content\" rather than a file upload>", "@size": 564, "@sourceForTree": "tree1", "@type": "newick", "@url": "/curator/default/to_nexson?output=input&uploadid=u252925aa-4dee-4768-bccf-16e8e86b2bfa", "description": {"$": "Source data for tree 'tree1'"}}]}}}]}, "^ot:nearestTaxonMRCAName": "Alcidae", "^ot:nearestTaxonMRCAOttId": "855478", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@source": "node1", "@target": "node2"}, "edge34": {"@source": "node1", "@target": "node35"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge13": {"@source": "node12", "@target": "node14"}}, "node15": {"edge15": {"@source": "node15", "@target": "node16"}, "edge16": {"@source": "node15", "@target": "node17"}}, "node18": {"edge18": {"@source": "node18", "@target": "node19"}, "edge21": {"@source": "node18", "@target": "node22"}}, "node19": {"edge19": {"@source": "node19", "@target": "node20"}, "edge20": {"@source": "node19", "@target": "node21"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge29": {"@source": "node2", "@target": "node30"}}, "node22": {"edge22": {"@source": "node22", "@target": "node23"}, "edge23": {"@source": "node22", "@target": "node24"}}, "node25": {"edge25": {"@source": "node25", "@target": "node26"}, "edge28": {"@source": "node25", "@target": "node29"}}, "node26": {"edge26": {"@source": "node26", "@target": "node27"}, "edge27": {"@source": "node26", "@target": "node28"}}, "node3": {"edge24": {"@source": "node3", "@target": "node25"}, "edge3": {"@source": "node3", "@target": "node4"}}, "node30": {"edge30": {"@source": "node30", "@target": "node31"}, "edge33": {"@source": "node30", "@target": "node34"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge32": {"@source": "node31", "@target": "node33"}}, "node35": {"edge35": {"@source": "node35", "@target": "node36"}, "edge44": {"@source": "node35", "@target": "node45"}}, "node36": {"edge36": {"@source": "node36", "@target": "node37"}, "edge43": {"@source": "node36", "@target": "node44"}}, "node37": {"edge37": {"@source": "node37", "@target": "node38"}, "edge40": {"@source": "node37", "@target": "node41"}}, "node38": {"edge38": {"@source": "node38", "@target": "node39"}, "edge39": {"@source": "node38", "@target": "node40"}}, "node4": {"edge17": {"@source": "node4", "@target": "node18"}, "edge4": {"@source": "node4", "@target": "node5"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge42": {"@source": "node41", "@target": "node43"}}, "node45": {"edge45": {"@source": "node45", "@target": "node46"}, "edge50": {"@source": "node45", "@target": "node51"}}, "node46": {"edge46": {"@source": "node46", "@target": "node47"}, "edge49": {"@source": "node46", "@target": "node50"}}, "node47": {"edge47": {"@source": "node47", "@target": "node48"}, "edge48": {"@source": "node47", "@target": "node49"}}, "node5": {"edge14": {"@source": "node5", "@target": "node15"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node6": {"edge11": {"@source": "node6", "@target": "node12"}, "edge6": {"@source": "node6", "@target": "node7"}}, "node7": {"edge10": {"@source": "node7", "@target": "node11"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node8": {"edge8": {"@source": "node8", "@target": "node9"}, "edge9": {"@source": "node8", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu2"}, "node11": {"@otu": "otu3"}, "node12": {}, "node13": {"@otu": "otu4"}, "node14": {"@otu": "otu5"}, "node15": {}, "node16": {"@otu": "otu6"}, "node17": {"@otu": "otu7"}, "node18": {}, "node19": {}, "node2": {}, "node20": {"@otu": "otu8"}, "node21": {"@otu": "otu9"}, "node22": {}, "node23": {"@otu": "otu10"}, "node24": {"@otu": "otu11"}, "node25": {}, "node26": {}, "node27": {"@otu": "otu12"}, "node28": {"@otu": "otu13"}, "node29": {"@otu": "otu14"}, "node3": {}, "node30": {}, "node31": {}, "node32": {"@otu": "otu15"}, "node33": {"@otu": "otu16"}, "node34": {"@otu": "otu17"}, "node35": {}, "node36": {}, "node37": {}, "node38": {}, "node39": {"@otu": "otu18"}, "node4": {}, "node40": {"@otu": "otu19"}, "node41": {}, "node42": {"@otu": "otu20"}, "node43": {"@otu": "otu21"}, "node44": {"@otu": "otu22"}, "node45": {}, "node46": {}, "node47": {}, "node48": {"@otu": "otu23"}, "node49": {"@otu": "otu24"}, "node5": {}, "node50": {"@otu": "otu25"}, "node51": {"@otu": "otu26"}, "node6": {}, "node7": {}, "node8": {}, "node9": {"@otu": "otu1"}}}}}}}}, "branch2sha": {"master": "6bed60428352c04d00341ad513a8efb9442e4d8a"}, "commentHTML": "<p>Aethia psittacula not mapped. Proposed synonym Cyclorrhynchus psittacula is not generally accepted (<a target=\"_blank\" href=\"http://avibase.bsc-eoc.org/species.jsp?lang=EN&amp;avibaseid=2B46719DC058D033\">http://avibase.bsc-eoc.org/species.jsp?lang=EN&amp;avibaseid=2B46719DC058D033</a>). Pinguinus impennis in taxonomy as Laridae instead of Alcidae (unmapped here).</p>", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "ef407b60d3d7433bb4da06fd9d29fdf153ea94ba", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 6 Aug 2014 03:53:42 +0000", "date_ISO_8601": "2014-08-06 03:53:42 +0000", "relative_date": "12 years ago", "message_subject": "Alcidae", "message_body": "(Update Study #ot_144 via OpenTree API)"}, {"id": "ab5b490b1b4dd26e64682b1eaab152426cb85474", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 6 Aug 2014 03:43:44 +0000", "date_ISO_8601": "2014-08-06 03:43:44 +0000", "relative_date": "12 years ago", "message_subject": "Update Study #ot_144 via OpenTree API"}]}