{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-02-27T02:06:22.280Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": true, "searchContext": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-02-27T02:06:22.280Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-02-27T02:06:22.280Z", "@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": "BybeeTaylor2004Asilidae.nwk", "@size": 523, "@type": "newick", "@url": "/curator/download/supporting_files.doc.9313b196dd30f564.42796265655461796c6f72323030344173696c696461652e6e776b.nwk", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "image.png", "@size": 570, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.89e32682f68f9c7f.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 798, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.a3ebabab1cee5c2b.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 1872, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.881add830636a9b3.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 2196, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.b794d1b5b03c69a9.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}]}}, "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": ["otu2", "otu26"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["highestMintedElementIDs"], "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"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu2", "otu26"], "@otusID": "otus1", "@otuID": ["otu2", "otu26"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["dchesters"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 653876, "^ot:focalCladeOTTTaxonName": "Asilidae", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_2533", "^ot:studyPublication": {"@href": "https://doi.org/10.1016/s1055-7903(03)00253-7"}, "^ot:studyPublicationReference": "Bybee, S. M., Taylor, S. D., Riley Nelson, C., & Whiting, M. F. (2004). A phylogeny of robber flies (Diptera: Asilidae) at the subfamilial level: molecular evidence. Molecular Phylogenetics and Evolution, 30(3), 789\u2013797. https://doi.org/10.1016/s1055-7903(03)00253-7\n", "^ot:studyYear": 2004, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 50, "message": 0, "node": 51, "otu": 26, "otus": 2, "tree": 1, "trees": 2}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Mydas clavatus", "^ot:ottId": 356517, "^ot:ottTaxonName": "Mydas clavatus"}, "otu10": {"^ot:originalLabel": "Philonicus arizonensis", "^ot:ottId": 153045, "^ot:ottTaxonName": "Philonicus arizonensis"}, "otu11": {"^ot:originalLabel": "Holopogon currani", "^ot:ottId": 153046, "^ot:ottTaxonName": "Holopogon currani"}, "otu12": {"^ot:originalLabel": "Senobasis corsair", "^ot:ottId": 520968, "^ot:ottTaxonName": "Senobasis corsair"}, "otu13": {"^ot:originalLabel": "Saropogon fletcheri", "^ot:ottId": 676333, "^ot:ottTaxonName": "Saropogon fletcheri"}, "otu14": {"^ot:originalLabel": "Diogmites grossus", "^ot:ottId": 153050, "^ot:ottTaxonName": "Diogmites grossus"}, "otu15": {"^ot:originalLabel": "Laphystia sp", "^ot:ottId": 841694, "^ot:ottTaxonName": "Laphystia"}, "otu16": {"^ot:originalLabel": "Andrenosoma fulvicauda", "^ot:ottId": 1098303, "^ot:ottTaxonName": "Andrenosoma fulvicauda"}, "otu17": {"^ot:originalLabel": "Adelodus sp", "^ot:ottId": 1098304, "^ot:ottTaxonName": "Adelodus"}, "otu18": {"^ot:originalLabel": "Smeryngolaphria sp", "^ot:ottId": 584224, "^ot:ottTaxonName": "Smeryngolaphria"}, "otu19": {"^ot:originalLabel": "Laphria sp", "^ot:ottId": 217442, "^ot:ottTaxonName": "Laphria"}, "otu2": {"^ot:altLabel": "Leptogaster", "^ot:originalLabel": "Leptogaster sp"}, "otu20": {"^ot:originalLabel": "Maira sp", "^ot:ottId": 623807, "^ot:ottTaxonName": "Maira"}, "otu21": {"^ot:originalLabel": "Stenopogon martini", "^ot:ottId": 1041295, "^ot:ottTaxonName": "Stenopogon martini"}, "otu22": {"^ot:originalLabel": "Ospriocerus latipennis", "^ot:ottId": 153051, "^ot:ottTaxonName": "Ospriocerus latipennis"}, "otu23": {"^ot:originalLabel": "Hypenetes critesi", "^ot:ottId": 1098300, "^ot:ottTaxonName": "Hypenetes critesi"}, "otu24": {"^ot:originalLabel": "Stichopogon trifasciatus", "^ot:ottId": 153053, "^ot:ottTaxonName": "Stichopogon trifasciatus"}, "otu25": {"^ot:originalLabel": "Creolestes nigribarbis", "^ot:ottId": 1098311, "^ot:ottTaxonName": "Creolestes nigribarbis"}, "otu26": {"^ot:originalLabel": "Obelopherus landbecki"}, "otu3": {"^ot:originalLabel": "Psilonyx annulatus", "^ot:ottId": 464490, "^ot:ottTaxonName": "Psilonyx annulatus"}, "otu4": {"^ot:originalLabel": "Holcocephala abdominalis", "^ot:ottId": 1098309, "^ot:ottTaxonName": "Holcocephala abdominalis"}, "otu5": {"^ot:originalLabel": "Promachus bastardii", "^ot:ottId": 623802, "^ot:ottTaxonName": "Promachus bastardii"}, "otu6": {"^ot:originalLabel": "Efferia nemoralis", "^ot:ottId": 464493, "^ot:ottTaxonName": "Efferia nemoralis"}, "otu7": {"^ot:originalLabel": "Proctacanthus nearno", "^ot:ottId": 464491, "^ot:ottTaxonName": "Proctacanthus nearno"}, "otu8": {"^ot:originalLabel": "Ommatius sp", "^ot:ottId": 623810, "^ot:ottTaxonName": "Ommatius"}, "otu9": {"^ot:originalLabel": "Machimus sp", "^ot:ottId": 464504, "^ot:ottTaxonName": "Machimus"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 4, ML", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node3", "^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"}, "edge2": {"@source": "node1", "@target": "node3"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge11": {"@source": "node10", "@target": "node12"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge15": {"@source": "node12", "@target": "node16"}}, "node13": {"edge13": {"@source": "node13", "@target": "node14"}, "edge14": {"@source": "node13", "@target": "node15"}}, "node16": {"edge16": {"@source": "node16", "@target": "node17"}, "edge17": {"@source": "node16", "@target": "node18"}}, "node18": {"edge18": {"@source": "node18", "@target": "node19"}, "edge19": {"@source": "node18", "@target": "node20"}}, "node21": {"edge21": {"@source": "node21", "@target": "node22"}, "edge28": {"@source": "node21", "@target": "node29"}}, "node22": {"edge22": {"@source": "node22", "@target": "node23"}, "edge23": {"@source": "node22", "@target": "node24"}}, "node24": {"edge24": {"@source": "node24", "@target": "node25"}, "edge25": {"@source": "node24", "@target": "node26"}}, "node26": {"edge26": {"@source": "node26", "@target": "node27"}, "edge27": {"@source": "node26", "@target": "node28"}}, "node29": {"edge29": {"@source": "node29", "@target": "node30"}, "edge40": {"@source": "node29", "@target": "node41"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge6": {"@source": "node3", "@target": "node7"}}, "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"}}, "node36": {"edge36": {"@source": "node36", "@target": "node37"}, "edge37": {"@source": "node36", "@target": "node38"}}, "node38": {"edge38": {"@source": "node38", "@target": "node39"}, "edge39": {"@source": "node38", "@target": "node40"}}, "node4": {"edge4": {"@source": "node4", "@target": "node5"}, "edge5": {"@source": "node4", "@target": "node6"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge44": {"@source": "node41", "@target": "node45"}}, "node42": {"edge42": {"@source": "node42", "@target": "node43"}, "edge43": {"@source": "node42", "@target": "node44"}}, "node45": {"edge45": {"@source": "node45", "@target": "node46"}, "edge46": {"@source": "node45", "@target": "node47"}}, "node47": {"edge47": {"@source": "node47", "@target": "node48"}, "edge48": {"@source": "node47", "@target": "node49"}}, "node49": {"edge49": {"@source": "node49", "@target": "node50"}, "edge50": {"@source": "node49", "@target": "node51"}}, "node7": {"edge20": {"@source": "node7", "@target": "node21"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node8": {"edge8": {"@source": "node8", "@target": "node9"}, "edge9": {"@source": "node8", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {"@otu": "otu5"}, "node12": {}, "node13": {}, "node14": {"@otu": "otu6"}, "node15": {"@otu": "otu7"}, "node16": {}, "node17": {"@otu": "otu8"}, "node18": {}, "node19": {"@otu": "otu9"}, "node2": {"@otu": "otu1"}, "node20": {"@otu": "otu10"}, "node21": {}, "node22": {}, "node23": {"@otu": "otu11"}, "node24": {}, "node25": {"@otu": "otu12"}, "node26": {}, "node27": {"@otu": "otu13"}, "node28": {"@otu": "otu14"}, "node29": {}, "node3": {}, "node30": {}, "node31": {"@otu": "otu15"}, "node32": {}, "node33": {"@otu": "otu16"}, "node34": {}, "node35": {"@otu": "otu17"}, "node36": {}, "node37": {"@otu": "otu18"}, "node38": {}, "node39": {"@otu": "otu19"}, "node4": {}, "node40": {"@otu": "otu20"}, "node41": {}, "node42": {}, "node43": {"@otu": "otu21"}, "node44": {"@otu": "otu22"}, "node45": {}, "node46": {"@otu": "otu23"}, "node47": {}, "node48": {"@otu": "otu24"}, "node49": {}, "node5": {"@otu": "otu2"}, "node50": {"@otu": "otu25"}, "node51": {"@otu": "otu26"}, "node6": {"@otu": "otu3"}, "node7": {}, "node8": {}, "node9": {"@otu": "otu4"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "c20d6dcd05c9d9ba3eb7bd8368cc2ad8d77bd56e", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Thu, 27 Feb 2025 02:08:50 +0000", "date_ISO_8601": "2025-02-27 02:08:50 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Initial commit Bybee, Taylor et al. (2004)", "message_body": "BybeeTaylor2004Asilidae.nwk\n\n(Update document 'ot_2533' via OpenTree API)"}, {"id": "414f358934b0d9895186c745097992a69b0a4d7e", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Thu, 27 Feb 2025 02:06:18 +0000", "date_ISO_8601": "2025-02-27 02:06:18 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Update document 'ot_2533' via OpenTree API"}]}