{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-02-28T09:18:39.623Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": true, "searchContext": {"$": "All life"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-02-28T09:18:39.623Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-02-28T09:18:39.623Z", "@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": "CastroDowton2007Endopterygota.nwk", "@size": 400, "@type": "newick", "@url": "/curator/download/supporting_files.doc.96e8e65f93ab8199.43617374726f446f77746f6e32303037456e646f7074657279676f74612e6e776b.nwk", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "image.png", "@size": 662, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.aa6c6d9ad514ee89.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 1816, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.97ba93fe1ca38c23.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 2475, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.8d56337b41d83cc0.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 5642, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.9e82151bcac0d96e.696d6167652e706e67.png", "description": {"$": ""}, "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": ["otu10", "otu12", "otu3"], "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": ["otu10", "otu12", "otu3"], "@otusID": "otus1", "@otuID": ["otu10", "otu12", "otu3"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["dchesters"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 1082885, "^ot:focalCladeOTTTaxonName": "Holometabola", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_2548", "^ot:studyPublication": {"@href": "https://doi.org/10.1111/j.1365-3113.2006.00356.x"}, "^ot:studyPublicationReference": "CASTRO, L. R., & DOWTON, M. (2006). Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers. Systematic Entomology, 32(1), 60\u201369. Portico. https://doi.org/10.1111/j.1365-3113.2006.00356.x\n", "^ot:studyYear": 2007, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 36, "message": 0, "node": 37, "otu": 19, "otus": 2, "tree": 1, "trees": 2}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Triatoma dimidiata", "^ot:ottId": 93952, "^ot:ottTaxonName": "Triatoma dimidiata"}, "otu10": {"^ot:originalLabel": "Ostrinia nubilaris"}, "otu11": {"^ot:originalLabel": "Antheraea pernyi", "^ot:ottId": 167955, "^ot:ottTaxonName": "Antheraea pernyi"}, "otu12": {"^ot:originalLabel": "Bombyx mandarina"}, "otu13": {"^ot:originalLabel": "Anopheles gambiae", "^ot:ottId": 553555, "^ot:ottTaxonName": "Anopheles gambiae"}, "otu14": {"^ot:originalLabel": "Bactrocera oleae", "^ot:ottId": 702964, "^ot:ottTaxonName": "Bactrocera oleae"}, "otu15": {"^ot:originalLabel": "Ceratitis capitata", "^ot:ottId": 34902, "^ot:ottTaxonName": "Ceratitis capitata"}, "otu16": {"^ot:originalLabel": "Drosophila melanogaster", "^ot:ottId": 505714, "^ot:ottTaxonName": "Drosophila melanogaster"}, "otu17": {"^ot:originalLabel": "Haematobia irritans", "^ot:ottId": 484743, "^ot:ottTaxonName": "Haematobia irritans"}, "otu18": {"^ot:originalLabel": "Cochliomyia hominivorax", "^ot:ottId": 358229, "^ot:ottTaxonName": "Cochliomyia hominivorax"}, "otu19": {"^ot:originalLabel": "Chrysomya chloropyga", "^ot:ottId": 971011, "^ot:ottTaxonName": "Chrysomya chloropyga"}, "otu2": {"^ot:originalLabel": "Perga condei", "^ot:ottId": 875712, "^ot:ottTaxonName": "Perga condei"}, "otu3": {"^ot:originalLabel": "Vanhornia eunemidarum"}, "otu4": {"^ot:originalLabel": "Primeuchroeus sp", "^ot:ottId": 93695, "^ot:ottTaxonName": "Primeuchroeus"}, "otu5": {"^ot:originalLabel": "Apis mellifera", "^ot:ottId": 461645, "^ot:ottTaxonName": "Apis mellifera (species in domain Eukaryota)"}, "otu6": {"^ot:originalLabel": "Melipona bicolor", "^ot:ottId": 1007167, "^ot:ottTaxonName": "Melipona bicolor"}, "otu7": {"^ot:originalLabel": "Pyrocoelia rufa", "^ot:ottId": 583618, "^ot:ottTaxonName": "Pyrocoelia rufa"}, "otu8": {"^ot:originalLabel": "Tribolium castaneum", "^ot:ottId": 148904, "^ot:ottTaxonName": "Tribolium castaneum"}, "otu9": {"^ot:originalLabel": "Crioceris duodecimpunctata", "^ot:ottId": 590209, "^ot:ottTaxonName": "Crioceris duodecimpunctata"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 2C", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Bayesian inference ", "^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"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge12": {"@source": "node11", "@target": "node13"}}, "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"}, "edge24": {"@source": "node19", "@target": "node25"}}, "node20": {"edge20": {"@source": "node20", "@target": "node21"}, "edge21": {"@source": "node20", "@target": "node22"}}, "node22": {"edge22": {"@source": "node22", "@target": "node23"}, "edge23": {"@source": "node22", "@target": "node24"}}, "node25": {"edge25": {"@source": "node25", "@target": "node26"}, "edge26": {"@source": "node25", "@target": "node27"}}, "node27": {"edge27": {"@source": "node27", "@target": "node28"}, "edge30": {"@source": "node27", "@target": "node31"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge29": {"@source": "node28", "@target": "node30"}}, "node3": {"edge18": {"@source": "node3", "@target": "node19"}, "edge3": {"@source": "node3", "@target": "node4"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge32": {"@source": "node31", "@target": "node33"}}, "node33": {"edge33": {"@source": "node33", "@target": "node34"}, "edge34": {"@source": "node33", "@target": "node35"}}, "node35": {"edge35": {"@source": "node35", "@target": "node36"}, "edge36": {"@source": "node35", "@target": "node37"}}, "node4": {"edge13": {"@source": "node4", "@target": "node14"}, "edge4": {"@source": "node4", "@target": "node5"}}, "node5": {"edge5": {"@source": "node5", "@target": "node6"}, "edge6": {"@source": "node5", "@target": "node7"}}, "node7": {"edge7": {"@source": "node7", "@target": "node8"}, "edge8": {"@source": "node7", "@target": "node9"}}, "node9": {"edge10": {"@source": "node9", "@target": "node11"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu4"}, "node11": {}, "node12": {"@otu": "otu5"}, "node13": {"@otu": "otu6"}, "node14": {}, "node15": {"@otu": "otu7"}, "node16": {}, "node17": {"@otu": "otu8"}, "node18": {"@otu": "otu9"}, "node19": {}, "node2": {"@otu": "otu1"}, "node20": {}, "node21": {"@otu": "otu10"}, "node22": {}, "node23": {"@otu": "otu11"}, "node24": {"@otu": "otu12"}, "node25": {}, "node26": {"@otu": "otu13"}, "node27": {}, "node28": {}, "node29": {"@otu": "otu14"}, "node3": {}, "node30": {"@otu": "otu15"}, "node31": {}, "node32": {"@otu": "otu16"}, "node33": {}, "node34": {"@otu": "otu17"}, "node35": {}, "node36": {"@otu": "otu18"}, "node37": {"@otu": "otu19"}, "node4": {}, "node5": {}, "node6": {"@otu": "otu2"}, "node7": {}, "node8": {"@otu": "otu3"}, "node9": {}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "d658bd3034b803ed2ebe57a991e9c9bd172bd850", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Fri, 28 Feb 2025 09:21:04 +0000", "date_ISO_8601": "2025-02-28 09:21:04 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Initial commit Castro and Dowton (2007)", "message_body": "CastroDowton2007Endopterygota.nwk\nJoint-first mitogenome phylogeny published by Systematic Entomology. Unstable inter order relationships, though authors appear to prefer Bayesian result with third codon removed, so selected that topology.\n\n(Update document 'ot_2548' via OpenTree API)"}, {"id": "d4662e8e20add7977b7ad6b655d33016c537a906", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Fri, 28 Feb 2025 09:18:35 +0000", "date_ISO_8601": "2025-02-28 09:18:35 +0000", "relative_date": "1 year, 2 months ago", "message_subject": "Update document 'ot_2548' via OpenTree API"}]}