{"sha": "e8a9c00dfe53f1b5d14873592fed3f756c0ffb31", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-07-08T15:38:02.548Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": false, "searchContext": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-07-08T15:38:02.547Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-07-08T15:38:02.548Z", "@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": "Bergsten_etal_2025.trees.nex", "@size": 2027, "@type": "nexus", "@url": "/curator/download/supporting_files.doc.9747fcae4a018b0b.426572677374656e5f6574616c5f323032352e74726565732e6e6578.nex", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "Bergsten_etal_2025_fixed.trees.nex", "@size": 1997, "@type": "nexus", "@url": "/curator/download/supporting_files.doc.85ed61c6904d1452.426572677374656e5f6574616c5f323032355f66697865642e74726565732e6e6578.nex", "description": {"$": "Fixed location of polytomies."}, "sourceForTree": [{"$": "tree2"}]}]}}, "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": "UNRECOGNIZED_KEY", "data": ["highestMintedElementIDs"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree2", "@treesID": "trees1", "@treeID": "tree2"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "Phylogeny reconstructed using whole genome sequencing.", "^ot:curatorName": ["Valeria Ensenat Rivera"], "^ot:dataDeposit": {"@href": "https://doi.org/10.17044/scilifelab.28868468.v1"}, "^ot:focalClade": 66507, "^ot:focalCladeOTTTaxonName": "Dytiscidae", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_2846", "^ot:studyPublication": {"@href": "https://doi.org/10.1111/syen.12685"}, "^ot:studyPublicationReference": "Bergsten, J., Nylander, J. A. A., Ospina, O. E., Lemmon, A. R., & Miller, K. B. (2025). Whole genome shotgun phylogenomics resolve the diving beetle tree of life. Systematic Entomology. Portico. https://doi.org/10.1111/syen.12685\n", "^ot:studyYear": 2025, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "^xhtml:license": {"@href": "https://creativecommons.org/licenses/by/4.0/", "@name": "CC-BY 4.0"}, "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 110, "message": 0, "node": 112, "otu": 62, "otus": 3, "tree": 2, "trees": 3}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Agabetini", "^ot:ottId": 367977, "^ot:ottTaxonName": "Agabetini"}, "otu10": {"^ot:originalLabel": "Cybistrinae", "^ot:ottId": 6521099, "^ot:ottTaxonName": "Cybistrinae"}, "otu11": {"^ot:originalLabel": "Dytiscus", "^ot:ottId": 304281, "^ot:ottTaxonName": "Dytiscus"}, "otu12": {"^ot:originalLabel": "Hyderodes", "^ot:ottId": 381008, "^ot:ottTaxonName": "Hyderodes"}, "otu13": {"^ot:originalLabel": "Hydaticini", "^ot:ottId": 716369, "^ot:ottTaxonName": "Hydaticini"}, "otu14": {"^ot:originalLabel": "Aubehyhdrini", "^ot:ottId": 805396, "^ot:ottTaxonName": "Aubehydrini"}, "otu15": {"^ot:originalLabel": "Eretini", "^ot:ottId": 716365, "^ot:ottTaxonName": "Eretini"}, "otu16": {"^ot:originalLabel": "Aciliini", "^ot:ottId": 716361, "^ot:ottTaxonName": "Aciliini"}, "otu17": {"^ot:originalLabel": "Matinae", "^ot:ottId": 813564, "^ot:ottTaxonName": "Matinae"}, "otu18": {"^ot:originalLabel": "Hydrodytinae", "^ot:ottId": 716364, "^ot:ottTaxonName": "Hydrodytinae"}, "otu19": {"^ot:originalLabel": "Methlini", "^ot:ottId": 813553, "^ot:ottTaxonName": "Methlini"}, "otu2": {"^ot:originalLabel": "Laccophilini", "^ot:ottId": 43048, "^ot:ottTaxonName": "Laccophilini"}, "otu20": {"^ot:originalLabel": "Laccornini", "^ot:ottId": 659647, "^ot:ottTaxonName": "Laccornini"}, "otu21": {"^ot:originalLabel": "Laccornellini", "^ot:ottId": 6521100, "^ot:ottTaxonName": "Laccornellini"}, "otu22": {"^ot:originalLabel": "Hydrovatini", "^ot:ottId": 659641, "^ot:ottTaxonName": "Hydrovatini"}, "otu23": {"^ot:originalLabel": "Pachydrini", "^ot:ottId": 6521098, "^ot:ottTaxonName": "Pachydrini"}, "otu24": {"^ot:originalLabel": "Vatellini", "^ot:ottId": 659654, "^ot:ottTaxonName": "Vatellini"}, "otu25": {"^ot:originalLabel": "Bidessini", "^ot:ottId": 294405, "^ot:ottTaxonName": "Bidessini"}, "otu26": {"^ot:originalLabel": "Hygrotini", "^ot:ottId": 1002814, "^ot:ottTaxonName": "Hygrotini"}, "otu27": {"^ot:originalLabel": "Hyphydrini", "^ot:ottId": 1073665, "^ot:ottTaxonName": "Hyphydrini"}, "otu28": {"^ot:originalLabel": "Sternopriscina", "^ot:ottId": 6521101, "^ot:ottTaxonName": "Sternopriscina"}, "otu29": {"^ot:originalLabel": "Siettitiina", "^ot:ottId": 6521102, "^ot:ottTaxonName": "Siettitiina"}, "otu3": {"^ot:originalLabel": "Lancetinae", "^ot:ottId": 331602, "^ot:ottTaxonName": "Lancetinae"}, "otu30": {"^ot:originalLabel": "Deronectina", "^ot:ottId": 6521103, "^ot:ottTaxonName": "Deronectina"}, "otu31": {"^ot:originalLabel": "Hydroporina", "^ot:ottId": 6521104, "^ot:ottTaxonName": "Hydroporina"}, "otu4": {"^ot:originalLabel": "Coptotominae", "^ot:ottId": 829712, "^ot:ottTaxonName": "Coptotominae"}, "otu5": {"^ot:originalLabel": "Copelatinae", "^ot:ottId": 331598, "^ot:ottTaxonName": "Copelatinae"}, "otu6": {"^ot:originalLabel": "Colymbetinae", "^ot:ottId": 331597, "^ot:ottTaxonName": "Colymbetinae"}, "otu7": {"^ot:originalLabel": "Platynectini", "^ot:ottId": 6521105, "^ot:ottTaxonName": "Platynectini"}, "otu8": {"^ot:originalLabel": "Hydrotrupini", "^ot:ottId": 6521106, "^ot:ottTaxonName": "Hydrotrupini"}, "otu9": {"^ot:originalLabel": "Agabini", "^ot:ottId": 192876, "^ot:ottTaxonName": "Agabini"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree2"], "treeById": {"tree2": {"@label": "Bergsten et al. 2025 (Figure 5)", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node58", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node58", "^ot:specifiedRoot": "node58", "^ot:tag": ["Dytiscidae"], "^ot:unrootedTree": false, "edgeBySourceId": {"node101": {"edge100": {"@source": "node101", "@target": "node102"}, "edge101": {"@source": "node101", "@target": "node103"}, "edge102": {"@source": "node101", "@target": "node104"}}, "node104": {"edge103": {"@source": "node104", "@target": "node105"}, "edge104": {"@source": "node104", "@target": "node106"}, "edge105": {"@source": "node104", "@target": "node107"}, "edge106": {"@source": "node104", "@target": "node108"}}, "node108": {"edge107": {"@source": "node108", "@target": "node109"}, "edge108": {"@source": "node108", "@target": "node110"}}, "node110": {"edge109": {"@source": "node110", "@target": "node111"}, "edge110": {"@source": "node110", "@target": "node112"}}, "node58": {"edge57": {"@source": "node58", "@target": "node59"}, "edge60": {"@source": "node58", "@target": "node62"}}, "node59": {"edge58": {"@source": "node59", "@target": "node60"}, "edge59": {"@source": "node59", "@target": "node61"}}, "node62": {"edge61": {"@source": "node62", "@target": "node63"}, "edge64": {"@source": "node62", "@target": "node66"}}, "node63": {"edge62": {"@source": "node63", "@target": "node64"}, "edge63": {"@source": "node63", "@target": "node65"}}, "node66": {"edge65": {"@source": "node66", "@target": "node67"}, "edge88": {"@source": "node66", "@target": "node90"}}, "node67": {"edge66": {"@source": "node67", "@target": "node68"}, "edge67": {"@source": "node67", "@target": "node69"}}, "node69": {"edge68": {"@source": "node69", "@target": "node70"}, "edge75": {"@source": "node69", "@target": "node77"}}, "node70": {"edge69": {"@source": "node70", "@target": "node71"}, "edge70": {"@source": "node70", "@target": "node72"}}, "node72": {"edge71": {"@source": "node72", "@target": "node73"}, "edge72": {"@source": "node72", "@target": "node74"}}, "node74": {"edge73": {"@source": "node74", "@target": "node75"}, "edge74": {"@source": "node74", "@target": "node76"}}, "node77": {"edge76": {"@source": "node77", "@target": "node78"}, "edge77": {"@source": "node77", "@target": "node79"}}, "node79": {"edge78": {"@source": "node79", "@target": "node80"}, "edge81": {"@source": "node79", "@target": "node83"}}, "node80": {"edge79": {"@source": "node80", "@target": "node81"}, "edge80": {"@source": "node80", "@target": "node82"}}, "node83": {"edge82": {"@source": "node83", "@target": "node84"}, "edge83": {"@source": "node83", "@target": "node85"}}, "node85": {"edge84": {"@source": "node85", "@target": "node86"}, "edge85": {"@source": "node85", "@target": "node87"}}, "node87": {"edge86": {"@source": "node87", "@target": "node88"}, "edge87": {"@source": "node87", "@target": "node89"}}, "node90": {"edge89": {"@source": "node90", "@target": "node91"}, "edge90": {"@source": "node90", "@target": "node92"}}, "node92": {"edge91": {"@source": "node92", "@target": "node93"}, "edge92": {"@source": "node92", "@target": "node94"}}, "node94": {"edge93": {"@source": "node94", "@target": "node95"}, "edge94": {"@source": "node94", "@target": "node96"}}, "node96": {"edge95": {"@source": "node96", "@target": "node97"}, "edge96": {"@source": "node96", "@target": "node98"}, "edge97": {"@source": "node96", "@target": "node99"}, "edge98": {"@source": "node96", "@target": "node100"}, "edge99": {"@source": "node96", "@target": "node101"}}}, "nodeById": {"node100": {"@otu": "otu20"}, "node101": {}, "node102": {"@otu": "otu24"}, "node103": {"@otu": "otu25"}, "node104": {}, "node105": {"@otu": "otu26"}, "node106": {"@otu": "otu27"}, "node107": {"@otu": "otu28"}, "node108": {}, "node109": {"@otu": "otu29"}, "node110": {}, "node111": {"@otu": "otu30"}, "node112": {"@otu": "otu31"}, "node58": {"@root": true}, "node59": {}, "node60": {"@otu": "otu2"}, "node61": {"@otu": "otu1"}, "node62": {}, "node63": {}, "node64": {"@otu": "otu3"}, "node65": {"@otu": "otu4"}, "node66": {}, "node67": {}, "node68": {"@otu": "otu5"}, "node69": {}, "node70": {}, "node71": {"@otu": "otu6"}, "node72": {}, "node73": {"@otu": "otu7"}, "node74": {}, "node75": {"@otu": "otu8"}, "node76": {"@otu": "otu9"}, "node77": {}, "node78": {"@otu": "otu10"}, "node79": {}, "node80": {}, "node81": {"@otu": "otu11"}, "node82": {"@otu": "otu12"}, "node83": {}, "node84": {"@otu": "otu13"}, "node85": {}, "node86": {"@otu": "otu14"}, "node87": {}, "node88": {"@otu": "otu15"}, "node89": {"@otu": "otu16"}, "node90": {}, "node91": {"@otu": "otu17"}, "node92": {}, "node93": {"@otu": "otu18"}, "node94": {}, "node95": {"@otu": "otu19"}, "node96": {}, "node97": {"@otu": "otu23"}, "node98": {"@otu": "otu22"}, "node99": {"@otu": "otu21"}}}}}}}}, "branch2sha": {"master": "e8a9c00dfe53f1b5d14873592fed3f756c0ffb31"}, "commentHTML": "<p>Phylogeny reconstructed using whole genome sequencing.</p>", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "a37811171aef4a1f4995e18448c0b77ddadda288", "author_name": "Valeria Ensenat Rivera", "author_email": "valeria.ensenatrivera@gwmail.gwu.edu", "date": "Tue, 8 Jul 2025 17:39:26 +0000", "date_ISO_8601": "2025-07-08 17:39:26 +0000", "relative_date": "10 months ago", "message_subject": "Added link to data repository", "message_body": "(Update document 'ot_2846' via OpenTree API)"}, {"id": "e2b7b29b803a71f8d83db7da91953710530dd6fd", "author_name": "Valeria Ensenat Rivera", "author_email": "valeria.ensenatrivera@gwmail.gwu.edu", "date": "Tue, 8 Jul 2025 16:38:06 +0000", "date_ISO_8601": "2025-07-08 16:38:06 +0000", "relative_date": "10 months ago", "message_subject": "Added Bergsten et al. 2025", "message_body": "July 8, 2025.\n\n(Update document 'ot_2846' via OpenTree API)"}, {"id": "39df5714de1bc2ee8b6ea4815620054de1808629", "author_name": "Valeria Ensenat Rivera", "author_email": "valeria.ensenatrivera@gwmail.gwu.edu", "date": "Tue, 8 Jul 2025 16:37:23 +0000", "date_ISO_8601": "2025-07-08 16:37:23 +0000", "relative_date": "10 months ago", "message_subject": "Added Bergsten et al. 2025", "message_body": "July 8, 2025.\n\n(Update document 'ot_2846' via OpenTree API)"}, {"id": "a9ff91b238258163f74739cf1d1208794387d505", "author_name": "Valeria Ensenat Rivera", "author_email": "valeria.ensenatrivera@gwmail.gwu.edu", "date": "Tue, 8 Jul 2025 16:31:22 +0000", "date_ISO_8601": "2025-07-08 16:31:22 +0000", "relative_date": "10 months ago", "message_subject": "Added Bergsten et al. 2025", "message_body": "July 8, 2025.\n\n(Update document 'ot_2846' via OpenTree API)"}, {"id": "c2dc43ccef74db5f0c528e5e873d60523a049bd8", "author_name": "Valeria Ensenat Rivera", "author_email": "valeria.ensenatrivera@gwmail.gwu.edu", "date": "Tue, 8 Jul 2025 15:37:58 +0000", "date_ISO_8601": "2025-07-08 15:37:58 +0000", "relative_date": "10 months ago", "message_subject": "Update document 'ot_2846' via OpenTree API"}]}