{"sha": "2aa180baef3c5e313da1e7f09c83ce2c0467b457", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "3.10.12"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2025-05-05T02:17:48.204Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": true, "searchContext": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-05-05T02:17:48.204Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2025-05-05T02:17:48.204Z", "@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": "Gray2020Gryllus.nwk", "@size": 863, "@type": "newick", "@url": "/curator/download/supporting_files.doc.ae9c061024415804.47726179323032304772796c6c75732e6e776b.nwk", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "image.png", "@size": 699, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.acf74775ad1544c6.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 932, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.a447677b9f8bed1e.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 1448, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.ab035887c15b5cd9.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 2197, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.8349aa94bed3b20a.696d6167652e706e67.png", "description": {"$": ""}, "sourceForTree": []}, {"@filename": "image.png", "@size": 1591, "@type": "", "@url": "/curator/supporting_files/download/supporting_files.doc.8a479a7108cf8668.696d6167652e706e67.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": ["otu1", "otu10", "otu11", "otu13", "otu18", "otu19", "otu2", "otu26", "otu3", "otu31", "otu33", "otu35", "otu4", "otu41", "otu5", "otu6", "otu7", "otu8", "otu9"], "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": ["otu1", "otu10", "otu11", "otu13", "otu18", "otu19", "otu2", "otu26", "otu3", "otu31", "otu33", "otu35", "otu4", "otu41", "otu5", "otu6", "otu7", "otu8", "otu9"], "@otusID": "otus1", "@otuID": ["otu1", "otu10", "otu11", "otu13", "otu18", "otu19", "otu2", "otu26", "otu3", "otu31", "otu33", "otu35", "otu4", "otu41", "otu5", "otu6", "otu7", "otu8", "otu9"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["dchesters"], "^ot:dataDeposit": {"@href": "https://datadryad.org/stash/dataset/doi:10.5061%2Fdryad.mkkwh70vf"}, "^ot:focalClade": 1077621, "^ot:focalCladeOTTTaxonName": "Gryllus", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_2781", "^ot:studyPublication": {"@href": "https://doi.org/10.11646/zootaxa.4750.3.2"}, "^ot:studyPublicationReference": "GRAY, D. A., WEISSMAN, D. B., COLE, J. A., LEMMON, E. M., & LEMMON, A. R. (2020). Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment. Zootaxa, 4750(3). https://doi.org/10.11646/zootaxa.4750.3.2\n", "^ot:studyYear": 2020, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "^xhtml:license": {"@href": "", "@name": ""}, "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 86, "message": 0, "node": 87, "otu": 44, "otus": 2, "tree": 1, "trees": 2}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Gryllus saxatilis"}, "otu10": {"^ot:originalLabel": "Gryllus veletisoides"}, "otu11": {"^ot:originalLabel": "Gryllus chisosensis"}, "otu12": {"^ot:originalLabel": "Gryllus lineaticeps", "^ot:ottId": 535629, "^ot:ottTaxonName": "Gryllus lineaticeps"}, "otu13": {"^ot:originalLabel": "Gryllus staccato"}, "otu14": {"^ot:originalLabel": "Gryllus personatus", "^ot:ottId": 16166, "^ot:ottTaxonName": "Gryllus personatus"}, "otu15": {"^ot:originalLabel": "Gryllus vocalis", "^ot:ottId": 16168, "^ot:ottTaxonName": "Gryllus vocalis"}, "otu16": {"^ot:originalLabel": "Gryllus cohni", "^ot:ottId": 3493203, "^ot:ottTaxonName": "Gryllus cohni"}, "otu17": {"^ot:originalLabel": "Gryllus veletis", "^ot:ottId": 381537, "^ot:ottTaxonName": "Gryllus veletis"}, "otu18": {"^ot:originalLabel": "Gryllus montis"}, "otu19": {"^ot:originalLabel": "Gryllus planeta"}, "otu2": {"^ot:originalLabel": "Gryllus makhosica"}, "otu20": {"^ot:originalLabel": "Gryllus cayensis", "^ot:ottId": 16173, "^ot:ottTaxonName": "Gryllus cayensis"}, "otu21": {"^ot:originalLabel": "Gryllus fultoni", "^ot:ottId": 50650, "^ot:ottTaxonName": "Gryllus fultoni"}, "otu22": {"^ot:originalLabel": "Gryllus vernalis", "^ot:ottId": 3493223, "^ot:ottTaxonName": "Gryllus vernalis"}, "otu23": {"^ot:originalLabel": "Gryllus armatus", "^ot:ottId": 3493209, "^ot:ottTaxonName": "Gryllus armatus"}, "otu24": {"^ot:originalLabel": "Gryllus integer", "^ot:ottId": 1005594, "^ot:ottTaxonName": "Gryllus integer"}, "otu25": {"^ot:originalLabel": "Gryllus texensis", "^ot:ottId": 709194, "^ot:ottTaxonName": "Gryllus texensis"}, "otu26": {"^ot:originalLabel": "Gryllus regularis"}, "otu27": {"^ot:originalLabel": "Gryllus rubens", "^ot:ottId": 1005588, "^ot:ottTaxonName": "Gryllus rubens"}, "otu28": {"^ot:originalLabel": "Gryllus firmus", "^ot:ottId": 178926, "^ot:ottTaxonName": "Gryllus firmus"}, "otu29": {"^ot:originalLabel": "Gryllus pennsylvanicus", "^ot:ottId": 957742, "^ot:ottTaxonName": "Gryllus pennsylvanicus"}, "otu3": {"^ot:originalLabel": "Gryllus leei"}, "otu30": {"^ot:originalLabel": "Gryllus multipulsator", "^ot:ottId": 72709, "^ot:ottTaxonName": "Gryllus multipulsator"}, "otu31": {"^ot:originalLabel": "Gryllus assimilis"}, "otu32": {"^ot:originalLabel": "Gryllus locorojo", "^ot:ottId": 116975, "^ot:ottTaxonName": "Gryllus locorojo"}, "otu33": {"^ot:originalLabel": "Gryllus veintinueve"}, "otu34": {"^ot:originalLabel": "Gryllus ovisopis", "^ot:ottId": 492011, "^ot:ottTaxonName": "Gryllus ovisopis"}, "otu35": {"^ot:originalLabel": "Gryllus thinos"}, "otu36": {"^ot:originalLabel": "Gryllus bryanti", "^ot:ottId": 3493174, "^ot:ottTaxonName": "Gryllus bryanti"}, "otu37": {"^ot:originalLabel": "Gryllus insularis", "^ot:ottId": 3493215, "^ot:ottTaxonName": "Gryllus insularis"}, "otu38": {"^ot:originalLabel": "Gryllus brevicaudus", "^ot:ottId": 620631, "^ot:ottTaxonName": "Gryllus brevicaudus"}, "otu39": {"^ot:originalLabel": "Gryllus alexanderi", "^ot:ottId": 3493191, "^ot:ottTaxonName": "Gryllus alexanderi"}, "otu4": {"^ot:originalLabel": "Gryllus navajo"}, "otu40": {"^ot:originalLabel": "Gryllus bimaculatus", "^ot:ottId": 1077624, "^ot:ottTaxonName": "Gryllus bimaculatus"}, "otu41": {"^ot:originalLabel": "Gryllus campestris"}, "otu42": {"^ot:originalLabel": "Nigrogryllus sibiricus", "^ot:ottId": 7903071, "^ot:ottTaxonName": "Nigrogryllus sibiricus"}, "otu43": {"^ot:originalLabel": "Acheta domesticus", "^ot:ottId": 1077640, "^ot:ottTaxonName": "Acheta domesticus"}, "otu44": {"^ot:originalLabel": "Teleogryllus emma", "^ot:ottId": 239435, "^ot:ottTaxonName": "Teleogryllus emma"}, "otu5": {"^ot:originalLabel": "Gryllus vulcanus"}, "otu6": {"^ot:originalLabel": "Gryllus longicercus"}, "otu7": {"^ot:originalLabel": "Gryllus sotol"}, "otu8": {"^ot:originalLabel": "Gryllus lightfooti"}, "otu9": {"^ot:originalLabel": "Gryllus transpecos"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Gray_et_al_Gryllus_RAxML_tree.nex", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum likelihood ", "^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"}, "edge82": {"@source": "node1", "@target": "node83"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge29": {"@source": "node10", "@target": "node30"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge28": {"@source": "node11", "@target": "node29"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge23": {"@source": "node12", "@target": "node24"}}, "node13": {"edge13": {"@source": "node13", "@target": "node14"}, "edge20": {"@source": "node13", "@target": "node21"}}, "node14": {"edge14": {"@source": "node14", "@target": "node15"}, "edge17": {"@source": "node14", "@target": "node18"}}, "node15": {"edge15": {"@source": "node15", "@target": "node16"}, "edge16": {"@source": "node15", "@target": "node17"}}, "node18": {"edge18": {"@source": "node18", "@target": "node19"}, "edge19": {"@source": "node18", "@target": "node20"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge79": {"@source": "node2", "@target": "node80"}}, "node21": {"edge21": {"@source": "node21", "@target": "node22"}, "edge22": {"@source": "node21", "@target": "node23"}}, "node24": {"edge24": {"@source": "node24", "@target": "node25"}, "edge27": {"@source": "node24", "@target": "node28"}}, "node25": {"edge25": {"@source": "node25", "@target": "node26"}, "edge26": {"@source": "node25", "@target": "node27"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge78": {"@source": "node3", "@target": "node79"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge34": {"@source": "node31", "@target": "node35"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge33": {"@source": "node32", "@target": "node34"}}, "node36": {"edge36": {"@source": "node36", "@target": "node37"}, "edge37": {"@source": "node36", "@target": "node38"}}, "node39": {"edge39": {"@source": "node39", "@target": "node40"}, "edge50": {"@source": "node39", "@target": "node51"}}, "node4": {"edge4": {"@source": "node4", "@target": "node5"}, "edge75": {"@source": "node4", "@target": "node76"}}, "node40": {"edge40": {"@source": "node40", "@target": "node41"}, "edge45": {"@source": "node40", "@target": "node46"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge42": {"@source": "node41", "@target": "node43"}}, "node43": {"edge43": {"@source": "node43", "@target": "node44"}, "edge44": {"@source": "node43", "@target": "node45"}}, "node46": {"edge46": {"@source": "node46", "@target": "node47"}, "edge49": {"@source": "node46", "@target": "node50"}}, "node47": {"edge47": {"@source": "node47", "@target": "node48"}, "edge48": {"@source": "node47", "@target": "node49"}}, "node5": {"edge5": {"@source": "node5", "@target": "node6"}, "edge74": {"@source": "node5", "@target": "node75"}}, "node51": {"edge51": {"@source": "node51", "@target": "node52"}, "edge54": {"@source": "node51", "@target": "node55"}}, "node52": {"edge52": {"@source": "node52", "@target": "node53"}, "edge53": {"@source": "node52", "@target": "node54"}}, "node55": {"edge55": {"@source": "node55", "@target": "node56"}, "edge58": {"@source": "node55", "@target": "node59"}}, "node56": {"edge56": {"@source": "node56", "@target": "node57"}, "edge57": {"@source": "node56", "@target": "node58"}}, "node6": {"edge59": {"@source": "node6", "@target": "node60"}, "edge6": {"@source": "node6", "@target": "node7"}}, "node60": {"edge60": {"@source": "node60", "@target": "node61"}, "edge71": {"@source": "node60", "@target": "node72"}}, "node61": {"edge61": {"@source": "node61", "@target": "node62"}, "edge64": {"@source": "node61", "@target": "node65"}}, "node62": {"edge62": {"@source": "node62", "@target": "node63"}, "edge63": {"@source": "node62", "@target": "node64"}}, "node65": {"edge65": {"@source": "node65", "@target": "node66"}, "edge70": {"@source": "node65", "@target": "node71"}}, "node66": {"edge66": {"@source": "node66", "@target": "node67"}, "edge69": {"@source": "node66", "@target": "node70"}}, "node67": {"edge67": {"@source": "node67", "@target": "node68"}, "edge68": {"@source": "node67", "@target": "node69"}}, "node7": {"edge38": {"@source": "node7", "@target": "node39"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node72": {"edge72": {"@source": "node72", "@target": "node73"}, "edge73": {"@source": "node72", "@target": "node74"}}, "node76": {"edge76": {"@source": "node76", "@target": "node77"}, "edge77": {"@source": "node76", "@target": "node78"}}, "node8": {"edge35": {"@source": "node8", "@target": "node36"}, "edge8": {"@source": "node8", "@target": "node9"}}, "node80": {"edge80": {"@source": "node80", "@target": "node81"}, "edge81": {"@source": "node80", "@target": "node82"}}, "node83": {"edge83": {"@source": "node83", "@target": "node84"}, "edge86": {"@source": "node83", "@target": "node87"}}, "node84": {"edge84": {"@source": "node84", "@target": "node85"}, "edge85": {"@source": "node84", "@target": "node86"}}, "node9": {"edge30": {"@source": "node9", "@target": "node31"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {}, "node12": {}, "node13": {}, "node14": {}, "node15": {}, "node16": {"@otu": "otu1"}, "node17": {"@otu": "otu2"}, "node18": {}, "node19": {"@otu": "otu3"}, "node2": {}, "node20": {"@otu": "otu4"}, "node21": {}, "node22": {"@otu": "otu5"}, "node23": {"@otu": "otu6"}, "node24": {}, "node25": {}, "node26": {"@otu": "otu7"}, "node27": {"@otu": "otu8"}, "node28": {"@otu": "otu9"}, "node29": {"@otu": "otu10"}, "node3": {}, "node30": {"@otu": "otu11"}, "node31": {}, "node32": {}, "node33": {"@otu": "otu12"}, "node34": {"@otu": "otu13"}, "node35": {"@otu": "otu14"}, "node36": {}, "node37": {"@otu": "otu15"}, "node38": {"@otu": "otu16"}, "node39": {}, "node4": {}, "node40": {}, "node41": {}, "node42": {"@otu": "otu17"}, "node43": {}, "node44": {"@otu": "otu18"}, "node45": {"@otu": "otu19"}, "node46": {}, "node47": {}, "node48": {"@otu": "otu20"}, "node49": {"@otu": "otu21"}, "node5": {}, "node50": {"@otu": "otu22"}, "node51": {}, "node52": {}, "node53": {"@otu": "otu23"}, "node54": {"@otu": "otu24"}, "node55": {}, "node56": {}, "node57": {"@otu": "otu25"}, "node58": {"@otu": "otu26"}, "node59": {"@otu": "otu27"}, "node6": {}, "node60": {}, "node61": {}, "node62": {}, "node63": {"@otu": "otu28"}, "node64": {"@otu": "otu29"}, "node65": {}, "node66": {}, "node67": {}, "node68": {"@otu": "otu30"}, "node69": {"@otu": "otu31"}, "node7": {}, "node70": {"@otu": "otu32"}, "node71": {"@otu": "otu33"}, "node72": {}, "node73": {"@otu": "otu34"}, "node74": {"@otu": "otu35"}, "node75": {"@otu": "otu36"}, "node76": {}, "node77": {"@otu": "otu37"}, "node78": {"@otu": "otu38"}, "node79": {"@otu": "otu39"}, "node8": {}, "node80": {}, "node81": {"@otu": "otu40"}, "node82": {"@otu": "otu41"}, "node83": {}, "node84": {}, "node85": {"@otu": "otu42"}, "node86": {"@otu": "otu43"}, "node87": {"@otu": "otu44"}, "node9": {}}}}}}}}, "branch2sha": {"master": "2aa180baef3c5e313da1e7f09c83ce2c0467b457"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "e01e592ce5374fa2c50451ade1a5028abd03e8f3", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Mon, 5 May 2025 02:21:13 +0000", "date_ISO_8601": "2025-05-05 02:21:13 +0000", "relative_date": "12 months ago", "message_subject": "Initial commit Gray et al. (2020)", "message_body": "Gray2020Gryllus.nwk\nSpecies Gryllus_montis paraphyletic.\n\n(Update document 'ot_2781' via OpenTree API)"}, {"id": "9a45e15650e3aa103c7d2748cb2ee4b2c04e827f", "author_name": "dchesters", "author_email": "dc0357548934@live.co.uk", "date": "Mon, 5 May 2025 02:17:44 +0000", "date_ISO_8601": "2025-05-05 02:17:44 +0000", "relative_date": "12 months ago", "message_subject": "Update document 'ot_2781' via OpenTree API"}]}