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"@idref": "otus2542", "@otusID": "otus2542"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu372322", "otu372323", "otu372324"], "refersTo": {"@top": "otus", "@idref": "otus2542", "@otusID": "otus2542"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu372330", "otu372331"], "refersTo": {"@top": "otus", "@idref": "otus2542", "@otusID": "otus2542"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu372334", "otu372335"], "refersTo": {"@top": "otus", "@idref": "otus2542", "@otusID": "otus2542"}, "@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": "tree5590", "@treesID": "trees2542", "@treeID": "tree5590"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu365311", "otu365312", "otu365313", "otu365331", "otu365673", "otu365674", "otu365675"], "@otusID": "otus2542", "@otuID": ["otu365311", "otu365312", "otu365313", "otu365331", "otu365673", "otu365674", "otu365675"]}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree5471", "@treesID": "trees2542", "@treeID": "tree5471"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree5471", "@treesID": "trees2542", "@treeID": "tree5471"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree5472", "@treesID": "trees2542", "@treeID": "tree5472"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree5588", "@treesID": "trees2542", "@treeID": "tree5588"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree5589", "@treesID": "trees2542", "@treeID": "tree5589"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree5590", "@treesID": "trees2542", "@treeID": "tree5590"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree5590"], "^ot:comment": "Rooting marked as confirmed due to being between archaea and bacteria. Rooting within each domain is not confirmed, but there is no way to mark it as such. (MW)\n* * *\nWas: \nNo trees have confirmed rooting. (JWB)\n", "^ot:curatorName": ["Jessica Grant", "Joseph W. Brown", "Benjamin Redelings", "Mingye Wang"], "^ot:dataDeposit": {"@href": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062510#s4"}, "^ot:focalClade": 844192, "^ot:focalCladeOTTTaxonName": "Bacteria", "^ot:otusElementOrder": ["otus2542"], "^ot:studyId": "pg_2542", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1371/journal.pone.0062510"}, "^ot:studyPublicationReference": "Lang, Jenna Morgan, Aaron E. Darling, Jonathan A. Eisen. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS ONE 8 (4): e62510.", "^ot:studyYear": 2013, "^ot:tag": [], "^ot:treesElementOrder": ["trees2542"], "highestMintedElementIDs": {"agent": 0, "annotation": 0, "edge": 966243, "message": 0, "node": 966243, "otu": 372349, "otus": 2542, "tree": 5590, "trees": 2542}, "otusById": {"otus2542": {"otuById": {"otu365080": {"^ot:originalLabel": "Thermovibrio ammonificans HB 1 uid62095", "^ot:ottId": 395426, "^ot:ottTaxonName": "Thermovibrio ammonificans HB-1"}, "otu365081": {"^ot:originalLabel": "Desulfurobacterium thermolithotrophum BSA DSM 11699 2503754020 faa", "^ot:ottId": 39906, "^ot:ottTaxonName": "Desulfurobacterium thermolithotrophum DSM 11699"}, "otu365082": {"^ot:originalLabel": "Persephonella marina EX H1 uid58119", "^ot:ottId": 764027, "^ot:ottTaxonName": "Persephonella marina EX-H1"}, "otu365083": {"^ot:originalLabel": "Sulfurihydrogenibium yellowstonense SS 5 uid54637", "^ot:ottId": 588444, "^ot:ottTaxonName": "Sulfurihydrogenibium yellowstonense SS-5"}, "otu365084": {"^ot:originalLabel": "Hydrogenivirga 128 5 R1 1 uid54685", "^ot:ottId": 536212, "^ot:ottTaxonName": "Hydrogenivirga sp. 128-5-R1-1"}, "otu365085": {"^ot:originalLabel": "Hydrogenobaculum Y04AAS1 uid58857", "^ot:ottId": 1053732, "^ot:ottTaxonName": "Hydrogenobaculum sp. Y04AAS1"}, "otu365086": {"^ot:originalLabel": "Thermocrinis albus HI 11 12 DSM 14484 646564582", "^ot:ottId": 47338, "^ot:ottTaxonName": "Thermocrinis albus DSM 14484"}, "otu365087": {"^ot:originalLabel": "Hydrogenobacter thermophilus TK 6 DSM 6534 2502957034", "^ot:ottId": 721428, "^ot:ottTaxonName": "Hydrogenobacter thermophilus TK-6"}, "otu365088": {"^ot:originalLabel": "Aquifex aeolicus VF5 uid57765", "^ot:ottId": 1068688, "^ot:ottTaxonName": "Aquifex aeolicus VF5"}, "otu365089": {"^ot:originalLabel": "Dictyoglomus turgidum DSM 6724 uid59177", "^ot:ottId": 742557, "^ot:ottTaxonName": "Dictyoglomus turgidum DSM 6724"}, "otu365090": {"^ot:originalLabel": "Thermodesulfobium narugense Na82 DSM 14796 2502894016", "^ot:ottId": 996390, "^ot:ottTaxonName": "Thermodesulfobium narugense DSM 14796"}, "otu365091": {"^ot:originalLabel": "Coprothermobacter proteolyticus DSM 5265 uid59253", "^ot:ottId": 300840, "^ot:ottTaxonName": "Coprothermobacter proteolyticus DSM 5265"}, "otu365092": {"^ot:originalLabel": "Thermosipho melanesiensis BI429 uid58683", "^ot:ottId": 389584, "^ot:ottTaxonName": "Thermosipho melanesiensis BI429"}, "otu365093": {"^ot:originalLabel": "Fervidobacterium nodosum Rt17 B1 uid58625", "^ot:ottId": 998293, "^ot:ottTaxonName": "Fervidobacterium nodosum Rt17-B1"}, "otu365094": {"^ot:originalLabel": "Thermotoga lettingae TMO uid58419", "^ot:ottId": 83398, "^ot:ottTaxonName": "Thermotoga lettingae TMO"}, "otu365095": {"^ot:originalLabel": "Thermotoga thermarum LA3 DSM 5069 2503508007", "^ot:ottId": 652294, "^ot:ottTaxonName": "Thermotoga thermarum DSM 5069"}, "otu365096": {"^ot:originalLabel": "Thermotoga petrophila RKU 1 uid58655", "^ot:ottId": 183077, "^ot:ottTaxonName": "Thermotoga petrophila RKU-1"}, "otu365097": {"^ot:originalLabel": "Petrotoga mobilis SJ95 uid58747", "^ot:ottId": 428768, "^ot:ottTaxonName": "Petrotoga mobilis SJ95"}, "otu365098": {"^ot:originalLabel": "Kosmotoga olearia TBF 19 5 1 uid59205", "^ot:ottId": 663037, "^ot:ottTaxonName": "Kosmotoga olearia TBF 19.5.1"}, "otu365099": {"^ot:originalLabel": "Thermotogales bacterium mesG1 Ag 4 2 uid52599", "^ot:ottId": 139416, "^ot:ottTaxonName": "Mesotoga prima MesG1.Ag.4.2"}, "otu365100": {"^ot:originalLabel": "Cloacibacillus evryensis 158 DSM 19522 2503423011", "^ot:ottId": 669316, "^ot:ottTaxonName": "Cloacibacillus evryensis DSM 19522"}, "otu365101": {"^ot:originalLabel": "Synergistes jonesii", "^ot:ottId": 304335, "^ot:ottTaxonName": "Synergistes jonesii"}, "otu365102": {"^ot:originalLabel": "Thermanaerovibrio acidaminovorans DSM 6589 uid41925", "^ot:ottId": 418171, "^ot:ottTaxonName": "Thermanaerovibrio acidaminovorans DSM 6589"}, "otu365103": {"^ot:originalLabel": "Aminomonas paucivorans DSM 12260 uid60577", "^ot:ottId": 121273, "^ot:ottTaxonName": "Aminomonas paucivorans DSM 12260"}, "otu365104": {"^ot:originalLabel": "Thermovirga lienii Cas60314 DSM 17291 2501025492", "^ot:ottId": 330861, "^ot:ottTaxonName": "Thermovirga lienii DSM 17291"}, 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Rooting within each domain is not confirmed, but there is no way to mark it as such. (MW)</p>\n<hr>\n<p>Was: \nNo trees have confirmed rooting. (JWB)</p>", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "6bed60428352c04d00341ad513a8efb9442e4d8a", "author_name": "Mingye Wang", "author_email": "arthur200126@gmail.com", "date": "Wed, 8 Apr 2026 07:59:36 +0000", "date_ISO_8601": "2026-04-08 07:59:36 +0000", "relative_date": "4 weeks ago", "message_subject": "Finish & check OTU mapping, mark as confirmed root", "message_body": "Root between bacteria and archaea can be nothing but confirmed.\n\nResolved OTU mapping errors made apparent by duplicate tips (the remaining dups cannot be resolved by name).\n\n(Update document 'pg_2542' via OpenTree API)"}, {"id": "564311022773d070238b158f1d411317ef200102", "author_name": "Benjamin Redelings", "author_email": "benjamin.redelings@gmail.com", "date": "Tue, 23 Feb 2016 19:48:59 +0000", "date_ISO_8601": "2016-02-23 19:48:59 +0000", "relative_date": "10 years ago", "message_subject": "Unmap remaining plastids.", "message_body": "(Update document 'pg_2542' via OpenTree API)"}, {"id": "9689c1c04ffb61a09b974a9f6d8d8bbf644b325b", "author_name": "Benjamin Redelings", "author_email": "benjamin.redelings@gmail.com", "date": "Tue, 23 Feb 2016 19:29:07 +0000", "date_ISO_8601": "2016-02-23 19:29:07 +0000", "relative_date": "10 years ago", "message_subject": "Unmap Malawimonas and Reclinomonas mitochondria.", "message_body": "These shouldn't be mapped to Eukaryotes in this context.\n\n(Update document 'pg_2542' via OpenTree API)"}, {"id": "845b406df5c754aad86f18677c86e7e634084421", "author_name": "Benjamin Redelings", "author_email": "benjamin.redelings@gmail.com", "date": "Tue, 23 Feb 2016 19:23:46 +0000", "date_ISO_8601": "2016-02-23 19:23:46 +0000", "relative_date": "10 years ago", "message_subject": "Unmap Nephroselmis mitochondria.", "message_body": "Nephroselmis, but its mitochondria is in some sense a Bacteria, and so shouldn't be mapped as a Eukaryote.\n\n(Update document 'pg_2542' via OpenTree API)"}, {"id": "708ff1dbf1597b1da749ef6d96af4c0602ba2771", "author_name": "Benjamin Redelings", "author_email": "benjamin.redelings@gmail.com", "date": "Tue, 23 Feb 2016 19:19:05 +0000", "date_ISO_8601": "2016-02-23 19:19:05 +0000", "relative_date": "10 years ago", "message_subject": "Unmap Paulinella chromatophora plastid.", "message_body": "Paulinella is a Eukaryote, but its plastid is in some sense a bacteria, and so shouldn't be mapped as a Eukaryote.\n\n(Update document 'pg_2542' via OpenTree API)"}, {"id": "4cdc7caa8eadc3273f6aa76dcab73110e2e84686", "author_name": "Joseph W. 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Brown", "author_email": "ANONYMOUS", "date": "Fri, 8 Aug 2014 13:38:15 +0000", "date_ISO_8601": "2014-08-08 13:38:15 +0000", "relative_date": "12 years ago", "message_subject": "citation, DIO", "message_body": "(Update Study #pg_2542 via OpenTree API)"}, {"id": "d33fb39501605772a074dffc82affa5344ea9a94", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Wed, 11 Jun 2014 22:18:34 -0500", "date_ISO_8601": "2014-06-11 22:18:34 -0500", "relative_date": "12 years ago", "message_subject": "corrected study ids"}, {"id": "593d6fbab385716dc0a12f3fc95133e8b7479b37", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Tue, 29 Apr 2014 20:05:19 -0500", "date_ISO_8601": "2014-04-29 20:05:19 -0500", "relative_date": "12 years ago", "message_subject": "initial commit with phylografter files from 29 Apr, 2014"}]}