{"sha": "19ec8a2da4b35c55075f155f9fb4d01281774fe5", "data": {"nexml": {"@generator": "Phylografter nexml-json exporter", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2015-09-29T15:58:33.969Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "All life"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}, {"@active": true, "@valid": true, "new": {"$": "$1"}, "old": {"$": "^(\\S*\\s+\\S*).*"}}]}, "useFuzzyMatching": true}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2015-09-29T15:58:33.969Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199095", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199095"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199096", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199096"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199097", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199097"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199099", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199099"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199100", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199100"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199101", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199101"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199104", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199104"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199105", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199105"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199108", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199108"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199109", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199109"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199110", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199110"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199111", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199111"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199112", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199112"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199113", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199113"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199116", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199116"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199117", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199117"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199118", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199118"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199119", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199119"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199120", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199120"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199121", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199121"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199122", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199122"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199129", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199129"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199130", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199130"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199131", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199131"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199132", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199132"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199135", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199135"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199136", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199136"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node199137", "@treesID": "trees352", "@treeID": "tree388", "@nodeID": "node199137"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75410", "otu75411", "otu75412", "otu75413", "otu75414", "otu75417", "otu75418", "otu75422", "otu75425", "otu75428", "otu75430", "otu75431", "otu75437", "otu75438"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75410", "otu75411", "otu75412", "otu75413", "otu75414", "otu75417", "otu75418", "otu75425", "otu75437", "otu75440", "otu75441", "otu75455", "otu75457", "otu75463", "otu75468"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75415", "otu75416", "otu75423", "otu75424", "otu75427", "otu75432", "otu75433"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75416", "otu75423", "otu75424", "otu75433", "otu75443", "otu75451", "otu75456", "otu75458", "otu75460", "otu75461", "otu75465", "otu75466", "otu75469"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75419", "otu75434", "otu75435"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75420", "otu75426", "otu75429", "otu75439"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75444", "otu75454"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75445", "otu75452"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75446", "otu75453", "otu75462"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75448", "otu75467"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75450", "otu75464"], "refersTo": {"@top": "otus", "@idref": "otus352", "@otusID": "otus352"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree387", "@treesID": "trees352", "@treeID": "tree387"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree388", "@treesID": "trees352", "@treeID": "tree388"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree388"], "^ot:comment": "", "^ot:curatorName": ["Romina Gazis"], "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S779"}, "^ot:focalClade": 359501, "^ot:focalCladeOTTTaxonName": "Trichoderma (genus in family Hypocreaceae)", "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus352"], "^ot:studyId": "pg_352", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.2307/3761854"}, "^ot:studyPublicationReference": "Samuels G., Dodd S., Gams W., Castlebury L., & Petrini O. 2002. Trichoderma species associated with the green mold epidemic of commercially grown Agaricus bisporus. Mycologia, 94(1): 146-170.", "^ot:studyYear": 2002, "^ot:tag": [], "^ot:treesElementOrder": ["trees352"], "^xhtml:license": {"@href": "http://creativecommons.org/publicdomain/zero/1.0/", "@name": "CC0"}, "otusById": {"otus352": {"otuById": {"otu75410": {"^ot:originalLabel": "Trichoderma harzianum GJS99.231", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl125412"}, "otu75411": {"^ot:originalLabel": "Trichoderma harzianum IMI359823", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl125417"}, "otu75412": {"^ot:originalLabel": "Trichoderma harzianum GJS99.230", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl125420"}, "otu75413": {"^ot:originalLabel": "Trichoderma harzianum CBS226.95", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl125421"}, "otu75414": {"^ot:originalLabel": "Trichoderma harzianum GJS99.225", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl125462"}, "otu75415": {"^ot:originalLabel": "Trichoderma aggressivum TH2 CBS100526", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl20999"}, "otu75416": {"^ot:originalLabel": "Trichoderma aggressivum TH2 CBS689.94", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21000"}, "otu75417": {"^ot:originalLabel": "Trichoderma harzianum NR6883", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21001"}, "otu75418": {"^ot:originalLabel": "Trichoderma harzianum CBS227.95", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21002"}, "otu75419": {"^ot:originalLabel": "Trichoderma atroviride GJS95.108", "^ot:ottId": 990757, "^ot:ottTaxonName": "Trichoderma atroviride", "^ot:treebaseOTUId": "Tl21003"}, "otu75420": {"^ot:originalLabel": "Trichoderma viride BBA70239", "^ot:ottId": 939823, "^ot:ottTaxonName": "Hypocrea rufa", "^ot:treebaseOTUId": "Tl21004"}, "otu75421": {"^ot:originalLabel": "Hypocrea sp. GJS96.132", "^ot:ottId": 359501, "^ot:ottTaxonName": "Trichoderma", "^ot:treebaseOTUId": "Tl21005"}, "otu75422": {"^ot:originalLabel": "Trichoderma harzianum NR6938", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21006"}, "otu75423": {"^ot:originalLabel": "Trichoderma aggressivum TH2 CBS100525", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21007"}, "otu75424": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS99.29", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21008"}, "otu75425": {"^ot:originalLabel": "Trichoderma harzianum GJS99.227", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21009"}, "otu75426": {"^ot:originalLabel": "Hypocrea rufa GJS99.140", "^ot:ottId": 939823, "^ot:ottTaxonName": "Hypocrea rufa", "^ot:treebaseOTUId": "Tl21010"}, "otu75427": {"^ot:originalLabel": "Trichoderma aggressivum TH4 DAOM222156", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21011"}, "otu75428": {"^ot:originalLabel": "Trichoderma harzianum NR6931", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21012"}, "otu75429": {"^ot:originalLabel": "Hypocrea rufa GJS99.203", "^ot:ottId": 939823, "^ot:ottTaxonName": "Hypocrea rufa", "^ot:treebaseOTUId": "Tl21013"}, "otu75430": {"^ot:originalLabel": "Trichoderma harzianum NR6950", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21014"}, "otu75431": {"^ot:originalLabel": "Trichoderma harzianum CBS273.78", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21015"}, "otu75432": {"^ot:originalLabel": "Trichoderma aggressivum TH2 CBS433.95", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21016"}, "otu75433": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS99.30", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21017"}, "otu75434": {"^ot:originalLabel": "Trichoderma atroviride GJS90.134", "^ot:ottId": 990757, "^ot:ottTaxonName": "Trichoderma atroviride", "^ot:treebaseOTUId": "Tl21018"}, "otu75435": {"^ot:originalLabel": "Trichoderma atroviride GJS95.10", "^ot:ottId": 990757, "^ot:ottTaxonName": "Trichoderma atroviride", "^ot:treebaseOTUId": "Tl21019"}, "otu75436": {"^ot:originalLabel": "Hypocrea vinosa GJS99.83", "^ot:ottId": 208923, "^ot:ottTaxonName": "Hypocrea vinosa", "^ot:treebaseOTUId": "Tl21020"}, "otu75437": {"^ot:originalLabel": "Trichoderma harzianum NR6929", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21021"}, "otu75438": {"^ot:originalLabel": "Trichoderma harzianum GJS95.81", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21022"}, "otu75439": {"^ot:originalLabel": "Hypocrea rufa GJS99.105", "^ot:ottId": 939823, "^ot:ottTaxonName": "Hypocrea rufa", "^ot:treebaseOTUId": "Tl21023"}, "otu75440": {"^ot:originalLabel": "Trichoderma harzianum TR108", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21024"}, "otu75441": {"^ot:originalLabel": "Trichoderma harzianum GJS99.226", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21025"}, "otu75442": {"^ot:originalLabel": "Trichoderma longibrachiatum AJ230665", "^ot:ottId": 939814, "^ot:ottTaxonName": "Trichoderma longibrachiatum", "^ot:treebaseOTUId": "Tl21026"}, "otu75443": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS95.111", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21027"}, "otu75444": {"^ot:originalLabel": "Trichoderma inhamatum CBS273.78", "^ot:ottId": 237873, "^ot:ottTaxonName": "Trichoderma inhamatum", "^ot:treebaseOTUId": "Tl21028"}, "otu75445": {"^ot:originalLabel": "Trichoderma viride X93986", "^ot:ottId": 939823, "^ot:ottTaxonName": "Hypocrea rufa", "^ot:treebaseOTUId": "Tl21029"}, "otu75446": {"^ot:originalLabel": "Trichoderma aureoviride NR6938", "^ot:ottId": 236001, "^ot:ottTaxonName": "Trichoderma aureoviride", "^ot:treebaseOTUId": "Tl21030"}, "otu75447": {"^ot:originalLabel": "Trichoderma koningii Z79628", "^ot:ottId": 855112, "^ot:ottTaxonName": "Trichoderma koningii", "^ot:treebaseOTUId": "Tl21031"}, "otu75448": {"^ot:originalLabel": "Trichoderma asperellum AJ230669", "^ot:ottId": 939390, "^ot:ottTaxonName": "Trichoderma asperellum", "^ot:treebaseOTUId": "Tl21032"}, "otu75449": {"^ot:originalLabel": "Trichoderma citrinoviride AJ230663", "^ot:ottId": 237866, "^ot:ottTaxonName": "Trichoderma citrinoviride", "^ot:treebaseOTUId": "Tl21033"}, "otu75450": {"^ot:originalLabel": "Trichoderma atroviride GJS95.12", "^ot:ottId": 990757, "^ot:ottTaxonName": "Trichoderma atroviride", "^ot:treebaseOTUId": "Tl21034"}, "otu75451": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS95.118", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21035"}, "otu75452": {"^ot:originalLabel": "Hypocrea rufa AJ230667", "^ot:ottId": 939823, "^ot:ottTaxonName": "Hypocrea rufa", "^ot:treebaseOTUId": "Tl21036"}, "otu75453": {"^ot:originalLabel": "Trichoderma aureoviride NR6931", "^ot:ottId": 236001, "^ot:ottTaxonName": "Trichoderma aureoviride", "^ot:treebaseOTUId": "Tl21037"}, "otu75454": {"^ot:originalLabel": "Trichoderma inhamatum Z68188", "^ot:ottId": 237873, "^ot:ottTaxonName": "Trichoderma inhamatum", "^ot:treebaseOTUId": "Tl21038"}, "otu75455": {"^ot:originalLabel": "Trichoderma harzianum AF055213", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21039"}, "otu75456": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS95.117", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21040"}, "otu75457": {"^ot:originalLabel": "Trichoderma harzianum NR5555", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21041"}, "otu75458": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS95.122", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21042"}, "otu75459": {"^ot:originalLabel": "Trichoderma hamatum Z48816", "^ot:ottId": 499334, "^ot:ottTaxonName": "Trichoderma hamatum", "^ot:treebaseOTUId": "Tl21043"}, "otu75460": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS95.115", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21044"}, "otu75461": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS95.128", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21045"}, "otu75462": {"^ot:originalLabel": "Trichoderma aureoviride NR6950", "^ot:ottId": 236001, "^ot:ottTaxonName": "Trichoderma aureoviride", "^ot:treebaseOTUId": "Tl21046"}, "otu75463": {"^ot:originalLabel": "Trichoderma harzianum NR5546", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21047"}, "otu75464": {"^ot:originalLabel": "Trichoderma atroviride CBS351.93", "^ot:ottId": 990757, "^ot:ottTaxonName": "Trichoderma atroviride", "^ot:treebaseOTUId": "Tl21048"}, "otu75465": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS99.31", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21049"}, "otu75466": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS99.32", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21050"}, "otu75467": {"^ot:originalLabel": "Trichoderma asperellum AJ230668", "^ot:ottId": 939390, "^ot:ottTaxonName": "Trichoderma asperellum", "^ot:treebaseOTUId": "Tl21051"}, "otu75468": {"^ot:originalLabel": "Trichoderma harzianum GJS95.14", "^ot:ottId": 939829, "^ot:ottTaxonName": "Trichoderma harzianum", "^ot:treebaseOTUId": "Tl21052"}, "otu75469": {"^ot:originalLabel": "Trichoderma aggressivum TH4 GJS99.33", "^ot:ottId": 151293, "^ot:ottTaxonName": "Trichoderma aggressivum", "^ot:treebaseOTUId": "Tl21053"}}}}, "treesById": {"trees352": {"@otus": "otus352", "^ot:treeElementOrder": ["tree387", "tree388"], "treeById": {"tree387": {"@label": "FIG. 1.\u2003Phylogenetic relations among 33 T. harzianum, eight T. sect Trichoderma and two T. sect Longibrachiatum isolates inferred by neighbor-joining analysis of ITS-1 sequences. ", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:changesCount", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Neighbor-joining ", "^ot:inGroupClade": "node199029", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node199026", "^ot:specifiedRoot": "node199026", "^ot:tag": ["ITS"], "^ot:unrootedTree": false, "edgeBySourceId": {"node199026": {"edge199027": {"@source": "node199026", "@target": "node199027"}, "edge199028": {"@source": "node199026", "@target": "node199028"}, "edge199029": {"@source": "node199026", "@target": "node199029"}}, "node199029": {"edge199030": {"@source": "node199029", "@target": "node199030"}, "edge199074": {"@source": "node199029", "@target": "node199074"}}, "node199030": {"edge199031": {"@source": "node199030", "@target": "node199031"}, "edge199056": {"@source": "node199030", "@target": "node199056"}}, "node199031": {"edge199032": {"@source": "node199031", "@target": "node199032"}, "edge199055": {"@source": "node199031", "@target": "node199055"}}, "node199032": {"edge199033": {"@source": "node199032", "@target": "node199033"}, "edge199043": {"@source": "node199032", "@target": "node199043"}}, "node199033": {"edge199034": {"@source": "node199033", "@target": "node199034"}, "edge199035": {"@source": "node199033", "@target": "node199035"}, "edge199036": {"@source": "node199033", "@target": "node199036"}, "edge199037": {"@source": "node199033", "@target": "node199037"}, "edge199038": {"@source": "node199033", "@target": "node199038"}, "edge199039": {"@source": "node199033", "@target": "node199039"}, "edge199040": {"@source": "node199033", "@target": "node199040"}, "edge199041": {"@source": "node199033", "@target": "node199041"}, "edge199042": {"@source": "node199033", "@target": "node199042"}}, "node199043": {"edge199044": {"@source": "node199043", "@target": "node199044"}, "edge199053": {"@source": "node199043", "@target": "node199053"}, "edge199054": {"@source": "node199043", "@target": "node199054"}}, "node199044": {"edge199045": {"@source": "node199044", "@target": "node199045"}, "edge199046": {"@source": "node199044", "@target": "node199046"}, "edge199047": {"@source": "node199044", "@target": "node199047"}, "edge199048": {"@source": "node199044", "@target": "node199048"}, "edge199049": {"@source": "node199044", "@target": "node199049"}, "edge199050": {"@source": "node199044", "@target": "node199050"}, "edge199051": {"@source": "node199044", "@target": "node199051"}, "edge199052": {"@source": "node199044", "@target": "node199052"}}, "node199056": {"edge199057": {"@source": "node199056", "@target": "node199057"}, "edge199058": {"@source": "node199056", "@target": "node199058"}, "edge199061": {"@source": "node199056", "@target": "node199061"}, "edge199062": {"@source": "node199056", "@target": "node199062"}, "edge199063": {"@source": "node199056", "@target": "node199063"}, "edge199064": {"@source": "node199056", "@target": "node199064"}, "edge199065": {"@source": "node199056", "@target": "node199065"}, "edge199066": {"@source": "node199056", "@target": "node199066"}, "edge199067": {"@source": "node199056", "@target": "node199067"}}, "node199058": {"edge199059": {"@source": "node199058", "@target": "node199059"}, "edge199060": {"@source": "node199058", "@target": "node199060"}}, "node199067": {"edge199068": {"@source": "node199067", "@target": "node199068"}, "edge199069": {"@source": "node199067", "@target": "node199069"}}, "node199069": {"edge199070": {"@source": "node199069", "@target": "node199070"}, "edge199071": {"@source": "node199069", "@target": "node199071"}}, "node199071": {"edge199072": {"@source": "node199071", "@target": "node199072"}, "edge199073": {"@source": "node199071", "@target": "node199073"}}, "node199074": {"edge199075": {"@source": "node199074", "@target": "node199075"}, "edge199083": {"@source": "node199074", "@target": "node199083"}}, "node199075": {"edge199076": {"@source": "node199075", "@target": "node199076"}, "edge199082": {"@source": "node199075", "@target": "node199082"}}, "node199076": {"edge199077": {"@source": "node199076", "@target": "node199077"}, "edge199078": {"@source": "node199076", "@target": "node199078"}, "edge199081": {"@source": "node199076", "@target": "node199081"}}, "node199078": {"edge199079": {"@source": "node199078", "@target": "node199079"}, "edge199080": {"@source": "node199078", "@target": "node199080"}}, "node199083": {"edge199084": {"@source": "node199083", "@target": "node199084"}, "edge199085": {"@source": "node199083", "@target": "node199085"}}, "node199085": {"edge199086": {"@source": "node199085", "@target": "node199086"}, "edge199087": {"@source": "node199085", "@target": "node199087"}}}, "nodeById": {"node199026": {"@root": true}, "node199027": {"@otu": "otu75442"}, "node199028": {"@otu": "otu75449"}, "node199029": {}, "node199030": {}, "node199031": {}, "node199032": {}, "node199033": {}, "node199034": {"@otu": "otu75413"}, "node199035": {"@otu": "otu75454"}, "node199036": {"@otu": "otu75425"}, "node199037": {"@otu": "otu75410"}, "node199038": {"@otu": "otu75418"}, "node199039": {"@otu": "otu75455"}, "node199040": {"@otu": "otu75446"}, "node199041": {"@otu": "otu75462"}, "node199042": {"@otu": "otu75412"}, "node199043": {}, "node199044": {}, "node199045": {"@otu": "otu75453"}, "node199046": {"@otu": "otu75414"}, "node199047": {"@otu": "otu75411"}, "node199048": {"@otu": "otu75417"}, "node199049": {"@otu": "otu75437"}, "node199050": {"@otu": "otu75444"}, "node199051": {"@otu": "otu75441"}, "node199052": {"@otu": "otu75440"}, "node199053": {"@otu": "otu75457"}, "node199054": {"@otu": "otu75463"}, "node199055": {"@otu": "otu75468"}, "node199056": {}, "node199057": {"@otu": "otu75443"}, "node199058": {}, "node199059": {"@otu": "otu75461"}, "node199060": {"@otu": "otu75424"}, "node199061": {"@otu": "otu75458"}, "node199062": {"@otu": "otu75456"}, "node199063": {"@otu": "otu75460"}, "node199064": {"@otu": "otu75466"}, "node199065": {"@otu": "otu75465"}, "node199066": {"@otu": "otu75451"}, "node199067": {}, "node199068": {"@otu": "otu75469"}, "node199069": {}, "node199070": {"@otu": "otu75433"}, "node199071": {}, "node199072": {"@otu": "otu75423"}, "node199073": {"@otu": "otu75416"}, "node199074": {}, "node199075": {}, "node199076": {}, "node199077": {"@otu": "otu75450"}, "node199078": {}, "node199079": {"@otu": "otu75447"}, "node199080": {"@otu": "otu75445"}, "node199081": {"@otu": "otu75464"}, "node199082": {"@otu": "otu75452"}, "node199083": {}, "node199084": {"@otu": "otu75448"}, "node199085": {}, "node199086": {"@otu": "otu75467"}, "node199087": {"@otu": "otu75459"}}}, "tree388": {"@label": "FIG. 2.\u2003Phylogenetic relations among 21 T. harzianum and nine T. sect. Trichoderma isolates inferred by maximum parsimony analysis (590 steps, CI = 0.736; RI = 0.898; RC = 0.661) of the translation elongation factor gene 1 alpha (EF-1\u03b1). ", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:changesCount", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Maximum parsimony ", "^ot:inGroupClade": "node199088", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node199088", "^ot:specifiedRoot": "node199088", "^ot:tag": ["MP", "EF-1", "Choose me"], "^ot:unrootedTree": false, "edgeBySourceId": {"node199088": {"edge199089": {"@source": "node199088", "@target": "node199089"}, "edge199123": {"@source": "node199088", "@target": "node199123"}}, "node199089": {"edge199090": {"@source": "node199089", "@target": "node199090"}, "edge199114": {"@source": "node199089", "@target": "node199114"}}, "node199090": {"edge199091": {"@source": "node199090", "@target": "node199091"}, "edge199113": {"@source": "node199090", "@target": "node199113"}}, "node199091": {"edge199092": {"@source": "node199091", "@target": "node199092"}, "edge199102": {"@source": "node199091", "@target": "node199102"}}, "node199092": {"edge199093": {"@source": "node199092", "@target": "node199093"}, "edge199101": {"@source": "node199092", "@target": "node199101"}}, "node199093": {"edge199094": {"@source": "node199093", "@target": "node199094"}, "edge199098": {"@source": "node199093", "@target": "node199098"}}, "node199094": {"edge199095": {"@source": "node199094", "@target": "node199095"}, "edge199096": {"@source": "node199094", "@target": "node199096"}, "edge199097": {"@source": "node199094", "@target": "node199097"}}, "node199098": {"edge199099": {"@source": "node199098", "@target": "node199099"}, "edge199100": {"@source": "node199098", "@target": "node199100"}}, "node199102": {"edge199103": {"@source": "node199102", "@target": "node199103"}, "edge199106": {"@source": "node199102", "@target": "node199106"}}, "node199103": {"edge199104": {"@source": "node199103", "@target": "node199104"}, "edge199105": {"@source": "node199103", "@target": "node199105"}}, "node199106": {"edge199107": {"@source": "node199106", "@target": "node199107"}, "edge199112": {"@source": "node199106", "@target": "node199112"}}, "node199107": {"edge199108": {"@source": "node199107", "@target": "node199108"}, "edge199109": {"@source": "node199107", "@target": "node199109"}, "edge199110": {"@source": "node199107", "@target": "node199110"}, "edge199111": {"@source": "node199107", "@target": "node199111"}}, "node199114": {"edge199115": {"@source": "node199114", "@target": "node199115"}, "edge199120": {"@source": "node199114", "@target": "node199120"}, "edge199121": {"@source": "node199114", "@target": "node199121"}, "edge199122": {"@source": "node199114", "@target": "node199122"}}, "node199115": {"edge199116": {"@source": "node199115", "@target": "node199116"}, "edge199117": {"@source": "node199115", "@target": "node199117"}, "edge199118": {"@source": "node199115", "@target": "node199118"}, "edge199119": {"@source": "node199115", "@target": "node199119"}}, "node199123": {"edge199124": {"@source": "node199123", "@target": "node199124"}, "edge199139": {"@source": "node199123", "@target": "node199139"}}, "node199124": {"edge199125": {"@source": "node199124", "@target": "node199125"}, "edge199138": {"@source": "node199124", "@target": "node199138"}}, "node199125": {"edge199126": {"@source": "node199125", "@target": "node199126"}, "edge199133": {"@source": "node199125", "@target": "node199133"}}, "node199126": {"edge199127": {"@source": "node199126", "@target": "node199127"}, "edge199132": {"@source": "node199126", "@target": "node199132"}}, "node199127": {"edge199128": {"@source": "node199127", "@target": "node199128"}, "edge199131": {"@source": "node199127", "@target": "node199131"}}, "node199128": {"edge199129": {"@source": "node199128", "@target": "node199129"}, "edge199130": {"@source": "node199128", "@target": "node199130"}}, "node199133": {"edge199134": {"@source": "node199133", "@target": "node199134"}, "edge199137": {"@source": "node199133", "@target": "node199137"}}, "node199134": {"edge199135": {"@source": "node199134", "@target": "node199135"}, "edge199136": {"@source": "node199134", "@target": "node199136"}}}, "nodeById": {"node199088": {"@root": true}, "node199089": {}, "node199090": {}, "node199091": {}, "node199092": {}, "node199093": {}, "node199094": {}, "node199095": {"@otu": "otu75413", "^ot:isTaxonExemplar": false}, "node199096": {"@otu": "otu75411", "^ot:isTaxonExemplar": false}, "node199097": {"@otu": "otu75418", "^ot:isTaxonExemplar": false}, "node199098": {}, "node199099": {"@otu": "otu75412", "^ot:isTaxonExemplar": false}, "node199100": {"@otu": "otu75410", "^ot:isTaxonExemplar": false}, "node199101": {"@otu": "otu75425", "^ot:isTaxonExemplar": false}, "node199102": {}, "node199103": {}, "node199104": {"@otu": "otu75428", "^ot:isTaxonExemplar": false}, "node199105": {"@otu": "otu75431", "^ot:isTaxonExemplar": false}, "node199106": {}, "node199107": {}, "node199108": {"@otu": "otu75414", "^ot:isTaxonExemplar": false}, "node199109": {"@otu": "otu75430", "^ot:isTaxonExemplar": false}, "node199110": {"@otu": "otu75417", "^ot:isTaxonExemplar": false}, "node199111": {"@otu": "otu75437", "^ot:isTaxonExemplar": false}, "node199112": {"@otu": "otu75422", "^ot:isTaxonExemplar": false}, "node199113": {"@otu": "otu75438", "^ot:isTaxonExemplar": true}, "node199114": {}, "node199115": {}, "node199116": {"@otu": "otu75416", "^ot:isTaxonExemplar": false}, "node199117": {"@otu": "otu75415", "^ot:isTaxonExemplar": false}, "node199118": {"@otu": "otu75423", "^ot:isTaxonExemplar": false}, "node199119": {"@otu": "otu75432", "^ot:isTaxonExemplar": false}, "node199120": {"@otu": "otu75424", "^ot:isTaxonExemplar": false}, "node199121": {"@otu": "otu75433", "^ot:isTaxonExemplar": false}, "node199122": {"@otu": "otu75427", "^ot:isTaxonExemplar": true}, "node199123": {}, "node199124": {}, "node199125": {}, "node199126": {}, "node199127": {}, "node199128": {}, "node199129": {"@otu": "otu75434", "^ot:isTaxonExemplar": false}, "node199130": {"@otu": "otu75419", "^ot:isTaxonExemplar": false}, "node199131": {"@otu": "otu75435", "^ot:isTaxonExemplar": true}, "node199132": {"@otu": "otu75420", "^ot:isTaxonExemplar": true}, "node199133": {}, "node199134": {}, "node199135": {"@otu": "otu75439", "^ot:isTaxonExemplar": false}, "node199136": {"@otu": "otu75429", "^ot:isTaxonExemplar": false}, "node199137": {"@otu": "otu75426", "^ot:isTaxonExemplar": false}, "node199138": {"@otu": "otu75436"}, "node199139": {"@otu": "otu75421"}}}}}}}}, "branch2sha": {"master": "19ec8a2da4b35c55075f155f9fb4d01281774fe5"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "44de55f25d4b4e55a903e7ed251d1256c1b1e8b0", "author_name": "Romina Gazis", "author_email": "gazisromina@gmail.com", "date": "Tue, 29 Sep 2015 16:06:14 +0000", "date_ISO_8601": "2015-09-29 16:06:14 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #pg_352 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": "fb9410bc19523ea9ec208a35959e8a4cab0030d5", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Thu, 29 May 2014 11:33:49 -0500", "date_ISO_8601": "2014-05-29 11:33:49 -0500", "relative_date": "12 years ago", "message_subject": "otu labels to the new system.", "message_body": "Ran peyotl/dev/phylografter_workaround.py to\nfix this.\nNoted (in phylografter issue 119), that study\n2918 is not valid."}, {"id": "4385c49fc293c1253bd478e49a5e5cd518652f18", "author_name": "Mark T. Holder", "author_email": "None", "date": "Thu, 29 May 2014 15:23:15 +0000", "date_ISO_8601": "2014-05-29 15:23:15 +0000", "relative_date": "12 years ago", "message_subject": "Sync from phylografter", "message_body": "(Update Study #pg_352 via OpenTree API)"}, {"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"}]}