{"id":"https://openalex.org/W7225813258","doi":"https://doi.org/10.64898/2026.11.09.765192","title":"TaxaAudit: A statistical model of consensus in phylogenetics identifies non-monophyletic taxa","display_name":"TaxaAudit: A statistical model of consensus in phylogenetics identifies non-monophyletic taxa","publication_year":2026,"publication_date":"2026-11-11","ids":{"openalex":"https://openalex.org/W7225813258","doi":"https://doi.org/10.64898/2026.11.09.765192"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.09.765192","doi":"https://doi.org/10.64898/2026.11.09.765192","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.09.765192","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.11.09.765192","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086474584","display_name":"John B. Allard","orcid":"https://orcid.org/0009-0000-7766-0769","observed_orcids":["https://orcid.org/0009-0000-7766-0769"]},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John Benjamin Allard","raw_affiliation_strings":["Temple University"],"raw_orcid":"https://orcid.org/0009-0000-7766-0769","affiliations":[{"raw_affiliation_string":"Temple University","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091689845","display_name":"Jack M. Craig","orcid":"https://orcid.org/0000-0003-0590-5944","observed_orcids":["https://orcid.org/0000-0003-0590-5944"]},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack M Craig","raw_affiliation_strings":["Temple University"],"raw_orcid":"https://orcid.org/0000-0003-0590-5944","affiliations":[{"raw_affiliation_string":"Temple University","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100680948","display_name":"Sudhir Kumar","orcid":"https://orcid.org/0000-0002-9918-8212","observed_orcids":["https://orcid.org/0000-0002-9918-8212","https://orcid.org/0000-0001-9673-5842"]},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Temple University"],"raw_orcid":"https://orcid.org/0000-0002-9918-8212","affiliations":[{"raw_affiliation_string":"Temple University","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5086474584"],"corresponding_institution_ids":["https://openalex.org/I84392919"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.003700000001117587,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10385","display_name":"Plant Diversity and Evolution","score":0.0017999999690800905,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[],"concepts":[{"id":"https://openalex.org/C12326286","wikidata":"https://www.wikidata.org/wiki/Q210958","display_name":"Monophyly","level":5,"score":0.9180999994277954},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.730400025844574},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7121000289916992},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6872000098228455},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6510999798774719},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6492999792098999},{"id":"https://openalex.org/C189592816","wikidata":"https://www.wikidata.org/wiki/Q427626","display_name":"Taxonomic rank","level":3,"score":0.5809999704360962},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.5227000117301941},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.42410001158714294},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.36970001459121704},{"id":"https://openalex.org/C195239911","wikidata":"https://www.wikidata.org/wiki/Q2007033","display_name":"Molecular phylogenetics","level":4,"score":0.34220001101493835},{"id":"https://openalex.org/C20822588","wikidata":"https://www.wikidata.org/wiki/Q192210","display_name":"Cladistics","level":4,"score":0.32100000977516174},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.3082999885082245},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.30730000138282776},{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.2955999970436096},{"id":"https://openalex.org/C41806617","wikidata":"https://www.wikidata.org/wiki/Q3516404","display_name":"Systematics","level":3,"score":0.2685000002384186},{"id":"https://openalex.org/C198260499","wikidata":"https://www.wikidata.org/wiki/Q2976606","display_name":"Phylogenetic nomenclature","level":5,"score":0.2628999948501587},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.2590999901294708}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.09.765192","doi":"https://doi.org/10.64898/2026.11.09.765192","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.09.765192","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.09.765192","doi":"https://doi.org/10.64898/2026.11.09.765192","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.09.765192","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Interpreting":[0],"variation":[1],"in":[2,150],"genes":[3],"and":[4,44,81,107,129],"traits":[5],"across":[6,51],"species":[7,87],"requires":[8,48],"understanding":[9],"their":[10,147],"evolutionary":[11,42,209],"relationships.":[12],"Taxonomic":[13],"hierarchies":[14],"provide":[15],"a":[16,59],"practical":[17],"approximation":[18],"of":[19,22,84,113,203],"the":[20,25,52,82,121,153,171,193,204],"tree":[21],"life,":[23],"with":[24,124,165],"NCBI":[26,102,205],"taxonomy":[27,206],"linking":[28],"this":[29],"framework":[30,210],"directly":[31],"to":[32,89,93,145,169],"public":[33],"sequence":[34],"data.":[35],"Some":[36],"named":[37],"groups,":[38],"however,":[39],"are":[40],"not":[41,180],"clades,":[43],"recognizing":[45],"these":[46,116,160],"exceptions":[47],"knowledge":[49,190],"scattered":[50],"phylogenetics":[53],"literature.":[54],"Here":[55],"we":[56],"introduce":[57],"TaxaAudit,":[58],"statistical":[60],"model":[61,75],"that":[62],"identifies":[63],"taxonomic":[64,79],"groups":[65,176],"whose":[66,177],"monophyly":[67,118,148,161,178],"is":[68],"repeatedly":[69],"contradicted":[70],"by":[71],"published":[72,188],"phylogenies.":[73],"The":[74],"accounts":[76],"for":[77,109,196,211],"background":[78],"conflict":[80],"ability":[83],"each":[85],"study's":[86],"sampling":[88],"expose":[90],"non-monophyly.":[91],"Applied":[92],"5,865":[94],"molecular":[95],"phylogenies":[96,130,167],"from":[97,132],"TimeTree,":[98],"TaxaAudit":[99,183],"flagged":[100],"516":[101],"taxa":[103,135],"at":[104],"family":[105],"rank":[106],"below":[108],"significant":[110],"recurrent":[111],"contradiction":[112],"monophyly.":[114],"Excluding":[115],"taxa's":[117],"requirements":[119],"improved":[120,163],"taxonomy's":[122],"agreement":[123,164],"independent":[125],"phylogenomic":[126],"reference":[127,166],"trees":[128],"withheld":[131],"discovery.":[133],"Flagged":[134],"were":[136],"also":[137],"3.61":[138],"times":[139],"as":[140,142,207],"likely":[141],"matched":[143],"controls":[144],"have":[146],"challenged":[149],"publications":[151],"outside":[152],"discovery":[154],"set.":[155],"In":[156],"tree-inference":[157],"experiments,":[158],"excluding":[159],"constraints":[162],"relative":[168],"enforcing":[170],"unmodified":[172],"taxonomy.":[173],"By":[174],"identifying":[175],"should":[179],"be":[181],"assumed,":[182],"lets":[184],"researchers":[185],"draw":[186],"on":[187],"phylogenetic":[189],"without":[191],"reviewing":[192],"specialist":[194],"literature":[195],"every":[197],"taxon.":[198],"This":[199],"supports":[200],"broader":[201],"use":[202],"an":[208],"biological":[212],"comparisons.":[213]},"counts_by_year":[],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2026-11-12T00:00:00"}