{"id":"https://openalex.org/W2134113602","doi":"https://doi.org/10.1080/10635150802166046","title":"A Bayesian Perspective on a Non-parsimonious Parsimony Model","display_name":"A Bayesian Perspective on a Non-parsimonious Parsimony Model","publication_year":2008,"publication_date":"2008-06-01","ids":{"openalex":"https://openalex.org/W2134113602","doi":"https://doi.org/10.1080/10635150802166046","mag":"2134113602","pmid":"https://pubmed.ncbi.nlm.nih.gov/18570035"},"language":"en","primary_location":{"id":"doi:10.1080/10635150802166046","doi":"https://doi.org/10.1080/10635150802166046","is_oa":false,"landing_page_url":"https://doi.org/10.1080/10635150802166046","pdf_url":null,"source":{"id":"https://openalex.org/S65478581","display_name":"Systematic Biology","issn_l":"1063-5157","issn":["1063-5157","1076-836X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-3","ki-jl-1","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Systematic Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068909032","display_name":"John P. Huelsenbeck","orcid":"https://orcid.org/0000-0002-3050-9997","observed_orcids":["https://orcid.org/0000-0002-3050-9997"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John P Huelsenbeck","raw_affiliation_strings":["Department of Integrative Biology, University of California, Berkeley 3060 VLSB No. 3140, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrative Biology, University of California, Berkeley 3060 VLSB No. 3140, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031584591","display_name":"C\u00e9cile An\u00e9","orcid":"https://orcid.org/0000-0002-4702-8217","observed_orcids":["https://orcid.org/0000-0002-4702-8217"]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C\u00e9cile An\u00e9","raw_affiliation_strings":["Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI, USA","Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053292653","display_name":"Bret R. Larget","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bret Larget","raw_affiliation_strings":["Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI, USA","Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048208979","display_name":"Fredrik Ronquist","orcid":"https://orcid.org/0000-0002-3929-251X","observed_orcids":["https://orcid.org/0000-0002-3929-251X"]},"institutions":[{"id":"https://openalex.org/I2801711128","display_name":"Swedish Museum of Natural History","ror":"https://ror.org/05k323c76","country_code":"SE","type":"archive","lineage":["https://openalex.org/I2801711128"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Fredrik Ronquist","raw_affiliation_strings":["Swedish Museum of Natural History, Box 50007, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swedish Museum of Natural History, Box 50007, Stockholm, Sweden","institution_ids":["https://openalex.org/I2801711128"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5068909032"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":2166,"currency":"USD","value_usd":2166},"apc_paid":null,"fwci":1.37,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.7966584,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"57","issue":"3","first_page":"406","last_page":"419"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8955000042915344,"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":0.8955000042915344,"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":0.015599999576807022,"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/T12056","display_name":"Markov Chains and Monte Carlo Methods","score":0.014399999752640724,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/maximum-parsimony","display_name":"maximum parsimony","score":0.8479999899864197},{"id":"https://openalex.org/keywords/bayesian-phylogenetics","display_name":"Bayesian phylogenetics","score":0.843999981880188},{"id":"https://openalex.org/keywords/marginal-likelihood","display_name":"marginal likelihood","score":0.7620000243186951}],"concepts":[{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.718027651309967},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6080805063247681},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5997969508171082},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.570192277431488},{"id":"https://openalex.org/C57830394","wikidata":"https://www.wikidata.org/wiki/Q278079","display_name":"Posterior probability","level":3,"score":0.5547639727592468},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5417355895042419},{"id":"https://openalex.org/C95923904","wikidata":"https://www.wikidata.org/wiki/Q6760420","display_name":"Marginal likelihood","level":3,"score":0.5367404818534851},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5182011723518372},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5171610713005066},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.4835614860057831},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4534088671207428},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.42667266726493835},{"id":"https://openalex.org/C73586568","wikidata":"https://www.wikidata.org/wiki/Q2600211","display_name":"Parameter space","level":2,"score":0.42481112480163574},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.247254878282547},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.186070054769516},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16212865710258484},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005914","descriptor_name":"Globins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1080/10635150802166046","doi":"https://doi.org/10.1080/10635150802166046","is_oa":false,"landing_page_url":"https://doi.org/10.1080/10635150802166046","pdf_url":null,"source":{"id":"https://openalex.org/S65478581","display_name":"Systematic Biology","issn_l":"1063-5157","issn":["1063-5157","1076-836X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-3","ki-jl-1","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Systematic Biology","raw_type":"journal-article"},{"id":"pmid:18570035","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18570035","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Systematic biology","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G173923842","display_name":null,"funder_award_id":"R01 GM-069801","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3184487981","display_name":null,"funder_award_id":"GM069801","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7396665720","display_name":"Extending Bayesian Phylogenetic Analysis","funder_award_id":"5r01gm069801-09","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7461682145","display_name":"Model Choice and Model Averaging in Molecular Phylogenetics","funder_award_id":"0445453","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W48223389","https://openalex.org/W1525734744","https://openalex.org/W1531406273","https://openalex.org/W1565693361","https://openalex.org/W1579352620","https://openalex.org/W1585365342","https://openalex.org/W1593676244","https://openalex.org/W1759730364","https://openalex.org/W1844951369","https://openalex.org/W1966972227","https://openalex.org/W1971273325","https://openalex.org/W1984965430","https://openalex.org/W1991965330","https://openalex.org/W2003197664","https://openalex.org/W2004239648","https://openalex.org/W2043379280","https://openalex.org/W2048335804","https://openalex.org/W2056760934","https://openalex.org/W2102424972","https://openalex.org/W2102528464","https://openalex.org/W2117752525","https://openalex.org/W2122082385","https://openalex.org/W2124988091","https://openalex.org/W2128706909","https://openalex.org/W2130416410","https://openalex.org/W2138309709","https://openalex.org/W2139421741","https://openalex.org/W2143183702","https://openalex.org/W2144427666","https://openalex.org/W2151949784","https://openalex.org/W2155343574","https://openalex.org/W2160364329","https://openalex.org/W2161647617","https://openalex.org/W2161836094","https://openalex.org/W2164406317","https://openalex.org/W2164789250","https://openalex.org/W2319943156","https://openalex.org/W2322461341","https://openalex.org/W2327660108","https://openalex.org/W2330719889","https://openalex.org/W2334679888","https://openalex.org/W2371818109","https://openalex.org/W2937773112","https://openalex.org/W3004825006","https://openalex.org/W3217097258","https://openalex.org/W4231958944","https://openalex.org/W4233815609","https://openalex.org/W4239617799","https://openalex.org/W4244797807","https://openalex.org/W4247332402","https://openalex.org/W4248373945","https://openalex.org/W4253882016"],"related_works":["https://openalex.org/W7095478943","https://openalex.org/W2125562015","https://openalex.org/W2168697257","https://openalex.org/W3151952724","https://openalex.org/W4239866432","https://openalex.org/W7097216327","https://openalex.org/W7097210869","https://openalex.org/W1974764231","https://openalex.org/W2757042507","https://openalex.org/W7098496177"],"abstract_inverted_index":{"Several":[0],"stochastic":[1],"models":[2,246],"of":[3,27,45,60,117,129,134,158,166,179,192,195,213,222,228,238],"character":[4,230],"change,":[5],"when":[6],"implemented":[7,149,244],"in":[8,56,225,247],"a":[9,17,72,176,184,196,251],"maximum":[10,21,28,203],"likelihood":[11,172],"framework,":[12],"are":[13,91],"known":[14],"to":[15,75,93,104,123,136,143,174],"give":[16],"correspondence":[18],"between":[19],"the":[20,25,46,58,66,76,87,97,115,126,140,144,156,164,167,180,187,193,202,207,210,214,226,236],"parsimony":[22,181,204],"method":[23,26,112,205,217],"and":[24,42,79,100,186,232],"likelihood.":[29],"One":[30],"such":[31],"model":[32,78],"has":[33],"an":[34,106,152],"independently":[35],"estimated":[36],"branch-length":[37,88,168,253],"parameter":[38],"for":[39,113,131,183,234,245],"each":[40,43,159],"site":[41],"branch":[44,98,197],"phylogenetic":[47,118,132],"tree.":[48,215],"This":[49],"model--the":[50],"no-common-mechanism":[51,77],"model--has":[52],"many":[53],"parameters,":[54],"and,":[55],"fact,":[57],"number":[59],"parameters":[61],"increases":[62],"as":[63,65,148],"fast":[64],"alignment":[67],"is":[68,198,221],"extended.":[69],"We":[70,90,120],"take":[71],"Bayesian":[73,141],"approach":[74,142],"place":[80],"independent":[81,153],"gamma":[82],"prior":[83,154],"probability":[84,190],"distributions":[85],"on":[86,155],"parameters.":[89,169],"able":[92,122],"analytically":[94],"integrate":[95],"over":[96],"lengths,":[99],"this":[101],"allowed":[102],"us":[103],"implement":[105],"efficient":[107],"Markov":[108,239],"chain":[109,240],"Monte":[110,241],"Carlo":[111,242],"exploring":[114],"space":[116],"trees.":[119],"were":[121],"reliably":[124],"estimate":[125],"posterior":[127,189],"probabilities":[128],"clades":[130],"trees":[133],"up":[135],"500":[137],"sequences.":[138],"However,":[139],"problem,":[145],"at":[146,209],"least":[147],"here":[150],"with":[151],"length":[157,194],"branch,":[160],"does":[161],"not":[162],"tame":[163],"behavior":[165,237],"The":[170,216],"integrated":[171],"appears":[173],"be":[175],"simple":[177],"rescaling":[178],"score":[182],"tree,":[185],"marginal":[188],"distribution":[191],"dependent":[199],"upon":[200],"how":[201],"reconstructs":[206],"characters":[208],"interior":[211],"nodes":[212],"we":[218],"describe,":[219],"however,":[220],"potential":[223],"importance":[224],"analysis":[227],"morphological":[229],"data":[231],"also":[233],"improving":[235],"methods":[243],"which":[248],"sites":[249],"share":[250],"common":[252],"parameter.":[254]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}