{"id":"https://openalex.org/W2123595455","doi":null,"title":"Improving the accuracy and realism of Bayesian phylogenetic analyses","display_name":"Improving the accuracy and realism of Bayesian phylogenetic analyses","publication_year":2009,"publication_date":"2009-08-01","ids":{"openalex":"https://openalex.org/W2123595455","mag":"2123595455"},"language":"en","primary_location":{"id":"pmh:oai:repositories.lib.utexas.edu:2152/6567","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2152/6567","pdf_url":"http://hdl.handle.net/2152/6567","source":{"id":"https://openalex.org/S4306400568","display_name":"Texas ScholarWorks (Texas Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210102904","host_organization_name":"Texas Digital Library","host_organization_lineage":["https://openalex.org/I4210102904"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2152/6567","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062412720","display_name":"Jeremy M. Brown","orcid":"https://orcid.org/0000-0002-1447-8633","observed_orcids":["https://orcid.org/0000-0002-1447-8633"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Jeremy M. Brown","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-1447-8633","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5062412720"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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":0.9247999787330627,"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":0.9247999787330627,"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":0.025200000032782555,"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":0.00930000003427267,"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":[{"id":"https://openalex.org/keywords/bayesian-phylogenetics","display_name":"Bayesian phylogenetics","score":0.8899999856948853},{"id":"https://openalex.org/keywords/model-heterogeneity","display_name":"model heterogeneity","score":0.6460000276565552},{"id":"https://openalex.org/keywords/partitioned-models","display_name":"partitioned models","score":0.8629999756813049},{"id":"https://openalex.org/keywords/branch-length-estimation","display_name":"branch length estimation","score":0.5699999928474426},{"id":"https://openalex.org/keywords/model-adequacy-testing","display_name":"model adequacy testing","score":0.6499999761581421},{"id":"https://openalex.org/keywords/posterior-probability","display_name":"posterior probability","score":0.5339999794960022},{"id":"https://openalex.org/keywords/model-selection","display_name":"model selection","score":0.41200000047683716},{"id":"https://openalex.org/keywords/simulation-study","display_name":"simulation study","score":0.49799999594688416}],"concepts":[{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.618710458278656},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.615621030330658},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.5327344536781311},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.5117142200469971},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4643476605415344},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.362011194229126},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3482261896133423},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33902686834335327},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3314933180809021}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:repositories.lib.utexas.edu:2152/6567","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2152/6567","pdf_url":"http://hdl.handle.net/2152/6567","source":{"id":"https://openalex.org/S4306400568","display_name":"Texas ScholarWorks (Texas Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210102904","host_organization_name":"Texas Digital Library","host_organization_lineage":["https://openalex.org/I4210102904"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.428.4217","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.428.4217","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://repositories.lib.utexas.edu/bitstream/handle/2152/6567/brownj27313.pdf","raw_type":"text"},{"id":"mag:2123595455","doi":null,"is_oa":false,"landing_page_url":"https://repositories.lib.utexas.edu/bitstream/2152/6567/2/brownj27313.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:repositories.lib.utexas.edu:2152/6567","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2152/6567","pdf_url":"http://hdl.handle.net/2152/6567","source":{"id":"https://openalex.org/S4306400568","display_name":"Texas ScholarWorks (Texas Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210102904","host_organization_name":"Texas Digital Library","host_organization_lineage":["https://openalex.org/I4210102904"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2123595455.pdf","grobid_xml":"https://content.openalex.org/works/W2123595455.grobid-xml"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W14699558","https://openalex.org/W56484600","https://openalex.org/W1509562192","https://openalex.org/W1565709818","https://openalex.org/W1638753340","https://openalex.org/W1966972227","https://openalex.org/W1982447955","https://openalex.org/W1996356638","https://openalex.org/W2006435864","https://openalex.org/W2006681603","https://openalex.org/W2012181955","https://openalex.org/W2018093010","https://openalex.org/W2025130480","https://openalex.org/W2030966943","https://openalex.org/W2041404167","https://openalex.org/W2042612610","https://openalex.org/W2045656233","https://openalex.org/W2051296828","https://openalex.org/W2060425093","https://openalex.org/W2082928585","https://openalex.org/W2092674070","https://openalex.org/W2095532262","https://openalex.org/W2096384485","https://openalex.org/W2096484952","https://openalex.org/W2097706568","https://openalex.org/W2098538101","https://openalex.org/W2101546326","https://openalex.org/W2101846955","https://openalex.org/W2102860463","https://openalex.org/W2104891575","https://openalex.org/W2106750393","https://openalex.org/W2108087670","https://openalex.org/W2110879928","https://openalex.org/W2111303992","https://openalex.org/W2121194856","https://openalex.org/W2124608480","https://openalex.org/W2125359798","https://openalex.org/W2125603395","https://openalex.org/W2126163471","https://openalex.org/W2126682991","https://openalex.org/W2128110103","https://openalex.org/W2128701823","https://openalex.org/W2129343067","https://openalex.org/W2129928578","https://openalex.org/W2130549894","https://openalex.org/W2132477986","https://openalex.org/W2140308583","https://openalex.org/W2141913814","https://openalex.org/W2142258617","https://openalex.org/W2142510328","https://openalex.org/W2146058063","https://openalex.org/W2147021949","https://openalex.org/W2147201983","https://openalex.org/W2147307434","https://openalex.org/W2152886327","https://openalex.org/W2153184851","https://openalex.org/W2155196220","https://openalex.org/W2156321798","https://openalex.org/W2156524622","https://openalex.org/W2159977619","https://openalex.org/W2161647617","https://openalex.org/W2161696685","https://openalex.org/W2166010426","https://openalex.org/W2167218332","https://openalex.org/W2168573791","https://openalex.org/W2168934042","https://openalex.org/W2169549534","https://openalex.org/W2169943826","https://openalex.org/W2171403786","https://openalex.org/W2172075237","https://openalex.org/W2807981689","https://openalex.org/W3005512703","https://openalex.org/W3029141791"],"related_works":["https://openalex.org/W3010636886","https://openalex.org/W7098939876","https://openalex.org/W7096901919","https://openalex.org/W7096447642","https://openalex.org/W3146346913","https://openalex.org/W4235539253","https://openalex.org/W4403856674","https://openalex.org/W2539079734","https://openalex.org/W2406495037","https://openalex.org/W191157447"],"abstract_inverted_index":{"Central":[0],"to":[1,43,109,131,173,255,268,291],"the":[2,10,17,51,67,85,112,122,244,250,259,262,284],"study":[3,172],"of":[4,48,54,70,114,151,160,179,208,222,246,261,281],"Life":[5],"is":[6,64,129,192,213],"knowledge":[7],"both":[8,34],"about":[9],"underlying":[11,152],"relationships":[12],"\\namong":[13],"living":[14],"things":[15],"and":[16,72,91,118,264,317],"processes":[18],"that":[19,107,200],"have":[20],"molded":[21],"them":[22],"into":[23,210],"their":[24],"diverse":[25],"forms.":[26],"\\nPhylogenetics":[27],"provides":[28],"a":[29,55,126,148,170,184,194,295,308,330],"powerful":[30],"toolkit":[31],"for":[32,162,177,215,235,322],"investigating":[33],"aspects.":[35],"Bayesian":[36,86,115,127,296],"\\nphylogenetics":[37],"has":[38],"gained":[39],"much":[40],"popularity,":[41],"due":[42],"its":[44,73,96],"readily":[45],"interpretable":[46],"notion":[47],"\\nprobability.":[49],"However,":[50],"posterior":[52],"probability":[53],"phylogeny,":[56],"as":[57,59],"well":[58],"any":[60],"dependent":[61],"\\nbiological":[62],"inferences,":[63],"conditioned":[65],"on":[66,95],"assumed":[68,124,279],"model":[69,78,123,280,325],"evolution":[71,282],"priors,":[74],"\\nnecessitating":[75],"care":[76],"in":[77,125,142,294,306],"formulation.":[79],"In":[80,165,239,312],"Chapter":[81,166,240,313],"1,":[82],"I":[83,100,168,242,315],"outline":[84],"perspective":[87],"\\nof":[88,187],"phylogenetic":[89,135,138,217,220,332],"inference":[90,117],"provide":[92],"my":[93],"view":[94],"most":[97,253],"outstanding":[98],"questions.":[99],"then":[101],"\\npresent":[102],"results":[103,198],"from":[104],"three":[105],"studies":[106],"aim":[108],"(i)":[110],"improve":[111],"accuracy":[113],"\\nphylogenetic":[116,310,324],"(ii)":[119],"assess":[120,274],"when":[121],"analysis":[128],"\\ninsufficient":[130],"produce":[132],"an":[133,278,289],"accurate":[134,216],"estimate.":[136],"As":[137],"data":[139,181,202,251,285],"sets":[140,182,252],"increase":[141],"size,":[143],"they":[144],"must":[145],"also":[146],"accommodate":[147],"greater":[149],"\\ndiversity":[150],"evolutionary":[153],"processes.":[154],"Partitioned":[155],"models":[156,212],"represent":[157],"one":[158],"way":[159],"\\naccounting":[161],"this":[163,247],"heterogeneity.":[164],"2,":[167],"describe":[169],"simulation":[171],"\\ninvestigate":[174],"whether":[175,190],"support":[176],"partitioning":[178],"empirical":[180],"represents":[183],"real":[185],"signal":[186],"heterogeneity":[188,209],"or":[189],"it":[191,301],"merely":[193],"statistical":[195],"artifact.":[196],"The":[197,206],"suggest":[199,265],"\\nempirical":[201],"are":[203,225,232],"extremely":[204],"heterogeneous.":[205],"incorporation":[207],"\\ninferential":[211],"important":[214,233],"inference.":[218],"\\nBayesian":[219],"estimates":[221],"branch":[223,230],"lengths":[224,231],"often":[226],"wildly":[227],"unreasonable.":[228],"\\nHowever,":[229],"input":[234],"many":[236],"other":[237],"analyses.":[238],"3,":[241],"\\nstudy":[243],"occurrence":[245],"phenomenon,":[248],"identify":[249],"likely":[254],"be":[256],"affected,":[257],"\\ndemonstrate":[258],"causes":[260],"bias,":[263],"several":[266],"solutions":[267],"avoid":[269],"inaccurate":[270],"\\ninferences.":[271],"\\nPhylogeneticists":[272],"rarely":[273],"absolute":[275],"fit":[276,293],"between":[277],"\\nand":[283],"being":[286],"analyzed.":[287],"While":[288],"approach":[290],"assessing":[292,323],"framework":[297],"\\nhas":[298],"been":[299],"proposed,":[300],"sometimes":[302],"performs":[303],"quite":[304],"poorly":[305],"predicting":[307],"model\u2019s":[309,331],"utility.":[311],"4,":[314],"propose":[316],"evaluate":[318,329],"new":[319],"test":[320],"statistics":[321],"adequacy,":[326],"which":[327],"directly":[328],"\\nperformance.":[333]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2016-06-24T00:00:00"}