{"id":"https://openalex.org/W4306149322","doi":"https://doi.org/10.1093/bioinformatics/btac679","title":"Estimation of speciation times under the multispecies coalescent","display_name":"Estimation of speciation times under the multispecies coalescent","publication_year":2022,"publication_date":"2022-10-13","ids":{"openalex":"https://openalex.org/W4306149322","doi":"https://doi.org/10.1093/bioinformatics/btac679","pmid":"https://pubmed.ncbi.nlm.nih.gov/36227122"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac679","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac679","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/23/5182/47465997/btac679.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/23/5182/47465997/btac679.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103026267","display_name":"Jing Peng","orcid":"https://orcid.org/0000-0002-8835-4545"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jing Peng","raw_affiliation_strings":["Division of Biostatistics, The Ohio State University , Columbus, OH 43210, USA"],"raw_orcid":"https://orcid.org/0000-0002-8835-4545","affiliations":[{"raw_affiliation_string":"Division of Biostatistics, The Ohio State University , Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073568173","display_name":"David L. Swofford","orcid":"https://orcid.org/0000-0003-0396-1395"},"institutions":[{"id":"https://openalex.org/I1313142568","display_name":"Florida Museum of Natural History","ror":"https://ror.org/02pjdv450","country_code":"US","type":"archive","lineage":["https://openalex.org/I1313142568","https://openalex.org/I33213144"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David L Swofford","raw_affiliation_strings":["Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida Museum of Natural History, University of Florida , Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I1313142568","https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080396236","display_name":"Laura Kubatko","orcid":"https://orcid.org/0000-0002-5215-7144"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laura Kubatko","raw_affiliation_strings":["Department of Evolution, Ecology, and Organismal Biology, The Ohio State University , Columbus, OH 43210, USA","Department of Statistics, The Ohio State University , Columbus, OH 43210, USA","Mathematical Biosciences Institute, The Ohio State University , Columbus, OH 43210, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Evolution, Ecology, and Organismal Biology, The Ohio State University , Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Department of Statistics, The Ohio State University , Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Mathematical Biosciences Institute, The Ohio State University , Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5103026267"],"corresponding_institution_ids":["https://openalex.org/I52357470"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":8.2537,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.9707334,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"23","first_page":"5182","last_page":"5190"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.39340001344680786,"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"}},"topics":[{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.39340001344680786,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.38850000500679016,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.06870000064373016,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/coalescent-theory","display_name":"Coalescent theory","score":0.9435628056526184},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.783325731754303},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.4481198787689209},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37316372990608215},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36756640672683716},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3009824752807617},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2837265431880951},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.26506245136260986},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16232284903526306},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.10793042182922363}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.9435628056526184},{"id":"https://openalex.org/C2776838516","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.783325731754303},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.4481198787689209},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37316372990608215},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36756640672683716},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3009824752807617},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2837265431880951},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.26506245136260986},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16232284903526306},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.10793042182922363},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac679","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac679","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/23/5182/47465997/btac679.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36227122","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36227122","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,"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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac679","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac679","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/23/5182/47465997/btac679.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4691280071","display_name":null,"funder_award_id":"DEB 1455399","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6001708135","display_name":null,"funder_award_id":"1610305","funder_id":"https://openalex.org/F4320337380","funder_display_name":"Division of Mathematical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337380","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W60603402","https://openalex.org/W1525734744","https://openalex.org/W1897064680","https://openalex.org/W1923274812","https://openalex.org/W1954989577","https://openalex.org/W2015929993","https://openalex.org/W2041177653","https://openalex.org/W2046132104","https://openalex.org/W2107608009","https://openalex.org/W2116811037","https://openalex.org/W2120663060","https://openalex.org/W2125024684","https://openalex.org/W2126786937","https://openalex.org/W2135046866","https://openalex.org/W2139050004","https://openalex.org/W2277574918","https://openalex.org/W2553089913","https://openalex.org/W2766449436","https://openalex.org/W2883170162","https://openalex.org/W2950847777","https://openalex.org/W2962714894","https://openalex.org/W2963101269","https://openalex.org/W3025561817","https://openalex.org/W3100438266","https://openalex.org/W3123097201","https://openalex.org/W4232111321","https://openalex.org/W4232936004","https://openalex.org/W6602539855","https://openalex.org/W6640330755"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2952954362","https://openalex.org/W3093602888","https://openalex.org/W2762052495","https://openalex.org/W3156045358","https://openalex.org/W2921578049","https://openalex.org/W2581424563","https://openalex.org/W2020599444","https://openalex.org/W2089205969","https://openalex.org/W3021715419"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,198],"multispecies":[2],"coalescent":[3,37,88],"model":[4,12,109],"is":[5],"now":[6],"widely":[7],"accepted":[8],"as":[9],"an":[10,190],"effective":[11,68],"for":[13,25,42,56,102,114,193,211],"incorporating":[14],"variation":[15],"in":[16,86,203],"the":[17,36,74,78,123,130,136,169,174,179,204],"evolutionary":[18],"histories":[19],"of":[20,47,58,76,80,110,125,168,181],"individual":[21],"genes":[22],"into":[23],"methods":[24],"phylogenetic":[26],"inference":[27],"from":[28],"genome-scale":[29],"data.":[30],"However,":[31],"because":[32],"model-based":[33],"analysis":[34],"under":[35,107,122],"can":[38,119,152],"be":[39,120,153],"computationally":[40,165],"expensive":[41],"large":[43],"datasets,":[44],"a":[45,84,87,92,94,108,126,163],"variety":[46],"inferential":[48],"frameworks":[49],"and":[50,61,67,142,146,186,214],"corresponding":[51],"algorithms":[52],"have":[53],"been":[54,201],"proposed":[55],"estimation":[57],"species-level":[59],"phylogenies":[60],"associated":[62],"parameters,":[63],"including":[64],"speciation":[65,81,105],"times":[66,106],"population":[69],"sizes.":[70],"RESULTS:":[71],"We":[72,90,133,160,177],"consider":[73],"problem":[75],"estimating":[77],"timing":[79],"events":[82],"along":[83],"phylogeny":[85],"framework.":[89],"propose":[91],"maximum":[93],"posteriori":[95],"estimator":[96,167],"based":[97,172],"on":[98,173],"composite":[99],"likelihood":[100],"(MAPCL)":[101],"inferring":[103],"these":[104],"DNA":[111],"sequence":[112],"evolution":[113],"which":[115],"exact":[116],"site-pattern":[117],"probabilities":[118],"computed":[121],"assumption":[124],"constant":[127],"\u03b8":[128],"throughout":[129],"species":[131],"tree.":[132],"demonstrate":[134],"that":[135],"MAPCL":[137],"estimates":[138],"are":[139,222],"statistically":[140],"consistent":[141],"asymptotically":[143],"normally":[144],"distributed,":[145],"we":[147],"show":[148],"how":[149],"this":[150],"result":[151],"used":[154],"to":[155,189],"estimate":[156],"their":[157],"asymptotic":[158,170],"variance.":[159],"also":[161],"provide":[162],"more":[164],"efficient":[166],"variance":[171],"non-parametric":[175],"bootstrap.":[176],"evaluate":[178],"performance":[180],"our":[182],"method":[183,199],"using":[184],"simulation":[185],"by":[187],"application":[188],"empirical":[191],"dataset":[192],"gibbons.":[194],"AVAILABILITY":[195],"AND":[196],"IMPLEMENTATION:":[197],"has":[200],"implemented":[202],"PAUP*":[205],"program,":[206],"freely":[207],"available":[208,223],"at":[209,224],"https://paup.phylosolutions.com":[210],"Macintosh,":[212],"Windows":[213],"Linux":[215],"operating":[216],"systems.":[217],"SUPPLEMENTARY":[218],"INFORMATION:":[219],"Supplementary":[220],"data":[221],"Bioinformatics":[225],"online.":[226]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}