{"id":"https://openalex.org/W2063433754","doi":"https://doi.org/10.1093/molbev/msv075","title":"A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla","display_name":"A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla","publication_year":2015,"publication_date":"2015-03-25","ids":{"openalex":"https://openalex.org/W2063433754","doi":"https://doi.org/10.1093/molbev/msv075","mag":"2063433754","pmid":"https://pubmed.ncbi.nlm.nih.gov/25808541","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4476164"},"language":"en","primary_location":{"id":"doi:10.1093/molbev/msv075","doi":"https://doi.org/10.1093/molbev/msv075","is_oa":false,"landing_page_url":"https://doi.org/10.1093/molbev/msv075","pdf_url":null,"source":{"id":"https://openalex.org/S57552105","display_name":"Molecular Biology and Evolution","issn_l":"0737-4038","issn":["0737-4038","1537-1719"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1"],"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":"Molecular Biology and Evolution","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4476164","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085701739","display_name":"Fabia Ursula Battistuzzi","orcid":"https://orcid.org/0000-0003-1852-2934","observed_orcids":["https://orcid.org/0000-0003-1852-2934"]},"institutions":[{"id":"https://openalex.org/I177721651","display_name":"Oakland University","ror":"https://ror.org/01ythxj32","country_code":"US","type":"education","lineage":["https://openalex.org/I177721651"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fabia U. Battistuzzi","raw_affiliation_strings":["Department of Biological Sciences, Oakland University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Oakland University","institution_ids":["https://openalex.org/I177721651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066122684","display_name":"Paul Billing-Ross","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210144145","display_name":"New York State University College of Human Ecology","ror":"https://ror.org/047g2xp14","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4210144145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Billing-Ross","raw_affiliation_strings":["Department of Molecular Biology and Genetics, College of Human Ecology, Cornell University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, College of Human Ecology, Cornell University","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210144145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101553389","display_name":"Oscar D. Murillo","orcid":"https://orcid.org/0000-0003-1938-3905","observed_orcids":["https://orcid.org/0000-0003-1938-3905"]},"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":"Oscar Murillo","raw_affiliation_strings":["Institute for Genomics and Evolutionary Medicine, Temple University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111452408","display_name":"Alan Filipski","orcid":null,"observed_orcids":[]},"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":"Alan Filipski","raw_affiliation_strings":["Institute for Genomics and Evolutionary Medicine, Temple University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, 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/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]},{"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":["SA","US"],"is_corresponding":true,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Institute for Genomics and Evolutionary Medicine, Temple University Department of Biology, Temple University Center for Genomic Medicine and Research, King Abdulaziz University, Jddah, Saudi Arabia s.kumar@temple.edu","Center for Genomic Medicine and Research, King Abdulaziz University, Jddah, Saudi Arabia","Department of Biology, Temple University","Institute for Genomics and Evolutionary Medicine, Temple University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University Department of Biology, Temple University Center for Genomic Medicine and Research, King Abdulaziz University, Jddah, Saudi Arabia s.kumar@temple.edu","institution_ids":["https://openalex.org/I185163786","https://openalex.org/I84392919"]},{"raw_affiliation_string":"Center for Genomic Medicine and Research, King Abdulaziz University, Jddah, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]},{"raw_affiliation_string":"Department of Biology, Temple University","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100680948"],"corresponding_institution_ids":["https://openalex.org/I185163786","https://openalex.org/I84392919"],"apc_list":{"value":3418,"currency":"USD","value_usd":3418},"apc_paid":null,"fwci":5.0349,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.95704422,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"7","first_page":"1907","last_page":"1912"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.4560999870300293,"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":0.4560999870300293,"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":0.37299999594688416,"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/T11879","display_name":"Protist diversity and phylogeny","score":0.03229999914765358,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/divergence-time-estimation","display_name":"divergence time estimation","score":0.8849999904632568},{"id":"https://openalex.org/keywords/cambrian-explosion","display_name":"Cambrian explosion","score":0.8859999775886536},{"id":"https://openalex.org/keywords/metazoan-diversification","display_name":"metazoan diversification","score":0.9139999747276306},{"id":"https://openalex.org/keywords/proterozoic","display_name":"Proterozoic","score":0.6710000038146973},{"id":"https://openalex.org/keywords/timetree","display_name":"timetree","score":0.5789999961853027},{"id":"https://openalex.org/keywords/divergence-time","display_name":"divergence time","score":0.4099999964237213}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9286252856254578},{"id":"https://openalex.org/C91066513","wikidata":"https://www.wikidata.org/wiki/Q38348","display_name":"Phylum","level":3,"score":0.7475560307502747},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.6935455203056335},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.5554354786872864},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.5050762295722961},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4395361542701721},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.3811001181602478},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3560035824775696},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.19610115885734558},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17250946164131165},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.12849661707878113},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.10501968860626221},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0947374701499939},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06019735336303711},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/molbev/msv075","doi":"https://doi.org/10.1093/molbev/msv075","is_oa":false,"landing_page_url":"https://doi.org/10.1093/molbev/msv075","pdf_url":null,"source":{"id":"https://openalex.org/S57552105","display_name":"Molecular Biology and Evolution","issn_l":"0737-4038","issn":["0737-4038","1537-1719"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1"],"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":"Molecular Biology and Evolution","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4476164","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4476164","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Mol Biol Evol","raw_type":"Text"},{"id":"pmid:25808541","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25808541","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":"Molecular biology and evolution","raw_type":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4476164","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4476164","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Mol Biol Evol","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3097176500","display_name":"Graduate and Undergraduate Training in Biomedicine at ASU","funder_award_id":"R25GM099650","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8030537233","display_name":null,"funder_award_id":"HG00296-12","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1507241016","https://openalex.org/W1605705157","https://openalex.org/W1634598038","https://openalex.org/W1964454133","https://openalex.org/W1970473208","https://openalex.org/W1975553093","https://openalex.org/W1980780818","https://openalex.org/W1992566665","https://openalex.org/W2003596334","https://openalex.org/W2005201180","https://openalex.org/W2032344982","https://openalex.org/W2045165720","https://openalex.org/W2052544560","https://openalex.org/W2059383371","https://openalex.org/W2059419868","https://openalex.org/W2064523628","https://openalex.org/W2067110477","https://openalex.org/W2096314092","https://openalex.org/W2097573355","https://openalex.org/W2100473357","https://openalex.org/W2101877523","https://openalex.org/W2102985891","https://openalex.org/W2104398544","https://openalex.org/W2107886421","https://openalex.org/W2111414198","https://openalex.org/W2112373839","https://openalex.org/W2113525598","https://openalex.org/W2121190890","https://openalex.org/W2122842112","https://openalex.org/W2133436664","https://openalex.org/W2143124634","https://openalex.org/W2149409778","https://openalex.org/W2150491897","https://openalex.org/W2152400281","https://openalex.org/W2157452947","https://openalex.org/W2158187424","https://openalex.org/W2159714622","https://openalex.org/W2160354623","https://openalex.org/W2163048979","https://openalex.org/W2164727170","https://openalex.org/W2166647921","https://openalex.org/W4388253203"],"related_works":["https://openalex.org/W7100064974","https://openalex.org/W7098142512","https://openalex.org/W2125241803","https://openalex.org/W2150491897","https://openalex.org/W2909712482","https://openalex.org/W2158187424","https://openalex.org/W2734462687","https://openalex.org/W1985490568","https://openalex.org/W6929554604","https://openalex.org/W2101877523"],"abstract_inverted_index":{"We":[0,34],"present":[1],"a":[2,16,42],"procedure":[3],"to":[4,41,85,177,184,190],"test":[5],"the":[6,32,70,79,86,89,94,101,107,110,114,142,167,172],"effect":[7],"of":[8,44,73,81,88,113,138,141,149,161,163,174],"calibration":[9,104,145,181],"priors":[10,105],"on":[11],"estimated":[12],"times,":[13],"which":[14,77],"applies":[15],"recently":[17],"developed":[18],"calibration-free":[19,175],"approach":[20],"(RelTime)":[21],"method":[22],"that":[23,100,133,158],"produces":[24,153],"relative":[25],"divergence":[26,64,80,116,131],"times":[27,117,132],"for":[28,155],"all":[29,140],"nodes":[30],"in":[31,69,106,121,166,188],"tree.":[33],"illustrate":[35],"this":[36,122],"protocol":[37],"by":[38],"applying":[39],"it":[40],"timetree":[43],"metazoan":[45,156],"diversification":[46],"(Erwin":[47],"DH,":[48],"Laflamme":[49],"M,":[50],"Tweedt":[51],"SM,":[52],"Sperling":[53],"EA,":[54],"Pisani":[55],"D,":[56],"Peterson":[57],"KJ.":[58],"2011.":[59],"The":[60,147],"Cambrian":[61,90],"conundrum:":[62],"early":[63,71],"and":[65,183],"later":[66],"ecological":[67],"success":[68],"history":[72],"animals.":[74],"Science":[75],"334:1091-1097.),":[76],"placed":[78],"animal":[82,119],"phyla":[83,120],"close":[84],"time":[87],"explosion":[91],"inferred":[92],"from":[93],"fossil":[95],"record.":[96],"These":[97],"analyses":[98],"revealed":[99],"two":[102,127],"maximum-only":[103,128],"pre-Cambrian":[108],"are":[109,159],"primary":[111],"determinants":[112],"young":[115],"among":[118],"study.":[123],"In":[124],"fact,":[125],"these":[126,150],"calibrations":[129,152],"produce":[130],"severely":[134],"violate":[135],"minimum":[136],"boundaries":[137],"almost":[139],"other":[143],"22":[144,151],"constraints.":[146],"use":[148,173],"dates":[154],"divergences":[157],"hundreds":[160],"millions":[162],"years":[164],"earlier":[165],"Proterozoic.":[168],"Our":[169],"results":[170],"encourage":[171],"approaches":[176],"identify":[178],"most":[179],"influential":[180],"constraints":[182],"evaluate":[185],"their":[186],"impact":[187],"order":[189],"achieve":[191],"biologically":[192],"robust":[193],"interpretations.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2}],"updated_date":"2026-11-03T10:50:19.383937","created_date":"2016-06-24T00:00:00"}