{"id":"https://openalex.org/W2096314092","doi":"https://doi.org/10.1093/sysbio/syr019","title":"Integrating Fossil Preservation Biases in the Selection of Calibrations for Molecular Divergence Time Estimation","display_name":"Integrating Fossil Preservation Biases in the Selection of Calibrations for Molecular Divergence Time Estimation","publication_year":2011,"publication_date":"2011-03-23","ids":{"openalex":"https://openalex.org/W2096314092","doi":"https://doi.org/10.1093/sysbio/syr019","mag":"2096314092","pmid":"https://pubmed.ncbi.nlm.nih.gov/21436104"},"language":"en","primary_location":{"id":"doi:10.1093/sysbio/syr019","doi":"https://doi.org/10.1093/sysbio/syr019","is_oa":false,"landing_page_url":"https://doi.org/10.1093/sysbio/syr019","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","is_traditional":true,"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/A5002799814","display_name":"Alex Dornburg","orcid":"https://orcid.org/0000-0003-0863-2283","observed_orcids":["https://orcid.org/0000-0003-0863-2283"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alex Dornburg","raw_affiliation_strings":["Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032882921","display_name":"Jeremy M. Beaulieu","orcid":"https://orcid.org/0000-0001-5953-1701","observed_orcids":["https://orcid.org/0000-0001-5953-1701"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy M. Beaulieu","raw_affiliation_strings":["Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061875763","display_name":"Jeffrey C. Oliver","orcid":"https://orcid.org/0000-0003-2160-1086","observed_orcids":["https://orcid.org/0000-0003-2160-1086","https://orcid.org/0000-0001-6354-8290"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey C. Oliver","raw_affiliation_strings":["Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088952270","display_name":"Thomas J. Near","orcid":"https://orcid.org/0000-0002-7398-6670","observed_orcids":["https://orcid.org/0000-0002-7398-6670"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4387153325","display_name":"Yale Peabody Museum","ror":"https://ror.org/03db5ay71","country_code":"US","type":"archive","lineage":["https://openalex.org/I32971472","https://openalex.org/I4387153325"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas J. Near","raw_affiliation_strings":["Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA","Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472","https://openalex.org/I4387153325"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5002799814"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":2166,"currency":"USD","value_usd":2166},"apc_paid":null,"fwci":5.1548,"has_fulltext":false,"cited_by_count":66,"citation_normalized_percentile":{"value":0.96650564,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"60","issue":"4","first_page":"519","last_page":"527"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.8715999722480774,"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":0.8715999722480774,"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":0.04390000179409981,"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/T10385","display_name":"Plant Diversity and Evolution","score":0.032600000500679016,"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/fossil-calibration","display_name":"fossil calibration","score":0.7950000166893005},{"id":"https://openalex.org/keywords/divergence-time-estimation","display_name":"divergence time estimation","score":0.7870000004768372},{"id":"https://openalex.org/keywords/taphonomic-bias","display_name":"taphonomic bias","score":0.9330000281333923},{"id":"https://openalex.org/keywords/turtles","display_name":"turtles","score":0.8040000200271606},{"id":"https://openalex.org/keywords/bayesian-phylogenetics","display_name":"Bayesian phylogenetics","score":0.6729999780654907},{"id":"https://openalex.org/keywords/first-occurrence","display_name":"first occurrence","score":0.3799999952316284}],"concepts":[{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.7846817970275879},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.6872873902320862},{"id":"https://openalex.org/C10277891","wikidata":"https://www.wikidata.org/wiki/Q596086","display_name":"Taphonomy","level":2,"score":0.6310999989509583},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.6244465112686157},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5687528848648071},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.5354125499725342},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5131062269210815},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.47410494089126587},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.46945852041244507},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.45599430799484253},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4418976306915283},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3520788550376892},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3244703412055969},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21602091193199158},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.18161532282829285},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17828452587127686},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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":"D005580","descriptor_name":"Fossils","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011309","descriptor_name":"Preservation, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014426","descriptor_name":"Turtles","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D014426","descriptor_name":"Turtles","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014426","descriptor_name":"Turtles","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D049810","descriptor_name":"Genetic Speciation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/sysbio/syr019","doi":"https://doi.org/10.1093/sysbio/syr019","is_oa":false,"landing_page_url":"https://doi.org/10.1093/sysbio/syr019","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:21436104","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21436104","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"},{"id":"mag:3151126744","doi":null,"is_oa":false,"landing_page_url":"http://sysbio.oxfordjournals.org/content/early/2011/03/23/sysbio.syr019.full.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":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":70,"referenced_works":["https://openalex.org/W976785850","https://openalex.org/W1807131829","https://openalex.org/W1968883957","https://openalex.org/W1969732390","https://openalex.org/W1970779668","https://openalex.org/W1978464139","https://openalex.org/W2005633246","https://openalex.org/W2006661252","https://openalex.org/W2013136111","https://openalex.org/W2020042837","https://openalex.org/W2036628186","https://openalex.org/W2038935556","https://openalex.org/W2039021716","https://openalex.org/W2045519929","https://openalex.org/W2049217528","https://openalex.org/W2051296828","https://openalex.org/W2051801987","https://openalex.org/W2059419868","https://openalex.org/W2061352595","https://openalex.org/W2062847946","https://openalex.org/W2070909443","https://openalex.org/W2073635400","https://openalex.org/W2077388150","https://openalex.org/W2081244377","https://openalex.org/W2087644815","https://openalex.org/W2091989118","https://openalex.org/W2094939159","https://openalex.org/W2099364951","https://openalex.org/W2100473357","https://openalex.org/W2101107494","https://openalex.org/W2102850151","https://openalex.org/W2102860463","https://openalex.org/W2106768037","https://openalex.org/W2110831582","https://openalex.org/W2110835349","https://openalex.org/W2112389780","https://openalex.org/W2117384519","https://openalex.org/W2121625232","https://openalex.org/W2122807348","https://openalex.org/W2124318470","https://openalex.org/W2125603395","https://openalex.org/W2128110103","https://openalex.org/W2128841626","https://openalex.org/W2128979083","https://openalex.org/W2129343067","https://openalex.org/W2132926880","https://openalex.org/W2137261417","https://openalex.org/W2139771752","https://openalex.org/W2141229554","https://openalex.org/W2143501660","https://openalex.org/W2146368901","https://openalex.org/W2149557149","https://openalex.org/W2151413057","https://openalex.org/W2155579386","https://openalex.org/W2157127204","https://openalex.org/W2158187424","https://openalex.org/W2160525739","https://openalex.org/W2160918824","https://openalex.org/W2168548796","https://openalex.org/W2170870306","https://openalex.org/W2172057351","https://openalex.org/W2176918263","https://openalex.org/W2178892563","https://openalex.org/W2204890871","https://openalex.org/W2225100815","https://openalex.org/W2478395683","https://openalex.org/W2732998557","https://openalex.org/W2733548038","https://openalex.org/W2745099866","https://openalex.org/W4211177544"],"related_works":["https://openalex.org/W2158187424","https://openalex.org/W2958638543","https://openalex.org/W1858638980","https://openalex.org/W2059419868","https://openalex.org/W2150491897","https://openalex.org/W6929554604","https://openalex.org/W2188917387","https://openalex.org/W3175697530","https://openalex.org/W2171217030","https://openalex.org/W2163048979"],"abstract_inverted_index":{"The":[0,48],"selection":[1,66,105],"of":[2,33,56,88,142,178],"fossil":[3,39,45,104,124],"data":[4],"to":[5,44,68,74,82,102,150,174,181],"use":[6],"as":[7,93,162],"calibration":[8,46,65,184],"age":[9,148],"priors":[10],"in":[11,37,157,185],"molecular":[12,120],"divergence":[13,86,117],"time":[14],"estimates":[15,149,160],"inherently":[16],"links":[17],"neontological":[18,25],"methods":[19],"with":[20],"paleontological":[21],"theory.":[22],"However,":[23],"few":[24],"studies":[26],"have":[27],"taken":[28],"into":[29,132],"account":[30,133],"the":[31,38,53,60,85,103,140,176,186],"possibility":[32],"a":[34,57,94,99],"taphonomic":[35,135],"bias":[36,52,147],"record":[40],"when":[41],"developing":[42],"approaches":[43,67],"selection.":[47],"Sppil-Rongis":[49],"effect":[50],"may":[51,146],"first":[54],"appearance":[55],"lineage":[58],"toward":[59],"recent":[61,153],"causing":[62],"most":[63],"objective":[64],"erroneously":[69],"exclude":[70],"appropriate":[71],"calibrations":[72,77,125,144,180],"or":[73],"incorporate":[75],"multiple":[76,123],"that":[78,130,145],"are":[79],"too":[80,152],"young":[81],"accurately":[83],"represent":[84],"times":[87,118],"target":[89],"lineages.":[90],"Using":[91],"turtles":[92],"case":[95],"study,":[96],"we":[97],"develop":[98],"Bayesian":[100],"extension":[101],"approach":[106],"developed":[107],"by":[108],"Marshall":[109],"(2008.":[110],"A":[111],"simple":[112],"method":[113,138,170],"for":[114],"bracketing":[115],"absolute":[116],"on":[119],"phylogenies":[121],"using":[122],"points.":[126],"Am.":[127],"Nat.":[128],"171:726-742)":[129],"takes":[131],"this":[134,169],"bias.":[136],"Our":[137],"has":[139],"advantage":[141],"identifying":[143],"be":[151],"while":[154],"incorporating":[155],"uncertainty":[156],"phylogenetic":[158],"parameter":[159],"such":[161],"tree":[163],"topology":[164],"and":[165],"branch":[166],"lengths.":[167],"Additionally,":[168],"is":[171],"easily":[172],"adapted":[173],"assess":[175],"consistency":[177],"potential":[179],"any":[182],"one":[183],"candidate":[187],"pool.":[188]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":9}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
