{"id":"https://openalex.org/W7213519145","doi":"https://doi.org/10.5281/zenodo.22810150","title":"Data and code from: Estimating divergence times and diversification rates with the unresolved fossilized birth-death process","display_name":"Data and code from: Estimating divergence times and diversification rates with the unresolved fossilized birth-death process","publication_year":2026,"publication_date":"2026-09-17","ids":{"openalex":"https://openalex.org/W7213519145","doi":"https://doi.org/10.5281/zenodo.22810150"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.22810150","doi":"https://doi.org/10.5281/zenodo.22810150","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22810150","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"volume":null,"type":"software","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.22810150","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109977045","display_name":"Wang-Jin Lim","orcid":"https://orcid.org/0009-0007-1004-2326","observed_orcids":["https://orcid.org/0009-0007-1004-2326"]},"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":false,"raw_author_name":"Lim, Wonseop","raw_affiliation_strings":["University of California, Berkeley"],"raw_orcid":"https://orcid.org/0009-0007-1004-2326","affiliations":[{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114499295","display_name":"Levi Yoder Raskin","orcid":"https://orcid.org/0009-0001-2680-8417","observed_orcids":["https://orcid.org/0009-0001-2680-8417"]},"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":false,"raw_author_name":"Raskin, Levi","raw_affiliation_strings":["University of California, Berkeley"],"raw_orcid":"https://orcid.org/0009-0001-2680-8417","affiliations":[{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126450178","display_name":"Jacky Li","orcid":null,"observed_orcids":[]},"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":false,"raw_author_name":"Li, Jacky","raw_affiliation_strings":["University of California, Berkeley"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","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":false,"raw_author_name":"Huelsenbeck, John","raw_affiliation_strings":["University of California, Berkeley"],"raw_orcid":"https://orcid.org/0000-0002-3050-9997","affiliations":[{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088476239","display_name":"Rasmus Nielsen","orcid":"https://orcid.org/0000-0003-0513-6591","observed_orcids":["https://orcid.org/0000-0003-0513-6591"]},"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":false,"raw_author_name":"Nielsen, Rasmus","raw_affiliation_strings":["University of California, Berkeley"],"raw_orcid":"https://orcid.org/0000-0003-0513-6591","affiliations":[{"raw_affiliation_string":"University of California, Berkeley","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.8974999785423279,"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":0.8974999785423279,"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":0.05420000106096268,"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":0.026399999856948853,"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/fossilized-birth-death-model","display_name":"fossilized birth-death model","score":0.8610000014305115},{"id":"https://openalex.org/keywords/tip-dating","display_name":"tip-dating","score":0.8650000095367432},{"id":"https://openalex.org/keywords/divergence-time-estimation","display_name":"divergence time estimation","score":0.9179999828338623},{"id":"https://openalex.org/keywords/diversification-rates","display_name":"diversification rates","score":0.9620000123977661},{"id":"https://openalex.org/keywords/cetaceans","display_name":"cetaceans","score":0.7879999876022339},{"id":"https://openalex.org/keywords/emydidae","display_name":"Emydidae","score":0.9990000128746033}],"concepts":[{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.6247000098228455},{"id":"https://openalex.org/C180916674","wikidata":"https://www.wikidata.org/wiki/Q3711935","display_name":"Diversification (marketing strategy)","level":2,"score":0.5364999771118164},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.5084999799728394},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5001999735832214},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.4771000146865845},{"id":"https://openalex.org/C196662502","wikidata":"https://www.wikidata.org/wiki/Q827541","display_name":"Molecular clock","level":4,"score":0.4607999920845032},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.4507000148296356},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4408000111579895},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4122999906539917},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.4072999954223633},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.390500009059906},{"id":"https://openalex.org/C2778012447","wikidata":"https://www.wikidata.org/wiki/Q1034415","display_name":"Scope (computer science)","level":2,"score":0.3528999984264374},{"id":"https://openalex.org/C2780586970","wikidata":"https://www.wikidata.org/wiki/Q1357284","display_name":"Popularity","level":2,"score":0.3398999869823456},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.3292999863624573},{"id":"https://openalex.org/C2780522230","wikidata":"https://www.wikidata.org/wiki/Q1140419","display_name":"Ambiguity","level":2,"score":0.32659998536109924},{"id":"https://openalex.org/C5274069","wikidata":"https://www.wikidata.org/wiki/Q2285707","display_name":"Categorical variable","level":2,"score":0.32600000500679016},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31130000948905945},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.31040000915527344},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.30720001459121704},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.30000001192092896},{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.28929999470710754},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.2847999930381775},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.2840000092983246},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.26159998774528503},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2574000060558319},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2540999948978424},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.25369998812675476},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.2513999938964844}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.22810150","doi":"https://doi.org/10.5281/zenodo.22810150","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22810150","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},{"id":"doi:10.5281/zenodo.22810151","doi":"https://doi.org/10.5281/zenodo.22810151","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22810151","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"doi:10.5281/zenodo.22810150","doi":"https://doi.org/10.5281/zenodo.22810150","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22810150","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7212379221","https://openalex.org/W4388635742","https://openalex.org/W4284883401","https://openalex.org/W6931419943","https://openalex.org/W6911188764","https://openalex.org/W2947631770","https://openalex.org/W4293529973","https://openalex.org/W4293862937","https://openalex.org/W2985039433","https://openalex.org/W2946805451"],"abstract_inverted_index":{"Tip-dating":[0],"using":[1],"Fossilized":[2],"Birth-Death":[3],"(FBD)":[4],"models":[5,73],"offers":[6],"a":[7,60,79,129,166,171,177,205],"favorable":[8],"alternative":[9],"to":[10,132,149,173,186],"conventional":[11],"node-dating":[12],"analyses":[13],"of":[14,42,63,92,189,208,213],"the":[15,43,90,139],"evolutionary":[16],"timescale,":[17],"bypassing":[18],"various":[19],"conceptual":[20],"and":[21,56,100,168,192,194,200],"technical":[22],"difficulties.":[23],"However,":[24],"despite":[25],"their":[26,32],"increasing":[27],"popularity":[28],"in":[29,38,45,78,89,113,116,157],"phylogenetic":[30],"studies,":[31,68],"use":[33],"has":[34],"remained":[35],"rather":[36],"limited":[37],"taxonomic":[39],"scope":[40],"because":[41],"difficulty":[44],"collecting":[46],"morphological":[47,93,124],"data,":[48,94],"which":[49,114,158],"is":[50,119],"often":[51],"required":[52],"for":[53,84],"tip-dating":[54],"analyses,":[55,87],"computational":[57],"intractability":[58],"when":[59,123,211],"large":[61],"number":[62],"fossils":[64,214],"are":[65,126,215],"present.":[66,216],"Recent":[67],"however,":[69],"suggest":[70],"that":[71,138,196],"FBD":[72,111],"can":[74,162],"also":[75],"be":[76,163],"used":[77,143],"principled":[80],"way":[81],"as":[82,165],"priors":[83],"molecular":[85],"clock":[86],"even":[88,210],"absence":[91],"relying":[95],"only":[96],"on":[97],"temporal":[98],"information":[99],"given":[101],"clade":[102],"assignments.":[103],"Heath":[104,145],"et":[105,146],"al.":[106,147],"(2014)":[107,148],"introduced":[108],"an":[109],"\"unresolved\"":[110],"model":[112],"uncertainty":[115],"fossil":[117,153,160],"placements":[118],"analytically":[120],"integrated":[121],"out":[122],"data":[125],"unavailable,":[127],"providing":[128],"potential":[130],"solution":[131],"this":[133,174],"problem.":[134],"Here,":[135],"we":[136,169],"show":[137,195],"topological":[140],"enumeration":[141],"scheme":[142],"by":[144],"marginalize":[150],"over":[151],"unresolved":[152,180],"attachments":[154],"overcounts":[155],"configurations":[156],"multiple":[159],"taxa":[161],"resolved":[164],"clade,":[167],"provide":[170],"correction":[172],"factor,":[175],"yielding":[176],"valid":[178],"marginalized":[179],"likelihood.":[181],"We":[182],"apply":[183],"our":[184,197],"implementation":[185],"empirical":[187],"datasets":[188],"Cetacea,":[190],"Emydidae,":[191],"Palaeodictyopterida,":[193],"method":[198],"converges":[199],"yields":[201],"reasonable":[202,206],"estimates":[203],"within":[204],"amount":[207],"time,":[209],"hundreds":[212]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-09-18T00:00:00"}