{"id":"https://openalex.org/W3040237290","doi":"https://doi.org/10.1101/2020.07.03.185074","title":"Prior hypotheses or regularization allow inference of diversification histories from extant timetrees","display_name":"Prior hypotheses or regularization allow inference of diversification histories from extant timetrees","publication_year":2020,"publication_date":"2020-07-04","ids":{"openalex":"https://openalex.org/W3040237290","doi":"https://doi.org/10.1101/2020.07.03.185074","mag":"3040237290"},"language":"en","primary_location":{"id":"doi:10.1101/2020.07.03.185074","doi":"https://doi.org/10.1101/2020.07.03.185074","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.07.03.185074","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/07/04/2020.07.03.185074.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2020/07/04/2020.07.03.185074.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084776094","display_name":"H\u00e9l\u00e8ne Morlon","orcid":"https://orcid.org/0000-0002-3195-7521","observed_orcids":["https://orcid.org/0000-0002-3195-7521"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I4210129409","display_name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure","ror":"https://ror.org/03mxktp47","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210096427","https://openalex.org/I4210129409"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"H\u00e9l\u00e8ne Morlon","raw_affiliation_strings":["Institut de Biologie de l\u2019Ecole Normale Sup\u00e9rieure (IBENS), Ecole Normale Sup\u00e9rieure, CNRS, INSERM, PSL Research University, 75005 Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-3195-7521","affiliations":[{"raw_affiliation_string":"Institut de Biologie de l\u2019Ecole Normale Sup\u00e9rieure (IBENS), Ecole Normale Sup\u00e9rieure, CNRS, INSERM, PSL Research University, 75005 Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I4210129409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002648105","display_name":"Florian Hartig","orcid":"https://orcid.org/0000-0002-6255-9059","observed_orcids":["https://orcid.org/0000-0002-6255-9059"]},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Florian Hartig","raw_affiliation_strings":["Theoretical Ecology, University of Regensburg, Regensburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-6255-9059","affiliations":[{"raw_affiliation_string":"Theoretical Ecology, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000329854","display_name":"Stephane S. Robin","orcid":"https://orcid.org/0000-0003-1045-069X","observed_orcids":["https://orcid.org/0000-0003-1045-069X"]},"institutions":[{"id":"https://openalex.org/I22248866","display_name":"AgroParisTech","ror":"https://ror.org/02kbmgc12","country_code":"FR","type":"education","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4387153087","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es","ror":"https://ror.org/00780az30","country_code":"FR","type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I4210088668","https://openalex.org/I4387153087"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"St\u00e9phane Robin","raw_affiliation_strings":["UMR MIA-Paris, AgroParisTech, INRA, Paris-Saclay University, 75005 Paris, France"],"raw_orcid":"https://orcid.org/0000-0003-1045-069X","affiliations":[{"raw_affiliation_string":"UMR MIA-Paris, AgroParisTech, INRA, Paris-Saclay University, 75005 Paris, France","institution_ids":["https://openalex.org/I22248866","https://openalex.org/I4387153087"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5084776094"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I4210129409"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":43,"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":0.8988999724388123,"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":0.8988999724388123,"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":0.0357000008225441,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.026100000366568565,"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/timetree","display_name":"timetree","score":0.7950000166893005},{"id":"https://openalex.org/keywords/speciation-and-extinction-rates","display_name":"speciation and extinction rates","score":0.8330000042915344},{"id":"https://openalex.org/keywords/phylogenetic-likelihood","display_name":"phylogenetic likelihood","score":0.4309999942779541}],"concepts":[{"id":"https://openalex.org/C178300618","wikidata":"https://www.wikidata.org/wiki/Q1898509","display_name":"Extant taxon","level":2,"score":0.7892801761627197},{"id":"https://openalex.org/C180916674","wikidata":"https://www.wikidata.org/wiki/Q3711935","display_name":"Diversification (marketing strategy)","level":2,"score":0.6730647087097168},{"id":"https://openalex.org/C101991246","wikidata":"https://www.wikidata.org/wiki/Q5422078","display_name":"Extinction (optical mineralogy)","level":2,"score":0.6079768538475037},{"id":"https://openalex.org/C2776838516","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.5745224952697754},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.511769711971283},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.4588371813297272},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.44513097405433655},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.4102938175201416},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.40985220670700073},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3707040548324585},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.25458192825317383},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.24737825989723206},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24346604943275452},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2009592056274414},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.10409292578697205},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.09944826364517212},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.07440409064292908},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.06625264883041382},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2020.07.03.185074","doi":"https://doi.org/10.1101/2020.07.03.185074","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.07.03.185074","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/07/04/2020.07.03.185074.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2020.07.03.185074","doi":"https://doi.org/10.1101/2020.07.03.185074","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.07.03.185074","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/07/04/2020.07.03.185074.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3040237290.pdf","grobid_xml":"https://content.openalex.org/works/W3040237290.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W123584386","https://openalex.org/W1554944419","https://openalex.org/W1964525108","https://openalex.org/W1990824786","https://openalex.org/W1999179318","https://openalex.org/W2034921015","https://openalex.org/W2039879168","https://openalex.org/W2058894350","https://openalex.org/W2081587468","https://openalex.org/W2098713714","https://openalex.org/W2122825543","https://openalex.org/W2142708736","https://openalex.org/W2151541130","https://openalex.org/W2210604002","https://openalex.org/W2308144904","https://openalex.org/W2308827608","https://openalex.org/W2478738321","https://openalex.org/W2593643174","https://openalex.org/W2604959477","https://openalex.org/W2766641567","https://openalex.org/W2898169259","https://openalex.org/W2947175105","https://openalex.org/W2971755138","https://openalex.org/W3008256015","https://openalex.org/W3016352084","https://openalex.org/W3097794559","https://openalex.org/W3122992882"],"related_works":["https://openalex.org/W3016352084","https://openalex.org/W4214753734","https://openalex.org/W3202100786","https://openalex.org/W2800772661","https://openalex.org/W4200071587","https://openalex.org/W6892165832","https://openalex.org/W3161837187","https://openalex.org/W4323810567","https://openalex.org/W4388021726","https://openalex.org/W4399726133"],"abstract_inverted_index":{"Abstract":[0],"Phylogenies":[1],"of":[2,24,66,70,98],"extant":[3,128],"species":[4],"are":[5],"widely":[6,112],"used":[7,113],"to":[8,20,51],"study":[9],"past":[10],"diversification":[11,77],"dynamics":[12,123],"1":[13],".":[14],"The":[15],"most":[16],"common":[17],"approach":[18],"is":[19],"formulate":[21],"a":[22,39,131],"set":[23],"candidate":[25],"models":[26,47,72],"representing":[27],"evolutionary":[28],"hypotheses":[29],"for":[30,82],"how":[31],"and":[32,35,44,101,121],"why":[33],"speciation":[34,120],"extinction":[36,122],"rates":[37],"in":[38,114],"clade":[40],"changed":[41],"over":[42],"time,":[43],"compare":[45],"those":[46],"through":[48],"their":[49],"probability":[50],"have":[52],"generated":[53],"the":[54,64,96,107,115],"corresponding":[55],"empirical":[56,84],"tree.":[57],"Recently,":[58],"Louca":[59],"&":[60,89],"Pennell":[61],"2":[62],"reported":[63],"existence":[65],"an":[67],"infinite":[68],"number":[69],"\u2018congruent\u2019":[71],"with":[73],"potentially":[74],"markedly":[75],"different":[76],"dynamics,":[78],"but":[79],"equal":[80],"likelihood,":[81],"any":[83],"tree":[85],"(see":[86],"also":[87],"Lambert":[88],"Stadler":[90],"3":[91],").":[92],"Here":[93],"we":[94],"explore":[95],"implications":[97],"these":[99],"results,":[100],"conclude":[102],"that":[103,119],"they":[104],"neither":[105],"undermine":[106],"hypothesis-driven":[108],"model":[109],"selection":[110],"procedure":[111],"field":[116],"nor":[117],"show":[118],"cannot":[124],"be":[125],"investigated":[126],"from":[127],"timetrees":[129],"using":[130],"data-driven":[132],"procedure.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":2}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2020-07-10T00:00:00"}