{"id":"https://openalex.org/W4409975418","doi":"https://doi.org/10.3389/fbinf.2025.1571568","title":"Integrating phylogenies with chronology to assemble the tree of life","display_name":"Integrating phylogenies with chronology to assemble the tree of life","publication_year":2025,"publication_date":"2025-04-30","ids":{"openalex":"https://openalex.org/W4409975418","doi":"https://doi.org/10.3389/fbinf.2025.1571568","pmid":"https://pubmed.ncbi.nlm.nih.gov/40370941"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1571568","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1571568","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1571568/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1571568/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000997109","display_name":"Jose Barba\u2010Montoya","orcid":"https://orcid.org/0000-0002-1337-8139"},"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"]},{"id":"https://openalex.org/I1338124936","display_name":"American Museum of Natural History","ror":"https://ror.org/03thb3e06","country_code":"US","type":"archive","lineage":["https://openalex.org/I1338124936"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose Barba-Montoya","raw_affiliation_strings":["Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","Richard Gilder Graduate School, American Museum of Natural History, New York, NY, United States"],"affiliations":[{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Richard Gilder Graduate School, American Museum of Natural History, New York, NY, United States","institution_ids":["https://openalex.org/I1338124936"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091689845","display_name":"Jack M. Craig","orcid":"https://orcid.org/0000-0003-0590-5944"},"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":"Jack M. Craig","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, United States","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","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"},"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":true,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Department of Biology, Temple University, Philadelphia, PA, United States","Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100680948"],"corresponding_institution_ids":["https://openalex.org/I84392919"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":3.8633,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.9053006,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"5","issue":null,"first_page":"1571568","last_page":"1571568"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9958999752998352,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9595999717712402,"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/chronology","display_name":"Chronology","score":0.963009238243103},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5958508849143982},{"id":"https://openalex.org/keywords/tree-of-life","display_name":"Tree of life (biology)","score":0.591040849685669},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4678286910057068},{"id":"https://openalex.org/keywords/genealogy","display_name":"Genealogy","score":0.41550299525260925},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3520314395427704},{"id":"https://openalex.org/keywords/history","display_name":"History","score":0.32162541151046753},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.2519916296005249},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.24834740161895752},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1616053283214569},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10796335339546204},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.05504634976387024}],"concepts":[{"id":"https://openalex.org/C181536285","wikidata":"https://www.wikidata.org/wiki/Q130788","display_name":"Chronology","level":2,"score":0.963009238243103},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5958508849143982},{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.591040849685669},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4678286910057068},{"id":"https://openalex.org/C53553401","wikidata":"https://www.wikidata.org/wiki/Q47307","display_name":"Genealogy","level":1,"score":0.41550299525260925},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3520314395427704},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.32162541151046753},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.2519916296005249},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.24834740161895752},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1616053283214569},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10796335339546204},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.05504634976387024},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1571568","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1571568","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1571568/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40370941","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40370941","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:38b825644dab4c13a35b75ef9c6fd51b","is_oa":true,"landing_page_url":"https://doaj.org/article/38b825644dab4c13a35b75ef9c6fd51b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12075222","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12075222","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,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1571568","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1571568","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1571568/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409975418.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1605984840","https://openalex.org/W1992566665","https://openalex.org/W1992800126","https://openalex.org/W2009596137","https://openalex.org/W2041187152","https://openalex.org/W2045517599","https://openalex.org/W2060425093","https://openalex.org/W2071465766","https://openalex.org/W2097706568","https://openalex.org/W2111647009","https://openalex.org/W2117260150","https://openalex.org/W2121552166","https://openalex.org/W2125359798","https://openalex.org/W2127779696","https://openalex.org/W2145100181","https://openalex.org/W2145769273","https://openalex.org/W2152529266","https://openalex.org/W2161973008","https://openalex.org/W2179623716","https://openalex.org/W2187450834","https://openalex.org/W2229908198","https://openalex.org/W2342704856","https://openalex.org/W2521268904","https://openalex.org/W2801361050","https://openalex.org/W2801982793","https://openalex.org/W2803572653","https://openalex.org/W2947934976","https://openalex.org/W2949972517","https://openalex.org/W2951002538","https://openalex.org/W2951664382","https://openalex.org/W2954312507","https://openalex.org/W2991998196","https://openalex.org/W3083304049","https://openalex.org/W4200339067","https://openalex.org/W4239632189","https://openalex.org/W4251751280","https://openalex.org/W4254717640","https://openalex.org/W4290075586","https://openalex.org/W4302763624","https://openalex.org/W4313236308","https://openalex.org/W4384819927","https://openalex.org/W4385567503","https://openalex.org/W4389788119","https://openalex.org/W4393055199","https://openalex.org/W6632899734","https://openalex.org/W6689475862","https://openalex.org/W6948047203"],"related_works":["https://openalex.org/W2004270443","https://openalex.org/W2207720026","https://openalex.org/W1766380752","https://openalex.org/W2901347066","https://openalex.org/W2146536773","https://openalex.org/W2011419188","https://openalex.org/W1976078150","https://openalex.org/W1923231248","https://openalex.org/W3047355839","https://openalex.org/W2955599956"],"abstract_inverted_index":{"Reconstructing":[0],"the":[1,64,180],"global":[2],"Tree":[3],"of":[4,24,56,74,137,182],"Life":[5],"necessitates":[6],"computational":[7],"approaches":[8,106,158],"to":[9,34,39,88,134,189],"integrate":[10],"numerous":[11],"molecular":[12,43,85,99],"phylogenies":[13,30,86,110,133,175],"with":[14,114,150],"limited":[15,152],"species":[16,50,75,153],"overlap":[17],"into":[18],"a":[19,53,60,72,92,125,129],"comprehensive":[20],"supertree.":[21],"Our":[22],"survey":[23],"published":[25,84],"literature":[26],"shows":[27],"that":[28,69,107,143,159,173,185],"individual":[29],"are":[31,186],"frequently":[32],"restricted":[33,148],"specific":[35],"taxonomic":[36],"groups":[37],"due":[38],"investigators'":[40],"expertise":[41],"and":[42,139],"evolutionary":[44],"considerations,":[45],"resulting":[46],"in":[47,52,83],"any":[48],"given":[49],"present":[51,59],"minuscule":[54],"fraction":[55],"phylogenies.":[57],"We":[58,171],"novel":[61],"approach,":[62],"called":[63],"chronological":[65,96],"supertree":[66,73,93],"algorithm":[67],"(Chrono-STA),":[68],"can":[70,145],"build":[71],"from":[76,98,104,111],"such":[77,156],"data":[78,97],"by":[79,94],"using":[80],"node":[81],"ages":[82],"scaled":[87,188],"time.":[89,190],"Chrono-STA":[90,118,144],"builds":[91],"integrating":[95,174],"timetrees.":[100],"It":[101],"fundamentally":[102],"differs":[103],"existing":[105],"generate":[108],"consensus":[109],"gene":[112],"trees":[113],"missing":[115,161],"taxa,":[116],"as":[117,128],"does":[119],"not":[120,168],"impute":[121,160],"nodal":[122],"distances,":[123],"use":[124],"guide":[126],"tree":[127],"backbone,":[130],"or":[131,163],"reduce":[132],"quartets.":[135],"Analyses":[136],"simulated":[138],"empirical":[140],"datasets":[141],"show":[142],"combine":[146],"taxonomically":[147],"timetrees":[149],"extremely":[151],"overlap.":[154],"For":[155],"data,":[157],"distances":[162],"assemble":[164],"phylogenetic":[165],"quartets":[166],"did":[167],"perform":[169],"well.":[170],"conclude":[172],"via":[176],"temporal":[177],"dimension":[178],"enhances":[179],"accuracy":[181],"reconstructed":[183],"supertrees":[184],"also":[187]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}