{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T01:54:16Z","timestamp":1775872456730,"version":"3.50.1"},"reference-count":116,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2027,2,23]],"date-time":"2027-02-23T00:00:00Z","timestamp":1803340800000},"content-version":"am","delay-in-days":387,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["7005101"],"award-info":[{"award-number":["7005101"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015814","name":"Great Lakes Bioenergy Research Center","doi-asserted-by":"publisher","award":["DE\\u2013SC0018409"],"award-info":[{"award-number":["DE\\u2013SC0018409"]}],"id":[{"id":"10.13039\/100015814","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Foundation for Science and Technology","doi-asserted-by":"publisher","award":["UIDP\/04378\/2020"],"award-info":[{"award-number":["UIDP\/04378\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Foundation for Science and Technology","doi-asserted-by":"publisher","award":["PTDC\/BIA-EVL\/0604\/2021"],"award-info":[{"award-number":["PTDC\/BIA-EVL\/0604\/2021"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-2305612"],"award-info":[{"award-number":["DBI-2305612"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-2110403"],"award-info":[{"award-number":["DEB-2110403"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-2110404"],"award-info":[{"award-number":["DEB-2110404"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006111","name":"Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior","doi-asserted-by":"publisher","award":["LA\/P\/0140\/2020"],"award-info":[{"award-number":["LA\/P\/0140\/2020"]}],"id":[{"id":"10.13039\/501100006111","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015691","name":"National Institute of Allergy and Infectious Diseases Division of Microbiology and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI153356"],"award-info":[{"award-number":["R01 AI153356"]}],"id":[{"id":"10.13039\/100015691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006206","name":"Biological and Environmental Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006206","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM151348"],"award-info":[{"award-number":["R35GM151348"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Current Biology"],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1016\/j.cub.2025.12.053","type":"journal-article","created":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T15:57:04Z","timestamp":1769615824000},"page":"1067-1075.e3","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["Discovery of additional ancient genome duplications in yeasts"],"prefix":"10.1016","volume":"36","author":[{"given":"Kyle T.","family":"David","sequence":"first","affiliation":[]},{"given":"Linda","family":"Horianopoulos","sequence":"additional","affiliation":[]},{"given":"Carla","family":"Gon\u00e7alves","sequence":"additional","affiliation":[]},{"given":"Jacob L.","family":"Steenwyk","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Pontes","sequence":"additional","affiliation":[]},{"given":"Paula","family":"Gon\u00e7alves","sequence":"additional","affiliation":[]},{"given":"Chris Todd","family":"Hittinger","sequence":"additional","affiliation":[]},{"given":"Matt","family":"Pennell","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7248-6551","authenticated-orcid":false,"given":"Antonis","family":"Rokas","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/j.cub.2025.12.053_bib1","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.cell.2007.10.022","article-title":"The evolutionary consequences of polyploidy","volume":"131","author":"Otto","year":"2007","journal-title":"Cell"},{"key":"10.1016\/j.cub.2025.12.053_bib2","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nrg.2017.26","article-title":"The evolutionary significance of polyploidy","volume":"18","author":"Van de Peer","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.cub.2025.12.053_bib3","doi-asserted-by":"crossref","first-page":"e314","DOI":"10.1371\/journal.pbio.0030314","article-title":"Two rounds of whole genome duplication in the ancestral vertebrate","volume":"3","author":"Dehal","year":"2005","journal-title":"PLOS Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib4","series-title":"Evolution by Gene Duplication","author":"Ohno","year":"1970"},{"key":"10.1016\/j.cub.2025.12.053_bib5","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41559-023-02299-z","article-title":"Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences","volume":"8","author":"Yu","year":"2024","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib6","doi-asserted-by":"crossref","first-page":"1808","DOI":"10.1093\/molbev\/msl049","article-title":"Gene loss and evolutionary rates following whole-genome duplication in teleost fishes","volume":"23","author":"Brunet","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib7","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1007\/s00438-014-0889-2","article-title":"Whole-genome duplication in teleost fishes and its evolutionary consequences","volume":"289","author":"Glasauer","year":"2014","journal-title":"Mol. Genet. Genomics"},{"key":"10.1016\/j.cub.2025.12.053_bib8","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/j.tree.2005.07.008","article-title":"Genome duplication and the origin of angiosperms","volume":"20","author":"De Bodt","year":"2005","journal-title":"Trends Ecol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib9","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1111\/nph.13491","article-title":"Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications","volume":"207","author":"Tank","year":"2015","journal-title":"New Phytol."},{"key":"10.1016\/j.cub.2025.12.053_bib10","doi-asserted-by":"crossref","first-page":"8362","DOI":"10.1073\/pnas.1503926112","article-title":"The butterfly plant arms-race escalated by gene and genome duplications","volume":"112","author":"Edger","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2025.12.053_bib11","series-title":"The Evolution of the Genome","first-page":"427","article-title":"Polyploidy in animals","author":"Gregory","year":"2005"},{"key":"10.1016\/j.cub.2025.12.053_bib12","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1146\/annurev.genet.34.1.401","article-title":"Polyploid incidence and evolution","volume":"34","author":"Otto","year":"2000","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.cub.2025.12.053_bib13","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1016\/j.molp.2018.01.002","article-title":"Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms","volume":"11","author":"Ren","year":"2018","journal-title":"Mol. Plant"},{"key":"10.1016\/j.cub.2025.12.053_bib14","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1016\/j.tplants.2018.07.006","article-title":"Whole-genome duplication and plant macroevolution","volume":"23","author":"Clark","year":"2018","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.cub.2025.12.053_bib15","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1002\/ajb2.1060","article-title":"Impact of whole-genome duplication events on diversification rates in angiosperms","volume":"105","author":"Landis","year":"2018","journal-title":"Am. J. Bot."},{"key":"10.1016\/j.cub.2025.12.053_bib16","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1086\/688763","article-title":"The case of the missing ancient fungal polyploids","volume":"188","author":"Campbell","year":"2016","journal-title":"Am. Nat."},{"key":"10.1016\/j.cub.2025.12.053_bib17","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1111\/brv.12605","article-title":"Fungal evolution: cellular, genomic and metabolic complexity","volume":"95","author":"Naranjo-Ortiz","year":"2020","journal-title":"Biol. Rev. Camb. Philos. Soc."},{"key":"10.1016\/j.cub.2025.12.053_bib18","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/42711","article-title":"Molecular evidence for an ancient duplication of the entire yeast genome","volume":"387","author":"Wolfe","year":"1997","journal-title":"Nature"},{"key":"10.1016\/j.cub.2025.12.053_bib19","doi-asserted-by":"crossref","first-page":"8397","DOI":"10.1073\/pnas.0608218104","article-title":"Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication","volume":"104","author":"Scannell","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2025.12.053_bib20","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msae052","article-title":"Aneuploidy can be an evolutionary diversion on the path to adaptation","volume":"41","author":"Kohanovski","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib21","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib22","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1111\/nph.14812","article-title":"Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events","volume":"217","author":"Yang","year":"2018","journal-title":"New Phytol."},{"key":"10.1016\/j.cub.2025.12.053_bib23","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.1501084","article-title":"Early genome duplications in conifers and other seed plants","volume":"1","author":"Li","year":"2015","journal-title":"Sci. Adv."},{"key":"10.1016\/j.cub.2025.12.053_bib24","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nature09916","article-title":"Ancestral polyploidy in seed plants and angiosperms","volume":"473","author":"Jiao","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.cub.2025.12.053_bib25","doi-asserted-by":"crossref","first-page":"R109","DOI":"10.1186\/gb-2007-8-6-r109","article-title":"The human phylome","volume":"8","author":"Huerta-Cepas","year":"2007","journal-title":"Genome Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib26","doi-asserted-by":"crossref","first-page":"e1002220","DOI":"10.1371\/journal.pbio.1002220","article-title":"Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the baker\u2019s yeast lineage","volume":"13","author":"Marcet-Houben","year":"2015","journal-title":"PLoS Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib27","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.molp.2018.12.019","article-title":"Finding evidence for whole genome duplications: a reappraisal","volume":"12","author":"Zwaenepoel","year":"2019","journal-title":"Mol. Plant"},{"key":"10.1016\/j.cub.2025.12.053_bib28","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1101\/gr.123901.111","article-title":"Unified modeling of gene duplication, loss, and coalescence using a locus tree","volume":"22","author":"Rasmussen","year":"2012","journal-title":"Genome Res."},{"key":"10.1016\/j.cub.2025.12.053_bib29","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/nrg1449","article-title":"Computational approaches to unveiling ancient genome duplications","volume":"5","author":"Van de Peer","year":"2004","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.cub.2025.12.053_bib30","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1126\/science.1153917","article-title":"Synteny and collinearity in plant genomes","volume":"320","author":"Tang","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.cub.2025.12.053_bib31","doi-asserted-by":"crossref","first-page":"1914","DOI":"10.1093\/molbev\/msu122","article-title":"ChromEvol: assessing the pattern of chromosome number evolution and the inference of polyploidy along a phylogeny","volume":"31","author":"Glick","year":"2014","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib32","series-title":"Fungal Biology","author":"Deacon","year":"2005"},{"key":"10.1016\/j.cub.2025.12.053_bib33","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.tibs.2009.08.006","article-title":"Plasticity of telomere maintenance mechanisms in yeast","volume":"35","author":"Lue","year":"2010","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.cub.2025.12.053_bib34","doi-asserted-by":"crossref","first-page":"12784","DOI":"10.1038\/s41598-021-92126-x","article-title":"Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae","volume":"11","author":"Peska","year":"2021","journal-title":"Sci. Rep."},{"key":"10.1016\/j.cub.2025.12.053_bib35","article-title":"Centromeres evolve progressively through selection at the kinetochore interface","author":"Helsen","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.cub.2025.12.053_bib36","article-title":"Ancient co-option of LTR retrotransposons as yeast centromeres","author":"Haase","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.cub.2025.12.053_bib37","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1007\/s00294-018-0904-y","article-title":"Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus","volume":"65","author":"Brejov\u00e1","year":"2019","journal-title":"Curr. Genet."},{"key":"10.1016\/j.cub.2025.12.053_bib38","doi-asserted-by":"crossref","first-page":"e00092-19","DOI":"10.1128\/MRA.00092-19","article-title":"Genome sequence of an arthroconidial yeast, Saprochaete fungicola CBS 625.85","volume":"8","author":"Brejov\u00e1","year":"2019","journal-title":"Microbiol. Resour. Announc."},{"key":"10.1016\/j.cub.2025.12.053_bib39","doi-asserted-by":"crossref","first-page":"e01366-19","DOI":"10.1128\/MRA.01366-19","article-title":"Genome sequence of the yeast Saprochaete ingens CBS 517.90","volume":"8","author":"Hodorov\u00e1","year":"2019","journal-title":"Microbiol. Resour. Announc."},{"key":"10.1016\/j.cub.2025.12.053_bib40","doi-asserted-by":"crossref","first-page":"e00094-19","DOI":"10.1128\/MRA.00094-19","article-title":"Genome sequence of flavor-producing yeast Saprochaete suaveolens NRRL Y-17571","volume":"8","author":"Lichancov\u00e1","year":"2019","journal-title":"Microbiol. Resour. Announc."},{"key":"10.1016\/j.cub.2025.12.053_bib41","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/S0168-1605(02)00023-5","article-title":"Intra-species chromosome-length polymorphism in Geotrichum candidum revealed by pulsed field gel electrophoresis","volume":"76","author":"Gente","year":"2002","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.cub.2025.12.053_bib42","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1023\/A:1013038610122","article-title":"Molecular differentiation of sibling species in the Galactomyces geotrichum complex","volume":"80","author":"Naumova","year":"2001","journal-title":"Antonie Leeuwenhoek"},{"key":"10.1016\/j.cub.2025.12.053_bib43","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/BF00313197","article-title":"Electrophoretic karyotype of Dipodascus (Endomyces) magnusii: two main intraspecific chromosomal polymorphisms associated with the difference in total genome size","volume":"29","author":"Filipp","year":"1995","journal-title":"Curr. Genet."},{"key":"10.1016\/j.cub.2025.12.053_bib44","doi-asserted-by":"crossref","first-page":"2495","DOI":"10.1016\/j.cub.2020.04.071","article-title":"Pathogenic allodiploid hybrids of Aspergillus fungi","volume":"30","author":"Steenwyk","year":"2020","journal-title":"Curr. Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib45","doi-asserted-by":"crossref","DOI":"10.1093\/femsyr\/foaf037","article-title":"Taxogenomic analysis of Pichia senei sp. nov. and new insights into hybridization events in the Pichia cactophila species complex","volume":"25","author":"Barros","year":"2025","journal-title":"FEMS Yeast Res."},{"key":"10.1016\/j.cub.2025.12.053_bib46","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1002\/yea.1598","article-title":"Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981","volume":"25","author":"Gordon","year":"2008","journal-title":"Yeast"},{"key":"10.1016\/j.cub.2025.12.053_bib47","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1093\/dnares\/dst058","article-title":"The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant","volume":"21","author":"Mira","year":"2014","journal-title":"DNA Res."},{"key":"10.1016\/j.cub.2025.12.053_bib48","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1093\/gbe\/evu082","article-title":"Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies","volume":"6","author":"Pryszcz","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib49","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0033840","article-title":"De-novo assembly and analysis of the heterozygous triploid genome of the wine spoilage yeast Dekkera bruxellensis AWRI1499","volume":"7","author":"Curtin","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.cub.2025.12.053_bib50","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1038\/s41559-019-0998-8","article-title":"Fermentation innovation through complex hybridization of wild and domesticated yeasts","volume":"3","author":"Langdon","year":"2019","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib51","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1038\/s41477-023-01513-x","article-title":"Evolution of phenotypic disparity in the plant kingdom","volume":"9","author":"Clark","year":"2023","journal-title":"Nat. Plants"},{"key":"10.1016\/j.cub.2025.12.053_bib52","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/ng1553","article-title":"Resurrecting ancestral alcohol dehydrogenases from yeast","volume":"37","author":"Thomson","year":"2005","journal-title":"Nat. Genet."},{"key":"10.1016\/j.cub.2025.12.053_bib53","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1093\/molbev\/msq184","article-title":"Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts","volume":"28","author":"Lin","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib54","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0068734","article-title":"Yeast \u201cmake-accumulate-consume\u201d life strategy evolved as a multi-step process that predates the whole genome duplication","volume":"8","author":"Hagman","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.cub.2025.12.053_bib55","article-title":"Convergent evolution of aerobic fermentation through divergent mechanisms acting on key shared glycolytic genes","author":"Horianopoulos","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.cub.2025.12.053_bib56","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1093\/sysbio\/syy031","article-title":"Rethinking phylogenetic comparative methods","volume":"67","author":"Uyeda","year":"2018","journal-title":"Syst. Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib57","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/sysbio\/syu070","article-title":"The unsolved challenge to phylogenetic correlation tests for categorical characters","volume":"64","author":"Maddison","year":"2015","journal-title":"Syst. Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib58","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gkaa977","article-title":"The InterPro protein families and domains database: 20 years on","volume":"49","author":"Blum","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2025.12.053_bib59","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2025.12.053_bib60","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1385\/ABAB:128:3:227","article-title":"Production of natural fruity aroma by Geotrichum candidum","volume":"128","author":"Mdaini","year":"2006","journal-title":"Appl. Biochem. Biotechnol."},{"key":"10.1016\/j.cub.2025.12.053_bib61","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ijfoodmicro.2004.12.028","article-title":"Interests in Geotrichum candidum for cheese technology","volume":"102","author":"Boutrou","year":"2005","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.cub.2025.12.053_bib62","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4236\/oalib.1108825","article-title":"Taxonomy and characterization of fungi isolated from cocoa beans during fermentation in Saf\u2019s agroforestry system in the Amazon","volume":"9","author":"Barros","year":"2022","journal-title":"OALib"},{"key":"10.1016\/j.cub.2025.12.053_bib63","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1016\/j.foodres.2016.04.010","article-title":"Contribution of predominant yeasts to the occurrence of aroma compounds during cocoa bean fermentation","volume":"89","author":"Kon\u00e9","year":"2016","journal-title":"Food Res. Int."},{"key":"10.1016\/j.cub.2025.12.053_bib64","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1016\/j.foodchem.2017.06.009","article-title":"Flavour production by Saprochaete and Geotrichum yeasts and their close relatives","volume":"237","author":"Grondin","year":"2017","journal-title":"Food Chem."},{"key":"10.1016\/j.cub.2025.12.053_bib65","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1038\/msb4100170","article-title":"Increased glycolytic flux as an outcome of whole-genome duplication in yeast","volume":"3","author":"Conant","year":"2007","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib66","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1002\/1097-0061(200010)16:14<1325::AID-YEA627>3.0.CO;2-E","article-title":"Simultaneous overexpression of enzymes of the lower part of glycolysis can enhance the fermentative capacity of Saccharomyces cerevisiae","volume":"16","author":"Peter Smits","year":"2000","journal-title":"Yeast"},{"key":"10.1016\/j.cub.2025.12.053_bib67","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1534\/genetics.112.140863","article-title":"Response to hyperosmotic stress","volume":"192","author":"Saito","year":"2012","journal-title":"Genetics"},{"key":"10.1016\/j.cub.2025.12.053_bib68","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1534\/genetics.111.128264","article-title":"Regulation of cell wall biogenesis in Saccharomyces cerevisiae: the cell wall integrity signaling pathway","volume":"189","author":"Levin","year":"2011","journal-title":"Genetics"},{"key":"10.1016\/j.cub.2025.12.053_bib69","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1128\/MMBR.62.4.1264-1300.1998","article-title":"MAP kinase pathways in the yeast Saccharomyces cerevisiae","volume":"62","author":"Gustin","year":"1998","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.cub.2025.12.053_bib70","doi-asserted-by":"crossref","first-page":"E1064","DOI":"10.1152\/ajpendo.00296.2003","article-title":"Insulin\/IGF-I-signaling pathway: an evolutionarily conserved mechanism of longevity from yeast to humans","volume":"285","author":"Barbieri","year":"2003","journal-title":"Am. J. Physiol. Endocrinol. Metab."},{"key":"10.1016\/j.cub.2025.12.053_bib71","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/msb.2009.2","article-title":"Glucose regulates transcription in yeast through a network of signaling pathways","volume":"5","author":"Zaman","year":"2009","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib72","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1046\/j.1365-2958.1999.01538.x","article-title":"Novel sensing mechanisms and targets for the cAMP\u2013protein kinase A pathway in the yeast Saccharomyces cerevisiae","volume":"33","author":"Thevelein","year":"1999","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.cub.2025.12.053_bib73","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.3390\/cancers11101618","article-title":"A comprehensive review on MAPK: a promising therapeutic target in cancer","volume":"11","author":"Braicu","year":"2019","journal-title":"Cancers"},{"key":"10.1016\/j.cub.2025.12.053_bib74","doi-asserted-by":"crossref","first-page":"R209","DOI":"10.1186\/gb-2007-8-10-r209","article-title":"All duplicates are not equal: the difference between small scale and genome duplication","volume":"8","author":"Hakes","year":"2007","journal-title":"Genome Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib75","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1101\/gr.3681406","article-title":"Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity","volume":"16","author":"Freeling","year":"2006","journal-title":"Genome Res."},{"key":"10.1016\/j.cub.2025.12.053_bib76","doi-asserted-by":"crossref","first-page":"R43","DOI":"10.1186\/gb-2006-7-5-r43","article-title":"The gain and loss of genes during 600 million years of vertebrate evolution","volume":"7","author":"Blomme","year":"2006","journal-title":"Genome Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib77","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s12915-017-0418-y","article-title":"Dosage-sensitive genes in evolution and disease","volume":"15","author":"Rice","year":"2017","journal-title":"BMC Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib78","doi-asserted-by":"crossref","first-page":"9270","DOI":"10.1073\/pnas.0914697107","article-title":"Ohnologs in the human genome are dosage balanced and frequently associated with disease","volume":"107","author":"Makino","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2025.12.053_bib79","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004394","article-title":"Identification of ohnolog genes originating from whole genome duplication in early vertebrates, based on synteny comparison across multiple genomes","volume":"11","author":"Singh","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib80","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2500165122","article-title":"Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts","volume":"122","author":"David","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2025.12.053_bib81","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1093\/molbev\/msx205","article-title":"The influence of polyploidy on the evolution of yeast grown in a sub-optimal carbon source","volume":"34","author":"Scott","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib82","doi-asserted-by":"crossref","first-page":"2421","DOI":"10.1534\/g3.116.029397","article-title":"Whole genome analysis of 132 clinical Saccharomyces cerevisiae strains reveals extensive ploidy variation","volume":"6","author":"Zhu","year":"2016","journal-title":"G3 (Bethesda)"},{"key":"10.1016\/j.cub.2025.12.053_bib83","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1016\/j.cub.2022.01.068","article-title":"Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts","volume":"32","author":"Saada","year":"2022","journal-title":"Curr. Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib84","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41559-018-0787-9","article-title":"The global biogeography of polyploid plants","volume":"3","author":"Rice","year":"2019","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib85","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2214070119","article-title":"Global gradients in the distribution of animal polyploids","volume":"119","author":"David","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2025.12.053_bib86","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1093\/jhered\/esp047","article-title":"Distinguishing among evolutionary models for the maintenance of gene duplicates","volume":"100","author":"Hahn","year":"2009","journal-title":"J. Hered."},{"key":"10.1016\/j.cub.2025.12.053_bib87","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.8813","article-title":"Patterns of gene evolution following duplications and speciations in vertebrates","volume":"8","author":"David","year":"2020","journal-title":"PeerJ"},{"key":"10.1016\/j.cub.2025.12.053_bib88","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nature06151","article-title":"Gene duplication and the adaptive evolution of a classic genetic switch","volume":"449","author":"Hittinger","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.cub.2025.12.053_bib89","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.cub.2025.12.053_bib90","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1101\/gr.214270.116","article-title":"Fast and accurate de novo genome assembly from long uncorrected reads","volume":"27","author":"Vaser","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.cub.2025.12.053_bib93","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.cub.2025.12.053_bib94","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s13742-015-0076-3","article-title":"LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads","volume":"4","author":"Warren","year":"2015","journal-title":"GigaScience"},{"key":"10.1016\/j.cub.2025.12.053_bib96","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cub.2025.12.053_bib97","series-title":"Funannotate v1.8.1: Eukaryotic genome annotation","author":"Palmer","year":"2020"},{"key":"10.1016\/j.cub.2025.12.053_bib98","doi-asserted-by":"crossref","first-page":"e23","DOI":"10.1093\/nar\/gkq1212","article-title":"A new repeat-masking method enables specific detection of homologous sequences","volume":"39","author":"Frith","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2025.12.053_bib99","doi-asserted-by":"crossref","first-page":"W435","DOI":"10.1093\/nar\/gkl200","article-title":"AUGUSTUS: ab initio prediction of alternative transcripts","volume":"34","author":"Stanke","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2025.12.053_bib100","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1471-2105-5-59","article-title":"Gene finding in novel genomes","volume":"5","author":"Korf","year":"2004","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.cub.2025.12.053_bib101","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1093\/bioinformatics\/bth315","article-title":"TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders","volume":"20","author":"Majoros","year":"2004","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2025.12.053_bib102","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1093\/molbev\/msx319","article-title":"BUSCO applications from quality assessments to gene prediction and phylogenomics","volume":"35","author":"Waterhouse","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2025.12.053_bib103","doi-asserted-by":"crossref","first-page":"D744","DOI":"10.1093\/nar\/gkw1119","article-title":"OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs","volume":"45","author":"Zdobnov","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2025.12.053_bib104","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2025.12.053_bib105","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.cub.2025.12.053_bib106","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cub.2025.12.053_bib107","doi-asserted-by":"crossref","first-page":"2251","DOI":"10.1093\/bioinformatics\/btz859","article-title":"KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold","volume":"36","author":"Aramaki","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2025.12.053_bib108","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2025.12.053_bib109","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae162","article-title":"AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss","volume":"40","author":"Morel","year":"2024","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2025.12.053_bib110","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae272","article-title":"wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication","volume":"40","author":"Chen","year":"2024","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2025.12.053_bib111","doi-asserted-by":"crossref","first-page":"e11","DOI":"10.1093\/nar\/gkr955","article-title":"i-ADHoRe 3.0\u2014fast and sensitive detection of genomic homology in extremely large data sets","volume":"40","author":"Proost","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2025.12.053_bib113","unstructured":"R Core Team (2017). R: A Language and Environment for Statistical Computing. https:\/\/www.R-project.org\/."},{"key":"10.1016\/j.cub.2025.12.053_bib112","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"},{"key":"10.1016\/j.cub.2025.12.053_bib116","doi-asserted-by":"crossref","first-page":"2216","DOI":"10.1093\/bioinformatics\/btu181","article-title":"geiger v2. 0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees","volume":"30","author":"Pennell","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2025.12.053_bib91","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1016\/j.cell.2018.10.023","article-title":"Tempo and mode of genome evolution in the budding yeast subphylum","volume":"175","author":"Shen","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.cub.2025.12.053_bib92","doi-asserted-by":"crossref","DOI":"10.1126\/science.adj4503","article-title":"Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts","volume":"384","author":"Opulente","year":"2024","journal-title":"Science"},{"key":"10.1016\/j.cub.2025.12.053_bib95","doi-asserted-by":"crossref","DOI":"10.1016\/j.xgen.2024.100656","article-title":"Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model","volume":"4","author":"Rojas","year":"2024","journal-title":"Cell Genomics"},{"key":"10.1016\/j.cub.2025.12.053_bib114","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. B (Methodol.)"},{"key":"10.1016\/j.cub.2025.12.053_bib115","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1101\/gr.3672305","article-title":"The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species","volume":"15","author":"Byrne","year":"2005","journal-title":"Genome Res."}],"container-title":["Current Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0960982225017063?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0960982225017063?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T21:11:45Z","timestamp":1772485905000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0960982225017063"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2]]},"references-count":116,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["S0960982225017063"],"URL":"https:\/\/doi.org\/10.1016\/j.cub.2025.12.053","relation":{},"ISSN":["0960-9822"],"issn-type":[{"value":"0960-9822","type":"print"}],"subject":[],"published":{"date-parts":[[2026,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Discovery of additional ancient genome duplications in yeasts","name":"articletitle","label":"Article Title"},{"value":"Current Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cub.2025.12.053","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}