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A major unanswered question is the degree to which an individual\u2019s genetic makeup influences its tolerance of karyotypic imbalance. Here we investigated within-species variation in aneuploidy prevalence and tolerance, using Saccharomyces cerevisiae as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000 S. cerevisiae strains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The relationships between lineages with high aneuploidy frequencies suggest that increased aneuploidy prevalence emerged multiple times in S. cerevisiae evolution. Separate from aneuploidy prevalence, analyzing growth phenotypes revealed that some genetic backgrounds\u2014such as the European Wine lineage\u2014show fitness costs in aneuploids compared to euploids, whereas other clades with high aneuploidy frequencies show little evidence of major deleterious effects. Our analysis confirms that chromosome gain can produce phenotypic benefits, which could influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution.<\/jats:p>","DOI":"10.1093\/genetics\/iyab015","type":"journal-article","created":{"date-parts":[[2021,2,3]],"date-time":"2021-02-03T17:56:54Z","timestamp":1612375014000},"source":"Crossref","is-referenced-by-count":51,"title":["Genetic variation in aneuploidy prevalence and tolerance across\n                    <i>Saccharomyces cerevisiae<\/i>\n                    lineages"],"prefix":"10.1093","volume":"217","author":[{"given":"Eduardo F C","family":"Scopel","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Hose","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics and Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9015-2707","authenticated-orcid":false,"given":"Douda","family":"Bensasson","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8182-257X","authenticated-orcid":false,"given":"Audrey P","family":"Gasch","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics and Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,3,4]]},"reference":[{"key":"2022030401093326100_iyab015-B1","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1111\/1567-1364.12120","article-title":"Improved sake metabolic profile during fermentation 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