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Whereas the genome of one isolate,\n                    <jats:italic>C<\/jats:italic>\n                    .\n                    <jats:italic>tropicalis<\/jats:italic>\n                    MYA-3404, was originally sequenced in 2009, there have been no large-scale, multi-isolate studies of the genetic and phenotypic diversity of this species. Here, we used whole genome sequencing and phenotyping to characterize 77 isolates of\n                    <jats:italic>C<\/jats:italic>\n                    .\n                    <jats:italic>tropicalis<\/jats:italic>\n                    from clinical and environmental sources from a variety of locations. We show that most\n                    <jats:italic>C<\/jats:italic>\n                    .\n                    <jats:italic>tropicalis<\/jats:italic>\n                    isolates are diploids with approximately 2\u20136 heterozygous variants per kilobase. The genomes are relatively stable, with few aneuploidies. However, we identified one highly homozygous isolate and six isolates of\n                    <jats:italic>C<\/jats:italic>\n                    .\n                    <jats:italic>tropicalis<\/jats:italic>\n                    with much higher heterozygosity levels ranging from 36\u201349 heterozygous variants per kilobase. Our analyses show that the heterozygous isolates represent two different hybrid lineages, where the hybrids share one parent (A) with most other\n                    <jats:italic>C<\/jats:italic>\n                    .\n                    <jats:italic>tropicalis<\/jats:italic>\n                    isolates, but the second parent (B or C) differs by at least 4% at the genome level. Four of the sequenced isolates descend from an AB hybridization, and two from an AC hybridization. The hybrids are\n                    <jats:italic>MTL<\/jats:italic>\n                    <jats:bold>a<\/jats:bold>\n                    \/\u03b1 heterozygotes. Hybridization, or mating, between different parents is therefore common in the evolutionary history of\n                    <jats:italic>C<\/jats:italic>\n                    .\n                    <jats:italic>tropicalis<\/jats:italic>\n                    . The new hybrids were predominantly found in environmental niches, including from soil. Hybridization is therefore unlikely to be associated with virulence. In addition, we used genotype-phenotype correlation and CRISPR-Cas9 editing to identify a genome variant that results in the inability of one isolate to utilize certain branched-chain amino acids as a sole nitrogen source.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1009138","type":"journal-article","created":{"date-parts":[[2021,3,31]],"date-time":"2021-03-31T13:48:02Z","timestamp":1617198482000},"page":"e1009138","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":52,"title":["Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7730-004X","authenticated-orcid":true,"given":"Caoimhe E.","family":"O\u2019Brien","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1894-3002","authenticated-orcid":true,"given":"Jo\u00e3o","family":"Oliveira-Pacheco","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3148-842X","authenticated-orcid":true,"given":"Eoin","family":"\u00d3 Cinn\u00e9ide","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8962-0446","authenticated-orcid":true,"given":"Max A. B.","family":"Haase","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5088-7461","authenticated-orcid":true,"given":"Chris Todd","family":"Hittinger","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4336-7729","authenticated-orcid":true,"given":"Thomas R.","family":"Rogers","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1581-0845","authenticated-orcid":true,"given":"Oscar","family":"Zaragoza","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2877-6460","authenticated-orcid":true,"given":"Ursula","family":"Bond","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1770-5301","authenticated-orcid":true,"given":"Geraldine","family":"Butler","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2021,3,31]]},"reference":[{"key":"ppat.1009138.ref001","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1128\/JCM.02117-09","article-title":"Results from the ARTEMIS DISK Global Antifungal Surveillance Study, 1997 to 2007: a 10.5-year analysis of susceptibilities of Candida Species to fluconazole and voriconazole as determined by CLSI standardized disk diffusion","volume":"48","author":"MA 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