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Tellini, Nicolò, De Chiara, Matteo, Mozzachiodi, Simone, Tattini, Lorenzo, Vischioni, Chiara, Naumova, Elena S., Warringer, Jonas, Bergström, Anders 
ORCID: https://orcid.org/0000-0002-4096-9268 and Liti, Gianni
(2024)
Ancient and recent origins of shared polymorphisms in yeast.
Nature Ecology & Evolution, 8 (4).
pp. 761-776.
ISSN 2397-334X
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Abstract
Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4–6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.
| Item Type: | Article |
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| Additional Information: | Data availability statement: The gVCF of the S. cerevisiae collection and raw data of the diagnostic markers and introgressed blocks coordinates are available at https://bitbucket.org/yeastgenomics. The genome sequences generated in this study are available at European Nucleotide Archive under the accession code PRJEB71987. Source data are provided with this paper. Code availability statement: The developed computational pipelines and scripts are available at https://bitbucket.org/yeastgenomics. Funding information: This work was supported by Agence Nationale de la Recherche (ANR-11-LABX-0028-01, ANR-15-IDEX-01, ANR-18-CE12-0004, ANR-20-CE12-0020, ANR-22-CE12-0015), Fondation pour la Recherche Médicale (EQU202003010413), UCA AAP Start-up Deep tech, CEFIPRA to G.L. N.T. was partially supported by the PhD fellowship programme Region PACA. E.S.N. was supported by the Ministry of Science and Higher Education of the Russian Federation grant for Kurchatov Center of Genome Research (075-15-2019-1659). |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| UEA Research Groups: | Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation |
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| Depositing User: | LivePure Connector |
| Date Deposited: | 07 Nov 2024 17:30 |
| Last Modified: | 13 Nov 2024 00:53 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97575 |
| DOI: | 10.1038/s41559-024-02352-5 |
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