Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle
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Edited by Mark Johnston, Washington University, St. Louis, MO, and accepted by the Editorial Board January 30, 2008 (received for review August 3, 2007)
Abstract
Most microbes have complex life cycles with multiple modes of reproduction that differ in their effects on DNA sequence variation. Population genomic analyses can therefore be used to estimate the relative frequencies of these different modes in nature. The life cycle of the wild yeast Saccharomyces paradoxus is complex, including clonal reproduction, outcrossing, and two different modes of inbreeding. To quantify these different aspects we analyzed DNA sequence variation in the third chromosome among 20 isolates from two populations. Measures of mutational and recombinational diversity were used to make two independent estimates of the population size. In an obligately sexual population these values should be approximately equal. Instead there is a discrepancy of about three orders of magnitude between our two estimates of population size, indicating that S. paradoxus goes through a sexual cycle approximately once in every 1,000 asexual generations. Chromosome III also contains the mating type locus (MAT), which is the most outbred part in the entire genome, and by comparing recombinational diversity as a function of distance from MAT we estimate the frequency of matings to be ≈94% from within the same tetrad, 5% with a clonemate after switching the mating type, and 1% outcrossed. Our study illustrates the utility of population genomic data in quantifying life cycles.
Footnotes
- †To whom correspondence should be addressed. E-mail: v.koufopanou{at}imperial.ac.uk
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Author contributions: A.B. and V.K. contributed equally to this work; A.B. and V.K. designed research; I.J.T., D.B., A.B., and V.K. analyzed data; and I.J.T., A.B., and V.K. wrote the paper.
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↵*Present address: Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom.
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The authors declare no conflict of interest.
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This article is a PNAS Direct Submission. M.J. is a guest editor invited by the Editorial Board.
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Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. EU444726 and EU519436-53).
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This article contains supporting information online at www.pnas.org/cgi/content/full/0707314105/DC1.
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Freely available online through the PNAS open access option.
- © 2008 by The National Academy of Sciences of the USA
