Population genomics of the wild yeast Saccharomyces paradoxus : Quantifying the life cycle
- 25 March 2008
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 105 (12), 4957-4962
- https://doi.org/10.1073/pnas.0707314105
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.Keywords
This publication has 63 references indexed in Scilit:
- The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxusPhilosophical Transactions Of The Royal Society B-Biological Sciences, 2006
- Sequence Diversity, Reproductive Isolation and Species Concepts in SaccharomycesGenetics, 2006
- High Nucleotide Polymorphism and Rapid Decay of Linkage Disequilibrium in Wild Populations of Caenorhabditis remaneiGenetics, 2006
- Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic DiversityGenetics, 2006
- Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparisonGenome Research, 2006
- Genome-Wide Detection of Polymorphisms at Nucleotide Resolution with a Single DNA MicroarrayScience, 2006
- Genomic Selective Constraints in Murid Noncoding DNAPLoS Genetics, 2006
- A haplotype map of the human genomeNature, 2005
- Repbase Update, a database of eukaryotic repetitive elementsCytogenetic and Genome Research, 2005
- Sequencing and comparison of yeast species to identify genes and regulatory elementsNature, 2003