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Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae
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Jenkins, Paul, Song, Yun S. and Brem, Rachel B. (2012) Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae. PLoS One, Volume 7 (Number 11). Article number e46947. doi:10.1371/journal.pone.0046947 ISSN 1932-6203.
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Official URL: http://dx.doi.org/10.1371/journal.pone.0046947
Abstract
Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Statistics | ||||
Library of Congress Subject Headings (LCSH): | Gene flow, Saccharomyces cerevisiae -- Genetics | ||||
Journal or Publication Title: | PLoS One | ||||
Publisher: | Public Library of Science | ||||
ISSN: | 1932-6203 | ||||
Official Date: | 30 November 2012 | ||||
Dates: |
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Volume: | Volume 7 | ||||
Number: | Number 11 | ||||
Article Number: | Article number e46947 | ||||
DOI: | 10.1371/journal.pone.0046947 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Date of first compliant deposit: | 28 December 2015 | ||||
Date of first compliant Open Access: | 28 December 2015 | ||||
Funder: | National Science Foundation (U.S.) (NSF), David & Lucile Packard Foundation, Ellison Medical Foundation | ||||
Grant number: | DBI-0846015 (NSF) |
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