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Exact calculation of the joint allele frequency spectrum for generalized isolation with migration models

Andrew D. Kern, Jody Hey
doi: https://doi.org/10.1101/065003
Andrew D. Kern
*Department of Genetics, Rutgers University, Piscataway, NJ 08554, USA
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Jody Hey
†Department of Biology, Temple University, Philadephia, PA 19122 USA
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Abstract

Population genomic datasets collected over the past decade have spurred interest in developing methods that can utilize massive numbers of loci for inference of demographic and selective histories of populations. The allele frequency spectrum (AFS) provides a convenient framework for such analysis and accordingly much attention has been paid to predicting theoretical expectations of the AFS under a number of different models. However, to date, exact solutions for the joint AFS of two or more populations under models of migration and divergence have not been found. Here we present a novel Markov chain representation of the coalescent on the state space of the joint AFS that allows for rapid, exact calculation of the joint AFS under generalized isolation with migration (IM) models. In turn, we show how our Markov chain method, in the context of composite likelihood estimation, can be used for accurate inference of parameters of the IM model using SNP data. Lastly, we apply our method to recent whole genome datasets from Drosophila melanogaster.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted July 21, 2016.
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Exact calculation of the joint allele frequency spectrum for generalized isolation with migration models
Andrew D. Kern, Jody Hey
bioRxiv 065003; doi: https://doi.org/10.1101/065003
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Exact calculation of the joint allele frequency spectrum for generalized isolation with migration models
Andrew D. Kern, Jody Hey
bioRxiv 065003; doi: https://doi.org/10.1101/065003

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