Exact Calculation of the Joint Allele Frequency Spectrum for Isolation with Migration Models. Issue 1 (10th July 2017)

• Record Type: Journal Article
• Authors: Kern, Andrew D; Hey, Jody
• Is Part Of: Genetics. Volume 207:Issue 1(2017)
• Page Start: 241
• Page End: 253
• Publication Date: 2017-07-10
• Subjects: isolation with migration -- AFS -- Markov chains -- composite likelihood; Genetics -- Periodicals; 576.5
• DOI: 10.1534/genetics.116.194019
• Languages: English
• ISSNs: 0016-6731

Abstract

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 statistic 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 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 African Drosophila melanogaster .