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Appears in Collections:Biological and Environmental Sciences Journal Articles
Peer Review Status: Refereed
Title: ABC inference of multi-population divergence with admixture from unphased population genomic data
Authors: Robinson, John D
Bunnefeld, Lynsey
Hearn, Jack
Stone, Graham N
Hickerson, Michael J
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Keywords: approximate Bayesian computation
Biorhiza pallida
gene flow
next-generation sequencing
Issue Date: Sep-2014
Publisher: Wiley-Blackwell
Citation: Robinson JD, Bunnefeld L, Hearn J, Stone GN & Hickerson MJ (2014) ABC inference of multi-population divergence with admixture from unphased population genomic data, Molecular Ecology, 23 (18), pp. 4458-4471.
Abstract: Rapidly developing sequencing technologies and declining costs have made it possible to collect genome-scale data from population-level samples in nonmodel systems. Inferential tools for historical demography given these data sets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large data sets that are now attainable from nonmodel taxa through current genomic sequencing technologies. We develop and test an ABC framework for model selection and parameter estimation, given histories of three-population divergence with admixture. We then explore different sampling regimes to illustrate how sampling more loci, longer loci or more individuals affects the quality of model selection and parameter estimation in this ABC framework. Our results show that inferences improved substantially with increases in the number and/or length of sequenced loci, while less benefit was gained by sampling large numbers of individuals. Optimal sampling strategies given our inferential models included at least 2000 loci, each approximately 2 kb in length, sampled from five diploid individuals per population, although specific strategies are model and question dependent. We tested our ABC approach through simulation-based cross-validations and illustrate its application using previously analysed data from the oak gall wasp, Biorhiza pallida.
Type: Journal Article
DOI Link:
Rights: © 2014 The Authors. Molecular Ecology published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Affiliation: City College of New York, USA
Biological and Environmental Sciences
University of Edinburgh
University of Edinburgh
City University of New York

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