Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers

Willing, Eva-Maria, Dreyer, Christine and Van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X (2012) Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. PLoS One, 7 (8). ISSN 1932-6203

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Abstract

Population genetic studies provide insights into the evolutionary processes that influence the distribution of sequence variants within and among wild populations. FST is among the most widely used measures for genetic differentiation and plays a central role in ecological and evolutionary genetic studies. It is commonly thought that large sample sizes are required in order to precisely infer FST and that small sample sizes lead to overestimation of genetic differentiation. Until recently, studies in ecological model organisms incorporated a limited number of genetic markers, but since the emergence of next generation sequencing, the panel size of genetic markers available even in non-reference organisms has rapidly increased. In this study we examine whether a large number of genetic markers can substitute for small sample sizes when estimating FST. We tested the behavior of three different estimators that infer FST and that are commonly used in population genetic studies. By simulating populations, we assessed the effects of sample size and the number of markers on the various estimates of genetic differentiation. Furthermore, we tested the effect of ascertainment bias on these estimates. We show that the population sample size can be significantly reduced (as small as n = 4–6) when using an appropriate estimator and a large number of bi-allelic genetic markers (k.1,000). Therefore, conservation genetic studies can now obtain almost the same statistical power as studies performed on model organisms using markers developed with next-generation sequencing.

Item Type:	Article
Additional Information:	© Willing et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Faculty \ School:	Faculty of Science > School of Environmental Sciences
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
Depositing User:	Katherine Humphries
Date Deposited:	21 Feb 2013 14:29
Last Modified:	23 Oct 2022 00:07
URI:	https://ueaeprints.uea.ac.uk/id/eprint/41484
DOI:	10.1371/journal.pone.0042649

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