Estimates of genetic differentiation measured by F(ST) do not necessarily require large sample sizes when using many SNP markers.
Estimates of genetic differentiation measured by F(ST) do not necessarily require large sample sizes when using many SNP markers.
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DOI：
10.1371/journal.pone.0042649
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
van Oosterhout C
中科院分区：
文献类型：
--
作者：
Willing EM;Dreyer C;van Oosterhout C
种群遗传学研究提供了对影响野生种群内和野生种群之间序列变异分布的进化过程的洞察。FST是最广泛使用的遗传分化指标之一，在生态和进化遗传学研究中发挥着核心作用。人们普遍认为，为了准确地推断FST，需要大样本量，而小样本量会导致对遗传分化的高估。直到最近，在生态模式生物中的研究纳入了有限数量的遗传标记，但自从下一代测序的出现以来，即使在非参考生物中也可以获得的遗传标记的小组规模迅速增加。在这项研究中，我们检验了在估计FST时，大量的遗传标记是否可以替代小样本容量。我们测试了三种推断FST的不同估计者的行为，这三种估计者通常用于群体遗传学研究。通过模拟种群，我们评估了样本大小和标记数量对遗传分化的各种估计的影响。此外，我们还检验了确定偏差对这些估计的影响。我们表明，当使用适当的估计器和大量的双等位基因标记(k>；1,000)时，总体样本量可以显著减少(小到n = 4-6)。因此，保护遗传研究现在可以获得几乎与使用下一代测序开发的标记对模型生物进行的研究相同的统计能力。
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.
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