A simple method of removing the effect of a bottleneck and unequal population sizes on pairwise genetic distances
A simple method of removing the effect of a bottleneck and unequal population sizes on pairwise genetic distances
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DOI：
10.1098/rspb.2000.0970
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发表时间：
2000-01-07
影响因子：
4.7
通讯作者：
Excoffier, L
中科院分区：
文献类型：
--
作者：
Gaggiotti, OE;Excoffier, L
在本文中，我们得到了两个流行的遗传距离的期望下的纯种群裂变模型允许不相等的人口规模。在该模型下，我们发现，传统的遗传距离是不成正比的分歧时间，并普遍高估它，由于不平等的遗传漂变和在分歧时间的瓶颈效应。即使知道目前的人口规模，也不能完全消除这种偏见。相反，我们提出了一种方法来估计种群之间的分歧时间，这是基于种群内和种群之间的核苷酸差异的平均数。该方法同时估计了种群的发散时间、祖先种群大小和衍生种群的相对大小。一项模拟研究表明，这种方法基本上是无偏的，它导致更好的估计比传统的方法为一个非常广泛的参数值。模拟结果还表明，适度的人口增长后，分歧的所有三个估计参数的估计几乎没有影响。应用我们的方法比较人类和黑猩猩的线粒体DNA多样性发现，普通黑猩猩有一个显着较大的女性人口规模比人类。
In this paper, we derive the expectation of two popular genetic distances under a model of pure population fission allowing for unequal population sizes. Under the model, we show that conventional genetic distances are not Proportional to the divergence time and generally overestimate it due to unequal genetic drift and to a bottleneck effect at the divergence time. This bias cannot be totally removed even if the present population sizes are known. Instead, we present a method to estimate the divergence times between populations which is based on the average number of nucleotide differences within and between populations. The method simultaneously estimates the divergence time, the ancestral population size and the relative sizes of the derived populations. A simulation study revealed that this method is essentially unbiased and that it leads to better estimates than traditional approaches for a very wide range of parameter values. Simulations also indicated that moderate population growth after divergence has little effect on the estimates of all three estimated parameters. An application of our method to a comparison of humans and chimpanzee mitochondrial DNA diversity revealed that common chimpanzees have a significantly larger female population size than humans.