Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent
Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent
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DOI：
10.1016/j.ajhg.2015.07.012
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发表时间：
2015-09-03
影响因子：
9.8
通讯作者：
Browning, Brian L.
中科院分区：
文献类型：
--
作者：
Browning, Sharon R.;Browning, Brian L.
从遗传数据估计历史有效群体大小的现有方法已经不能准确地估计最近的过去期间的有效群体大小。我们提出了一个非参数的方法，准确估计最近的有效人口规模，通过使用推断的长段身份的下降（IBD）。我们发现，IBD的推断片段包含SNP阵列数据从大约4代到大约50代前以及序列数据到超过200代前的有效群体大小的信息。在我们研究的人群中，有效规模的估计值约为人口普查规模的三分之一。我们估计四代前英国欧洲血统个体的有效人口规模为800万，四代前芬兰的有效人口规模为70万。我们的方法是在开源的IBDNe软件包中实现的。
Existing methods for estimating historical effective population size from genetic data have been unable to accurately estimate effective population size during the most recent past. We present a non-parametric method for accurately estimating recent effective population size by using inferred long segments of identity by descent (IBD). We found that inferred segments of IBD contain information about effective population size from around 4 generations to around 50 generations ago for SNP array data and to over 200 generations ago for sequence data. In human populations that we examined, the estimates of effective size were approximately one-third of the census size. We estimate the effective population size of European-ancestry individuals in the UK four generations ago to be eight million and the effective population size of Finland four generations ago to be 0.7 million. Our method is implemented in the open-source IBDNe software package.