Szpiech Zachary A, Jakobsson Mattias, Rosenberg Noah A
Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.
Bioinformatics. 2008 Nov 1;24(21):2498-504. doi: 10.1093/bioinformatics/btn478. Epub 2008 Sep 8.
Analysis of the distribution of alleles across populations is a useful tool for examining population diversity and relationships. However, sample sizes often differ across populations, sometimes making it difficult to assess allelic distributions across groups.
We introduce a generalized rarefaction approach for counting alleles private to combinations of populations. Our method evaluates the number of alleles found in each of a set of populations but absent in all remaining populations, considering equal-sized subsamples from each population. Applying this method to a worldwide human microsatellite dataset, we observe a high number of alleles private to the combination of African and Oceanian populations. This result supports the possibility of a migration out of Africa into Oceania separate from the migrations responsible for the majority of the ancestry of the modern populations of Asia, and it highlights the utility of our approach to sample size correction in evaluating hypotheses about population history.
We have implemented our method in the computer pro-gram ADZE, which is available for download at http://rosenberglab.bioinformatics.med.umich.edu/adze.html.
分析等位基因在群体中的分布是检验群体多样性和关系的一种有用工具。然而，不同群体的样本量往往不同，有时难以评估不同群体间的等位基因分布。
我们引入了一种广义稀疏化方法来计算群体组合特有的等位基因数量。我们的方法评估一组群体中每个群体所发现的但在其余所有群体中不存在的等位基因数量，同时考虑从每个群体中抽取的大小相等的子样本。将此方法应用于一个全球人类微卫星数据集时，我们观察到非洲和大洋洲群体组合特有的大量等位基因。这一结果支持了存在一次从非洲迁移到大洋洲的可能性，这次迁移独立于导致现代亚洲人群大部分祖先的迁移，并且突出了我们的样本量校正方法在评估关于群体历史的假设时的实用性。
我们已将我们的方法在计算机程序ADZE中实现，该程序可从http://rosenberglab.bioinformatics.med.umich.edu/adze.html下载。
