Efficient moment-based inference of admixture parameters and sources of gene flow.
Efficient moment-based inference of admixture parameters and sources of gene flow.
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DOI：
10.1093/molbev/mst099
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发表时间：
2013-08
影响因子：
10.7
通讯作者：
Berger B
中科院分区：
文献类型：
--
作者：
Lipson M;Loh PR;Levin A;Reich D;Patterson N;Berger B
最近可用遗传数据的爆炸性增长使人们在了解人口统计历史和人口之间的关系方面取得了重大进展。它仍然是一个挑战，但是，推断可靠的参数值复杂的模型，涉及许多人口。在这里，我们提出了MixMapper，一个有效的，交互式的方法构建系统发育树，包括混合事件使用单核苷酸多态性（SNP）基因型数据。MixMapper使用矩统计实现了一种新的两阶段混合推理方法，首先构建一个未混合的支架树，然后通过求解混合参数表达等位基因频率差异的方程组来添加混合种群。重要的是，模型的所有特征，包括拓扑结构、基因流来源、分支长度和混合比例，都是根据数据自动优化的，并包括统计不确定性的估计。MixMapper还使用了一种新的方法，以易于解释的漂移单位表示分支长度。我们将MixMapper应用于最近发表的人类基因组多样性细胞系面板个体基因分型的SNP阵列上的数据，该SNP阵列专门用于群体遗传学研究，获得了30个群体的可靠结果，其中20个是混合的。值得注意的是，我们确认了一个信号的古代混合物在欧洲人口，包括以前未被发现的混合物在撒丁岛和巴斯克，涉及20-40%的比例古北方欧亚血统。
The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for complicated models involving many populations. Here, we present MixMapper, an efficient, interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the model, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units. We apply MixMapper to recently published data for Human Genome Diversity Cell Line Panel individuals genotyped on a SNP array designed especially for use in population genetics studies, obtaining confident results for 30 populations, 20 of them admixed. Notably, we confirm a signal of ancient admixture in European populations—including previously undetected admixture in Sardinians and Basques—involving a proportion of 20–40% ancient northern Eurasian ancestry.
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影响因子：
10.7
作者：
Dupanloup, I;Bertorelle, G;Barbujani, G
通讯作者：
Barbujani, G
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
56.9
作者：
Abdulla, Mahmood Ameen;Ahmed, Ikhlak;Zilfalil, Bin Alwi
通讯作者：
Zilfalil, Bin Alwi
影响因子：
30.8
作者：
Keinan, Alon;Mullikin, James C.;Reich, David
通讯作者：
Reich, David
影响因子：
3.3
作者：
Loh PR;Lipson M;Patterson N;Moorjani P;Pickrell JK;Reich D;Berger B
通讯作者：
Berger B