A method for genome-wide genealogy estimation for thousands of samples.
A method for genome-wide genealogy estimation for thousands of samples.
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DOI：
10.1038/s41588-019-0484-x
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发表时间：
2019-09
期刊：
影响因子：
30.8
通讯作者：
Myers SR
中科院分区：
文献类型：
--
作者：
Speidel L;Forest M;Shi S;Myers SR
数千个个体的全基因组谱系知识将简化人类和其他物种的大多数进化分析，但在计算上仍然是不可行的。我们开发了一种方法，Relate，扩展到> 10，000个序列，同时估计分支长度，突变年龄和可变的历史群体大小，以及允许数据错误。应用1000个基因组计划单倍型产生26个人类种群的联合系谱历史。高度分化的谱系存在于所有群体中，但最常见于非洲。在非洲以外，这些信号主要反映了与尼安德特人和丹尼索瓦人有关的群体的古老渗入，而非洲的信号则反映了该大陆特有的未知事件。我们的方法允许比以前更强大的自然选择的推论。我们确定了强阳性选择下的多个新区域，以及多等位基因特征，包括头发颜色，身体质量指数（BMI）和血压，显示了定向选择的强有力证据，在人类群体中各不相同。
Knowledge of genome-wide genealogies for thousands of individuals would simplify most evolutionary analyses for humans and other species, but has remained computationally infeasible. We developed a method, Relate, scaling to > 10,000 sequences while simultaneously estimating branch lengths, mutational ages, and variable historical population sizes, as well as allowing for data errors. Application to 1000 Genomes Project haplotypes produces joint genealogical histories for 26 human populations. Highly diverged lineages are present in all groups, but most frequent in Africa. Outside Africa, these mainly reflect ancient introgression from groups related to Neanderthals and Denisovans, while African signals instead reflect unknown events, unique to that continent. Our approach allows more powerful inferences of natural selection than previously possible. We identify multiple novel regions under strong positive selection, and multi-allelic traits including hair color, body mass index (BMI), and blood pressure, showing strong evidence of directional selection, varying among human groups.