Department of Statistics, University of Oxford, Oxford, UK.
Université du Québec à Montréal, Montréal, Canada.
Nat Genet. 2019 Sep;51(9):1321-1329. doi: 10.1038/s41588-019-0484-x. Epub 2019 Sep 2.
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 have 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 1,000 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 has previously been possible. We identify multiple regions under strong positive selection, and multi-allelic traits including hair color, body mass index and blood pressure, showing strong evidence of directional selection, varying among human groups.
对数千个人的全基因组谱系的了解将简化人类和其他物种的大多数进化分析，但在计算上仍然不可行。我们开发了一种方法，名为 Relate，可以同时估计分支长度、突变年龄和可变历史人口规模，以及允许数据错误，其规模可扩展到>10000 个序列。将 1000 基因组计划的单倍型应用于 26 个人类群体，可产生共同的谱系历史。所有群体中都存在高度分化的谱系，但在非洲最为常见。在非洲以外，这些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基因渗入，而非洲的信号则反映了该大陆特有的未知事件。我们的方法允许对自然选择进行比以前更强大的推断。我们确定了多个受到强烈正向选择的区域，以及多等位基因特征，包括头发颜色、体重指数和血压，这些特征显示出在人类群体中存在强烈的定向选择的证据。
