Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania
Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania
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DOI：
10.1038/s41467-018-08089-7
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发表时间：
2019-01-16
影响因子：
16.6
通讯作者：
Lao, Oscar
中科院分区：
文献类型：
--
作者：
Mondal, Mayukh;Bertranpetit, Jaume;Lao, Oscar
自从解剖学意义上的现代人分散到非洲以外，欧亚种群的进化史就以目前已灭绝的古人类的渗入为标志。其中一些基因渗入已经通过对古代基因组（尼安德特人和丹尼索瓦人）的测序得到了鉴定。其他的基因渗入已经被提出，利用目前人类种群中存在的遗传多样性，对尚未确定的群体进行渗透。我们在近似贝叶斯计算框架中建立了一个基于深度学习的人口统计模型，以推断欧亚种群的进化史，包括非洲以外种群的过去渗入事件，以符合当前的遗传证据。除了已报道的尼安德特人和丹尼索瓦人基因渗入外，我们的研究结果还支持在所有亚洲和大洋洲人群中存在第三种来自古代人群的基因渗入。这个种群要么与尼安德特人-丹尼索瓦人分支有关，要么与丹尼索瓦人谱系早期分化。我们建议使用深度学习方法来澄清进化基因组学中高度复杂的情况。
Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.