<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hubisz, Melissa J.</style></author><author><style face="normal" font="default" size="100%">Williams, Amy L.</style></author><author><style face="normal" font="default" size="100%">Siepel, Adam</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph</style></title><secondary-title><style face="normal" font="default" size="100%">PLOS Genetics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020/08/06</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008895</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">16</style></volume><pages><style face="normal" font="default" size="100%">e1008895 - </style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;We present ARGweaver-D, an extension of the ARGweaver algorithm which can be applied under a user-defined demographic model including population splits and migration events. Given genome sequence data from a collection of individuals across multiple closely related populations or subspecies, ARGweaver-D can infer trees describing the genetic relationships among these individuals at every location along the genome, conditional on the demographic model. Like ARGweaver, ARGweaver-D is a Bayesian method, sampling trees from the posterior distribution in order to account for uncertainty. Using simulations, we show that ARGweaver-D can successfully identify regions introgressed from Neanderthals and Denisovans into modern humans. It is also well-powered to detect introgressed regions stemming from older gene-flow events. We apply ARGweaver-D to the genomes of two Neanderthals, a Denisovan, and two African humans. We identify 3% of the Neanderthal genome which is likely derived from gene flow from ancient humans. We also identify about 1% of the Denisovan genome that may be traced to an unsequenced archaic hominin; 15% of these regions were subsequently passed to modern humans. We find no convincing evidence that selection acted against any of these introgressed regions.&lt;/p&gt;
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