@article {322085,
	title = {Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph},
	journal = {PLOS Genetics},
	volume = {16},
	year = {2020},
	month = {2020/08/06},
	pages = {e1008895 - },
	abstract = {<p>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.</p>
},
	doi = {https://doi.org/10.1371/journal.pgen.1008895},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008895},
	author = {Hubisz, Melissa J. and Williams, Amy L. and Siepel, Adam}
}
