Abstract
Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins, such as Neanderthals and Denisovans, interbred or admixed with the ancestors of present-day humans. Central to these analyses are methods for inferring archaic ancestry along the genomes of present-day individuals (archaic local ancestry). Methods for archaic local ancestry inference rely on the availability of reference genomes from the ancestral archaic populations for accurate inference. However, several instances of archaic admixture lack reference archaic genomes, making it difficult to characterize these events. We present a statistical method that combines diverse population genetic summary statistics to infer archaic local ancestry without access to an archaic reference genome. We validate the accuracy and robustness of our method in simulations. When applied to genomes of European individuals, our method recovers segments that are substantially enriched for Neanderthal ancestry, even though our method did not have access to any Neanderthal reference genomes.
Highlights
Admixture, the exchange of genes among previously isolated populations, is increasingly being recognized as an important force in shaping genetic variation in natural populations
Recent analyses of modern human genomes have shown that archaic hominins like Neanderthals and Denisovans contribute a few percentage of ancestry to many populations
Due to the difficulty in sequencing these genomes, we lack a complete collection of reference genomes with which to identify archaic ancestry
Summary
The exchange of genes among previously isolated populations, is increasingly being recognized as an important force in shaping genetic variation in natural populations. Analyses of large collections of genome sequences have shown that admixture events have been prevalent throughout human history [1] These studies have shown that modern human populations outside of Africa trace a small percentage of their ancestry to admixture events from populations related to archaic hominins like Neanderthals and Denisovans [1, 2, 3]. Studies of the functional impact of archaic ancestry have suggested that Neanderthal DNA contributes to phenotypic variation in modern humans [4, 5]. Central to these studies is the problem of archaic local ancestry inference—the pinpointing of segments of an individual genome that trace their ancestry to archaic hominin populations. Ta is the admixture time and mu rho refers to the experiment that uses realistic recombination and mutation rates, estimated from the human genome (see Methods for more details). (PDF)
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