Model‐based detection and analysis of introgressed Neanderthal ancestry in modern humans

Abstract

Genetic evidence has revealed that the ancestors of modern human populations outside Africa and their hominin sister groups, notably Neanderthals, exchanged genetic material in the past. The distribution of these introgressed sequence tracts along modern-day human genomes provides insight into the selective forces acting on them and the role of introgression in the evolutionary history of hominins. Studying introgression patterns on the X-chromosome is of particular interest, as sex chromosomes are thought to play a special role in speciation. Recent studies have developed methods to localize introgressed ancestries, reporting long regions that are depleted of Neanderthal introgression and enriched in genes, suggesting negative selection against the Neanderthal variants. On the other hand, enriched Neanderthal ancestry in hair- and skin-related genes suggests that some introgressed variants facilitated adaptation to new environments. Here, we present a model-based introgression detection method called dical-admix. We demonstrate its efficiency and accuracy through extensive simulations and apply it to detect tracts of Neanderthal introgression in modern human individuals from the 1000 Genomes Project. Our findings are largely concordant with previous studies, consistent with weak selection against Neanderthal ancestry. We find evidence that selection against Neanderthal ancestry was due to higher genetic load in Neanderthals resulting from small effective population size, rather than widespread Dobzhansky-Müller incompatibilities (DMIs) that could contribute to reproductive isolation. Moreover, we confirm the previously reported low level of introgression on the X-chromosome, but find little evidence that DMIs contributed to this pattern.

Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

“…Few others studies (Galaverni et al, 2017;Nelson et al, 2017;VonHoldt et al, 2016) also explored this issue, but this certainly has to be expanded further. For example, an in-depth analysis of the genomewide landscape of introgression would be useful to further identify genomic regions where introgression departs from neutral expectations and is potentially adaptive or maladaptive (Duranton et al, 2018;Edmands, 2007;Hedrick, 2013;Racimo et al, 2015;Sankararaman et al, 2014;Steinrücken, Spence, Kamm, Wieczorek, & Song, 2018; reviewed in Dannemann & Racimo, 2018). This is of prime importance for future conservation and management actions (Allendorf, Leary, Spruell, & Wenburg, 2001;Allendorf et al, 2010;Frankham, 2010;Garner et al, 2016;Stronen & Paquet, 2013), and more generally, the haplotype-based approach associated with recent theoretical findings will provide new ways to explore genomic data over a broad scope of both applied and fundamental evolutionary topics (Dannemann & Racimo, 2018;Hvala, Frayer, & Payseur, 2018;Janzen, Nolte, & Traulsen, 2018;Ni et al, 2018).…”

Introduction: Sex chromosomes and speciation

“…The authors argue that inferred population expansions do not explain these patterns, instead viewing them as consistent with a special role for the X in reproductive isolation Steinrücken, Spence, Kamm, Wieczorek, and Song (2018). revisit evidence for gene flow between Neanderthals and modern humans.Building on their earlier approach for reconstructing demographic history,Steinrücken et al (2018) present a new model-based method for inferring admixed ancestry along chromosomes. Applying this demography-informed strategy to population genomic data, the authors confirm that the human X harbours relatively less Neanderthal ancestry than autosomes.…”

“…Applying this demography-informed strategy to population genomic data, the authors confirm that the human X harbours relatively less Neanderthal ancestry than autosomes. After investigating genomic correlates of admixture,Steinrücken et al (2018) conclude that selection against gene flow stems from a higher load of deleterious mutations in Neanderthals and not hybrid incompatibilities.…”

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph

“…While we identified 3% of the Neanderthal genome as introgressed, a rough 389 extrapolation based on our estimated rates of true and false positives suggests that the 390 true amount is around 6%. Thus, the Neanderthal genome was likely more influenced recently called into question [11,20]. The strongest remaining pieces of evidence for 403 negative selection against Nea→Hum introgression are the depletion on the X 404 chromosome and several other genomic deserts.…”