Natural selection interacts with the local recombination rate to shape the evolution of hybrid genomes

Schumer, Molly; Xu, Chenwu; Dl, Powell; Durvasula, Arun; Skov, Laurits; Holland, C. D.; Sankararaman, Sriram; Andolfatto, Peter; Rosenthal, Gil G.; Przeworski, Molly

doi:10.1101/212407

Cited by 20 publications

(25 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similar to Schumer et al. (), we found a positive association between local population‐scaled recombination rate and frequency of introgression (Spearman's ρ = 0.055, p < .001 in CEU and ρ = .054, p < .001 in CHB + CHS, bootstrap‐like test) lending further credence to the hypothesis that selection is acting against certain regions of Neanderthal ancestry.…”

Section: Resultssupporting

confidence: 89%

“…()), which would be suggestive of selection against Neanderthal ancestry because regions of high recombination would be more likely to separate neutral regions of Neanderthal ancestry from linked deleterious regions, an idea recently explored elegantly and in more detail by Schumer et al. (). Similar to Schumer et al.…”

Section: Resultsmentioning

confidence: 99%

“…The studies also reported enriched Neanderthal ancestry in hair‐ and skin‐related genes (keratin pathways), which suggests that these introgressed variants could have helped modern non‐African populations to adapt to their local environments. All in all, the availability of Neanderthal introgression maps in modern humans has led to numerous follow‐up studies investigating the various functional, evolutionary and medical implications of archaic hominin introgression into modern humans (Dannemann, Prüfer, & Kelso, ; Gittelman et al., ; Rogers, ; Schumer et al., ; Simonti et al., ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

et al. 2018

View full text Add to dashboard Cite

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.

show abstract

Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2018

View full text Add to dashboard Cite

show abstract

Section: Prospects For the Futurementioning

confidence: 99%

“…As a complement to these theoretical approaches, it will also be key to study empirical patterns of introgression in non-human populations that admixed after being separated for some time. These "natural experiments", in which certain historical or biological parameters may already be known a priori , can be compared and contrasted with hypothesized human evolutionary scenarios [50] .Additionally, the first empirical results from studies of archaic human introgression have led to an increasing interest in developing methods for the spatio-temporal localization of adaptive events. This is especially important when studying complex evolutionary histories involving many populations, as these often include multiple divergence and admixture processes.…”

mentioning

confidence: 99%

Something old, something borrowed: Admixture and adaptation in human evolution

Dannemann

Racimo

2018

Preprint

View full text Add to dashboard Cite

Almost a decade ago, the sequencing of ancient DNA from archaic humans -Neanderthals and Denisovans -revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Were introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time. Genome-wide patterns of archaic admixtureIn 2010, the first sequenced Neanderthal genome provided evidence for gene flow from Neanderthals into the ancestors of present-day non-Africans, around 50,000-60,000 years ago [1][2][3] . Since then, archaic human genomes have yielded ever more insightful discoveries. A few years later, a high coverage genome sequence from a Neanderthal found in the Altai mountains allowed researchers to pin down the proportion of Neanderthal ancestry in non-Africans to be ~2% [4] . In 2017, a second high coverage genome sequence from a Neanderthal in Croatia showed that this individual was more closely related to the introgressing Neanderthal population than the Altai Neanderthal, allowing researchers to detect even slightly higher levels of Neanderthal DNA [5] . In 2018, low-coverage genomes of five additional Neanderthals living between 39,000 and 47,000 years ago allowed a first glimpse at population structure in Neanderthals and showed indications of population turnover in late Neanderthal history [6] . But admixture between different human groups has not been limited to modern humans and Neanderthals. The genome sequence of a previously unknown group, the Denisovans (a sister group to Neanderthals), also contributed to the genomes of present-day people in Oceania, and, to a lower extent, to mainland East and South Asians [7][8][9][10][11][12] . Further admixture episodes have also been suggested, including gene flow from an unsampled "super-archaic" human group into Denisovans [4] , from eastern Neanderthals into Denisovans [4] and from modern humans into Neanderthals [13] (Figure 1). While the signals of shared ancestry between modern and archaic human groups are quite evident, the exact processes by which introgression occurred remain unclear. For example, higher levels of Neanderthal ancestry have been observed in...

show abstract

Asymmetric introgression reveals the genetic architecture of a plumage trait

et al. 2021

View full text Add to dashboard Cite

Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.

show abstract

Natural selection interacts with the local recombination rate to shape the evolution of hybrid genomes

Cited by 20 publications

References 55 publications

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

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

Something old, something borrowed: Admixture and adaptation in human evolution

Asymmetric introgression reveals the genetic architecture of a plumage trait

Contact Info

Product

Resources

About