Admixture in Mammals and How to Understand Its Functional Implications

Abstract

Admixture, the genetic exchange between differentiated populations appears to be common in the history of species, but has not yet been comparatively studied across mammals. This limits the understanding of its mechanisms and potential role in mammalian evolution. The authors want to summarize the current knowledge on admixture in non-human primates, and suggest that it is important to establish a comparative framework for this phenomenon in humans. Genetic observations in domesticated mammals and their wild counterparts are discussed, and a brief global overview on other clades is presented. Based on this, some of the consequences of gene flow, including incompatibilities and their genomic footprint, as well as adaptive introgression are discussed, and suggestions for a functional genomics approach are made. It is proposed that the field is moving beyond descriptive observations in single species, to a comprehensive analysis of admixture and its impact. Admixture is becoming an integral part of mammalian evolution.

Ghost Introgression: Spooky Gene Flow in the Distant Past

“…Introgression—the exchange of genetic material through hybridization and backcrossing—is a common phenomenon across the Tree of Life. [ 1–4 ] Numerous studies have reported ancient or contemporary gene flow between extant lineages. In some cases, introgression from an extinct lineage could be uncovered by sequencing ancient DNA from fossils.…”

sstar: A Python package for detecting archaic introgression from population genetic data with S*

“…Admixture between populations is a topic of great interest (Fontsere et al 2019), especially since we know that it does affect our own species. For example, we have direct evidence for genetic exchange with other hominins like Neandertals (Green et al 2010).…”

A Brain Region-Specific Expression Profile for Genes Within Large Introgression Deserts and Under Positive Selection in Homo sapiens

“…While it is important to ask whether our species benefited from these admixture events (so-called adaptive introgression, where alleles inherited from other hominins rose to high frequency as a result of positive selection after gene flow), it is also worth examining regions of the genomes that are depleted of alleles resulting from gene flow from other hominins ( Sankararaman et al, 2016 ; Vernot et al, 2016 ; Chen et al, 2020 ; Skov et al, 2020 ; Rinker et al, 2020 ). Such regions are called introgression deserts (sometimes also “genomic islands of divergence/speciation” ( Wang et al, 2020 ) and have now been identified in a range of species ( Fontsere et al, 2019 ).…”

“…It is reasonable to expect, and indeed has been shown, that the X chromosome constitutes such a desertic region [not only in our species ( Kuhlwilm et al, 2019 ; Martin and Jiggins, 2017 )]. This could be due to repeated selective sweeps on this chromosome: genes involved in reproduction on this chromosome might act as strong reproductive barriers between populations ( Fontsere et al, 2019 ).…”