Evidence for archaic adaptive introgression in humans

Abstract

As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments - a process known as adaptive introgression. Within the past few years, a series of studies have identified genomic regions that show strong evidence for archaic adaptive introgression. Here, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments. We review recently reported examples of adaptive introgression, grouped by selection pressure, and consider the level of supporting evidence for each. Finally, we discuss challenges and recommendations for inferring selection on introgressed regions.

Figure 1. Expected length of archaic tracts under admixture and ancestral structure scenarios

Schematic comparison of expected tract length of archaic-like tracts for a scenario of admixture (left panel) and a scenario of ancestral population structure (right panel). Because there is less time for recombination to break down the migrant tracts (red) in the admixed population, the expected tract length in this case will be longer than in the case of ancestral structure.

Figure 2. Example coalescent genealogy of uniquely shared mutations

Several DNA fragments from two modern populations (pink and light-blue chromosomes) are sequenced. A diploid sequence is also obtained from an extinct archaic population (yellow chromosomes) that split from the population tree more anciently than the two modern populations split from each other. Uniquely shared mutations (red stars) occur in the archaic population, but are passed on to the ancestors of the light-blue modern population via admixture (dashed line). These are then are swept to high frequency by selection, producing a shallow local coalescent genealogy. This process results in sites with high-frequency derived alleles in the light-blue samples that are present in the archaic sample but not the pink samples from the other modern population. Mutations in the genealogy that are not uniquely shared are shown as green stars.