VolcanoFinder: Genomic scans for adaptive introgression

Abstract

Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method-VolcanoFinder-to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder.

Learning the properties of adaptive regions with functional data analysis

“…We find that regardless of the types of statistics used, we classify the majority of the genome as neutral, and classify more of the genome as sweep than as adaptive introgression (S16-S19 Tables). Importantly, we find that we are able to recapitulate signals of previously-identified regions of adaptive introgression in the CEU population with SURFDAWave, such as BNC2 [50,51] and APOL4 [4]…”

“…Adaptive introgression is a complex form of natural selection that produces genetic diversity footprints distinct from typical selective sweeps [4]. In both selective sweeps and adaptive introgression, diversity generally decreases surrounding the beneficial mutation.…”

“…Moreover, ref. [4] shows that their method for detecting adaptive introgression from distortions in the site frequency spectrum has the ability to uncover soft adaptive introgression sweeps from multiple introgressed haplotypes, demonstrating that there is even a difference in the spatial signature of nucleotide diversity for soft sweeps and soft introgression sweeps. Indeed, the authors note that both hard and soft introgression sweeps leave more similar genomic footprints to each other than do non-introgression hard and soft sweeps, with both modes of introgression sweeps displaying the crests and troughs of nucleotide diversity characteristic of adaptive introgression.…”

“…For example, if the crest of the wave extends above the rest position (neutrality), then this may be the signal of adaptive introgression as shown in ref. [4].…”

The timing of human adaptation from Neanderthal introgression

“…While, on average, Neanderthal-derived alleles have been selected against, a few alleles exist at high frequency in present-day non-African populations and reflect putative cases of adaptive introgression (Abi-Rached et al, 2011;Sankararaman et al, 2014;Khrameeva et al, 2014;Vernot and Akey, 2014;Dannemann et al, 2016;Deschamps et al, 2016;Gittelman et al, 2016;Racimo et al, 2017;Jagoda et al, 2018;Quach et al, 2016;Sams et al, 2016;Setter et al, 2020). These alleles have been identified based on the characteristic patterns left behind by adaptive introgression, namely high haplotype similarity between Eurasian modern humans and Neanderthals, and the deep divergence of haplotypes within modern human populations.…”