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.
Highlights
While classic species concepts imply genetic isolation [1], research of the past 30 years shows that hybridization between closely related species is widespread [2]
The process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression
Such adaptive introgressions occurred in modern humans [13,14,15]: local adaptation to hypoxia at high-altitude was shown to be associated with selection for a Denisovanrelated haplotype at the EPAS1 hypoxia pathway gene in Tibetan populations [16]; positive selection has been characterized for three archaic haplotypes, independently introgressed from Denisovans or Neanderthals in a cluster of genes involved in the innate immune response [17], and immunity related genes show evidence of selection for Neanderthal and Denisovan haplotypes [18, 19]
Summary
While classic species concepts imply genetic isolation [1], research of the past 30 years shows that hybridization between closely related species (or diverged subspecies) is widespread [2]. Well-documented examples cover a wide range of taxa, including the transfer of wing-pattern mimicry genes in Heliconius butterflies [7], herbivore resistance and abiotic tolerance genes in wild sunflowers [8, 9], pesticide resistance in mice [10] and mosquitoes [11], and new mating and vegetative incompatibility types in an invasive fungus [12] Such adaptive introgressions occurred in modern humans [13,14,15]: local adaptation to hypoxia at high-altitude was shown to be associated with selection for a Denisovanrelated haplotype at the EPAS1 hypoxia pathway gene in Tibetan populations [16]; positive selection has been characterized for three archaic haplotypes, independently introgressed from Denisovans or Neanderthals in a cluster of genes involved in the innate immune response [17], and immunity related genes show evidence of selection for Neanderthal and Denisovan haplotypes [18, 19]. Our work aims to bridge the gap between classes (i) and (ii), and detect the specific genomic signature of an introgression sweep
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