15 years of introgression studies: quantifying gene flow across Eukaryotes

Abstract

With the rise of affordable next generation sequencing technology, introgression - or the exchange of genetic materials between taxa - is widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment on the frequency of introgression in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by providing a meta-analysis of the most comprehensive survey of introgression studies in Eukaryotes to date (724 papers with claims of introgression). We first examined the evidence given to support introgression, and if/how the lines of evidence have changed across time. We then collated a single statistic, Patterson's D, that quantifies the strength of introgression across 123 studies to further assess how taxonomic group, divergence time, and aspects of life history influence introgression. We find three main results. Studies on introgression are much more frequent in plants and mammals than any other taxonomic group. The study of introgression has shifted from a largely qualitative assessment of whether introgression happens, to a focus on when and how much introgression has occurred across taxa. The most-often used introgression statistic, Patterson's D, shows several intriguing patterns suggesting introgression reports may be biased by both differences in reporting criteria and sequencing technology, but may also differ across taxonomic systems and throughout the process of speciation. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities, and highlight important areas of future research that can be better assessed once this unified approach is met.

The dynamics of introgression across an avian radiation

“…Contrary to other studies (Dagilis et al. 2021 ; Hamlin et al. 2020 ), we find no evidence for increased introgression between more recently diverged taxa (Fig.…”

“…Hybridization between nonoverlapping species might reflect shifting geographic ranges through time and the high dispersal capacity of birds. Contrary to other studies (Dagilis et al 2021;Hamlin et al 2020), we find no evidence for increased introgression between more recently diverged taxa (Fig. 4A).…”

“…Further, species that originate in variable environments, like the historically unstable regions of the temperate zone (Hewitt 2004), tend to have more dynamic ranges that might lead to secondary contact between species before reproductive barriers have evolved (Cutter and Gray 2016). Together, these verbal arguments suggest that when and where hybridization occurs might be predictable based on both their intrinsic properties and the geographic and environmental context in which they form (Dagilis et al 2021;Hamlin et al 2020;Leighton et al 2021;Mitchell et al 2019).…”

“…Together, these verbal arguments suggest that when and where hybridization occurs might be predictable based on both their intrinsic properties and the geographic and environmental context in which they form (Dagilis et al. 2021 ; Hamlin et al. 2020 ; Leighton et al.…”

Leveraging shared ancestral variation to detect local introgression

“…Introgression has been found in swordtail fish [1], Heliconius butterflies [2,3], and from Neanderthals and Denisovans to modern-day non-African populations [4][5][6][7][8] as well as many other systems. These observations suggest that introgression is pervasive and thus determining its relative contribution to the evolution of a species is of evolutionary interest [9]. Therefore, detecting and quantifying introgressed segments in the genome is necessary to begin measuring its biological importance.…”