Widespread introgression across a phylogeny of 155Drosophilagenomes

Abstract

Genome-scale sequence data has invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred, with introgression at the base of species radiations being particularly common. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.

15 years of introgression studies: quantifying gene flow across Eukaryotes

“…researchers must either shift their focus from taxa-centric studies of introgression to more clade-centric studies (e.g. Malinsky, et al (2018); Hamlin, et al (2020);Small, et al (2020);Suvorov, et al (2021)), however, we recognize that this may not always be possible or feasible. Alternatively, we suggest the following unified reporting standard, to further advance the field's abilities to perform comparative analyses of introgression across the tree of life.…”

Phylogenomic approaches to detecting and characterizing introgression

“…In fact, Huson et al (2005) proposed such a test, using a statistic they called ∆. Significance in genome-scale datasets can be evaluated by bootstrap-sampling the estimated gene trees (Vanderpool et al 2020) or by assuming a  2 distribution (Suvorov et al 2021), with ∆ = 0 again representing the null hypothesis under ILS alone. While ∆ has greater potential to be affected by sources of technical error such as systematic bias in gene tree inference-and may have limited power to detect very ancient introgression-it has the advantage of being more robust to the infinite-sites assumption and allows for testing of introgression along deep, internal branches of a phylogeny.…”

“…Therefore, one of the simplest ways to test for introgression is to test for an asymmetry in pairwise sequence divergence. This logic has been informally applied to test for introgression (Brandvain et al 2014) and has recently been formalized in several test statistics including D3 (Hahn and Hibbins 2019) and the branch-length test (Suvorov et al 2021). D3 is straightforward, and has the following definition (changed from the original to be consistent with the notation used here):…”

“…The mostly widely used methods are formulated to test for the presence of introgression versus no introgression, but provide no rigorous way to evaluate the number of distinct introgression events. One approach is to perform many quartet-based tests, and then to infer the most parsimonious set of introgression events by collapsing sets of positive tests that share the same ancestral populations (Pease et al 2016, Suvorov et al 2021. However, this approach is highly conservative, as it can collapse cases where there truly are multiple instances of post-speciation introgression within a clade.…”

Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

“…In sum, incomplete lineage sorting and ancient hybridization are known to contribute to levels of shared variation among species (Pease et al, 2016;Malinsky et al, 2018;Edelman et al, 2019), even at deep evolutionary levels (Song et al, 2015;Suh, Smeds & Ellegren, 2015). The development of tools which employ the substantial amount of modern genomic data has allowed separating cases of ILS and ancient admixture, showing that ancient hybridization can have a strong impact in the levels of shared variation among species complexes (Malinsky et al, 2018;Li et al, 2019;Taylor & Larson, 2019;Ferreira et al, 2020), even after several million years of divergence (Barth et al, 2020;Suvorov et al, 2020). Future work should employ multispecies-network methods or coalescent simulations (Joly, McLenachan & Lockhart, 2009) to determine the relative role of ILS and ancient admixture.…”