Widespread introgression across a phylogeny of 155 Drosophila genomes

• Published in: Current biology 2022-01, Vol.32 (1), p.111-123.e5
• Main Authors: Suvorov, Anton, Kim, Bernard Y., Wang, Jeremy, Armstrong, Ellie E., Peede, David, D’Agostino, Emmanuel R.R., Price, Donald K., Waddell, Peter J., Lang, Michael, Courtier-Orgogozo, Virginie, David, Jean R., Petrov, Dmitri, Matute, Daniel R., Schrider, Daniel R., Comeault, Aaron A.
• Format: Article
• Language: English
• Subjects: Animal genetics; Animals; Biodiversity; Biological Evolution; Drosophila - genetics; gene flow; Genetics; Genome; Hybridization, Genetic; introgression; Life Sciences; phylogenetic discordance; Phylogenomics; Phylogeny; Populations and Evolution; reticulate evolution
• ISSN: 0960-9822; 1879-0445
• DOI: 10.1016/j.cub.2021.10.052

Genome-scale sequence data have 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 across most of the 9 clades that we examined. 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. •Resolved fossil-calibrated evolutionary history of 155 Drosophila genomes•Phylogenomic evidence of widespread introgression in Drosophila•Evidence of both phylogenetically deep and recent gene flow events in multiple clades•Conservative detection of gene flow via discordant gene tree counts and branch lengths Suvorov et al. use multi-locus data from 155 Drosophila genome assemblies to reconstruct the phylogeny of the genus and estimate divergence times. They used multiple phylogenomic methods to shed light on patterns of gene flow within the genus. Their results suggest multiple instances of introgression across the Drosophila tree of life.