Patterns of Population Structure and Introgression Among Recently Differentiated Drosophila melanogaster Populations

Authors

Jenn M. Coughlan, University of North Carolina, Yale University
Andrius J. Dagilis, University of North Carolina
Antonio Serrato-Capuchina, Harvard University
Hope Elias, University of North Carolina
David Peede, Brown University
Kristin Isbell, University of North Carolina
Dean M. Castillo, University of Nebraska-LincolnFollow
Brandon S. Cooper, University of Montana
Daniel R. Matute, University of North Carolina

Document Type

Article

Date of this Version

10-17-2022

Citation

Mol. Biol. Evol. 39(11):msac223 https://doi.org/10.1093/molbev/msac223

Comments

Open access.

Abstract

Despite a century of genetic analysis, the evolutionary processes that have generated the patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic variation is partitioned within its putative ancestral range in Southern Africa remains unresolved. Here, we study patterns of population genetic structure, admixture, and the spatial structuring of candidate incompatibility alleles across a global sample, including 223 new accessions, predominantly from remote regions in Southern Africa. We identify nine major ancestries, six that primarily occur in Africa and one that has not been previously described. We find evidence for both contemporary and historical admixture between ancestries, with admixture rates varying both within and between continents. For example, while previous work has highlighted an admixture zone between broadly defined African and European ancestries in the Caribbean and southeastern USA, we identify West African ancestry as the most likely African contributor. Moreover, loci showing the strongest signal of introgression between West Africa and the Caribbean/southeastern USA include several genes relating to neurological development and male courtship behavior, in line with previous work showing shared mating behaviors between these regions. Finally, while we hypothesized that potential incompatibility loci may contribute to population genetic structure across the range of D. melanogaster; these loci are, on average, not highly differentiated between ancestries. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the partitioning of diversity across its range.