Inferring the Demographic History and Rate of Adaptive Substitution in Drosophila

Abstract

An important goal of population genetics is to determine the forces that have shaped the pattern of genetic variation in natural populations. We developed a maximum likelihood method that allows us to infer demographic changes and detect recent positive selection (selective sweeps) in populations of varying size from DNA polymorphism data. Applying this approach to single nucleotide polymorphism data at more than 250 noncoding loci on the X chromosome of Drosophila melanogaster from an (ancestral) African population and a (derived) European, we found that the African population expanded about 60,000 y ago and that the European population split off from the African lineage about 15,800 y ago, thereby suffering a severe population size bottleneck. We estimated that about 160 beneficial mutations (with selection coefficients s between 0.05% and 0.5%) were fixed in the euchromatic portion of the X in the African population since population size expansion, and about 60 mutations (with s around 0.5%) in the diverging European lineage. The authors provide evidence for the recent action of positive selection in the fruit fly Drosophila melanogaster. They describe a new statistical method to detect footprints of selection in the genome of this species and apply it to a large set of DNA polymorphism data from the X chromosome. They find that numerous selective events occurred in the past 60,000 y, while D. melanogaster expanded its ancestral range in Africa and subsequently colonized temperate zones in the rest of the world after the last ice age. The findings of this paper are important as they indicate where in the genome the genes are located that have been involved in the adaptation of D. melanogaster to environmental changes in the recent past. The approach developed here for the model species D. melanogaster can be readily extended to study adaptation in humans and other species.