Disentangling Types of Linked Selection Using Patterns of Nucleotide Variation in Drosophila pseudoobscura

Abstract

A central goal in evolutionary genetics is to understand the forces that drive patterns of nucleotide variation within species. Recombination rate and nucleotide diversity are positively correlated across loci within many species. Selective sweeps and background selection both may contribute to this pattern by reducing nucleotide variation disproportionately in regions of low recombination. While there is unambiguous documentation of some forms of selective sweeps, it is less clear how much background selection and soft selective sweeps contribute. Here, we discuss the study of these different types of linked selection, paying particular attention to the large body of work devoted to linked selection in Drosophila. We discuss patterns of nucleotide variation in the classic model system Drosophila pseudoobscura, and we leverage this system to test for the effects of linked selection in the near absence of hard, complete selective sweeps. Our case study of variation in sets of loci shared between Drosophila pseudoobscura and D. miranda suggests that selection at linked sites may reduce nucleotide variation even in the absence of hard selective sweeps. We discuss how this work relates to recent approaches and challenges in the study of how selection at linked sites influences patterns of nucleotide variation.