Characterization of Genetic Diversity in the Nematode Pristionchus pacificus from Population-Scale Resequencing Data
Christian Rödelsperger, Richard A. Neher, Andreas M. Weller, Gabi Eberhardt, Hanh Witte, Werner E. Mayer, Christoph Dieterich, Ralf J. Sommer

Abstract

The hermaphroditic nematode Pristionchus pacificus is an established model system for comparative studies with Caenorhabditis elegans in developmental biology, ecology and population genetics. In this study, we present whole genome sequencing data of 104 P. pacificus strains and the draft assembly of the obligate outcrossing sister species Pristionchus exspectatus. We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. P. pacificus is ten times more diverse than C. elegans and exhibits substantial population structure that allows us to probe its evolution on multiple time scales. Consistent with reduced effective recombination in this self-fertilizing species, we find haplotype blocks that span several megabases. Using the P. exspectatus genome as outgroup, we polarized variation in P. pacificus and found a site frequency spectrum (SFS) that decays more rapidly than expected in neutral models. The SFS at putatively neutral sites is U-shaped, which is a characteristic feature of pervasive linked selection. Based on the additional findings i) that the majority of non-synonymous variation is eliminated over time scales on the order of the separation between clades, ii) that diversity is reduced in gene rich regions, and iii) that highly differentiated clades show very similar patterns of diversity, we conclude that purifying selection on many mutations with weak effects is a major force shaping genetic diversity in P. pacificus.

  • Received November 17, 2013.
  • Accepted January 16, 2014.