A population genomic resource for Drosophila pseudoobscura

Drosophila pseudoobscura is an historically important organism in evolutionary genetics, serving as a model system in studies of chromosomal inversions, speciation, sex chromosome evolution, and sex-ratio drive. However, previous population genetics analysis of D. pseudoobscura focused on individual chromosomes or used fragmented genome assemblies as a reference. To address these shortcomings, we generated a D. pseudoobscura population genomics resource consisting of newly sequenced genomes from 60 inbred lines sampled across the species' geographic range in North America. Using these data and a chromosome-scale reference genome, we examined patterns of nucleotide diversity and population structure across the chromosomes. We found no strong evidence of population structure on most chromosomes, consistent with prior results. In contrast, we identified population structure on the third chromosome, which we attributed to a well-characterized inversion polymorphism. We assigned individual third chromosome haplotypes to inversion arrangements, demonstrating how tests for population structure can be used to identify polymorphic chromosomal rearrangements. Tajima's D was negative across most of the genome, consistent with a recent population expansion. However, the distribution of genetic variation differed across third chromosome inversion arrangements in ways that were consistent with their hypothesized evolutionary histories, and we identified inter-arrangement genetic differentiation that could be attributed to the inversions suppressing genetic exchange. The population genomic data we have collected are publicly available and will support future research on evolutionary genetics.