Abstract
By shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage-disequilibrium pre-speciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of chromosomal inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and D. persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between Drosophila pseudoobscura and D. persimilis over three distinct timescales: 1) pre-speciation segregation of ancestral polymorphism, 2) post-speciation ancient gene flow, and 3) recent gene flow. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in similar datasets in other systems.
Footnotes
Data Accessibility Statement:
All raw sequence data will be provided on NCBI’s Short Read Archive by the time of publication, with all sequence accession numbers in Supplementary Table 1. Scripts used for data analysis are available on GitHub: https://github.com/kkorunes/Dpseudoobscura_Introgression
Updated Fig 3 with smaller window size and accompanying boxplots. Added new figure (Fig 4) to show fd statistics. Added Tajima relative rate test. Updated figures and tables to show results for both all collinear regions and a more conservative subset predicted to be freely-recombining.
