Genetic and evolutionary consequences of fine-scale recombination rate variation in Drosophila persimilis

Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act. Identifying local recombination rates across a genome and their correlates can yield insights into the processes leading to adaptation or speciation. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of recombination rates in Drosophila persimilis. We observed no significant difference between sex chromosome and autosome recombination rates. We documented broad-scale patterning of recombination rates as interpreted by a significant autocorrelation between adjacent sites. We further found significant associations of fine-scale recombination rate with repetitive element abundance and a human recombination sequence motif. We calculated crossover interference and note strong interference as far as 5-7Mb away from the focal crossover event. Further, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sibling species D. pseudoobscura. We documented a significant relationship between recombination rates and nucleotide diversity within species, but no relationship between recombination rate and nucleotide divergence between species, consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining patterns of variation within species. Finally, we found a significant correlation between recombination rate and total GC content, third position codon GC content, supporting both biased GC gene conversion models and selection-driven codon bias models. Overall, we confirm predictions and findings of many previous analyses and report several novel findings.