Fine-scale mapping of recombination rate in Drosophila
Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence
 Regional rates of recombination often correlate with levels of nucleotide diversity and either selective or neutral hypotheses can explain this relationship.  Regional recombination rates also correlate with nucleotide divergence between human and chimpanzee, consistent with models where recombination is mutagenic, however a lack of correlation is observed in the Drosophila melanogaster group, consistent with models invoking natural selection.  Here, we revisit the relationship between recombination, diversity and divergence by generating fine-scale empirical estimates of these parameters in Drosophila pseudoobscura.  To measure recombination rate, we genotyped 1294 backcross hybrids at 50 markers across the largest assembled linkage group in this species.  Genome-wide diversity was estimated by sequencing a second isolate of D. pseudoobscura at shallow coverage.  Alignment to the sequenced genome of the closely related species, D. persimilis, provided orthology at each nucleotide site.  Our findings demonstrate that scale is critical in determining correlates to recombination rate: fine-scale crossover rate estimates are far stronger predictors of both diversity and divergence than broad-scale estimates.  The correlation of fine-scale recombination rate to diversity and divergence appears to be genome-wide, evidenced by examination of an X-linked region in greater detail.  Because we observe a strong correlation of crossover rate with divergence, even after correcting for segregating ancestral variation, we suggest that both mutagenic and selective forces generate these correlations, the latter particularly in regions of low crossing over.  We propose that it is not crossovers per se that are mutagenic, but rather repair of DNA double-strand break precursors via crossing over and gene conversion.        
454 sequences from total genomic DNA of Flagstaff 1993 strain of Drosophila pseudoobscura to examine patterns of nucleotide diversity within species.