Recombination in the threespine stickleback genome – patterns and consequences

Heterogeneity in recombination rate may strongly influence genome evolution and entail methodological challenges in genomic investigations. Nevertheless, a solid understanding of these issues awaits detailed information across a broad range of taxa. Based on 282 F2 individuals and 1,872 single nucleotide polymorphisms, we characterize recombination in the threespine stickleback fish genome. We find an average genome-wide recombination rate of 3.11 cM/Mb. Crossover frequencies are dramatically elevated in the chromosome peripheries as compared to the centers, and are consistent with one obligate crossover per chromosome (but not chromosome arm). Along the sex chromosome, we show that recombination is restricted to a small pseudoautosomal domain of c. 2 Mb, spanning only 10% of that chromosome. Comparing female versus male RAD sequence coverage allows us to identify two discrete levels of degeneration on the Y chromosome, one of these ‘evolutionary strata’ coinciding with a previously inf...