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Meiotic recombination is one of the major molecular mechanisms generating genetic diversity and influencing genome evolution. By shuffling allelic combinations, it can directly influence the patterns and efficacy of natural selection. The rate and the placement of recombination varies substantially within the genome, among individuals, sexes, and different species. Using the threespine stickleback fish, an evolutionary model organism, we investigated the extent and molecular basis of recombination variation to further understand its evolutionary implications. We used both ChIP-sequencing and whole genome sequencing of pedigrees to empirically identify and quantify double strand breaks (DSBs) and meiotic crossovers (COs). High-resolution maps of crossover events were constructed for 36 individuals of diverging marine and freshwater ecotypes and their hybrids. We produced the first genome-wide high-resolution sex-specific and ecotype-specific maps of contemporary recombination events in sticklebacks. We report striking differences in the crossover number and placement between sexes, with male crossovers occurring predominantly near the chromosomal periphery and female crossovers distributed throughout the chromosome. Under conditions of on-going gene flow between diverging forms, theory predicts natural selection will favor recombination modifiers that suppress recombination. In this study, we find empirical support 229TAGC20 Online: Abstract Book for a reduction in overall recombination rate in hybrids compared to pure forms – a phenomena that is stronger in females. Further we see that, even though the loci underlying freshwater-marine adaptation fall in regions of low recombination, females recombine considerably in the regions between adaptive loci. This suggests that the sexual dimorphism in recombination phenotype may have important evolutionary implications. The fine scale recombination landscape is highly non-uniform with both recombination hot- and cold-spots. Male crossover landscape broadly mirrors DSB landscape and both DSB as well as crossover hotspots are significantly associated with open chromatin regions like transcription start sites. Whereas, female crossovers do not show an association more than expected by chance. A substantial number of hotspots away from open chromatin marks suggests the possibility of additional novel mechanisms of recombination regulation in sticklebacks. Overall, our study provides insight into the pattern and molecular regulators of recombination variation in the context of adaptive divergence and speciation.
