Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish [ChIP-Seq]

Despite deep evolutionary conservation, recombination varies greatly across the genome, among individuals, sexes and populations and can be a major evolutionary force in the wild. Yet this variation in recombination and its impact on adaptively diverging populations is not well understood. To elucidate the nature and potential consequences of recombination rate variation, we characterized fine-scale recombination landscapes by combining pedigrees, functional genomics and field fitness measurements in an adaptively divergent pair of marine and freshwater threespine stickleback populations from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic location of almost 50,000 crossovers and built recombination maps for 36 marine, freshwater, and hybrid individuals at 3.8 kilobase resolution. Using these maps, we quantified the factors driving variation in recombination rate: we find strong heterochiasmy between sexes (68% of the variation) but also differences among ecotypes (21.8%). Hybrids show evidence of significant recombination suppression, both in overall map length and in individual loci. We further tested and found reduced recombination rates both within single marine–freshwater adaptive loci and between loci on the same chromosome, suggestive of selection on linked ‘cassettes’. We tested theory supporting the evolution of linked selection using temporal sampling along a natural hybrid zone, and found that recombinants with shuffled alleles across loci show traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers whose mechanisms are disrupted in hybrids, may have an important role to play in the maintenance of differences among adaptively diverging populations. This GEO data deposit is part of a multipart study that includes functional genomic data related to meiosis in stickleback fish as described in Venu et al 2024. This particular data series includes a ChIPseq dataset using a stickleback fish-specific DMC1 antibody and commercially available H3K4me3 antibody raised against a synthetic H3K4me3 peptide (Millipore; cat#07-473; testes only). The experiments were performed in meiotic tissue (testes) of marine and freshwater strains of stickleback fish and ChIPseq in a control-somatic tissue (liver). The ChIP pulldown of DMC1-bound single stranded DNA was performed with "kinetic enrichment" following the protocols described in Smagulova et al (2011) Nature 472:375-8 and Khil et al (2012) Genome Research 22:957-65 and was followed sequentially by a ChIP pull down H3K4me3 on the same tissue lysate. Meiotic tissue lysates comprised of a "freshwater ecotype testes pool" from 15 pairs of testes from freshwater-strain sticklebacks, a "marine ecotype testes pool" from 18 pairs of testes marine-strain sticklebacks. Somatic-control tissue lysates comprised of a "freshwater ecotype liver pool" from tissue samples from 15 freshwater-strain stickleback livers. No replicates were performed.