Fine-scale map reveals highly variable recombination rates associated
with genomic features in the European blackcap
Abstract
Recombination is responsible for breaking up haplotypes, influencing
genetic variability, and the efficacy of selection. Bird genomes lack
the protein PRDM9, a key determinant of recombination dynamics in most
metazoans. The historical recombination maps in birds show an apparent
stasis in the positioning of recombination events. This highly conserved
recombination pattern over long timescales should constrain the
evolution of recombination in birds, but extensive variation in
recombination rate across the genome and between different species has
been reported. Here, we characterise a fine-scale historical
recombination map of an iconic migratory songbird, the European blackcap
(Sylvia atricapilla) using a LD-based approach which accounts for
population demography. We found variable recombination rates among and
within chromosomes, which associate positively with nucleotide diversity
and GC content, and a negatively with chromosome size. The recombination
rates increased significantly at regulatory regions and not necessarily
at high-dense gene regions. CpG islands associated strongly with
recombination rates; however, their specific position and local DNA
methylation patterns likely influenced this relationship. The
association with retrotransposons varied according to specific family
and location. Our results also provide evidence of a heterogeneous
conservation of recombination maps between the blackcap and its closest
sister taxon, the garden warbler at the intra-chromosomal level. These
findings highlight the considerable variability of recombination rates
at different scales and the role of specific genomic features at shaping
this variation. This study opens the possibility of further
investigating the impact of recombination in specific population-genomic
features.