Data from: Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

Recombination rate is heterogeneous across the genome of various species,
and so are genetic diversity and differentiation as a consequence of
linked selection. However, we still lack a clear picture of the underlying
mechanisms for regulating recombination. Here we estimated fine-scale
population recombination rate based on the patterns of linkage
disequilibrium (LD) across the genomes of multiple populations of two
closely related flycatcher species (Ficedula albicollis and F. hypoleuca).
This revealed an overall conservation of the recombination landscape
between these species at the scale of 200-kb, but we also identified
differences in the local rate of recombination despite their recent
divergence (<1 million years). Genetic diversity and
differentiation were associated with recombination rate in a
lineage-specific manner, indicating differences in the extent of linked
selection between species. We detected 400-3,085 recombination hotspots
per population. Location of hotspots was conserved between species, but
the intensity of hotspot activity varied between species. Recombination
hotspots were primarily associated with CpG islands (CGIs), regardless of
whether CGIs were at promoter regions or away from genes. Recombination
hotspots were also associated with specific transposable elements (TEs),
but this association appears indirect due to shared preferences of the
transposition machinery and the recombination machinery for accessible
open chromatin regions. Our results suggest that CGIs are a major
determinant of the localization of recombination hotspots, and we propose
that both the distribution of TEs and fine-scale variation in
recombination rate may be associated with the evolution of the epigenetic
landscape.