Data from: Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence

Recombination between loci underlying mate choice and ecological traits is
a major evolutionary force acting against speciation with gene flow. The
evolution of linkage disequilibrium between such loci is therefore a
fundamental step in the origin of species. Here, we show that this process
can take place in the absence of physical linkage in hamlets—a group of
closely related reef fishes from the wider Caribbean that differ
essentially in colour pattern and are reproductively isolated through
strong visually-based assortative mating. Using full-genome analysis, we
identify four narrow genomic intervals that are consistently
differentiated among sympatric species in a backdrop of extremely low
genomic divergence. These four intervals include genes involved in
pigmentation (sox10), axial patterning (hoxc13a), photoreceptor
development (casz1) and visual sensitivity (SWS and LWS opsins) that
develop islands of long-distance and inter-chromosomal linkage
disequilibrium as species diverge. The relatively simple genomic
architecture of species differences facilitates the evolution of linkage
disequilibrium in the presence of gene flow.