Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

Speciation is a continuous process. Although it is known that differential
adaptation can initiate divergence even in the face of gene flow, we know
relatively little about the mechanisms driving complete reproductive
isolation and the genomic patterns of divergence and introgression at the
later stages of speciation. Sticklebacks contain many pairs of sympatric
species differing in levels of reproductive isolation and divergence
history. Nevertheless, most previous studies have focused on young species
pairs. Here, we investigated two sympatric stickleback species, Pungitius
pungitius and P. sinensis, whose habitats overlap in eastern Hokkaido;
these species show hybrid male sterility, suggesting that they may be at a
late stage of speciation. Our demographic analysis using whole genome
sequence data showed that these species split 1.73 million years ago and
came into secondary contact 37,200 years ago after a period of allopatry.
This long period of allopatry might have promoted the evolution of
intrinsic incompatibility. Although we detected on-going gene flow and
signatures of introgression, overall genomic divergence was high, with
considerable heterogeneity across the genome. The heterogeneity was
significantly associated with variation in recombination rate. This
sympatric pair provides new avenues to investigate the late stages of the
stickleback speciation continuum.