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 Ma 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.
This article is part of the theme issue ‘Towards the completion of
speciation: the evolution of reproductive isolation beyond the first barriers’.