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Abstract
With only a few absolute geographic barriers in marine environments, the factors maintaining
reproductive isolation among marine organisms remain elusive. However, spatial structuring
in breeding habitat can contribute to reproductive isolation. This is particularly
important for marine organisms that migrate to use fresh- or brackish water environments
to breed. The Japanese Gasterosteus stickleback species, the Pacific Ocean three-spined
stickleback (G. aculeatus) and the Japan Sea stickleback (G. nipponicus) overwinter
in the sea, but migrate to rivers for spawning. Although they co-occur at several
locations across the Japanese islands, they are reproductively isolated. Our previous
studies in Bekanbeushi River showed that the Japan Sea stickleback spawns in the estuary,
while the Pacific Ocean stickleback mainly spawns further upstream in freshwater.
Overall genomic divergence was very high with many interspersed regions of introgression.
Here, we investigated genomic divergence and introgression between the sympatric species
in the much shorter Tokotan River, where they share spawning sites. The levels of
genome-wide divergence were reduced and introgression was increased, suggesting that
habitat isolation substantially contributes to a reduction in gene flow. We also found
that genomic regions of introgression were largely shared between the two systems.
Furthermore, some regions of introgression were located near loci with a heterozygote
advantage for juvenile survival. Taken together, introgression may be partially driven
by adaptation in this system. Although, the two species remain clearly genetically
differentiated. Regions with low recombination rates showed especially low introgression.
Speciation reversal is therefore likely prevented by barriers other than habitat isolation.