There have been many studies in genetic structuring of the Baltic Sea organism, and people have made ad hoc attempts compare similarities and differences in patterning of genetic variability across the species. The problem faced by such studies is that the sampling schemes for different species have often been quite different.
In a paper to appear soon in Marine Biology we sampled three- and nine-spined sticklebacks from the same areas across the Baltic Sea basin to compare patterns of genetic differentiation, variability and gene flow in comparable fashion. The results reveal contrasting population structures for the two species in neutral marker genes: the nine-spined stickleback is much more structured than the three-spined stickleback.
DeFaveri J., T. Shikano, I.N. Ab Ghani & J. Merilä (2012) Contrasting population structures in two sympatric fishes in the Baltic Sea basin. Marine Biology, in press.