Despite the growing recognition of an important role of ecological speciation in evolution, the mechanisms driving sympatric divergence within a single population are not fully understood. We documented a series of parallel divergence events and tried to assess general regularities of the diversification of the ancestral gene pool. For that we analysed variation at microsatellite loci in populations of a highly polymorphic complex species Salvelinus alpinus from 14 Transbaikalian lakes, 10 of them hosting two or three forms: dwarf, small, and large. Our results suggest sympatric or parapatric origin of forms in all 10 lakes (in one lake, two forms out of three). Gene diversity and allelic richness of form populations are positively correlated with lake size and negatively correlated with modal length of mature fish, so that the dwarf form typically has the highest, and the large form, the lowest indices of genetic variation. The latter effect might be caused by differences in life histories, thus reflecting adaptive divergence. Sympatric forms have differently segregated gene pools (FST = 0.030–0.497, RST = 0.011–0.440) and restricted (m = 0.002–0.042) typically asymmetric long-term gene flow. The level of reproductive isolation among forms assessed using putatively neutral microsatellite loci is correlated with their differentiation in morphology, including trophic-related gill raker number, and with lake depth (i.e., with segregation of diets and with habitat diversity), which corresponds to “isolation-by-adaptation” pattern. Our data suggest that the advance in speciation stage apparently more depends upon ecological opportunities of lake ecosystems than upon their age.
