Generation of a neutral FST baseline for testing local adaptation on gill-raker number within and between European whitefish ecotypes in the Baltic Sea basin

Divergent selection at ecologically important traits is thought to be a major factor driving phenotypic differentiation between populations. To elucidate the role of different evolutionary processes shaping the variation in gill-raker number of European whitefish (Coregonus lavaretus sensu lato) in the Baltic Sea basin, we assessed the relationships between genetic and phenotypic variation among and within three whitefish ecotypes (sea-, river and lake-spawners). To generate expected neutral distribution of FST and to evaluate whether highly variable microsatellite loci resulted in deflated FST estimates compared to less variable markers we performed population genetic simulations under finite island and hierarchical island models. The genetic divergence observed among (FCT=0.010) and within (FST=0.014–0.041) ecotypes was rather low. The divergence in gill-raker number, however, was substantially higher between sea- and river-spawners compared to observed microsatellite data and simulat...