Data from: 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 simulated neutral baseline (PCT>FCT). This suggests that the differences in gill-raker number between sea- and river-spawners are likely driven by divergent natural selection. We also found strong support for divergent selection on gill-raker number among different populations of sea-spawners (PST>FST), most likely caused by highly variable habitat use and diverse diet. The putative role of divergent selection within lake-spawners initially inferred from empirical microsatellite data, was not supported by simulated FST distributions. This work provides a first formal test of divergent selection on gill-raker number in Baltic whitefish, and demonstrates the usefulness of population genetic simulations to generate informative neutral baselines for PST–FST analyses helping to disentangle the effects of stochastic evolutionary processes from natural selection.

生态重要性状的趋异选择被认为是驱动种群间表型分化的核心因素。为阐明不同进化过程对波罗的海流域欧洲白鲑（Coregonus lavaretus sensu lato）鳃耙数量变异的塑造作用，我们评估了3种白鲑生态型（海产卵型、河产卵型与湖产卵型）内部及之间的遗传变异与表型变异间的关联。为生成FST的期望中性分布，并评估相较于低变异分子标记，高变异微卫星位点是否会导致FST估计值被低估，我们在有限岛模型与层级岛模型下开展了群体遗传模拟。生态型间（FCT=0.010）及生态型内（FST=0.014–0.041）观测到的遗传分化程度较低。然而，相较于观测到的微卫星数据与模拟中性基线，海产卵型与河产卵型之间的鳃耙数量分化程度显著更高（PCT>FCT）。这表明海产卵型与河产卵型之间的鳃耙数量差异可能由趋异自然选择驱动。我们还发现，海产卵型不同种群间的鳃耙数量存在趋异选择的强力证据（PST>FST），这极有可能源于生境利用的高度多样性与食性分化。最初基于经验微卫星数据推断的湖产卵型内部趋异选择的假定作用，并未得到模拟FST分布的支持。本研究首次对波罗的海白鲑的鳃耙数量趋异选择开展了正式检验，并证实了群体遗传模拟可为PST-FST分析生成有效中性基线，从而助力区分随机进化过程与自然选择的效应。