Data from: A gene with major phenotypic effects as a target for selection versus homogenizing gene flow

Genes with major phenotypic effects facilitate quantifying the contribution of genetic vs. plastic effects to adaptive divergence. A classical example is Ectodysplasin (Eda), the major gene controlling lateral plate phenotype in three-spined stickleback. Completely plated marine stickleback populations evolved repeatedly towards low-plated freshwater populations, representing a prime example of parallel evolution by natural selection. However, many populations remain polymorphic for lateral plate number. Possible explanations for this polymorphism include relaxation of selection, disruptive selection, or a balance between divergent selection and gene flow. We investigated 15 polymorphic stickleback populations from brackish and freshwater habitats in coastal North-western Europe. At each site, we tracked changes in allele frequency at the Eda gene between subadults in fall, adults in spring, and juveniles in summer. Eda genotypes were also compared for body size and reproductive investment. We observed a fitness advantage for the Eda allele for low-platedness in freshwater, and for the allele for completely-platedness in brackish water. Despite these results, the differentiation at the Eda gene was poorly correlated with habitat characteristics. Neutral population structure was the best predictor of spatial variation in lateral plate number, suggestive of a substantial effect of gene flow. A meta-analysis revealed that the signature of selection at Eda was weak compared to similar studies in stickleback. We conclude that a balance between divergent selection and gene flow can maintain stickleback populations polymorphic for lateral plate number, and that ecologically relevant genes may not always contribute much to local adaptation, even when targeted by selection.

具有主要表型效应的基因，可用于量化遗传效应与表型塑性效应对适应性分化的贡献。外异蛋白（Ectodysplasin, Eda）便是典型范例，它是调控三棘刺鱼侧板表型的关键主效基因。完全骨板的海洋刺鱼种群曾多次演化出低骨板的淡水种群，这是自然选择驱动平行演化的经典例证。然而，仍有众多种群维持着侧板数量的多态性。针对这一多态性的潜在解释包括选择松弛、歧化选择，或是歧化选择与基因流之间的平衡。
本研究对西北欧沿海咸淡水与淡水生境中的15个刺鱼多态种群开展了调查。在每个采样位点，我们追踪了秋季亚成体、春季成体与夏季幼体三个阶段之间Eda基因的等位基因频率变化，并比较了不同Eda基因型个体的体型与繁殖投入。
研究结果显示，淡水生境中与低骨板相关的Eda等位基因具备适合度优势，而咸淡水生境中则是与完全骨板相关的等位基因占据优势。尽管得到上述结果，Eda基因的分化程度与生境特征的相关性却极低。中性种群结构是侧板数量空间变异的最佳预测因子，这暗示基因流发挥了显著作用。
荟萃分析结果表明，相较于其他刺鱼相关研究，Eda基因上的选择信号较为微弱。本研究得出结论：歧化选择与基因流之间的平衡可维持刺鱼种群的侧板数量多态性，且即便受到选择作用，生态相关基因也未必总能对局部适应做出显著贡献。