Data from: Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish

Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Due to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analyzing coding-gene single nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest.

生境破碎化（habitat fragmentation）与种群大小是否以及如何共同影响适应性遗传变异（adaptive genetic variation）与适应性种群分化（adaptive population differentiation），迄今尚未得到广泛深入的研究。由于显著的遗传漂变（genetic drift）效应，相较于大型种群，小型破碎化种群的适应性遗传变异水平被认为有所降低。但已有研究表明，随着种群规模减小，生境破碎化会加剧生境内部及生境间的异质性。这种生境异质性反而可能有助于适应性多态性的维持，或是在更小的种群规模下，为适应性分化带来更多变异。我们通过分析不同大小的破碎化溪鳟种群中与不同生物学功能相关的编码基因单核苷酸多态性（coding-gene single nucleotide polymorphisms），对这两种对立假说进行了验证。研究发现，小型种群与大型种群之间，或是小型种群内部之间的推定适应性分化程度，均高于大型种群之间的分化程度。相较于遗传种群大小（genetic population size）指标，基于种群统计大小指标得到的上述趋势更为显著，且即便小型种群存在显著的遗传漂变效应，该趋势依然存在。本研究结果表明，生境破碎化会对自然选择产生影响，且破碎化种群的适应性遗传组成与分化所发生的改变，会随种群大小而变化。生境破碎化过程中选择压力的改变，会通过产生更多样化的进化响应，独立于甚至可能早于种群统计随机性与遗传随机性的效应显现之前，影响种群未来的存续能力。