Data from: Managing cryptic biodiversity: Fine-scale intralacustrine speciation along a benthic gradient in Alpine whitefish (Coregonus spp.)

Whitefish (Coregonus spp.) are an important catch for many freshwater fisheries, particularly in Switzerland. In support of this, supplemental stocking of whitefish species is carried out, despite lacking complete knowledge of the extent, distribution and origin of whitefish diversity in these lakes, potentially threatening local endemics via artificial gene flow. Here, we investigate phenotypic and genetic differentiation among coexisting whitefish species spawning along a depth gradient in a subalpine Swiss lake to better delineate intralacustrine whitefish biodiversity. We find depth-related clines in adaptive morphology and in neutral genetic markers. This individual variation is structured in three distinct clusters with spatial overlap. Individual genetic distances correlate strongly with differences in growth rate and gill-raker number, consistent with predictions of isolation-by-adaptation and ecological speciation. Genetic differentiation between species suggests reproductive isolation, despite demographic admixture on spawning grounds. Our results are consistent with clinal speciation resulting in three species coexisting in close ecological parapatry, one (C. sp. “benthic intermediate”) being previously unknown. A second unknown species spawning in close proximity was found to be of potential allochthonous origin. This study highlights the importance of taxonomically unbiased sampling strategies to both understand evolutionary mechanisms structuring biodiversity and to better inform conservation and fisheries management.

白鲑（Coregonus spp.）是众多淡水渔业的重要捕捞对象，在瑞士的淡水渔业中地位尤为重要。为保障该渔业资源，相关方会对该属鱼类实施补充放养，但目前对瑞士这些湖泊中白鲑多样性的分布范围、分布格局与起源仍缺乏完整认知，此举可能通过人工基因流（artificial gene flow）威胁本地特有种的生存。本研究针对瑞士某亚高山湖泊中沿深度梯度（depth gradient）产卵的共存白鲑物种，探究其表型与遗传分化（phenotypic and genetic differentiation）特征，以期更清晰地界定湖内白鲑的生物多样性。研究发现，适应性形态（adaptive morphology）与中性遗传标记（neutral genetic markers）均呈现与深度相关的渐变格局。这种个体变异可被划分为三个存在空间重叠（spatial overlap）的不同聚类簇。个体遗传距离（individual genetic distances）与生长速率（growth rate）、鳃耙数（gill-raker number）的差异呈显著相关，这与适应隔离（isolation-by-adaptation）和生态物种形成（ecological speciation）的理论预测相符。尽管产卵场（spawning grounds）存在种群混合（demographic admixture），但不同物种间的遗传分化表明其存在生殖隔离（reproductive isolation）。本研究结果支持渐变式物种形成（clinal speciation）理论，即三个物种以紧密的生态邻域分布（parapatry）模式共存，其中一种为此前未被记录的底栖中间型白鲑（C. sp. "benthic intermediate"）。此外，研究还发现另一种在邻近区域产卵的未知物种，其起源为异源起源（allochthonous origin）。本研究凸显了采用分类学无偏采样（taxonomically unbiased sampling）策略的重要性，这既有助于理解塑造生物多样性的进化机制，也能为生物保护（conservation）与渔业管理（fisheries management）提供更科学的参考依据。