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.）是诸多淡水渔业的重要捕捞对象，在瑞士尤为突出。尽管对瑞士境内湖泊中白鲑多样性的范围、分布与起源尚缺乏完整认知，当地仍开展了白鲑物种的补充放养工作，这可能通过人工基因流威胁本地特有物种。本研究针对瑞士一座亚高山湖泊中沿深度梯度产卵的共存白鲑物种展开表型与遗传分化分析，以期更精准地刻画湖内白鲑的生物多样性。研究发现，适应性形态特征与中性遗传标记（neutral genetic markers）均呈现与水深相关的梯度变异。该个体层面的变异可划分为三个空间分布存在重叠的不同聚类簇。个体间遗传距离与生长速率及鳃耙数差异显著相关，符合适应性分化隔离（isolation-by-adaptation）与生态物种形成（ecological speciation）的理论预测。尽管产卵场存在种群基因混合（demographic admixture），但物种间的遗传分化表明其存在生殖隔离（reproductive isolation）。本研究结果支持梯度物种形成（clinal speciation）模式，即三个物种以紧密的生态邻域（parapatry）关系共存，其中一个（C. sp. "底栖中间型"）此前未被记录。另一个在邻近区域产卵的未记录物种，经分析推测其为异地起源（allochthonous origin）。本研究强调了采用分类学无偏采样策略（taxonomically unbiased sampling strategies）的重要性：这既有助于解析塑造生物多样性的进化机制，也能为生物保护与渔业管理提供更科学的参考依据。