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.白鱼（Coregonus spp.）是诸多淡水渔业的重要捕捞对象，在瑞士境内尤为突出。尽管目前对瑞士境内这些湖泊中白鱼多样性的分布范围、分布格局及起源尚缺乏完整认知，相关方仍开展了白鱼物种的补充放养工作，该行为可能通过人工基因流对当地特有物种造成潜在威胁。本研究针对瑞士一座亚高山湖泊中沿深度梯度产卵的共栖白鱼物种，开展表型与遗传分化分析，以期更清晰地界定湖内白鱼的生物多样性。研究发现，适应性形态特征与中性遗传标记均呈现与深度相关的梯度变异。该个体水平的变异可划分为三个具有空间重叠分布特征的聚类类群。个体遗传距离与生长速率及鳃耙数的差异呈显著正相关，这与适应性分化隔离（isolation-by-adaptation）与生态物种形成（ecological speciation）的理论预测相符。不同物种间的遗传分化表明其存在生殖隔离，尽管在产卵场存在种群遗传混合现象。本研究结果支持梯度物种形成（clinal speciation）理论，即三个物种在紧密的生态邻域（parapatry）中共存，其中一个被命名为‘底栖中间型（C. sp. "benthic intermediate"）’的物种此前尚未被报道。另一种在邻近区域产卵的未知物种，经分析发现其可能为异地起源（allochthonous origin）。本研究凸显了采用分类学无偏采样策略的重要性，该策略不仅有助于理解塑造生物多样性的进化机制，还能为生物保护及渔业管理提供更科学的决策支撑。