Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (Mean FST = 0.016) than between ecotypes within sites (Mean FST = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions support the presence of a continuum of divergence in Lake Trout.

通过生态物种形成过程解析物种起源，是进化生物学的核心议题之一，同时也对物种保护与资源管理具有重要意义。湖红点鲑（Lake Trout, *Salvelinus namaycush*）以其在北美广泛分布的、与资源利用和栖息地选择相关的不同生态型（ecotype）而闻名。本研究旨在解析苏必利尔湖内4种湖红点鲑生态型的精细遗传结构。研究采用RADseq技术，对来自4个采样点的共486尾个体进行了6822个过滤后单核苷酸多态性位点（Single Nucleotide Polymorphism, SNP）的基因分型。研究结果表明，不同采样点内的形态分化与遗传分化程度均存在差异。总体而言，遗传分化程度较弱但显著，且采样点间的平均遗传分化水平（平均固定指数（Fixation Index, FST）= 0.016）约为采样点内生态型间的3倍（平均FST = 0.005），这提示同一采样点内的生态型间基因流水平更高，或二者共享祖先的时间晚于同生态型不同种群间的共享祖先。此外，研究还发现了生态型间或与形态变异相关的歧化选择证据。在脂代谢与视觉敏锐度相关基因中检出的离群位点，在生态型分化的研究背景下具有重要研究价值。尽管不同采样点的部分生态型间存在表型平行性，但本研究并未在基因组水平发现明确的平行演化迹象。综上，各采样点内生态型间的基因组与表型分化程度存在差异，且多个分化位点与重要生物学功能相关，这些结果支持湖红点鲑的物种分化存在分化连续体。