Data from: Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses

Repeated adaptive ecological diversification has commonly been reported in fish, and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous Lake Trout ecotypes from Laurentian Shield lakes, Canada. This was achieved by documenting the extent of morphological differentiation using geometric morphometrics and linear measurements as well as the pattern of genomic divergence by means of RADseq genotyping (3,925 filtered SNPs) in 12 lakes. Our results indicate that the two ecotypes evolved distinct body shape and several linear measurements in parallel. Neutral genetic differentiation was pronounced between all isolated populations (Mean FST = 0.433), indicating no or very limited migration and pronounced genetic drift. Significant genetic differentiation also suggested partial reproductive isolation between ecotypes in the two lakes where they are found in sympatry. Combining different outlier detection methods, we identified 48 SNPs putatively under divergent selection between ecotypes, among which 10 could be annotated and related to functions such as developmental processes and ionic regulation. Finally, our results indicate that parallel morphological divergence is accompanied by both parallel and non-parallel genomic divergence, which is associated with the use of different trophic niches between ecotypes. The results are also discussed in the context of management and conservation of this highly exploited species throughout northern North America.

在鱼类中，重复适应性生态分化现象已被广泛报道，且常与营养生态位多样性密切相关。本研究的核心目标，是探究加拿大劳伦琴盾地湖泊中食鱼型与浮游生物食性型湖鳟（Lake Trout）生态型之间，基因组与表型分化的平行程度。本研究通过对12个湖泊的样本开展分析达成上述目标：一方面利用几何形态测量法（geometric morphometrics）与线性测量法量化形态分化程度，另一方面通过限制性位点相关DNA测序（RADseq）基因分型（共筛选得到3925个经过滤的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs））解析基因组分化模式。研究结果显示，两种湖鳟生态型已平行演化出显著差异化的躯体形态与多项线性测量指标。所有隔离种群间的中性遗传分化均极为显著（平均固定指数（Fixation Index, FST）=0.433），表明种群间几乎不存在基因交流或交流程度极低，且遗传漂变效应显著。在两种生态型同域分布的两个湖泊中，显著的遗传分化同样表明二者存在部分生殖隔离。通过整合多种异常值检测方法，本研究共鉴定出48个可能处于生态型间分化选择下的SNPs，其中10个可被功能注释，且与发育过程、离子调控等生物学功能相关。最终，本研究结果表明，平行的表型形态分化同时伴随平行与非平行的基因组分化，这与不同生态型对营养生态位的差异化利用密切相关。本研究还结合北美北部地区该高开发强度物种的管理与保护需求，对研究结果进行了讨论。