Data from: Genetic evidence for ecological divergence in kokanee salmon

The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has provided tools for investigating the genetic basis of this process in natural populations of non-model organisms. Kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in spawning habitat (tributaries vs. shorelines), however outside of the spawning season the two ecotypes co-occur in many lakes and lack diagnostic morphological characteristics. We used restriction site associated DNA (RAD) sequencing to identify 6,145 SNPs and genotype kokanee from multiple spawning sites in Okanagan Lake (British Columbia, Canada). Outlier tests revealed 18 loci putatively under divergent selection between ecotypes, all of which exhibited temporally stable allele frequencies within ecotypes. Six outliers were annotated to sequences in the NCBI database, two of which matched genes associated with early development. There was no evidence for neutral genetic differentiation, however, outlier loci demonstrated significant structure with respect to ecotype and had high assignment accuracy in mixed composition simulations. The absence of neutral structure combined with a small number of highly divergent outlier loci is consistent with theoretical predictions for the early stages of ecological divergence. These outlier loci were then applied to a realistic fisheries scenario in which additional RAD sequencing was used to genotype kokanee collected by trawl in Okanagan Lake, providing preliminary evidence that this approach may be an effective tool for conservation and management.

经历差异化选择压力的种群中，本地适应性表型的演化是产生并维持生物多样性的核心机制。近年来，高通量DNA测序技术（high-throughput DNA sequencing technology）的出现为研究非模式生物（non-model organisms）自然种群中该过程的遗传基础提供了工具。科卡尼鲑（Kokanee）是红大马哈鱼（Oncorhynchus nerka）的淡水形态，存在两种繁殖生态型（ecotype），二者的产卵栖息地分别为支流与岸线；但在非产卵季，两种生态型会在多个湖泊中共存，且缺乏可用于区分的诊断形态特征。本研究利用限制性酶切位点相关DNA测序（restriction site associated DNA sequencing, RAD）技术，对加拿大不列颠哥伦比亚省奥卡诺根湖多个产卵位点的科卡尼鲑进行基因分型，共鉴定出6145个单核苷酸多态性位点（single nucleotide polymorphism, SNP，复数为SNPs）。离群位点检测（outlier tests）共发现18个可能在两种生态型间受到差异化选择的基因座，且这些基因座在各自生态型内的等位基因频率均表现出时间稳定性。其中6个离群位点可在NCBI数据库中注释到同源序列，另有2个位点匹配与早期发育相关的基因。未检测到中性遗传分化的信号，但离群位点在生态型层面表现出显著的群体结构，且在混合组成模拟中具有较高的个体归属准确率。中性群体结构的缺失结合少量高度分化的离群位点，与生态分化早期阶段的理论预测相符。随后，本研究将这些离群位点应用于真实渔业场景：利用额外的RAD测序技术对奥卡诺根湖拖网采集的科卡尼鲑样本进行基因分型，初步证据表明该方法可作为物种保护与资源管理的有效工具。