Exploring a Pool-seq only approach for gaining population genomic insights in non-model species

Developing genomic insights is challenging in non-model species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data is used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta); one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual based SNPs) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (FST) between the two introduced populations exceeds that of the naturally sympatric populations (FST = 0.13 and 0.03 between the introduced and the natural...对于资源往往匮乏且成本高企的非模式物种（non-model species）而言，开展基因组研究并获取相关认知颇具挑战。本研究探索了一种新近建立的分析方法的应用潜力：该方法借助混池测序（Pool-seq）数据开展外显子（exon）挖掘并构建从头基因组组装（de novo genome assembly），随后基于该组装利用混池测序数据估算种群分化与多样性水平。我们针对两对褐鳟（*Salmo trutta*）同域种群开展研究：一组为自然同域种群，另一组为被引入同一环境的种群对。我们通过将本方法的分析结果与此前用于表征该种群的分子标记（同工酶（allozymes）与基于个体的单核苷酸多态性（SNP））的所得结果，以及将混池测序数据比对至近缘物种大西洋鲑（*Salmo salar*）参考基因组得到的结果进行对比，验证了本方法的有效性。研究发现，两个被引入种群间的基因组遗传分化指数（FST）高于自然同域种群间的分化水平（引入种群与自然种群间的FST分别为0.13与0.03……