Developing genomic insights is challenging in nonmodel 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 are 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 single nucleotide polymorphisms [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 (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.

Population translocations occur for a variety of reasons, from displacement due to climate change, to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor genomic effects of population translocations. In 1979, fish from each of two genetically and ecologically separate populations were released at one point in time to the same lake system. Whole-genome sequencing data is used to characterize diversity within and divergence between introduced fish from different source populations and fish inhabiting two lakes down-stream of the release sites, sampled 30 years later (c. 5 generations). Diversity and divergence among introduced populations and fish sampled in the wild c. 5 generations later suggest extensive hybridization. Introduced fish are unequally represented in the lakes down-stream of the release sites, with fish from one population mainly contributing to the lake closest to the release site, and the fish from the other dominating the lake further downstream. We also identify genomic regions putatively under directional selection in the new lake system, where genes from one of the introduced populations, regulating metabolism, appear advantageous. Our results demonstrate that genetic effects of population translocations e.g., establishment, hybridization, and adaptation can be rapid after release into novel environments – even for a species with relatively small local effective population sizes and a large, complex genome. This is an important contribution to understanding the microevolutionary effects population translocations have on intraspecific diversity.