Population genomics as a tool for management and conservation of brown trout (Salmo trutta) in the Iberian Peninsula

Abstract

Brown trout (Salmo trutta) is a cold-water salmonid with ecological, commercial and recreational importance. Previous genetic studies highlighted a notable genetic structure in natural populations, which is a fundamental biological feature for the conservation of the species. Nevertheless, many factors threaten this genetic richness. One of the most important is genetic introgression, that originated from the introduction of aquaculture individuals in the wild environment in the last decades. This genetic erosion can have adverse consequences in brown trout adaptation capacity, especially in the context of a reduction of available habitats driven, among other causes, by global warming. This doctoral thesis had two main strands: (1) A bioinformatic benchmark to evaluate the biological conclusion robustness drawn from diverse SNP panels derived from different building-loci pipelines. For this strand, a broad of five aquatic species representing different genomic and/or population structure scenarios was used. This strand was performed in a context in which, due to the irruption of new techniques as RAD-seq (Restricion site-associated DNA sequencing) for the library preparation and Next Generation DNA Sequencing (NGS), the volume of data generated has grown exponentially in the last decade, promoting the development of new bioinformatics tools to process it. On the other side, (2) a genomic approach was used for the first time on brown trout populations from the Iberian Peninsula, to evaluate genetic diversity levels, population structure, natural hybridization patterns, evaluation of population introgression with aquaculture individuals of the same species and the detection of candidate genomic regions under selection pressure. The information obtained will allow the improvement of current management and conservation strategies of wild brown trout genetic resources.