Comparative population genomics provides insights on the evolutionary history of marine fishes

Abstract

The study of evolutionary mechanisms that shape the divergence continuum whereby populations diverge, adapt to new environments, accumulate reproductive barriers to gene flow and evolve into new species, is a central topic in evolutionary biology. With the arrival of new sequencing techniques, we have the opportunity to advance our knowledge within this field, as well as to ask and answer fundamental research questions previously impossible to explore. While previous decades of research mainly relied on specific case studies with relatively few model species, comparative frameworks are now commonly used to understand the divergence continuum and to derive general patterns behind divergence processes. This PhD thesis provides an insight into the evolutionary history involved during the divergence process of populations in marine fishes. These species are often characterised by their ability to disperse, with larvae drifting with ocean currents for several weeks, and their large population sizes, which together result in limited population structure. As such, these species provide interesting models to study the role of evolutionary forces promoting population divergence, for example linked to demographic histories or local environmental adaptations. The North Sea – Baltic Sea transition zone is an ideal framework to study these evolutionary forces, as the Baltic Sea was connected to the Atlantic Ocean only 8 000 years ago, and presents steep environmental gradients (e.g. salinity) along the transition zone. This environmental gradient is associated with major breaks in the population genetic structure of several marine species. Yet, little is known about the demographic history and the genomic architecture that underlie population divergence and adaptation to this environment in marine fishes. The main goal of this PhD was to fill this knowledge gap by using a comparative population genomics approach on several marine flatfishes that have colonized the Baltic Sea. We found that this colonization was associated with a diversity of divergence patterns, with heterogeneous signals of divergence found across the genome of each species, but also in the genomic architecture of the divergence across species. Therefore, the populations from the North Sea and the Baltic Sea appear to have diverged through species-specific factors. Nevertheless, the presence of ancient lineages and ancient standing genetic variation seem to have fuelled the local adaptation of these species during the colonization of the Baltic Sea.