Genomic divergence in Atlantic cod populations

Abstract

The core of this thesis has been to address the genomic basis that underlies adaptation to environmental differences in the marine environment. We use Atlantic cod (Gadus morhua L.) to enhance our understanding of several ecological and evolutionary questions, where we seek not only to identify the sheer genetic differences between populations, but also seek to identify what these genomic elements are and try to unravel some of the genetic mechanisms that are involved in maintaining and creating such differences. To put the work into context, I first explain the general principles of population genetics/genomics for non-model species. Furthermore, I describe some key biological features and previous population genetic work in Atlantic cod, which makes a relevant background for interpreting and discussing our results in a general context. The development of a SNParray and linkage maps has provided a valuable tool that is used throughout the thesis. By using this resource in different populations of Atlantic cod, we describe genomic regions likely to be involved in adaptation to different salinity and temperature conditions or differences associated with behavior. The genomic basis of migratory and non-migratory ecotype divergence is explored between the adjacent North East arctic cod and Norwegian coastal cod populations as well as at a trans-Atlantic scale, while adaptation to oceanic and coastal behavioral types is explored at a local scale in the North Sea and at the Skagerrak coast. Our analyses of these data indicate that a range of genomic regions of several megabases each – which combined span more than 6% of the Atlantic cod genome – play a central role in the genetic divergence between various populations. Novel findings in this thesis are that some of the most prominent genomic ‘islands of divergence’ are chromosomal rearrangements in the form of large inversions. Our data suggests a central role for these inversions, each containing hundreds of genes, in maintaining and creating genomic divergence in Atlantic cod. These ‘islands’ are likely to foster the evolution of co-adapted genes or ‘supergenes’ by protecting adaptive loci from recombination and thereby facilitating adaptive genomic divergence across different environments and behavioral ecotypes throughout the distribution range. As such, we have provided new insight into the genomic architecture of distinct ecotypes that constitute different life history strategies as well as for populations facing distinctly different environmental conditions. Such knowledge could eventually warrant a more sustainable exploitation and management of Atlantic cod as a species and contribute to a better protection of marine biodiversity in general.