Evolutionary genomics in Corvids : – From single nucleotides to structural variants

Heritable genetic variation is the raw material of evolution and can occur in many different forms, from altering single nucleotides to rearranging stretches of millions at once. DNA mutations that result in phenotypic differences are the basis upon which natural selection can act, leading to a shift of the frequency of those mutations. In this thesis I aim to comprehensively characterize and quantify genetic variation in a natural system, the songbird genus Corvus. First, we expand on previous work from a hybrid zone of different populations of Eurasian crows. All black carrion crows and black-and-grey hooded crows meet in a narrow hybrid zone in central Europe, and also in central and Southeast Asia. Comparing population genetic data acquired from these three hybrid zones yielded no single genetic region as a candidate responsible for phenotypic divergence, yet a parallelism in sets of genes and gene networks was evident. Second, we capitalize on varying evolutionary timescales to investigate the driver of the heterogeneous genetic differentiation landscape observed in multiple avian species. Genetic diversity, and thus differentiation, seems to be correlated both between populations within single species and between species which diverged 50 million years ago. This pattern is best explained by conserved broad-scale recombination rate variation, which is in turn likely associated with chromosomal features such as centromeres and telomeres. Third, we introduce a de-novo assembly of the hooded crow based on long-read sequencing and optical mapping. The use of this technology allowed a glimpse into previously hidden regions of the genome, and uncovered large-scale tandem repeat arrays consisting of a 14-kbp satellite repeat or its 1.2-kpb subunit. Furthermore, these tandem repeat arrays are associated with regions of reduced recombination rate. Lastly, we extend the population genetic analysis to structural genomic variation, such as insertions and deletions. A large-scale population re-sequencing data set based on short-read and long-read technologies, spread across the entire genus is the foundation of a fine-scale genome-wide map of structural variation. A differentiation outlier approach between all-black carrion and black-and-grey hooded crows identified a 2.25-kilobase LTR retrotransposon inserted 20-kb upstream of the NDP gene. The element, which is fixed in the hooded crow population, is associated with decreased expression of NDP and may be responsible for differences in plumage color