Identification of regions of differentiation and study speciation patterns across the genome of European and Siberian chiffchaff. This project includes reference based genome assembly of European chiffchaff and whole genome sequencing of 40 chiffchaffs.

Identification of candidate genes for trait variation in diverging lineages is a key step towards understanding the processes underlying the formation of new species. Of particular interest is also to understand the mechanistic underpinnings of genome differentiation as lineages diverge. Hybrid zones provide a valuable resource for such investigations since they allow for studying how genomes evolve as species exchange genetic material and for associating particular genetic regions with phenotypic traits of interest. Here we use whole-genome resequencing of both allopatric and hybridising populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis) - two recently diverged species which differ in morphology, plumage characters, song, habitat preference and migration patterns – to quantify the regional variation in genome-wide genetic diversity and differentiation and to identify potential candidate regions for trait variation across the species. The results show that the levels of genetic diversity, differentiation and divergence are highly heterogeneous with significantly reduced global differentiation and more pronounced differentiation peaks in sympatry than in allopatry. We conclude that this is mainly an effect of regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but that post-divergence selection also has played a role resulting in increased differentiation and fixed differences in some regions. The data also shows that hybridization and backcrossing is common and that phenotype is a pore predictor of the genomic composition of birds in the sympatric region. A combination of differentiation scan approaches and identification of fixed differences in coding and splice altering parts of genes pinpoints a handful of candidate regions that might be important for trait variation between the two species.