Mapping the genomic diversity of the Eurasian blackcap, a songbird with a wide range of migratory behaviour
More and more diverse sequencing technologies and analysis tools are being developed to understand genomic, transcriptomic, and epigenomic variation. Understanding how this variation leads to phenotypic variation has become an integral question in studying complex behavioural traits. My PhD research focuses on understanding the complex behavioural trait of bird migration and its phenotypic variation as seen in the Eurasian blackcap (Sylvia atricapilla). In Chapter 1, I investigate the dichotomy between blackcap populations and their propensity to migrate by comparing seasonal migratory populations with year-round residential populations. Population structure analyses improved our understanding of where and how often residency evolved in the species. This informed my analysis of genomic signatures of selection for residency. A lack of overlap of these genomic regions is recovered, underlining convergent selection for this phenotype. Using a transcriptomic dataset of three brain regions (cluster N, hippocampus and hypothalamus), which either showed migratory behaviour or not. I investigated the allele-specific expression (ASE) patterns in these birds in Chapter 2. The three brain regions showed distinct ASE patterns, and the hippocampus and hypothalamus showed differentiation by behavioural state, which could be linked to the circadian clock. Lastly, transposable elements (TEs) can result in genomic variability. Chapter 3 presents a high-quality TE annotation for the blackcap genome. I investigated the TE distribution along the genome and how this distribution correlates with other genomic features (recombination rate, gene coverage, CpG island coverage and GC content). Recovering a recent accumulation of LTRs in the genome. Together, the work presented in my thesis emphasises the importance of understanding genomic variation at different levels: base pair, structural and allelic variation, for furthering the study of bird migration.
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