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要旨:
Meiotic recombination involves the exchange of genetic information between parental chromosomes generating new combinations of alleles in the offspring. Recombination is a crucial determinant for reproductive success, proper chromosomal segregation, genetic variability, adaptation rates, and influencing the efficacy of selection. The historical recombination landscape comprises all recombination events captured in DNA sequences among individuals over many generations. Recombination involves different molecular mechanisms and recombining events are not spread randomly across the genome. The placement of recombination events in most mammals is defined by the protein PRDM9, a key player in the initiation of recombination dynamics. However, some organismal groups, such as birds, have lost this protein enabling them with unique recombining properties and conferring an apparent stasis in the positioning of recombination events. However, recent studies in species lacking PRDM9 demonstrated that recombination rates differ widely across the genome and between species. The variation in recombination rates, its causes, and its impact on evolutionary and behavioral processes remain poorly understood, particularly in natural bird populations. Here, I studied the variation of the historical recombination landscape in the Eurasian blackcap, Sylvia atricapilla, and the interplay of recombination rate variation with specific genomic and epigenetic features at different scales: across the genome, at inter- and intraspecific levels. The Eurasian blackcap is an excellent model for bird migration and evolutionary research due to its vast repertoire of migratory phenotypes across a wide geographical range. The initial characterization of recombination rates at the genome level revealed a heterogeneous recombination landscape in this species. Specific genomic features such as nucleotide diversity, GC content, CpG islands, and retrotransposons contribute to this variation. The analysis including annotation features confirmed that most recombination events are prevalent in regulatory regions, particularly cis-regulatory regions. Additionally, the work presented here reveals that the density of CpG islands, location, and methylation patterns are essential determinants in shaping the recombination landscape in blackcaps. Increased methylation levels of shared CpG sites among different tissues were associated with low recombining regions, particularly in shorter chromosomes. Our analyses within the framework of TE characterization suggested that the association with recombination rates could be influenced by TE family, location, and age.
