Genomic studies of sex differences : On mutations, recombination, and sexual antagonism in songbirds

Abstract: Many organisms have separate sexes, i.e., males and females. The presence of separate sexes causes sex-specific selection regimes and sexual antagonism, which can lead to sex differences in morphology, physiology, and behaviours. Sex and sex differences can be genetically governed and regulated by a pair of sex chromosomes (e.g., X and Y, or Z and W), on which there often are regions without recombination. In this thesis, I used genomic approaches to study sex differences in a songbird, the great reed warbler (Acrocephalus arundinaceus), in which male and females are monochromatic and genetically determined by a pair of sex chromosomes. The thesis starts with a study presenting and evaluating two alternative phylogenetic approaches (the expected likelihood weight (ELW) and the BEAST approach) to determine when different parts of the sex chromosomes stop recombining. My findings highlight the benefits of using fixed topologies to estimate the timing of recombination cessation as done by these approaches. Thereafter, I focus on molecular sex differences using genomic and bioinformatic methods to specifically investigate sex biases in de novo mutations and in recombination patterns, and search for sexually antagonistic loci in the genome.By using whole genome sequencing data from a three-generation pedigree of the great reed warbler, I found a strong sex bias in the numbers of de novo mutations, with males having three times as many mutations as females. Regarding recombination, I found no statistical support for sex-specific recombination rates, but the recombination landscape differed between sexes, with males having more crossovers towards the chromosome ends compared to females. Besides, I developed an interactive R application, RecView ShinyApp, to implement the methodology of locating recombination for future studies within similar topic.Finally, I used statistical approaches based on allele frequency differences and associations with sex per se to search for sexually antagonistic loci with whole genome sequencing data from 100 old great reed warblers that aged between 3 and 5 years. By comparing the top 100 SNPs with the strongest allelic differentiation between the sexes, and the most significant associations with sex, I discovered 50 overlapping SNPs that constitute candidates for future studies of sexual antagonistic selection. To conclude, this thesis has improved the methodology for studying the timing of recombination cessation on sex chromosomes as well as to study recombination per se, identified sex-specific de novo mutation rates and sexually dimorphic recombination landscapes, and obtained candidate loci for sexual antagonism.