Evolutionary genomics of avian sex chromosomes

Luohao Xu
2019 unpublished
The processes and underlying forces of the evolution of avian sex chromosomes remain to be elucidated, despite decades of cytogenetic and molecular studies. In recent years, with the increasing availability of avian genomes, it becomes possible to revisit classical questions in avian sex chromosome evolution, including what are the causes and consequences of recombination suppression, at a fine-scale genomic level. In this thesis, I start tackling this task by focusing on two important clades:
more » ... ongbirds and paleognathous birds. The former clade represents more than half of the bird species of diverse morphological, ecological and behavioral traits, while the latter is a basal and unique clade with unusually homomorphic sex chromosomes. Through a comparative analysis of 13 genomes of paleognathous birds, I uncovered various stages of sex chromosome evolution, from complete degeneration in some tinamous to nearly stalled evolution in most ratites that show a large pseudoautosomal region (PAR) that is still recombining. Unexpectedly, I found evidence of reduced efficacy of selection for PAR-linked genes in species with large PARs, likely due to a reduced recombination rate. On the contrary, all the 11 songbird genomes analyzed here have fully differentiated sex chromosomes. I dated each event of recombination suppression in songbird sex chromosomes, and found there are in total four such events and they all occurred before the rapid speciation of songbirds. Interestingly, I found that the genes survived on the heterochromatic W chromosomes, despite in small numbers, are very conserved across songbirds, and their retention is likely due to the selection for dosage balance and their regulatory roles in the genomes. I further discovered 3 Z-to-W transposition events involving 7 haploinsufficient and house-keeping genes. All together, my work on diverse paleognathous birds and songbirds provides new insights into the dynamic evolutionary history of avian sex chromosomes.
doi:10.25365/thesis.60467 fatcat:zsdxcb3bzzhv5psl4lpnyhzx6a