Evolutionary Genomics of Xenopus: Investigations Into Sex Chromosomes, Whole Genome Duplication, Speciation, and Hybridization

Abstract

African clawed frogs (Xenopus) have been scientific and medical model species for decades. These frogs present many curious features, and their genomic history is no exception. As such, a variety of evolutionary genomic questions can be addressed with these species in a comparative framework, owing to the great array of genetic tools available and a large number of abundant species. The sex chromosomes of this group are evolutionarily young, and this thesis establishes that there has been an additional change in what constitutes the sex chromosomes in one species of Xenopus. This allows us to compare the evolutionary trajectory of newly established sex chromosomes. By exploring the genetic content of these systems, profiling their recombinational activity, and assessing the extent of nucleotide divergence between the sex chromosomes, we find that sex chromosome evolution may be predictable in some aspects, and highly unpredictable in others. In addition, this genus is uncharacteristic for vertebrates in the frequency with which lineages undergo whole genome duplication. In this thesis, we explore the selective dynamics operating on duplicate genes over time, and the rate at which duplicate copies are purged from the genome from multiple Xenopus species. These investigations provide an animal perspective on the subject of biased subgenome evolution, characteristic of allopolyploids. The last two chapters of this thesis redefine the species boundaries for the most intensively studied Xenopus species (X. laevis), and explore the genetic extent of hybridization between the common X. laevis and the endangered X. gilli. Overall, this thesis provides a broad look at several aspects of Xenopus evolutionary genomics, providing novel contributions to the fields of sex chromosome research, whole genome duplication, and speciation and hybridization.