The Evolution and Adaptive Effects of Transposable Elements in Birds and Elapids

Abstract

Transposable elements (TEs) are genetic sequences able to copy or move themselves across their host genome. As TEs move within their host they can act as a source of genetic novelty, and hence are often described as \drivers of evolution". This novelty includes contributing or altering regulatory and coding regions, and promoting non- allelic homologous recombination and, in turn, major structural rearrangements. In some cases, TEs can further contribute to genomic change by jumping between organisms in a process known as horizontal transposon transfer (HTT). HTT is the passing of TEs between organisms by means other than parent to offspring, and has been well described across vertebrates, with multiple events noted in both birds and squamates. Birds are the most diverse class of reptiles, encompassing over 10,000 species, however studies in TE evolution in birds have focused on single lineages. Early findings from the chicken genome led to the assumption that avian TEs are largely stable and inactive. More recent studies have similarly focused on single lineages of birds, revealing some variation in TE activity across birds. In contrast to birds, few studies have explored the evolution of TEs in squamates (lizards and snakes) at a class or family level, instead examining their evolution either across the order or comparing two long diverged species. As such, it is unknown whether patterns seen across all squamates occur at shorter time scales. At lower levels many squamate families are highly diverse, rapidly adapting to new environments and ecological niches. One such family is Hydrophiinae, a family of elapid snakes containing ~100 terrestrial snakes, ~60 marine sea snakes and 6 amphibious sea kraits. In this thesis I investigate the evolution of TEs in two diverse groups of rep- tiles: birds and Australo-Melanesian elapid snakes (Hydrophiinae). I provide the first comprehensive study of TE activity across all orders of birds, focusing on the dominant superfamily, Chicken Repeat 1 (CR1) retrotransposons. By performing comparative genomic analyses I have identified significant variation in the rate of TE expansion both between and within avian orders. Clades including parrots, kiwis and waterfowl show high diversity and large, recent expansions of CR1 retrotransposons, while in various ratites and songbirds CR1s have been near inactive for tens of millions of years. The rest of the chapters focus on the evolution of TEs in hydrophiines, finding repeated HTT events into marine hydrophiines from other marine organisms. TEs in hydrophiines that were acquired via HTT appear to have played a role in their adaptation to the marine environment, with insertions found throughout regulatory regions. In the sea kraits, one horizontally transferred TE has rapidly expanded to make up 8-12% of the sea krait genome in a timespan of just 15-25 million years, the fastest known expansion of TEs in amniotes following a HTT event. Together this thesis presents bioinformatic analyses of two diverse clades of rep- tiles, Aves and Hydrophiine, finding that to truly understand TEs, their evolution and the potential adaptive effects they can cause, we must examine life on both a broad and fine scale.