The role of transposable elements in driving evolution and adaptation in the deep sea

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An enduring and perplexing puzzle in evolution is why species often undergo rapid diversification and adaptive radiation when they enter a new ecological niche or undergo range shifts. Theory predicts that those few pioneering individuals involved in the colonisation process will experience a population bottleneck or founder event which will erode genetic variation and actually hamper any potential for adaptation. There is increasing recognition that transposable elements (TE) may explain this "genetic paradox of invasion" and provide the evolutionary innovation that drives adaptive radiation following colonisation. TE are parasitic mobile genetic elements that propagate through a host genome by copy-and-paste or cut-and-paste mechanisms. This transposition can lead to evolutionary novelty by disrupting host coding sequences or gene regulation, and inducing structural variation such as gene duplications, inversions and translocations.This study will examine the role that TE played in facilitating the colonisation of the deep oceans by the amphipod crustacea. Few metazoan species managed to evolve the capacity to cope with the extreme environmental conditions associated with life at full ocean depth. Those that did tend to have large genomes consistent with the proliferation of TE, and some key genetic adaptations in deep sea animals are also clearly associated with previous TE activity. The latest advances in DNA sequencing technology are, for the first time, providing opportunities to examine the genome-wide effects of TE on gene content and structure, and a hosts capacity to police and so understand the mechanics of how TE may have driven evolution and adaptation during the colonisation of the deep sea.The project will use the very latest DNA sequencing approaches in a unique sample set of deep sea amphipods collected from across the World's oceans to: 1) compare and contrast the diversity, location, activity and abundance of TE in deep versus shallow water species; 2) examine the evolutionary history of transposition across the phylogeny of deep sea amphipods; 3) link TE activity to genes that affect fitness to deep ocean conditions and so shaped adaptation and evolution in the deep sea; 4) characterise levels of DNA CpG methylation in deep sea amphipods to examine capacity to affect TE activity.This lab-based project offers outstanding training opportunities in state-of-the-art 'omics approaches and bioinformatic and evolutionary analyses, coupled with a programme of broad core and generic skills development that is central to the Quadrat DTP training programme. The student will become part of a dynamic and vibrant multidisciplinary postgraduate community, and have the opportunity to make a major contribution to our understanding of fundamental issues in both evolutionary biology and deep sea ecology and biogeography.