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

在进化中，一个经久不衰且令人困惑的问题是，当物种进入一个新的生态位或经历范围转移时，为什么它们经常经历快速的多样化和适应性辐射。理论预测，那些参与殖民化过程的少数先锋个体将经历种群瓶颈或创始人事件，这将侵蚀遗传变异，实际上阻碍任何适应的潜力。越来越多的人认识到，转座因子（TE）可能解释了这种“入侵的遗传悖论”，并提供了驱动殖民化后适应性辐射的进化创新。TE是寄生的可移动遗传元件，通过复制-粘贴或剪切-粘贴机制在宿主基因组中传播。这种转位可以通过破坏宿主编码序列或基因调控，并诱导结构变异，如基因复制、倒位和易位，从而导致进化的新颖性。这项研究将研究TE在促进片脚类甲壳类动物在深海的殖民中所起的作用。很少有后生动物能够进化出应对海洋深处极端环境条件的能力。那些具有与TE增殖一致的大基因组的动物，深海动物的一些关键遗传适应也明显与先前的TE活动有关。DNA测序技术的最新进展首次为研究TE对基因含量和结构的全基因组影响以及宿主的监管能力提供了机会，从而了解TE如何在深海殖民期间推动进化和适应的机制。该项目将使用最新的DNA测序方法，对从世界各地海洋中收集的一组独特的深海片脚类动物样本进行分析：1)比较和对比深海和浅水物种TE的多样性、位置、活动和丰度；2)研究深海片脚类动物系统发育中的转位演化历史；3)将TE活性与影响深海环境适应性的基因联系起来，从而形成深海的适应和进化；4)表征深海片脚类动物DNA CpG甲基化水平，以检验其影响TE活性的能力。这个以实验室为基础的项目为最先进的组学方法、生物信息学和进化分析提供了出色的培训机会，同时还提供了一个广泛的核心和通用技能发展计划，这是Quadrat DTP培训计划的核心。该学生将成为一个充满活力和活力的多学科研究生社区的一员，并有机会为我们对进化生物学和深海生态学和生物地理学的基本问题的理解做出重大贡献。

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.