The evolutionary genomics of life-history adaptations and disease susceptibility in pinnipeds

鳍足类生活史适应和疾病易感性的进化基因组学

• 批准号: 2743369
• 金额: --
• 依托单位: University of Leeds
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2743369
• 关键词: evolutionary; genomics; life; history; adaptations

Pinnipeds (seals, sea lions, fur seals and walrus) are keystone marine predators, and sentinels for marine ecosystem health. Advances in genomics technologies are opening up the possibility to identify and dissect the genetics and molecular evolution underlying the adaptions of pinnipeds to the marine environment and the startling variation in ecology and life history present within the family. Understanding these mechanisms not only provides fundamental insights into the process of evolution, but is also important for assessing species vulnerability and responses to potential future environmental change. Some of the unique adaptions of pinnipeds may also be of relevance to human health and therapeutics, such as adaptations in fat metabolism.This project will build on rapidly growing genomic resources for pinnipeds, including de novo seal genome assemblies generated by the Goodman/O'Connell lab and other colleagues in the Pinniped Genome Consortium. These provide an opportunity to use comparative genomics to examine key aspects of pinniped ecology and evolution including physiological adaptations underpinning different life-history strategies and among species variation in disease susceptibility. We will use a variety of genomic approaches including de novo sequencing of seal genomes, and population genetic studies at the genomic level using methods such as ddRAD. Among the 33 extant species of pinnipeds there are a diverse array of adaptations to varying ecological conditions and life histories. One of the most striking aspects of pinnipeds is the variation exhibited in foraging and reproductive strategies, which are associated with among species body size variation, and the habitats they exploit. The harbour seal (Phoca vitulina) is the world's most widely distributed pinniped species, and in Europe has a range extending from Svarlbard to Northern France, and from the Baltic to the west coast of Ireland. Within this distribution the species exploits a wide variety of habitats and experiences a large range of environmental conditions. The species has also experienced 2 mass mortalities from phocine distemper virus (PDV; a member of the morbillivirus family), which killed more than 50% of the European population in 1988 and 2002. Levels of mortality varied substantially among populations, and intriguingly, grey seals (Halichoreus grypus), which are sympatric with harbour seals in much of Europe, were exposed to PDV during the epizootics but did not suffer extensive mortality. The species is therefore is a good model for examining how environmental and ecological conditions influence population structure in marine mammals and for evaluating how genetic variation might contribute to within and among species susceptibility to morbilliviruses.In addition to whole genome comparisons we will also use ddRAD, and MiSeq sequencing of immune related candidate genes to examine population structure, demographic history, and associations between PDV mortality and genetic variation.Expected outcomes: New knowledge on the molecular adaptions underpinning variation in pinniped life-history strategies; a detailed understanding of the way environmental factors influence population structure in a long-lived, marine mammal; insights into the population demographic history of harbour seals over long and short timescales in relation to past environmental change; potential identification of adaptations and functional genetic variation in harbour seals from across their geographic range and their genomic basis; identification of genetic variation contributing to within and among species variability in susceptibility to PDV; generation of data relevant to the conservation management of seal populations.

鳍足类动物（海豹、海狮、海狗和海象）是重要的海洋捕食者，也是海洋生态系统健康的哨兵。基因组学技术的进步为识别和剖析鳍足类适应海洋环境的遗传学和分子进化以及家族内生态和生活史的惊人变化提供了可能性。了解这些机制不仅可以提供对进化过程的基本见解，而且对于评估物种脆弱性和对未来潜在环境变化的反应也很重要。鳍足类动物的一些独特适应也可能与人类健康和治疗相关，例如脂肪代谢的适应。该项目将建立在快速增长的鳍足类基因组资源的基础上，包括由 Goodman/O' 生成的从头海豹基因组组装。康奈尔实验室和鳍足类基因组联盟的其他同事。这些提供了使用比较基因组学来研究鳍足类生态和进化的关键方面的机会，包括支持不同生活史策略的生理适应以及疾病易感性的物种变异。我们将使用各种基因组方法，包括海豹基因组的从头测序，以及使用 ddRAD 等方法进行基因组水平的群体遗传学研究。现存的 33 种鳍足类动物对不同的生态条件和生活史有着多种多样的适应。鳍足类动物最引人注目的方面之一是觅食和繁殖策略的差异，这与物种体型差异及其利用的栖息地有关。斑海豹（Phoca vitulina）是世界上分布最广泛的鳍足类物种，在欧洲的分布范围从斯瓦尔巴群岛延伸到法国北部，从波罗的海延伸到爱尔兰西海岸。在这个分布范围内，该物种利用各种各样的栖息地并经历各种各样的环境条件。该物种还经历过两次由福辛犬瘟热病毒（PDV；麻疹病毒科成员）造成的大规模死亡，该病毒在 1988 年和 2002 年导致欧洲 50% 以上的人口死亡。不同人群的死亡率水平差异很大，有趣的是，灰色海豹 (Halichoreus grypus) 与欧洲大部分地区的斑海豹同居，在流行病但并未造成大量死亡。因此，该物种是一个很好的模型，可用于检查环境和生态条件如何影响海洋哺乳动物的种群结构，以及评估遗传变异如何影响物种内部和物种间对麻疹病毒的易感性。除了全基因组比较外，我们还将使用 ddRAD，免疫相关候选基因的 MiSeq 测序，以检查种群结构、人口统计历史以及 PDV 死亡率和遗传变异之间的关联。预期结果：关于支持鳍足类生活史变异的分子适应的新知识策略；详细了解环境因素如何影响长寿的海洋哺乳动物的种群结构；深入了解与过去环境变化相关的长、短时间尺度上斑海豹的种群统计历史；从斑海豹的地理范围和基因组基础上潜在地识别斑海豹的适应和功能性遗传变异；鉴定导致种内和种间 PDV 易感性变异的遗传变异；生成与海豹种群保护管理相关的数据。