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

鳍足动物(海豹、海狮、毛海豹和海象)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鉴定和剖析鳍足动物适应海洋环境的遗传学和分子进化以及科内生态和生活史的惊人变化提供了可能性。了解这些机制不仅提供了对进化过程的基本见解，而且对于评估物种脆弱性和应对未来潜在的环境变化也很重要。鳍足动物的一些独特的适应也可能与人类健康和治疗相关，例如脂肪代谢的适应。这个项目将建立在快速增长的鳍足动物基因组资源的基础上，包括由Goodman/O‘Connell实验室和Pinniped Genome Consortium的其他同事生成的从头开始的基因组组装。这为利用比较基因组学研究羽足类生态和进化的关键方面提供了机会，包括支持不同生活史策略的生理适应以及物种间疾病易感性的差异。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等方法在基因组水平上进行种群遗传学研究。在现存的33种鳍脚类动物中，有一系列不同的适应不同的生态条件和生活史。鳍足类最引人注目的方面之一是觅食和繁殖策略上的差异，这与物种之间身体大小的差异及其所利用的栖息地有关。海豹(Phoca Vitulina)是世界上分布最广泛的羽足动物物种，在欧洲，从斯瓦尔巴群岛到法国北部，从波罗的海到爱尔兰西海岸，都有分布范围。在这种分布范围内，该物种利用了各种各样的栖息地，并经历了广泛的环境条件。该物种还经历了两次由鼠疫病毒(PDV)造成的大规模死亡，该病毒是麻疹病毒家族的成员，在1988年和2002年导致超过50%的欧洲人口死亡。不同种群的死亡率差异很大，有趣的是，在欧洲大部分地区与港海豹共处一地的灰海豹(Halichoreus Grypus)在疫情期间接触了PDV，但没有出现广泛的死亡。因此，该物种是研究环境和生态条件如何影响海洋哺乳动物种群结构以及评估遗传变异如何导致物种内和物种间对麻疹病毒易感性的一个很好的模型。除了全基因组比较，我们还将使用免疫相关候选基因的ddRAD和MiSeq测序来检查种群结构、人口学历史以及PDV死亡率和遗传变异之间的关联。预期结果：关于支持羽足类生活史策略变异的分子适应的新知识；对环境因素如何影响长寿海洋哺乳动物种群结构的详细了解；对与过去环境变化有关的长时间和短时间的海豹种群人口历史的洞察；从其地理范围及其基因组基础确定海豹的适应和功能性遗传变异的可能性；确定导致物种内和物种间对PDV易感性的遗传变异；生成与海豹种群养护管理相关的数据。

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.