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

鳍足类动物（海豹、海狮、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使鉴定和剖析鳍足类动物适应海洋环境的遗传学和分子进化，以及鳍足类动物家族中存在的生态和生活史的惊人变化成为可能。了解这些机制不仅提供了对进化过程的基本见解，而且对评估物种脆弱性和对未来潜在环境变化的反应也很重要。鳍足动物的一些独特适应也可能与人类健康和治疗有关，例如脂肪代谢的适应。该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Goodman/O'Connell实验室和鳍足动物基因组联盟的其他同事生成的从头海豹基因组组装。这为使用比较基因组学来研究鳍足类生态学和进化的关键方面提供了一个机会，包括支撑不同生活史策略的生理适应以及疾病易感性的物种差异。我们将使用多种基因组方法，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研究。在现存的33种鳍足动物中，有各种各样的适应不同的生态条件和生活史的物种。鳍足类动物最引人注目的特点之一是其觅食和繁殖策略的变化，这与物种之间体型的变化以及它们所利用的栖息地有关。斑海豹（Phoca vitulina）是世界上分布最广泛的鳍足动物，在欧洲的活动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。在这种分布中，该物种利用了各种各样的栖息地，并经历了各种各样的环境条件。该物种还经历了两次猪瘟热病毒（PDV；麻疹病毒家族的一员）的大规模死亡，该病毒在1988年和2002年杀死了50%以上的欧洲人口。不同种群的死亡率差异很大，有趣的是，灰海豹（Halichoreus grypus）在动物流行病期间暴露于PDV，但并没有大量死亡。灰海豹与欧洲大部分地区的斑海豹是同域的。因此，该物种是一个很好的模型，用于研究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有助于物种内部和物种之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和MiSeq对免疫相关候选基因进行测序，以检查人群结构、人口统计学历史以及PDV死亡率与遗传变异之间的关系。预期结果：关于支持鳍状生命史策略变化的分子适应的新知识；详细了解环境因素影响长寿海洋哺乳动物种群结构的方式；与过去环境变化有关的长、短时间尺度斑海豹人口统计历史研究确定斑海豹在不同地理范围内的适应性和功能基因变异的可能性及其基因组基础；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有关的数据。

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.