Adapting to life in metal polluted rivers: implications for conservation, genetic diversity and fisheries management in the brown trout (Salmo trutta)

鳟鱼（Salmo trutta）在最后一个冰河时代之后通过河流和沿海扩张路线重新殖民了许多英国河流，当代英国人口包括欧洲血统的混合物，占据了不同的景观，水质和化学成分根据当地的地质和地理而变化。此外，人类活动，包括工业和农业污染，影响水道，并对居住的鱼类种群构成重大的生理挑战。在水生污染的众多来源中，金属开采自工业革命以来一直是英国和爱尔兰的一个重要因素，特别是在康沃尔和威尔士中部，这两个地区都有大量的锡和铅开采。了解进化和人口统计过程，维持包括渔业在内的重要社会经济野生物种的自然种群，是未来可持续保护和管理这些物种的关键，也是《联合国生物多样性和可持续发展公约》所载的内容。在英国和爱尔兰，从社会经济和生态系统服务的角度来看，鳟鱼（Salmo trutta）渔业在当地很重要；因此，鳟鱼一直是最近几个研究项目的重点。该博士学位将以这些先前的项目为基础，并将使用最先进的基因组测序来探索英格兰西南部、威尔士中部和爱尔兰东南部（所有鳟鱼种群受到持续金属污染影响的地区）鳟鱼种群的进化适应，以理清最有可能影响鳟鱼适应能力的三个因素的相对重要性：进化史（冰期后的殖民谱系）、当地适应（自然地球化学、河流位置）和人为污染（采矿和持续的重金属污染）。这些问题为环境基因组学方法提供了帮助，该方法旨在识别单个鱼类基因组中的选择特征。在这里，我们将利用来自英格兰西南部、威尔士中部和北部以及爱尔兰东南部的现有样本。在每个地点，我们将使用现有样品的混合物，并将进行实地调查，从已知污染源（锡和铅矿）的上游和下游地点收集新的样品；众所周知，这些地点的下游鱼类在形态和生理上往往是不同的（例如，威尔士Dyfi的黑鳍鱼）。Bruford等人最近使用类似的方法成功地在绵羊和山羊中检测到驯化的基因组特征（Nature Communications, 2018）。该奖学金将形成一个CASE项目，由游戏和野生动物保护信托基金（GWCT）和西部国家河流信托基金（WRT）合作资助，威尔士自然资源部（抽样）提供实物捐款。除了标准的NERC资金外，布鲁福德和史蒂文斯还将提供资金，以确保所有相关样本的测序。

Trout (Salmo trutta) recolonised many UK rivers via riverine and coastal expansion routes after the last ice age, and the contemporary UK population comprises a mixture of European lineages occupying diverse landscapes, with water quality and chemistry varying according to local geology and geography. In addition, human activities, including industrial and agricultural pollution, affect water-courses and pose significant physiological challenges to resident fish populations. Among the many sources of aquatic pollution, metal mining has been a significant factor in Britain and Ireland since the industrial revolution, particularly in Cornwall and mid-Wales, both areas of intensive tin and lead mining. Understanding the evolutionary and demographic processes maintaining natural populations of socio-economically important wild species, including fisheries, is key to conserving and managing them sustainably into the future, and is enshrined in UN Conventions on Biological Diversity and Sustainable Development. In Britain and Ireland, trout (Salmo trutta) fisheries are locally important from a socio-economic and ecosystem service perspective; as such, trout have been the focus of several recent research projects. This PhD will build on these previous projects and will use state-of-the-art genomic sequencing to explore the evolutionary adaptations of trout populations in SW England, central Wales and SE Ireland (all regions with trout populations affected by continuing metal pollution), to disentangle the relative importance of the three factors most likely to affect the ability of trout to adapt: evolutionary history (post-glacial colonisation lineage), local adaptation (natural geochemistry, river location) and human-driven pollution (mining and persistent heavy metal contamination). These questions lend themselves to an environmental genomics approach designed to identify signatures of selection in the genomes of individual fish. Here we will take advantage of existing samples from SW England, central and north Wales and SE Ireland. At each location we will use a mix of existing samples and will undertake fieldwork to collect new samples from sites up- and down-river of known contamination sources (tin and lead mines); it is known that fish down-river of these sites are often morphologically and physiologically distinct (e.g. black-finned in the Dyfi, Wales). Bruford et al. recently successfully detected genomic signatures of domestication using a similar approach in sheep and goats (Nature Communications, 2018). This studentship will form a CASE project - funded in partnership with The Game and Wildlife Conservation Trust (GWCT) and Westcountry Rivers Trust (WRT), with in-kind contributions from Natural Resources Wales (sampling). Additional to standard NERC funding, Bruford and Stevens will contribute funds to ensure sequencing of all relevant samples.