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

鳟鱼（萨尔莫trutta）在最后一个冰河时代后通过沿河和沿海扩张路线使许多英国河流成为海洋，当代英国人口包括占据不同景观的欧洲血统的混合物，水质和化学根据当地地质和地理而变化。此外，人类活动，包括工业和农业污染，影响到水道，对常驻鱼类种群构成重大的生理挑战。在众多的水污染源中，自工业革命以来，金属开采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，这两个地区都是锡和铅的密集开采区。了解维持具有社会经济重要性的野生物种（包括渔业）的自然种群的进化和人口统计过程，是未来可持续地保护和管理它们的关键，并载于联合国生物多样性公约和可持续发展公约。在英国和爱尔兰，鳟鱼（萨尔莫trutta）渔业是当地重要的社会经济和生态系统服务的角度来看，因此，鳟鱼一直是最近的几个研究项目的重点。这个博士学位将建立在这些以前的项目，并将使用国家的最先进的基因组测序，以探讨在英格兰西南部，威尔士中部和东南爱尔兰鳟鱼种群的进化适应（所有鳟鱼种群受到持续金属污染影响的地区），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（冰川期后的殖民血统）、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）。这些问题有助于环境基因组学的方法，旨在确定个别鱼类的基因组中的选择签名。在这里，我们将利用现有的样本从西南英格兰，中部和北部威尔士和东南爱尔兰。在每个地点，我们将使用现有样本的组合，并将进行实地工作，从已知污染源（锡矿和铅矿）的上游和下游地点收集新样本;众所周知，这些地点下游的鱼类在形态和生理上往往不同（例如，威尔士Dyfi的黑鳍鱼）。Bruford等人最近在绵羊和山羊中使用类似的方法成功地检测到驯化的基因组特征（Nature Communications，2018）。该奖学金将形成一个案例项目-与游戏和野生动物保护信托基金（GWCT）和Westcountry Rivers Trust（WRT）合作资助，并由威尔士自然资源部（抽样）提供实物捐助。除了标准的NERC资金，布鲁福德和史蒂文斯将提供资金，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.