Adapting to life in an increasingly acid world: understanding tolerance to acidic waters in populations of trout (Salmo trutta)

在其生命周期的淡水阶段，褐鳟（Salmo trutta）和大西洋鲑鱼（Salmo salar）生活在广泛的环境中，从酸性高地溪流到中性碱性白垩溪流。主要由于人为驱动的生态扰动的影响，例如森林砍伐和酸流失，许多这些系统的pH值现在的波动远远超过以前记录的水平。达特穆尔国家公园是英格兰西南部一个独特的高地栖息地。该地区的许多河流流经花岗岩和泥炭，呈明显的酸性；然而，与英国和爱尔兰其他地方类似的高地溪流相比，当地的管理活动，如森林砍伐，导致pH值大幅波动，记录到的pH值低于4。尽管如此，达特穆尔河的大部分溪流都有健康的鳟鱼和鲑鱼，分子分析表明，来自酸性河流的鳟鱼在基因上是不同的。本项目旨在通过分析褐鳟对酸性水体的单核苷酸多态性（snp）和基因表达的变化，确定褐鳟对酸性水体耐受的基础。我们建议使用限制性内切位点相关DNA测序（RADseq）和转录组学（RNA测序[RNAseq]）的互补方法来研究生活在英国南部酸性、中性和碱性河流中的鳟鱼种群。这将使我们能够探索耐酸性的共同/趋同进化“解决方案”。此外，学生将获得实地经验，并与现代保护组织合作。我们的主要目标是了解褐鳟耐酸的遗传基础。我们建议使用RADseq分析来自低pH值河流（达特穆尔河）、中性河流（康沃尔和德文郡的其他河流）和碱性更强的河流（多塞特/汉普郡的白垩河）的鱼类。我们已经从这些地区收集了当地鳟鱼的组织样本，学生将有机会参加实地考察，收集更多的鳟鱼组织样本。采样设计包括来自酸性高沼泽地区和中性低地地区的支流的鱼（允许我们消除差异遗传漂变和流域特定选择压力的影响）。这将使我们能够确定在生态型之间明确分离的snp，并确定鳟鱼基因组中与适应低pH环境相关的区域。该研究将更好地了解鲑鱼耐酸的基础，并解决该物种在物种贫乏（高酸性）生态系统中持续存在的长期问题。它还提供了揭示局部适应机制和这一过程背后的遗传结构的潜力。面对全球对水生系统的压力，例如大气中二氧化碳增加的酸化作用，这种资料在鱼类养护和水产养殖方面也将有价值。与CASE合作伙伴，西部国家河流信托基金和野生动物保护信托基金的合作也提供了一个难得的机会来寻找与暴露在高酸性条件下有关的基因表达变化。然后，RNAseq的分析将描述与酸度相关的基因表达变化的特征，识别对野生鳟鱼种群的生理反应重要的基因。通过结合种群基因组学和基因表达方法，这项令人兴奋的研究为解决这种鱼的耐酸性和适应性等更广泛的问题提供了潜力。埃克塞特大学和布里斯托尔大学的研究小组在这一领域拥有丰富的经验，我们预计我们的研究成果将被渔业管理者、自然资源保护主义者和其他利益相关者用来帮助监测危险环境，检测可能威胁鱼类健康和种群数量的水质变化。

During the freshwater phases of their lifecycles, brown trout (Salmo trutta) and Atlantic salmon (Salmo salar) inhabit a broad range of environments, ranging from acidic upland streams to neutral-alkaline chalk streams. Due primarily to the impacts of human-driven ecological perturbations, e.g. forestry clearance and acid run-off, the pH of many of these systems is now fluctuating far beyond previously recorded levels. Dartmoor National Park is a unique upland habitat in southwest England. Flowing over granite and peat, many rivers of the region are markedly acidic; nonetheless, compared to similar upland streams elsewhere in Britain and Ireland, local management activities, e.g. forestry clearance, have led to large fluctuations in pH, with readings of less than pH 4 being recorded. Despite this, most Dartmoor streams host healthy populations of trout and salmon, and molecular analysis shows trout from acid rivers to be genetically distinct.This project aims to identify the basis of tolerance to acid waters in brown trout through analysis of single nucleotide polymorphisms (SNPs) and changes in gene expression. We propose to use the complementary approaches of restriction site associated DNA sequencing (RADseq) and transcriptomics (RNA sequencing [RNAseq]) to study trout populations inhabiting acid, neutral and alkaline rivers in southern Britain. This will allow us to explore common/convergent evolutionary 'solutions' to acid tolerance. Additionally, the student will gain field experience and work with a modern conservation organisation.Our primary objective is to understand the genetic basis of acid tolerance in brown trout. We propose to use RADseq analysis of fish from rivers with low pH (Dartmoor streams), neutral rivers (other rivers in Cornwall and Devon) and more alkaline waters (chalk streams, Dorset/Hampshire). We already hold tissue samples from resident trout collected from across these regions, and the student will have the opportunity to partake in fieldwork to collect additional trout tissue samples. The sampling design includes fish from tributaries running off acid high-moor sites and neutral lowland locations (allowing us to eliminate the effects of differential genetic drift and catchment-specific selective pressures). This will allow us to identify SNPs that segregate definitively between the ecotypes and to identify regions of the trout genome associated with adaptations to living in a low pH environment. The study will provide a better understanding of the basis of acid tolerance in salmonids and addresses long-standing questions regarding persistence of this species in an otherwise species-poor (highly acid) ecosystem. It also offers the potential to reveal the mechanisms of local adaptation and the genetic architecture underlying this process. Such information will also be of value in fish conservation and aquaculture in the face of global pressures on aquatic systems, e.g. the acidifying effects of increased atmospheric CO2.Collaboration with the CASE partner, Westcountry Rivers Trust, and The Game & Wildlife Conservation Trust also provides a rare opportunity to look for changes in gene expression in relation to exposure to highly acidic conditions. Analysis by RNAseq will then characterise changes in gene expression related to acidity, identifying genes important to physiological responses in wild trout populations. By combining population genomic and gene expression approaches, this exciting studentship offers the potential to address broader questions of acid tolerance and adaptation in this fish. The team at Exeter and Bristol have extensive experience in this field and we anticipate that our research findings will be used by fisheries managers, conservationists and other stakeholders to help in monitoring at-risk environments and detecting changes in water quality that may threaten fish health and population numbers.