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

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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.