Crayfish conservation: using eDNA to detect endangered and invasive species

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The detection of species using environmental DNA (eDNA) is proving invaluable in conservation biology for the detection of rare and invasive taxa (Bohmann et al. 2014; Deiner et al. 2017). Small fragments of species-specific DNA are amplified, and can be used for surveys of crayfish species in the UK. The white-clawed crayfish Austropotamobius pallipes is now classified as 'Endangered' in the IUCN Red List, and has declined by 50-80% globally in the last decade, largely because of interactions with invasive crayfish species, but also because of pollution and habitat degradation (IUCN Red List). A. pallipes is native and indigenous to the UK, and populations have been decimated by predation/competition with the larger and more aggressive American signal crayfish Pacifastacus leniusculus, and by crayfish plague (caused by a fungus Apanomyces astaci) often transmitted by invasive taxa. A further seven invasive crayfish taxa pose further threats to our native species. Conservation of the remaining populations of A. pallipes is therefore of high priority, and large-scale supplementation and reintroduction of populations now occurs through captive breeding programmes, yet the rapid assessment of current populations is still hamperedby the time it takes to survey crayfish using more 'traditional' methodology. We aim 1) to continue the development of DNA markers in order to detect eDNA from all invasive crayfish taxa in the UK. 2) To evaluate the sensitivity of existing markers developed by MS for A. pallipes, P. leniusculus and crayfish plague under natural conditions using high-throughput metabarcoding. We will determine the potential for false positive and false negative (lack of sensitivity) findings, and will also evaluate whether shotgun barcoding can be used to assess other aquatic taxa that may impact upon A. pallipes populations. 3) To use eDNA data to better assess the distribution of crayfish taxa and crayfish plague in the UK. This will involve species distribution and occupancy models to predict distributions so that effective sites for reintroductions can be determined, and will enable end users (governmental policy makers, ecological consultants and conservation charities) to predict changes in distribution that may occur under climate change scenarios and various land use scenarios (housing developments, road works etc.). The project is relevant to three of the FRESH priorities (1) quantifying and managing emerging risks to freshwaters (in this case risks caused by invasive species and climate change); (2) developing and testing next generation tools for monitoring ecosystems (eDNA) and (3) tacking extinction (of the Endangered A. pallipes) in freshwater ecosystems. Our work will have support from the UK's leading captive breeding facility for A. pallipes (Bristol Zoo Gardens), and Applied Genomics will provide £1K/year towards running costs, in addition to supplying sampling kits for use in the PhD. The supervisory team contains expertise from two FRESH institutions, and additional input from Dr Michael Sweet (University of Derby) who has pioneered the development of eDNA methods for crayfish in the UK. The student will be trained in molecular methods, field sampling, and will be trained in university, education charity and consultancy environments, giving exposure to a wide range of career options.