Crayfish conservation: using eDNA to detect endangered and invasive species

使用环境DNA（eDNA）检测物种在保护生物学中被证明是非常宝贵的，用于检测稀有和入侵分类群（Bohmann et al. 2014; Deiner et al. 2017）。物种特异性DNA的小片段被扩增，可用于英国小龙虾物种的调查。白爪小龙虾Austropotamobius pallipes在IUCN红色名录中被列为“濒危”，在过去十年中全球下降了50-80%，主要是因为与入侵的小龙虾物种的相互作用，但也因为污染和栖息地退化（IUCN红色名录）。A. pallipes是土生土长的英国，和人口已被大量的捕食/竞争与更大和更具侵略性的美国信号小龙虾lefastacus leniusculus，并通过小龙虾鼠疫（由真菌Apanomyces astaci引起）经常传播的入侵类群。另外七种入侵的小龙虾类群对我们的本土物种构成了进一步的威胁。保护A.因此，pallipes是高度优先事项，现在通过圈养繁殖方案进行大规模补充和重新引入种群，但由于使用更“传统”的方法调查小龙虾所需的时间，目前种群的快速评估仍然受到阻碍。我们的目标是1）继续发展DNA标记，以检测来自英国所有入侵小龙虾类群的eDNA。2)评价MS开发的现有标记物对A. pallipes，P. leniusculus和小龙虾鼠疫在自然条件下使用高通量metabarcoding。我们将确定假阳性和假阴性（缺乏敏感性）结果的可能性，并将评估鸟枪条形码是否可用于评估其他可能影响A. pallipes种群。3)利用eDNA数据更好地评估英国小龙虾分类群和小龙虾瘟疫的分布。这将涉及物种分布和占用模型，以预测分布情况，从而确定重新引入的有效地点，并使最终用户（政府决策者、生态顾问和保护慈善机构）能够预测在气候变化情景和各种土地使用情景（住房开发、道路工程等）下可能发生的分布变化。该项目与FRESH的三个优先事项有关：（1）量化和管理淡水新出现的风险（在这种情况下，由入侵物种和气候变化引起的风险）;（2）开发和测试下一代生态系统监测工具（eDNA）和（3）跟踪灭绝（濒危物种）。pallipes）在淡水生态系统中。我们的工作将得到英国领先的圈养繁殖设施的支持。pallipes（布里斯托动物园），和应用基因组学将提供£ 1 K/年的运行成本，除了提供采样套件用于博士。监督团队包含来自两个FRESH机构的专业知识，以及来自英国小龙虾eDNA方法开发先驱Michael Sweet博士（德比大学）的额外投入。学生将接受分子方法，实地采样的培训，并将在大学，教育慈善机构和咨询环境中接受培训，从而获得广泛的职业选择。

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.