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对于检测稀有和入侵的分类群是非常有价值的(Bohmann等人。2014年；Deiner等人。2017年)。物种特定DNA的小片段被扩增出来，可以用于英国的小龙虾物种调查。白爪小龙虾现在被列入世界自然保护联盟红色名录中的濒危物种，在过去十年中全球减少了50%-80%，这主要是由于与入侵小龙虾物种的相互作用，但也是因为污染和栖息地退化(国际自然保护联盟红色名录)。答：苍白龙虾原产于英国，由于捕食/竞争更大、更具攻击性的美国小龙虾Pacifastacus leniusculus，以及经常通过入侵分类群传播的小龙虾鼠疫(由一种真菌Apanmyces astaci引起)，种群已被大量灭绝。另外七个入侵的小龙虾分类群对我们的本土物种构成了进一步的威胁。因此，保护剩余的苍白对虾种群是当务之急，现在通过圈养繁殖计划进行大规模的种群补充和重新引入，但对现有种群的快速评估仍然受制于使用更传统的方法调查小龙虾所需的时间。我们的目标是1)继续开发DNA标记，以便从英国所有入侵的小龙虾分类群中检测EDNA。2)利用高通量MetabarCoding技术评估现有MS标记在自然条件下对苍白对虾、对虾和小龙虾鼠疫的敏感性。我们将确定假阳性和假阴性(缺乏敏感性)发现的可能性，并将评估猎枪条形码是否可用于评估可能影响苍白线虫种群的其他水生分类群。3)利用EDNA数据更好地评估英国小龙虾分类群和小龙虾鼠疫的分布情况。这将涉及物种分布和占用模型来预测分布，以便确定有效的重新引入地点，并使最终用户(政府政策制定者、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。该项目与三个新的优先事项有关：(1)量化和管理新出现的淡水风险(在这种情况下是由入侵物种和气候变化造成的风险)；(2)开发和测试下一代监测生态系统的工具(EDNA)和(3)跟踪淡水生态系统中(濒危的苍白对虾)的灭绝。我们的工作将得到英国领先的灰斑潜蝇人工繁殖设施(布里斯托尔动物园花园)的支持，应用基因组学公司将提供1K GB/年的运营成本，此外还将提供用于博士学位的采样试剂盒。监督团队包括来自两个新机构的专业知识，以及来自迈克尔·斯威特博士(德比大学)的补充意见，他是英国小龙虾Edna方法开发的先驱。学生将接受分子方法、现场采样方面的培训，并将在大学、教育慈善机构和咨询环境中接受培训，从而接触到广泛的职业选择。

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.