Bulletin of the Chartered Institute of Ecology and Environmental Management Issue 99 | March 2018 Genetic Techniques and Technologies In this issue Developing DNA-based Finding Newts – Using Practical Application of Techniques in Natural Environmental DNA to Genetic Technology in England for Surveying and Detect Great Crested Newts Mammal Research Monitoring Biodiversity Welcome Information Genetic Techniques and Technologies In Practice No. 99 March 2018 Back in 2012, when I was a PhD student at the University of East Anglia, ISSN 1754-4882 groundbreaking molecular methods for ecology were regularly being published in Editor scientific journals. Researchers claimed these methods would solve age-old problems Dr Gillian Kerby ([email protected]) faced by environmental managers in species detection and identification - yet Internal contributions the studies were never disseminated in an accessible way, nor the methods made coordinator available for routine use. I remember giving a talk at the BTO and explaining that Mr Jason Reeves ([email protected]) you could use high-throughput DNA sequencing to identify all the insects in a trap sample in a single reaction. Someone said they had thought such a thing might be Editorial Board Mr Jonathan Barnes, Dr Kate Bayley, possible in twenty years’ time but had no idea it could already be done. Dr Andrew Cherrill, Mr Dominic Coath, Likewise, the use of environmental DNA (eDNA) for species monitoring was first Mr Neil Harwood, Dr Caroline McParland, demonstrated in the scientific literature as early as 2008, when a study showed Mrs Kate Morris, Mr Paul Rooney, that American bullfrogs could be detected by analysing samples of pond water. Mr Paul Scott, Miss Katrena Stanhope, When a researcher at Central Michigan University read this and proposed using the Mr Darren Towers same approach for monitoring the invasion of Asian carp, he was nearly laughed Opinions expressed by contributors out of academia. Thankfully for him, their subsequent study showed that eDNA to In Practice are those of the authors was the most sensitive tool in the box for detecting the presence of the fish at low and not necessarily supported by the Institute. Readers should seek appropriate population levels and it has now become deeply embedded in the US Fish and professional guidance relevant to their Wildlife Service’s ongoing monitoring programme as they try to limit the ecological individual circumstances before following damage caused by these disruptive species. any advice provided herein. In the UK, eDNA first gained prominence in 2014 with the publication of the DEFRA- Information on advertising, including funded trial for great crested newt (GCN) monitoring. Four years on and thousands rates and deadlines, can be found at of eDNA samples are now analysed every spring. A generation of ecologists are www.cieem.net/ip-advertising. The becoming familiar with DNA as a powerful tool for monitoring species, and the UK is Institute does not accept responsibility for leading the way in adoption and standardisation of cutting-edge molecular methods. advertising content or policy of advertisers, nor does the placement of advertisements The use of DNA monitoring comes with a set of limitations, which vary among within In Practice imply support for environments and sample types. Ecologists should seek to develop an understanding companies, individuals or their products or of the methods (hopefully the articles in this issue should help!), including their services advertised herein. limitations and the factors that influence their performance. This will allow informed CIEEM Office decision-making about whether DNA is the right tool for addressing any specific 43 Southgate Street, Winchester, question, together with robust interpretation of results. At the same time, it is Hampshire, SO23 9EH, UK important to remember that all survey methods are subject to inherent limitations and biases - this is not something that is unique to DNA! T: 01962 868626 As with any new technology, some teething problems are inevitable as we all find E: [email protected] our feet and explore how to integrate new tools with more familiar ones. But W: www.cieem.net DNA monitoring has the potential to dramatically increase the scale at which we In Practice is printed on paper using can monitor species in the environment, providing data on groups that have been 100% post-consumer, de-inked waste. extremely difficult to survey in the past. This will help us to better understand the This is manufactured by an ISO14001 impacts of our actions on biodiversity, and ultimately to achieve better outcomes. and EMAS accredited company. The publication of this issue of In Practice is a real marker of how far we have come © Chartered Institute of Ecology and in just a few years, but I believe this is only the beginning of our journey with DNA. Environmental Management Kat Bruce Managing Director, NatureMetrics [email protected] Front cover image: Electrophoresis is used to identify, quantify, and purify DNA fragments. 2 Issue 99 | March 2018 Contents Developing DNA-based Techniques Great Crested Newt eDNA Laboratory in Natural England for Surveying and Quality Systems, Proficiency Testing Monitoring Biodiversity and Interpretation of Results PG 07 Andy Nisbet and Kat Bruce PG 24 Helen Rees and Kevin Gough Pollen Analysis Could Be Revolutionised Practical Application of Genetic with DNA Techniques Technology in Mammal Research PG 10 Cuong Q. Tang and Hannah Norman PG 32 Denise O’Meara DNA Metabarcoding of Invertebrates Use of Environmental DNA Analysis to to Evaluate Outcomes of Ecological Detect the Presence of Water Vole Restoration Carl M. Halford, Karl J. Jones, PG 13 Kat Bruce PG 35 David J. Hill and Wera M. Schmerer Bringing Beavers Back to Britain Finding Newts – Using – Genetic Considerations in the Environmental DNA to Detect Restoration of the Eurasian Beaver Great Crested Newts Róisín Campbell-Palmer PG 18 Jeremy Biggs PG 40 and Helen Senn 02 Editorial 40 – Bringing Beavers Back to Britain – Genetic Considerations 03 Contents in the Restoration of the Eurasian Beaver 04 Chartered Institute News and Activities Róisín Campbell-Palmer and Helen Senn 05 News in Brief 44 – Measuring Connectivity and Gene Flow: An Example in the Hazel Dormouse Feature Articles Fraser Combe 06 – Genetic Techniques and Technologies – Glossary of Terms 07 – Developing DNA-based Techniques in Natural England Professional Updates for Surveying and Monitoring Biodiversity 47 – Natural England Appoints New Panel on Bat Conservation Andy Nisbet and Kat Bruce 47 – DNA Working Group for the UK 10 – Pollen Analysis Could Be Revolutionised 48 – CIEEM’s Policy Activities with DNA Techniques Cuong Q. Tang and Hannah Norman Jason Reeves 13 – DNA Metabarcoding of Invertebrates to Evaluate 50 – Employment and Salary Survey – a Snapshot Outcomes of Ecological Restoration Sally Hayns Kat Bruce 52 – New Special Interest Group: Ecological Restoration 18 – Finding Newts – Using Environmental DNA to Detect and Habitat Creation Great Crested Newts Nick Coppin, John Box, Penny Anderson and David Parker Jeremy Biggs 24 – Great Crested Newt eDNA Laboratory Quality Systems, 56 – Student Hub Proficiency Testing and Interpretation of Results 58 – Why should you be a Chartered Ecologist? Helen Rees and Kevin Gough 59 – Meet the Member Networks Team 28 – eDNA Metabarcoding for Non-Invasive Fish Surveys 60 – British Ecological Society Kat Bruce, Cuong Q. Tang and Mark Parry Richard English 32 – Practical Application of Genetic Technology in Mammal Research 61 CIEEM’s Member Networks Denise O’Meara 62 New Members 35 – Use of Environmental DNA Analysis to Detect the 63 Recent Publications and Journals Presence of Water Vole Carl M. Halford, Karl J. Jones, David J. Hill 69 Diary and Wera M. Schmerer 70 External Advertisements Issue 99 | March 2018 3 Chartered Institute News and Activities CIEEM Conferences 2018 Date Title Location Irish Section Conference 2018 26 April 2018 Dublin Making Mitigation Work Spring Conference 2018 22 March 2018 The Nature of Buildings: Designing Effective Birmingham Mitigation and Enhancement Summer Conference 2018 Natural History 4 July 2018 Fit for the future: Developing an Ecologically Museum, London Resilient Protected Sites Network 21-22 Autumn Conference 2018 Glasgow November 2018 Habitat Re-creation and Ecological Restoration Visit the CIEEM website to book on the Spring Conference and to find out more information. Relaunching the Academia 25-Year Environment Plan Special Interest Group CIEEM responded to Natural England consultation on CIEEM has responded to the government’s This year sees the relaunch of CIEEM’s licence charges 25-Year Environment Plan, which is Academia Special Interest Group (SIG). for England only. CIEEM applauds the CIEEM has responded to Natural The Academia SIG aims to provide support Secretary of State, Michael Gove, for England’s consultation on charging the ambition of the Plan and its long- to members working in the academic field for licences. and their students through networking, term vision. There are many aspects of CIEEM understands the reasons for providing a focus for sharing good practice the Plan that CIEEM believes, if properly introducing charges for licences and funded and implemented, could make and acting as a valuable consultative and supports Natural England’s ambition to communication function for the Institute in a real difference to halting the current improve the licensing system. However, rate of environmental degradation, understanding and responding to the needs we have pointed out that charging is not helping to build a healthier, more resilient of academic members. the only way to deliver improvements. environment for future generations. CIEEM is also committed to supporting In general terms, CIEEM is not against CIEEM President, Dr Stephanie Wray, said: students looking to enter the sector and the principle of charging for site-specific “The Plan rightly sets out the importance of the SIG will provide a link between the mitigation licences. We do however have the natural environment to people and the Institute and the next generation of concerns about charging for individual CIEEM members.