Uncovering the hidden biodiversity benefits of beavers using environmental DNA

Uncovering the hidden biodiversity benefits of beavers using environmental DNA

Project partners: Dr. Lori Lawson Handley (contact and lead supervisor: l.lawson-handley@hull.ac.uk) and Dr. Bernd Hänfling (University of Hull), Dr. Lynsey Harper, (Liverpool John Moores University), Dr. Nigel Willby and Dr. Alan Law (University of Stirling), Dr. Allan McDevitt (University of Salford), Dr. Mark Smith and Dr. Megan Klaar (University of Leeds)

CASE partner: Forestry England (Cropton beaver Trial: https://www.forestryengland.uk/beaver-trial-cropton-forest)

Biodiversity is being lost at an unparalleled rate, particularly in freshwater ecosystems. Reintroduction of keystone species is considered part of the solution to the freshwater biodiversity crisis. Beavers, which were common in the UK until the 16th Century, are ecosystem engineers; altering the physical and chemical properties of their habitat, creating nutrient-rich ponds, and slowing the flow of water. Beaver reintroduction is gaining traction throughout the UK for improving biodiversity, carbon sequestration, and Natural Flood Management, with trials in >10 counties. A primary motivation for reintroducing beavers is to create heterogeneous habitats that support novel communities of animals and plants compared to the surrounding landscape, but so far we only understand impacts on a small number of species. This is largely because conventional approaches for studying biodiversity are time-consuming, challenging and can cause disturbance or harm to wildlife.

Environmental DNA (eDNA) metabarcoding offers a new, non-invasive alternative for describing entire ecological communities. eDNA is released into the environment in the form of shed cells, waste material or decaying matter, captured by sampling water, soil, air or other environmental samples, and sequenced using High Throughput Sequencing technology, generating millions of DNA sequences in a single experiment. Our group at the University of Hull has pioneered this method for describing vertebrate and invertebrate communities in lakes, rivers and ponds.

Beaver activity
Tree felled by beavers at Cropton Forest

This CASE studentship will use eDNA metabarcoding of entire habitats to investigate the impacts of beaver activity across freshwater and terrestrial communities, providing novel insights into the role of these ecosystem engineers in shaping biodiversity. The project will focus primarily on two reintroduction sites: Cropton Forest in North Yorkshire (established in 2019 and managed by our CASE partner, Forestry England) and the Bamff Estate in Scotland, providing two contrasting habitats and temporal scales of reintroduction.

More specifically, you will investigate 1) how beavers impact freshwater macroinvertebrate communities at different temporal and spatial scales, 2) the impact of beavers on conservation priority vertebrates, 3) the structure of aquatic-terrestrial linkages in beaver reintroduction sites, and 4) the role of beavers in shaping entire ecological networks. eDNA data will be analysed using Site Occupancy Modelling, in conjunction with habitat data from 3D High Resolution Topographic Surveys (HRTS).


Project Objectives: 

Obj1. Determine how beaver activity impacts freshwater macroinvertebrate biodiversity on different temporal scales. Freshwater macroinvertebrates are important indicators of water quality, but the role of beavers in shaping their communities is poorly understood. We predict macroinvertebrate communities to be highly dynamic, and to have higher richness and abundance in beaver-altered landscapes, compared to the surrounding landscape, benefitting species further up the food chain (Obj2). The student will generate macroinvertebrate community data using eDNA metabarcoding and relate this to changes in the environment due to beaver activity, quantified using HRTS.

Obj2. Investigate whether beavers benefit conservation priority vertebrates. Beaver ponds are expected to provide important habitats and food sources (Obj1) for conservation priority species such as otters, water voles, bats, eels, great crested newts etc. However there are also potential negative impacts; higher abundance of predatory fish may reduce amphibian abundance. The student will use eDNA metabarcoding and site occupancy modelling to test the hypothesis that beaver activity benefits conservation priority vertebrates compared to the surrounding landscape.

Obj3. Investigate aquatic-terrestrial linkages in beaver reintroduction sites: do beavers benefit terrestrial invertebrate consumers and species at higher trophic levels? Beavers are thought to play a significant role in the movement of energy and materials across the aquatic-terrestrial boundary, but we have very little understanding of the impact of beavers on terrestrial biodiversity. The student will use DNA metabarcoding of soil, combined with HRTS, to test the hypothesis that beaver activity increases richness, abundance and turnover of terrestrial invertebrates.

Obj4. Understand the role of beavers in shaping ecological networks. Ecological Networks Analysis (ENA) can be used to describe interactions between species and examine impacts on entire communities. Combining data from objectives 1-3, the student will use ENA to test the impact of beavers on structure, complexity and stability of species networks, which will provide a holistic insight into the role of beavers within the landscape.

Training and supervision:

You will be supervised by Dr. Lori Lawson Handley and Dr. Bernd Hänfling from the EvoHull Group at the University of Hull, which is one of the most experienced groups in the UK for eDNA analyses. The project is a CASE studentship with the Forestry England Cropton Forest Beaver Trial (https://www.forestryengland.uk/beaver-trial-cropton-forest). Our partners Dr Lynsey Harper and Dr. Allan McDevitt have also worked extensively on eDNA including other beaver eDNA projects.  Drs Nigel Willby and Alan Law are leading experts on the impacts of beavers, having studied the Bamff populations since 2002. Drs Megan Klaar and Mark Smith are specialists in HRTS and have already conducted surveys of the Cropton site. The project team have an excellent track record in training PhD students, publishing high impact research, and are highly active in national and international networks that will help you to develop external contacts and career prospects. The project will provide specialist training in environmental DNA sampling, capture and analysis, High Throughput Sequencing (metabarcoding), bioinformatics, and statistical modelling (including site occupancy modelling and Ecological Networks Analysis) in R.

Entry Requirements:

We are looking for a motivated student with a keen interest in molecular ecology and biodiversity. Experience with fieldwork, molecular tools (e.g. PCR), using R, and/or bioinformatics would be useful. You must hold an Honours (2.1. or higher) or Masters degree in a related subject, such as Biology, Ecology, Genetics or Zoology

Background reading:

Harper, L. R. et al. (2019) ‘Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian’, Environmental DNA, 60, p. 255. doi: 10.1002/edn3.57.

Harper, L. R. et al. (2019) ‘Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals’, Biological conservation, 238, p. 108225. doi: 10.1016/j.biocon.2019.108225.

Harper, L. R. et al. (2020) ‘Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity: A comparison of conventional and molecular tools’, Molecular Ecology. doi: 10.1111/mec.15670.

Hänfling, B. et al. (2016) ‘Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods’, Molecular ecology, 25(13), pp. 3101–3119. doi: 10.1111/mec.13660.

Law, A. et al. (2019) ‘Are beavers a solution to the freshwater biodiversity crisis?’, Diversity & distributions. Edited by X. Liu, 25(11), pp. 1763–1772. doi: 10.1111/ddi.12978.

Lawson Handley, L. et al. (2019) ‘Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake’, Environmental DNA, 1(1), pp. 26–39. doi: 10.1002/edn3.5.

Sales, N. G. et al. (2020) ‘Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems’, Journal of Applied Ecology, 57, pp. 707-716 doi: 10.1111/1365-2664.13592

Willby, N. J. et al. (2018) ‘Rewilding wetlands: beaver as agents of within-habitat heterogeneity and the responses of contrasting biota’, Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 373(1761). doi: 10.1098/rstb.2017.0444.