“eDNA: Challenges and Opportunities”; RSS meeting on the 7th of May 2020

Environmental DNA (eDNA) is an increasingly popular survey tool for monitoring species distribution. eDNA surveys have been used with a wide variety of species in different landscapes and there is growing evidence that they suffer from lower observation error than existing methods relying on direct observation of the target species.

From detecting single species using quantitative polymerase chain reaction (qPCR), to studying whole communities using metabarcoding, eDNA is showing great promise in helping us understand species distributions and community compositions.

However, we are yet to fully understand the properties of eDNA, and hence are only beginning to appreciate the opportunities that eDNA surveys bring or the challenges that we need to overcome in the field, in the lab or in implementing eDNA surveys into policy.

This meeting brings together researchers who are leading in the development of new statistical methods for analysing eDNA data, in evaluating the use of eDNA surveys with different species and landscapes, or in embedding eDNA techniques into national or international policy.

Speakers and talks

10.15-11 Kerry Walsh, Environment Agency: “Challenges and opportunities: A regulator’s perspective.”
11-11.30 break and refreshments
11.30-12.15 Naomi Ewald, FreshWater Habitats Trust: “Analysis of eDNA data to inform conservation priorities: case studies of long term species monitoring and short term before-after surveys.”
12.15-13 Francesco Ficetola, University of Milan: “Environmental DNA to track long-term changes of mountain ecosystem.”
13-14 lunch
14-14.45 Jim Griffin, University College London: “Modelling environmental DNA data; Bayesian variable selection accounting for false positive and false negative errors.”
14.45-15.30
Doug Yu, University of East Anglia: “Managing wildlife with eDNA data: salmon, leeches, insects, and forests.”
15.30-16.00 Discussion

The meeting, organised by the Environmental Statistics Section and the Emerging Applications Section of the Royal Statistical Society (RSS) will take place on the 7th of May 2020 at the RSS headquarters (12 Errol St, London EC1Y 8LX).

Follow this link to register for the event.

If you have any questions email e.matechou@kent.ac.uk.

Uncategorized

Paper co-authored by Eleni is top cited in Ecological Monographs

The paper Model averaging in ecology: a review of Bayesian, information‐theoretic, and tactical approaches for predictive inference, first published on the the 2nd of May 2018, was among the top cited articles in recent publication history for Ecological Monographs.

Conferences

Eleni gave a talk at the UK DNA working group

Eleni presented recent work with collaborators Jim Griffin, Andrew Buxton, Dimitrios Bormpoudakis and Richard Griffiths on modelling eDNA data at the 2-day conference, which took place at the Natural History Museum in London.

Her talk was on the new model, presented at the recently published JRSS C paper and the associated R-Shiny app.

grants

NERC-funded project on “Integrating new statistical frameworks into eDNA survey and analysis at the landscape scale”

The NERC-funded project, led by Dr Eleni Matechou, with Dr Alex Bush, University of Lancaster, Professor Jim Griffin, Statistical Science, UCL, Professor Richard Griffiths, Durrell Institute of Conservation and Ecology, University of Kent, and Professor Doug Yu, UEA as co-Investigators, is part of NERC’s Strategic Priorities Fund on Landscape Decisions: Towards a new framework for using land assets programme.

The RA on the project will be in place until 31st January 2022 and will work on meeting the four model development and two implementation and knowledge exchange objectives of the project.

Model Development (MD) objectives:
MD1 Account for sampling and analysis errors and taxonomic uncertainty in DNA-based data
Single-species (barcoding) and multi-species (metabarcoding) DNA data sets have more complicated properties than data
collected using traditional techniques using visual, aural or physical observations. For example, eDNA surveys are prone to
false-positive and false-negative errors at both the sampling and analysis stages as well as to taxonomic mismatches. We
will develop new statistical models that account for the probabilistic nature of eDNA data, reliably quantifying all levels of
uncertainty in eDNA surveys.

MD2 Identify important landscape predictors for site-specific species composition and metacommunity structure
The probability of species presences, species interactions and metacommunity structures is affected by landscape
characteristics. Accounting for these effects is necessary to obtain an understanding of the system and how to maintain it
or improve it. Failing to account for important effects can lead to inaccurate inference and biased results. However, the
strength and direction of these effects are typically unknown and we will develop a novel Bayesian modelling framework
and sophisticated algorithms for inferring landscape effects efficiently at the species and metacommunity levels using
eDNA data.

MD3 Perform simulations to identify the optimal study design for DNA-based surveys under different scenarios
The power to correctly infer the metacommunity structure and the landscape effects that shape it using eDNA data
depends on the number of sites sampled, the number of samples collected from each site, the number of PCR replicates
performed for each sample, as well as on landscape characteristics. We will perform extensive simulations to identify the
optimal study design under different scenarios and levels of error to provide practitioners with informed guidelines on how
to design eDNA surveys.

MD4 Identify the effects of errors in survey data or suboptimal study design on the selection of conservation priorities (e.g.
high-value habitat or restoration priorities)
Several conservation planning software exist that aim to infer the most efficient allocation of resources. Our Bayesian
model defined by MD1-2 as well as the power analysis resulting from MD3 provide a valuable predictive tool for species
presences and metacommunity structures, with corresponding measures of uncertainty, across the landscape. Using the
predictions generated by the fitted model in our case study system of UK ponds, we will obtain and compare different
solutions provided by planning software that are frequently employed in decision-making processes and assess how and if
decision-making is informed when uncertainty in inference is explicitly accounted for.

Implementation and Knowledge Exchange (IKE) objectives:

IKE1 Develop R-Shiny apps to implement MD1-4, making them accessible to users
The new statistical framework for eDNA data (MD1-4) will be implemented into R-Shiny apps and be accompanied by
examples of data analyses and corresponding interpretation to enable practitioners with limited understanding of statistics
and no prior knowledge of programming to employ our methods when analysing eDNA data.

IKE2 Disseminate project outputs and software to users via training workshops and project partners
We will organise two training workshops to take place in the last quarter of the project and after MD1-4 and IKE1 are
complete to disseminate the new methods to research users. These will complement ongoing – and fully subscribed –
training workshops that the research team have been running for practitioners in the general area of eDNA and statistical
modelling.

A more detailed description of the project can be found here

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New paper: Assessing heterogeneity in transition propensity in multistate capture–recapture data

Rachel has published a new paper in the Journal of the Royal Statistical Society with former SE@K PhD student Anita Jeyam and co-supervisor Roger Pradel from CEFE, CNRS Montpellier.

The paper is available open access so you are able to download the pdf of the full paper. The work proposes a new test which allows you to test for heterogeneity in transition probabilities from capture-recapture data before you fit any models to the data.

Assessing heterogeneity in transition propensity in multistate capture–recapture data

Multistate capture–recapture models are a useful tool to help to understand the dynamics of movement within discrete capture–recapture data. The standard multistate capture–recapture model, however, relies on assumptions of homogeneity within the population with respect to survival, capture and transition probabilities. There are many ways in which this model can be generalized so some guidance on what is really needed is highly desirable. Within the paper we derive a new test that can detect heterogeneity in transition propensity and show its good power by using simulation and application to a Canada goose data set. We also demonstrate that existing tests which have traditionally been used to diagnose memory are in fact sensitive to other forms of transition heterogeneity and we propose modified tests which can distinguish between memory and other forms of transition heterogeneity.

Statistical Ecology at Kent