Invited paper in JSTP

More than presence-absence; modelling (e)DNA concentration across time and space from qPCR survey data

Authors:
Milly Jones, Eleni Matechou, Diana Cole, Alex Diana, Jim Griffin, Sara Peixoto, Lori Lawson Handley & Andrew Buxton

Notes:
This article was invited as part of the Ecological Statistics Topical Collection in Journal of Statistical Theory and Practice — a curated series on advancing statistical methodology in ecological science.

Abstract:
Environmental DNA (eDNA) surveys offer a revolutionary approach to species monitoring by detecting DNA traces left by organisms in environmental samples. Quantitative PCR (qPCR) is commonly used not only to determine presence or absence but also to infer DNA concentration—information that can be directly connected to species’ abundance patterns.

Here, we introduce a sophisticated modeling framework that estimates DNA concentration across space and time as a function of environmental and technical covariates. The model explicitly addresses key issues such as contamination, inhibition, heteroscedastic variance, and stochastic noise—challenges especially pronounced at low DNA concentrations. Our framework was validated via simulations and further applied to three survey case studies in the UK. Results show increased accuracy and robustness in estimating DNA concentrations, contributing powerful new tools for ecological monitoring and conservation.

Supplementary materials are available online with standardized protocols for reproducing the analyses.

The work was very well received at the annual UKDNA working group meeting, hosted by the Royal Society, 13th-14th May 2025 (photo of Milly presenting the work below)