This project will address two major challenges to realizing the potential of environmental DNA (eDNA) data to contribute to species conservation and management through the development and integration of new approaches from across spatial, population, and molecular ecology. First, the project will address shortcomings in species detection when population densities are very low by investigating the spatial dispersion process of eDNA and using the results to improve sampling methods at wetlands of increasing complexity on Department of Defense (DoD) installations. Second, novel laboratory and population estimation methods will be used to integrate this spatial dispersion information with multilocus genomic data to estimate population size as well as other population parameters (genetic diversity, age structure, effective population size, gene flow), and demonstrate the utility of these methods for threatened and endangered species on DoD installations.

This project will increase the power of existing environmental DNA detection techniques for rare species in water samples to inform management using a combination of field experiments, simulations, laboratory optimizations, and field applications. First, the spatial dispersion of the eDNA signature of rare species in wetlands will be estimated in relation to degradative conditions in a field experiment, then that model will be used to inform improved sampling design for rare species and utilized as a baseline input for simulations to estimate population size using multi-locus genotypes. The cost efficiency of spatially-informed point sampling and continuous sampling with a purpose-built backpack sampler will be analyzed for improved detection of rare species in comparison with current field methods. The results from these two eDNA sampling designs will be applied to expand on and develop novel methods for estimating population size eDNA via two approaches: 1) building models to predict population size from eDNA quantity considering site covariates and 2) developing methods for harvesting and analyzing signals of individuals from water sampling through improved laboratory and spatial analyses. Finally, the use of additional genomic information in water samples will be explored to estimate age structure of populations.

Nine threatened or endangered amphibian species and 23 threatened or endangered fish species are known to occur on DoD lands, creating potential constraints on readiness training and resource management. These and other aquatic species pose unique challenges for inventory and monitoring due to the difficulty of thoroughly surveying aquatic environments. Environmental DNA analysis has great potential to contribute to the conservation and management of these species due to high detection rates and low impact of sampling. This project will address two current limitations on the application of eDNA for resource management by developing cost-effective sampling techniques for detecting species reliably at very low densities and developing and expanding methods for population estimation from eDNA data. Additionally, methods developed during this project will enable estimation of additional population parameters from water samples, including population genetic diversity, age structure, effective population size, and functional connectivity among populations.