Environmental DNA at the Population Level: Advancing Conservation Through Non‐Invasive Genetic and Genomic Approaches

ABSTRACT

Environmental DNA (eDNA) has emerged as a transformative, non‐invasive tool for ecological monitoring and conservation biology. Beyond its widespread use for species detection and community assessment, there is growing interest in applying eDNA‐based tools to evaluate genetic variability and monitor ecosystem health. This is particularly valuable for elusive or endangered species, for which traditional population genetic approaches are often limited by the necessity to avoid invasive sampling and by small sample sizes. In this systematic review, we synthesize recent advances in eDNA based population genetics based on a dataset of 83 studies (72 research articles and 11 reviews). We place particular emphasis on the potential of nuclear DNA (nuDNA) to capture intraspecific genetic variation. We identify several technical limitations such as low DNA copy number, allelic dropout and the inability to assign individual genotypes, that currently hinder the direct application of eDNA in conservation genomics. We propose the use of allele frequency‐based methods to estimate population genetic parameters, such as effective population size ( N _e ), from eDNA data. These approaches are especially valuable for non‐model species lacking reference genomes and are well suited to situations where direct sampling is not feasible. We also explore the application of eDNA Pool‐seq technologies to improve cost‐efficiency, suggesting a potential strategy to estimate the minimum number of contributing individuals. Integrating these approaches has the potential to expand the application of eDNA from biodiversity monitoring to a comprehensive framework for non‐invasive population genetic inference.