Environmental DNA at the population level: advancing conservation through non-invasive genetic and genomic approaches

Environmental DNA (eDNA) has emerged as a transformative, non-invasive tool for ecological monitoring and conservation biology. Beyond species detection and community assessments, there is growing interest in applying eDNA to evaluate genetic variability and monitor ecosystem health, particularly for elusive or endangered species where traditional sampling is invasive or limited. In this systematic review, we synthesize recent advances in eDNA based population genetics based on a final dataset of 83 studies (72 research articles and 11 reviews), with special emphasis on the use of nuclear DNA (nuDNA) to capture intraspecific genetic diversity. We identify several technical challenges, including low DNA copy number, allelic dropout and the lack of individual genotypes. To address these constraints, we highlight allele frequency-based approaches as a promising strategy to estimate effective population size (Ne) directly from eDNA. These methods are particularly suitable for non-model species without reference genomes and for contexts where invasive sampling is not feasible. We further discuss the potential of eDNA Pool-seq technologies to improve cost efficiency and to infer the minimum number of contributing individuals. Together, these advances provide a pathway to extend the use of eDNA beyond biodiversity monitoring toward a comprehensive, non-invasive framework for population genetic inference in conservation.