Segregating Sites Enhance Accuracy of Species Abundance Estimates From eDNA.

Abstract

Species abundance is a fundamental metric in ecology and conservation. Assessing how populations change across space time enables the identification of population trends and informs management and conservation decisions. However, measuring species abundance can be a challenging task, with logistical constraints, sampling biases, and detection limits inhibiting meaningful abundance estimates. Environmental DNA (eDNA) approaches have improved our ability to monitor species presence and biodiversity and may also serve as a tool for measuring species abundance. However, abundance estimates from eDNA typically rely on the correlation between species abundance and the concentration of target species' DNA in a sample, which may be hindered by complex interactions including variable amounts of DNA being shed by different individuals and environmental factors affecting DNA persistence. In this issue, Ai et al. (2025) present a new framework for estimating species abundance from eDNA that uses the amount of genetic diversity detected in a sample, specifically the number of segregating sites, to predict species abundance. The approach was developed and validated using in silico, in vitro, and in situ experiments, demonstrating improved correlations with species abundance compared to estimates based on eDNA concentration. With further improvements in detecting rare genetic variants, this approach has the potential to enhance our ability to quantify species abundance using eDNA.