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Dryad

Estimation of species abundance based on the number of segregating sites using environmental DNA (eDNA)

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Apr 24, 2024 version files 3.38 MB

Abstract

The advancement of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. While most studies focus on detecting species presence or absence, recent research has explored using eDNA data to quantify species abundance. This estimation usually is based on the concentration of targeted eDNA. However, eDNA concentration can be influenced by various factors, both biotic and abiotic, which can obscure the relationship between concentration and species abundance. In this study, we suggest using the number of segregating sites as a proxy for estimating species abundance. We investigated this relationship in silico, in vitro, and in situ (mesocosm experiments) using two brackish goby species, Acanthogobius hasta and Tridentiger bifasciatus. Analysis of simulated and in vitro data, where DNA was mixed from a known number of individuals, revealed a strong correlation between the number of segregating sites and species abundance (R2 > 0.9; P < 0.01). Results from the mesocosm experiment confirmed this correlation (R2 = 0.70, P < 0.01). This correlation remained consistent despite biotic factors such as body size and feeding behavior of the fish (P > 0.05). Cross-validation tests demonstrated that the number of segregating sites predicts species abundance more accurately and reliably than eDNA concentration. In conclusion, the number of segregating sites is a precise and robust indicator of species abundance compared to eDNA concentration, offering a significant enhancement to the quantitative capabilities of eDNA technology.