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

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.