DOI: 10.5061/dryad.w3r2280zz
title: Estimation of species abundance based on the number of segregating sites using environmental DNA (eDNA)

description: 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 &gt; 0.9; P &lt; 0.01). Results from the mesocosm experiment
 confirmed this correlation (R2 = 0.70, P &lt; 0.01). This correlation
 remained consistent despite biotic factors such as body size and feeding
 behavior of the fish (P &gt; 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.
description: We first assessed the relationship between the number of
 segregating sites and species abundance by entirely simulated sequences.
 The length of simulated sequences was set at 17,000 bp, close to the total
 size of 11 target segments. The number of simulated sequences/individuals
 was 1000, and sequences were generated at the mutation rate of 10-6
 /bp/gen. To account for mutation rate variation among different species,
 we also generated another two datasets at the mutation rate of 10-7
 /bp/gen and 10-8 /bp/gen. All data were generated using the software
 Fastsimcoal2 (Excoffier
 & Foll, 2011). A subset of sequences were randomly
 chosen from the simulated data, ranging from 20 to 980 sequences with
 intervals of 20. Selected sequences were aligned using MUSCLE v1.0 (Edgar,
 2004), then the number of segregating sites was counted from
 alignments. The simulation process was repeated three times at each
 specified number of sequences. The correlation between the number of
 segregating sites and the number of individuals/sequences was estimated by
 regression analysis using Microsoft Excel, in which the number of
 segregating sites was the dependent variable (y), the number of
 individuals/sequences was the independent variable (x) and the
 significance of the correlation was estimated by R2, and P
 values.
description: # Estimation of Species Abundance Based on the Number of Segregating Sites
 using Environmental DNA (eDNA)
 [https://doi.org/10.5061/dryad.w3r2280zz](https://doi.org/10.5061/dryad.w3r2280zz) This is a set of simulated sequences to explore the relationship between number of segregation site and species abundance. ## Description of the data and file structure We generated the sequence at three mutation rate: 10<sup>-6</sup>/bp/gen, 10<sup>-7</sup>/bp/gen and 10<sup>-8</sup>/bp/gen, correponding to `Simulated_seq__mutation_rate-10-6.fa`, `Simulated_seq__mutation_rate-10-7.fa`, `Simulated_seq__mutation_rate-10-8.fa`. We generated 1,000 sequences with the sequence length of 17,000 bp for each mutation rate. No insertion or deletion was simulated in the simulated sequences. Only loci with mutations are included. ## Code/Software All data were generated using the software Fastsimcoal2 (Excoffier & Foll, 2011).