A Model and Simulation of the Influence of Temperature and Amplicon Length on Environmental DNA Degradation Rates: A Meta-Analysis Approach

Tatsuya Saito,Hideyuki Doi

doi:10.3389/fevo.2021.623831

Abstract

Environmental DNA (eDNA) analysis can detect aquatic organisms, including rare and endangered species, in a variety of habitats. Degradation can influence eDNA persistence, impacting eDNA-based species distribution and occurrence results. Previous studies have investigated degradation rates and associated contributing factors. It is important to integrate data from across these studies to better understand and synthesize eDNA degradation in various environments. We complied the eDNA degradation rates and related factors, especially water temperature and amplicon lengths of the measured DNA from 28 studies, and subjected the data to a meta-analysis. In agreement with previous studies, our results suggest that water temperature and amplicon length are significantly related to the eDNA degradation rate. From the 95% quantile model simulation, we predicted the maximum eDNA degradation rate in various combinations of water temperature and amplicon length. Predicting eDNA degradation could be important for evaluating species distribution and inducing innovation (e.g., sampling, extraction, and analysis) of eDNA methods, especially for rare and endangered species with small population size.

Highlights

Environmental DNA methods are innovative methods developed for monitoring macroorganisms, especially aquatic species (Ficetola et al, 2008; Minamoto et al, 2012; Taberlet et al, 2012; Takahara et al, 2012; Ushio et al, 2018; Kakuda et al, 2019; Tsuji et al, 2019)
Previous studies have suggested that Environmental DNA (eDNA) is mainly derived from fractions of cells or cellular organs, but it can be derived from fragmented DNA in the water (Turner et al, 2014; Minamoto et al, 2016)
We evaluated the quantile models (QM) models using the Akaike information criteria (AIC), in which the best QM is identified by having the lowest AIC

Summary

Introduction

Environmental DNA (eDNA) methods are innovative methods developed for monitoring macroorganisms, especially aquatic species (Ficetola et al, 2008; Minamoto et al, 2012; Taberlet et al, 2012; Takahara et al, 2012; Ushio et al, 2018; Kakuda et al, 2019; Tsuji et al, 2019). EDNA methods have been used to detect rare and endangered species in various taxa, such as fish, salamander, and aquatic insects (Fukumoto et al, 2015; Sigsgaard et al, 2015; Pfleger et al, 2016; Doi et al, 2017; Sakata et al, 2017). Previous studies have suggested that eDNA is mainly derived from fractions of cells or cellular organs (i.e., mitochondria and nuclei), but it can be derived from fragmented DNA (degraded DNA) in the water (Turner et al, 2014; Minamoto et al, 2016)

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Conclusion