Validating eDNA measurements of the richness and abundance of anurans at a large scale

Abstract

In some situations, environmental DNA (eDNA) metabarcoding is a more accurate tool for measuring species richness of a taxon than conventional methods. Whether this tool can reliably estimate the abundance of a taxon remains unresolved. We examined the reliability of metabarcoding for measuring anuran diversity compared to a commonly used traditional line transect method (TLTM) through the replicate sampling of three visits across 71 waterbodies (ponds or reservoirs) in Liuheng, China. We also investigated the relative contributions of species‐specific characteristics and the physiochemical properties of a waterbody on the relative read count across species and waterbodies. We found that eDNA metabarcoding had a higher detection probability for each of seven anuran species found in the sampling region than TLTM. Furthermore, the relative read count estimated by metabarcoding was positively correlated with the density or relative density of individuals identified with the TLTM across waterbodies for every species. Species‐specific characteristics of anurans, such as density, relative density, body mass, biomass and relative biomass, accounted for substantial variations in the read count across species and waterbodies, while physiochemical factors, including pH, temperature, water volume, vegetation and elevation, had little effect on the read count. Our results based on robust sampling suggest that metabarcoding enables more reliable and efficient measurements of anuran occurrence at a large scale during a short‐term survey (within 15 days) than that obtained by the TLTM, and offers an alternative tool for quantifications of anuran abundance. Density or biomass is better and more reliable indicator of anuran abundance associated with read count than relative density or relative biomass.

Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem

“…As a standard processing pipeline we selected OBITools 10 , which is commonly used in eDNA metabarcoding studies 15 , 47 , 78 . We processed the reads from the sequencing following Valentini et al 77 .…”

Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia

“…In the case of amphibians, previous studies have used eDNA metabarcoding in various aquatic ecosystems, such as wetlands (Kačergytė et al 2021;Saenz-Agudelo et al 2021), tropical forests (Lopes et al 2017;Sasso et al 2017;Li et al 2021a) and ponds (Bálint et al 2018;Charvoz et al 2021). The technique has been used for multiple purposes, including monitoring biodiversity (Li et al 2021a;Saenz-Agudelo et al 2021), estimating abundance (Li et al 2021b), investigating co-occurrence with fish (Kačergytė et al 2021) and examining the properties of eDNA (Evans et al 2016;Brys et al 2021). However, there has been no comparison or evaluation amongst universal primer sets, as has been performed in eDNA metabarcoding studies on fish.…”

Next-generation sequencing and targeted quantitative real-time polymerase chain reaction for detection of Akebiae Caulis in the traditional Chinese medical formula Longdan Xiegan Wan

“…However, the DNA of species in TCM compete with DNA barcode primers in the PCR process, where the more common templates are more easily amplified. This results in false negatives for low-abundance species (10,11). However, qPCR primers only specifically bind to the target gene, providing the possibility of detecting low-abundance species.…”