DNA metabarcoding of mock communities highlights potential biases when assessing Neotropical fish diversity

Abstract

Despite the increasing popularity of DNA metabarcoding in the assessment of aquatic ecosystems using fish eDNA or ichthyoplankton, challenges have hampered its broader application in the Neotropical freshwaters. Using five mock communities composed of fish species from two Neotropical River basins, we evaluated the influence of DNA concentration and choice of mitochondrial 12S molecular markers (MiFish, NeoFish, and Teleo) on species detection and relative read abundance (RRA) using DNA metabarcoding. Of the three 12S markers analyzed, only MiFish detected all species from all mock communities. The performance of a taxonomy‐free approach using ASV/MOTUs was not as precise as assigning DNA reads to species using a curated 12S library that includes approximately 100 fish species since more than one ASV/MOTU was observed for the same specimen. Thus, here we showcase the importance of a custom reference database to allow precise assignment of Neotropical fish species in metabarcoding studies and that the RRA is dependent on community composition, marker, and DNA concentration. We highlight the importance of controlled experiments using known species communities before large investments are made in assessing biodiversity using non‐invasive methods that apply DNA metabarcoding.

DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent

“…However, despite the significant positive correlation between MiFish and COI, many identified species were detected by only one of these markers (Figure 2). The inefficiency of the Neofish marker to amplify Siluriformes has already been reported using DNA metabarcoding of Neotropical fish mock communities (Hilário et al, 2023).…”

Environmental DNA captures diurnal fluctuations of surface eukaryotes on a tropical coral reef

“…Demonstrated by the above examples, the inference of presence/absence of species using eDNA approaches has been well documented across multiple taxonomic groups. Moving beyond this, several laboratory studies have found positive correlations between species abundance/biomass and eDNA particle concentration or relative read abundance (Hilário et al, 2023;Jo & Yamanaka, 2022). However, in the natural environment, these relationships have been found to be weaker, most likely due to more dilute DNA concentrations and stochasticity in environmental parameters and organism behavior that are known to impact the release, transport, and degradation of eDNA (Rourke et al, 2021;Yates et al, 2019).…”