Environmental DNA reflects common haplotypic variation

Abstract

CIMA, CH, MK, GJJ, MB, and NJG helped to conceive and design the study. CIMA acquired the data with help from CH and analysed it with the guidance of HC. CIMA wrote the manuscript with input from HRT, MK, MB, NJG, and CH.

The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

“…The emergent field of eDNA‐based population genetics could have a great potential to study fish population connectivity across depths (Adams et al, 2019 ). For instance, eDNA has been recently used to investigate diversity within populations of Striped red mullet ( Mullus surmuletus ; e.g., Macé et al, 2022 ), or Blackfoot pāua ( Haliotis iris ; Adams et al, 2022 ), and to successfully estimate population genetic differentiation like for the whale shark (Sigsgaard et al, 2016 ). Only through standard, sustained and multi‐objectives observations at all depths we could get the insights needed to understand the fundamental ecological processes that govern the dynamics of marine ecosystems, and design depth‐specific strategies to effectively protect them in the future.…”

Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation

“…This suggests that our approach has high sensitivity and accuracy, but a slight risk of false negatives, in return for the least possibility of false positives. We consider that the use of such a stringent denoising approach is essential in evaluating the genetic structure of populations with low nucleotide diversity, where the specious error sequences may easily lead to overestimation of the genetic diversity (Adams et al, 2022; Elbrecht et al, 2018). We also confirmed that our approach is more sensitive than or as sensitive as the traditional sampling‐based approaches.…”

Beyond species detection—leveraging environmental DNA and environmental RNA to push beyond presence/absence applications

“…Comparisons between population genetic data obtained from eDNA and traditional tissue sampling can help identify genetic variation that may otherwise be missed in eDNA samples. This was explored by Adams et al (2023) in their study investigating haplotypic variation in Blackfoot Pãua (Haliotis iris), a species of abalone. The authors demonstrate the potential for eDNA sampling to uncover common haplotypic variation but concluded that rare (<5%) haplotypes were seldom recovered.…”

“…While some of these limitations are inherent, others may be overcome through technological or methodological improvements. For example, research byAdams et al (2023) andWakimura et al (2023) provides valuable insight into the issues of sensitivity and reliability of population genetic data obtained from eDNA samples and suggests methods for improvement.…”