Environmental DNA reflects common haplotypic variation

Abstract

Analysis of environmental DNA (eDNA) has gained widespread usage for taxonomically based biodiversity assessment. While interest in applying non-invasive eDNA monitoring for population genetic assessments has grown, its usage in this sphere remains limited. One barrier to uptake is that the effectiveness of eDNA detection below the species level remains to be determined for multiple species and environments. Here, we test the utility of this emergent technology in a population genetic framework using eDNA samples derived from water along New Zealands South Island (Otago Coast: n=9; Kaikōura: n=7) and DNA obtained from tissue samples (n=76) of individual blackfoot pāua (Haliotis iris) sampled from New Zealands Otago coast. We recovered four mitochondrial haplotypes from eDNA versus six from the tissue samples collected. Three common haplotypes were recovered with both eDNA and tissue samples, while only one out of three rare haplotypes, represented in tissue samples by one individual each, was recovered with our eDNA methods. We demonstrate that eDNA monitoring is an effective tool for recovering common genetic diversity from pāua, although rare (< 5%) haplotypes are seldom recovered. Our results show the potential of eDNA to identify population-level haplotypes for gastropods in the marine environment identification below the species level and for studying the population genetic diversity of gastropods. This work supports eDNA methods as effective, non-invasive tools for genetic monitoring. Non-invasive eDNA sampling could minimize target organism stress and human interaction enabling population genetic research for hard-to-sample, delicate, or sensitive species.

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.…”

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

“…While some of these limitations are inherent, others may be overcome through technological or methodological improvements. For example, research by Adams et al (2023) and Wakimura 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.…”

“…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.…”

Estimating number of European eel (Anguilla anguilla) individuals using environmental DNA and haplotype count in small rivers

“…Uchii et al ( 2016 ) estimated the degree of invasion of non‐native genotypes of common carp by eDNA, and Sigsgaard et al ( 2016 ) used eDNA from seawater to study mitochondrial haplotypes of whale sharks ( Rhincodon typus ) and assessed the population structure. In addition, Parsons et al ( 2018 ) developed an approach for generating population‐specific mitochondrial sequence data from eDNA using seawater samples, and Adams et al ( 2022 ) recovered haplotypes from New Zealand blackfoot pāua ( Haliotis iris ) from marine eDNA samples. Concerning the challenges associated with eDNA concentration surveys, more accurate information about population size can be estimated by examining the DNA sequence differences between individuals.…”