Environmental DNA: The next chapter

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 16, 2024

Abstract Molecular tools are an indispensable part of ecology and biodiversity sciences implemented across all biomes. About a decade ago, the use implementation environmental DNA (eDNA) to detect signals extracted from samples opened new avenues research. Initial eDNA research focused on understanding population dynamics target species. Its scope thereafter broadened, uncovering previously unrecorded via metabarcoding in both well‐studied understudied ecosystems taxonomic groups. The application rapidly became established research, field by its own. Here, we revisit key expectations made land‐mark special issue Ecology 2012 frame development six areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour environment (6) reference database development. We pinpoint success eDNA, yet also discuss shortfalls not met, highlighting areas priority identify unexpected developments. In parallel, our retrospective couples screening peer‐reviewed literature with survey users including academics, end‐users commercial providers, which address focus efforts advance eDNA. With rapid ever‐increasing pace technical advances, future looks bright, successful applications best practices must become more interdisciplinary reach full potential. Our retrospect gives towards concretely moving forward.

Language: Английский

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Estimation of Species Abundance Based on the Number of Segregating Sites Using Environmental DNA (eDNA)

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

ABSTRACT The advance of environmental DNA ( eDNA ) has enabled rapid and non‐invasive species detection in aquatic environments. While most studies focus on detection, recent works explored using concentration to quantify abundance. However, the differential individual contribution samples could easily obscure concentration‐species abundance relationship. We propose number segregating sites as a proxy for estimating Segregating reflect genetic diversity population, which is less sensitive than concentration. examined relationship between silico, vitro, situ experiments, two brackish goby species, Acanthogobius hasta Tridentiger bifasciatus . Analyses simulated vitro data with mixed from known individuals showed strong correlation R 2 > 0.9; p < 0.01). In we analysed collected mesocosm. results further validated that = 0.70, 0.01) was not affected by biotic factors, including body size feeding behaviour 0.05). cross‐validation test also predicted bias variability Overall, among compared This advancement can significantly enhance proficiency

Language: Английский

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Environmental DNA reveals the genetic diversity and population structure of an invasive species in the Laurentian Great Lakes

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(37)

Published: Sept. 5, 2023

Environmental DNA (eDNA) has been established as a noninvasive and efficient approach to sample genetic material from aquatic environments. Although most commonly used determine species presence measure biodiversity, eDNA approaches also hold great potential obtain population-level information water samples. In this study, we sequenced panel of multiallelic microsatellite markers filtered fish tissue samples uncover patterns intraspecific diversity in the freshwater Round Goby (Neogobius melanostomus) across their invaded range Laurentian Great Lakes region. found that concentration nuclear is lower than mitochondrial eDNA, nonetheless detected over two-thirds all alleles identified genotyped tissues our samples, with greatest recovery common population. Estimates allele frequencies variability within between populations were consistent individual tissue-based estimates differentiation. The strongest differentiation both exists an isolation by distance pattern. Our study demonstrates for eDNA-based characterize key population parameters required effectively monitor, manage, or sustain species.

Language: Английский

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A vision for global eDNA-based monitoring in a changing world

Cell, Journal Year: 2024, Volume and Issue: 187(17), P. 4444 - 4448

Published: May 15, 2024

Language: Английский

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Use of eDNA to Determine Source Locations of Deadly Jellyfish (Cubozoa) in an Open Coastal System

Coasts, Journal Year: 2024, Volume and Issue: 4(1), P. 198 - 212

Published: March 5, 2024

Challenges associated with cubozoan jellyfish detection and the limitations of current techniques limit ability scientists to fill critical knowledge gaps surrounding their ecology. Environmental DNA (eDNA), however, has proven useful as an ecological survey tool detect study these deadly jellyfish. This aimed leverage power eDNA explore distribution Australian box (Chironex fleckeri), encompassing both its medusae polyp life history stages, within open coastal bay (Horseshoe Bay) Magnetic Island, Queensland, Australia. Our investigation focused on a hypothesis concerning source locations Horseshoe Bay and, through comparison stage distributions, determine potential population stock boundaries. results aligned predicted nearshore medusae. Further, elusive benthic was also detected. These findings confirmed location Moreover, our evidence supported model that area likely represents species. adds growing suggesting some have stocks small spatial scales in relatively closed ecosystems such estuaries. In conclusion, this serves notable example eDNA’s resolve ecology enhance management reduce envenomations.

Language: Английский

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eDNA for monitoring and conserving terrestrial arthropods: Insights from a systematic map and barcode repositories assessments

Insect Conservation and Diversity, Journal Year: 2024, Volume and Issue: 17(4), P. 565 - 578

Published: March 8, 2024

Abstract In the past decade, environmental DNA (eDNA) assays have become an essential tool to investigate species presence with samples from environment instead of collected specimens. eDNA sampling techniques proved their worth in freshwater and marine studies; now, some trends emerge for use terrestrial habitats particularly study arthropods. After a systematic review literature, we illustrate analyse diversity such studies discuss benefits drawbacks. We identified most relevant research themes focused on (i) taxa sample types targeted (ii) details survey scheme. parallel, also assessed available number sequences cytochrome c oxidase subunit I (COI), 16S 18S barcode regions four major (spiders, centipedes, springtails insects) relation diversity. found strong taxonomic geographic biases regarding coverage per barcode. arthropods mainly focuses insect that affect humanity positive or negative way, availability is much higher temperate‐developed countries than tropical ones. Moreover, although high variety are being used, do not assess completeness target nor compare efficacy monitoring technique other well established known traditional techniques. Careful workflow designs comparisons needed before giving any management conservation advice as does come without error. Strengths weaknesses discussed.

Language: Английский

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Environmental DNA and biodiversity patterns: a call for a community phylogenetics approach

Perspectives in Ecology and Conservation, Journal Year: 2024, Volume and Issue: 22(1), P. 15 - 23

Published: Jan. 1, 2024

Environmental DNA (eDNA) metabarcoding is a relatively new technology allowing effective non-invasive analyses and monitoring of biodiversity patterns. Studies on eDNA focus using sequence data to delimit basic units (i.e., such as Molecular Operational Taxonomic Units – MOTUS or Amplicon Sequence Variation ASVs), after this definition standard analytical approaches from community ecology are applied. However, there more information inherent it now straightforward use general in which based directly phylogenies genetic distances between MOTUs ASVs, rather than discrete without any accounting for hierarchical structure, providing continuum understanding Here we briefly review the concepts methods incorporate phylogenetic patterns into analyses, illustrating some main issues with eukaryote diversity along Araguaia River Basin. Hopefully perspective stimulates researchers obtaining perform their under phylogenetics framework instead (or addition to) approach.

Language: Английский

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Segregating Sites Enhance Accuracy of Species Abundance Estimates From eDNA

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: March 24, 2025

Species abundance is a fundamental metric in ecology and conservation. Assessing how populations change across space time enables the identification of population trends informs management conservation decisions. However, measuring species can be challenging task, with logistical constraints, sampling biases, detection limits inhibiting meaningful estimates. Environmental DNA (eDNA) approaches have improved our ability to monitor presence biodiversity may also serve as tool for abundance. estimates from eDNA typically rely on correlation between concentration target species' sample, which hindered by complex interactions including variable amounts being shed different individuals environmental factors affecting persistence. In this issue, Ai et al. (2025) present new framework estimating that uses amount genetic diversity detected specifically number segregating sites, predict The approach was developed validated using silico, vitro, situ experiments, demonstrating correlations compared based concentration. With further improvements detecting rare variants, has potential enhance quantify eDNA.

Language: Английский

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Reconstruction of Marimo Population Dynamics Over 200 Years Using Molecular Markers and Fossil Plankton Remains

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Recent efforts have focused on reconstructing the historical abundance of unfossilized organisms using environmental DNA preserved in sediments (sedDNA). This information is crucial for understanding long‐term changes ecosystems. However, because sedDNA prone to degradation, its quantification may not always provide accurate estimates past abundances. To address this issue, we developed a novel method correct degradation by incorporating plankton remains and applied it estimate marimo—large spherical colonies green alga Aegagropila brownii (formerly A. linnaei )—in Lake Akan, Japan, which only known habitat large marimo. We first quantified marimo lake dating back over 200 years. then used our new their from sedDNA. Analyses revealed that were historically 10–100 times more abundant than they are today, but declined early 20th century when influxes muddy water level fluctuations occurred due deforestation operation hydroelectric power plant. These findings align with eyewitness accounts, indicating that, corrected fossilized remains, can be powerful tool organisms.

Language: Английский

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Environmental DNA exploring the distribution of Indo-Pacific humpback dolphins and fish diversity from the Pearl River Estuary, China

Marine Pollution Bulletin, Journal Year: 2025, Volume and Issue: 216, P. 118026 - 118026

Published: April 24, 2025

Language: Английский

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