Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(9), P. 4803 - 4815

Published: March 18, 2021

Decades of environmental DNA (eDNA) method application, spanning a wide variety taxa and habitats, has advanced our understanding eDNA underlined its value as tool for conservation practitioners. The general consensus is that methods are more accurate cost-effective than traditional survey methods. However, they formally approved just few species globally (e.g., Bighead Carp, Silver Great Crested Newt). We conducted meta-analysis studies directly compare with surveys to evaluate the assertion consistently "better."Environmental publications multiple or single macro-organism detection were identified using Web Science, by searching "eDNA" "environmental DNA" across papers published between 1970 2020. used, focal taxa, habitats surveyed, quantitative categorical results collated analyzed determine whether under what circumstances outperforms surveys.Results show cheaper, sensitive, detect This is, however, taxa-dependent, amphibians having highest potential survey. Perhaps most strikingly, 535 reviewed 49 quantified probability both three times likely give qualitative statements performance.

Language: Английский

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Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(6), P. 1820 - 1835

Published: Jan. 25, 2022

Abstract DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated consistency this technique with traditional morpho‐taxonomic approaches. These individual to assess diversity community structure organisms both in marine freshwater systems globally over last decade. However, a systematic analysis comparability effectiveness DNA‐based across all these has hitherto been lacking. Here, we performed first meta‐analysis available comparing methods measure biological key groups, including plankton, microphytobentos, macroinvertebrates, fish. Across 215 data sets, found that provides richness estimates are consistent those obtained using methods, at local regional scale. also generates species inventories highly congruent Contrastingly, microphytobenthos macroinvertebrates by showed pronounced differences missing some taxa but same time detecting otherwise overseen diversity. The method generally sufficiently advanced study composition fish communities replace more invasive methods. For smaller organisms, like plankton microphytobenthos, may continue give complementary rather than identical compared Systematic comparable collection will increase understanding different aspects complementarity, adequate interpretation results.

Language: Английский

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Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities

Annual Review of Marine Science, Journal Year: 2021, Volume and Issue: 14(1), P. 161 - 185

Published: Aug. 5, 2021

Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection multiple species) a noninvasive and cost-effective approach monitoring marine fish communities discusses prospects this growing field. coamplifies short fragments across wide variety taxa and, coupled with high-throughput sequencing technologies, allows massively parallel to be performed simultaneously dozens hundreds samples. can predict species richness in given area, detect habitat segregation biogeographic patterns small large spatial scales, monitor spatiotemporal dynamics communities. In addition, it anthropogenic impact on through evaluation their functional diversity. Recognizing strengths limitations will help ensure continuous at sites useful ecosystem conservation sustainable use fishery resources, possibly contributing achieving targets United Nations' Sustainable Development Goal 14 2030.

Language: Английский

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Meta‐analyses of environmental DNA downstream transport and deposition in relation to hydrogeography in riverine environments

Freshwater Biology, Journal Year: 2022, Volume and Issue: 67(8), P. 1333 - 1343

Published: May 10, 2022

Abstract Environmental DNA (eDNA) analysis is a promising tool to monitor species distribution and abundance in aquatic ecosystems. These estimates can be biased lotic environments by the effects of eDNA transport deposition processes. However, our understanding downstream dynamics limited because it fluctuate greatly depending on target quantity source site design sampling. Furthermore, into bottom substrates also determines availability aqueous eDNA, but knowledge about much more limited. Consequently, there little consensus deposition, as well their interactions with hydrogeographic conditions. In this study, we compiled previous papers concerning riverine synthesised deposition. A few studies have recently applied hydrodynamic modelling approach calculated average length ( S w ) velocity V dep ). Referring those studies, manually calculated, or directly extracted, from nine conducted meta‐analyses reveal association these river discharges. simulated mean channel given The estimated values ranged 2.6 13,187.4 m 0.003 1.900 mm/s, respectively. When log‐transformed, median were 10 2.188 (= 154.1) –1.387 0.041) mm/s. maximum distances until 95% 99% particles are deposited 334.0 1,272.7 513.5 1,956.4 m, Moreover, found that discharges positively associated , whereas was lower for natural than mesocosms. This trend could due other environmental factors, such substrates. Our meta‐analysis implied that, under ordinary conditions, most travel less 2 km even when considering resuspension riverbeds. By contrast, study did not consider multiple factors potentially affect would accordingly introduce moderate high degree heterogeneity across studies. issues will addressed future To knowledge, first quantitatively synthesise infer general properties distance velocity. According results, released individuals might effect detection sampling sites downstream. Although further accumulation empirical necessary, findings propose groundwork optimal designs ecosystems reduce false‐positive inference presence false‐negative detection.

Language: Английский

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Navigating the trade‐offs between environmental DNA and conventional field surveys for improved amphibian monitoring

Ecosphere, Journal Year: 2022, Volume and Issue: 13(2)

Published: Feb. 1, 2022

Abstract The need for efficient, accurate biodiversity monitoring is growing, especially globally imperiled taxa, such as amphibians. Environmental DNA (eDNA) analysis holds enormous potential enhancing programs, but this tool increasingly adopted, it imperative users to understand its benefits and shortcomings. We conducted a comparative study evaluate the efficacy of two eDNA methodologies (quantitative (q)PCR metabarcoding) conventional field sampling approaches (seining, dipnetting, visual encounter surveys) in system 20 ponds containing six different amphibian species. Using an occupancy modeling framework, we estimated differences detection sensitivity across methods, with focus on how survey design could be further optimized. Overall, both metabarcoding qPCR were competitive or improved upon methods. Specifically, (species‐specific approach) was most effective technique detecting rare species, California tiger salamander ( Ambystoma californiense ) red‐legged frog Rana draytonii ), probability >0.80 per survey. Metabarcoding (community diversity comparable rates techniques average, detected additional 41 vertebrate taxa. However, abundant species (western toads, Anaxyrus boreas , Pacific chorus frogs, Pseudacris regilla outperformed metabarcoding, individuals metamorphosed. Our results indicate that would when paired surveys detect terrestrial life stages, more optimization, specifically primer choice validation, needed. By comparing methods diverse set provide guidance future studies integrating into monitoring.

Language: Английский

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Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(4), P. 771 - 786

Published: Jan. 4, 2023

Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for filtration required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies investigate similarity between aquatic and filter-feeder eDNA signals essential. Here, we investigated differences among four sources (water; bivalve gill-tissue; sponges; ethanol in which filter-feeding organisms were stored) along vertically stratified transect Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish vertebrates. Combined, detected 59 vertebrates, while concurrent diver observed eight species. There no significant alpha beta diversity water sponge both highly correlated. Vertebrate was successfully extracted from sponges stored, although reduced number species detected. Bivalve gill-tissue dissections, on other hand, failed reliably detect eDNA. Overall, our results show vertebrate obtained samples concordant. strong demonstrates potential as an additional tool eDNA-based biodiversity surveys, by enabling incorporation larger sample numbers reducing plastic waste, simplifying collection, cost-efficient alternative. However, note importance not detrimentally impact communities by, example, nonlethal subsampling, specimen cloning, or bycatch specimens.

Language: Английский

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The Application of eDNA for Monitoring Aquatic Non-Indigenous Species: Practical and Policy Considerations

Diversity, Journal Year: 2023, Volume and Issue: 15(5), P. 631 - 631

Published: May 6, 2023

Aquatic non-indigenous species (NIS) threaten biodiversity, ecosystem functions, and the economy worldwide. Monitoring NIS is of immediate concern to identify newly arriving species, assess efficacy mitigation measures, report long-term indicators introduction, spread, impacts. The challenges associated with conventional methods specimen collection morphological identification have led development alternative methods, such as DNA-based which could offer rapid cost-effective detection NIS. Depending on whether a few (targeted monitoring) or many (passive are being monitored, environmental DNA (eDNA) can infer presence-absence relative abundances, enabling informed decisions actions be made based patterns detection. Compared more eDNA tools increase levels sensitivity for rare elusive even noticeable some taxa when using targeted monitoring. use not only minimizes onus taxonomic expertise reduces resource demands but also sensitive cost-efficient in detecting NIS, thus proving its value an early warning tool. As nucleic acid (DNA/RNA) advance rapidly detection, there must balance between method sensitivity, logistical requirements, costs, factored into future management decisions. While complementary reviews available, our aim emphasize importance incorporating surveys highlight available opportunities this field.

Language: Английский

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Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e14993 - e14993

Published: March 24, 2023

The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR–findable, accessible, interoperable, and reusable–despite growing awareness the importance such practices. In order to better understand these usability challenges, we systematically reviewed 60 peer articles conducting a specific subset eDNA research: metabarcoding studies in marine environments. For each article, characterized approximately 90 features across several categories: general article attributes topics, methodological choices, types metadata included, availability storage sequence data. Analyzing characteristics, identified barriers accessibility, including lack common context vocabulary articles, missing metadata, supplementary information limitations, concentration both sample collection analysis United States. While some require significant effort address, also found many instances where small choices made by authors journals could have an outsized influence on discoverability reusability Promisingly, showed consistency creativity as well strong trend toward open access publishing. Our underscores need think critically about accessibility studies, projects more broadly, continue proliferate.

Language: Английский

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Detecting and analysing intraspecific genetic variation with eDNA: From population genetics to species abundance

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(15), P. 4118 - 4132

Published: May 30, 2023

Abstract Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections diverse environments. Although most eDNA research is focused on leveraging genetic diversity to identify taxa, some recent studies explored the potential these detect within‐species variation, allowing population assessments abundance estimates from samples. However, we currently lack a framework outlining key considerations specific generating, analysing applying data two purposes. Here, discuss how various markers differ with regard information detectability samples analysis of differs common tissue‐based analyses. We then outline it may be possible obtain absolute by detecting intraspecific variation mixtures under multiple scenarios. also major causes contributing allele detection frequency errors data, their consequences population‐level analyses bioinformatic remove erroneous sequences. This review summarizes advances required harness full eDNA‐based inform questions ecology, evolutionary biology conservation management.

Language: Английский

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Soil biodiversity needs policy without borders

Science, Journal Year: 2023, Volume and Issue: 379(6627), P. 32 - 34

Published: Jan. 5, 2023

Soil health laws should account for global soil connections.

Language: Английский

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