Environmental RNA can distinguish life stages in amphibian populations

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 24(4)

Published: Aug. 18, 2023

Abstract Applications of environmental DNA (eDNA) analysis methods for biomonitoring have grown exponentially over the last decade and provide a wealth new information on distribution species. However, eDNA limited application estimating population‐level metrics. Environmental RNA (eRNA) has potential to address ecological questions by gathering population demographic from media but may be challenging detect analyze. We developed gene‐specific eRNA assays targeting keratin‐associated genes in two focal species, American bullfrogs ( Lithobates catesbeianus ) tiger salamanders Ambystoma mavortium answer an important question amphibian management: whether species detections represent breeding populations versus transitory adults. performed extensive laboratory validation with amphibians housed across development stages, where we collected 95 127 samples salamanders, respectively. Both were highly specific larval stage amplified high sensitivity (90% bullfrog 88.4% salamander samples). then applied our validated multiple natural systems. When larvae present, found 74.1% overall detection field 70.8% 48.5% ponds A. macrodactylum californiense larvae, correlating rates. only adults did not larvae‐specific ponds, despite Although much work is ahead optimizing assay design, sampling filtering methods, demonstrate that can successfully used discern life stages direct ecology conservation management.

Language: Английский

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Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 290(1999)

Published: May 30, 2023

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to aged that has long since been released from individual is more likely be detected at site further away its source. In order address issue, this manuscript focuses on state eDNA, proposing new methodologies estimate age eDNA: (1) damage rate, (2) particle size distribution, (3) viable cell-derived eDNA. addition, also shorter persistence environmental RNA (eRNA) compared highlighting application eRNA nucleic acid ratio for assessing genetic materials water. Although substantial research essential support feasibility these methodologies, incorporating time-scale information into would update current analysis, improve accuracy reliability eDNA-based monitoring, refine as useful monitoring tool ecology, fisheries various sciences.

Language: Английский

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Transcriptional responses to changing environments: insights from salmonids

Reviews in Fish Biology and Fisheries, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

Language: Английский

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Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1133 - 1147

Published: Sept. 28, 2023

Abstract Molecular technologies have facilitated the expansion of biodiversity assessments across a broad range organisms and aquatic systems. Environmental DNA (eDNA) environmental RNA (eRNA), collectively referred to as nucleic acids (eNAs), revolutionized monitoring due their noninvasive nature high‐resolution capabilities when compared traditional survey methods. While eNA applications grown exponentially over past decade, methodological inconsistencies hinder reproducibility comparability. To assess current state methodologies in ecology, we conducted systematic review 300 peer‐reviewed studies that ecological communities diverse Of these papers, 291 examine eDNA, four eRNA, five consider both eDNA eRNA. The small number eRNA highlights field is its infancy. looked at, found clear geographic bias, with approximately 50% all occurring six high‐income countries, while less than 10% occur South America Africa. Further, report lack standardization studies, showing high variability water filtration volume, filter material, pore size, extraction method, marker choice, bioinformatic pipelines. We further highlight incomplete reference sequence databases for limit taxonomic assignment inferences. Finally, identify issue community ecology: missing details, which compromise reproducibility, especially newly emerging applications. facilitate systems permit integration monitoring, recommend improvement alongside guidelines encourage transparency.

Language: Английский

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Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution

Chemosphere, Journal Year: 2024, Volume and Issue: 351, P. 141238 - 141238

Published: Jan. 21, 2024

Language: Английский

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A renaissance of microRNAs as taxonomic and phylogenetic markers in animals

Zoologica Scripta, Journal Year: 2024, Volume and Issue: 53(6), P. 754 - 762

Published: June 21, 2024

Abstract Molecular markers for tracing animal sample origins and compositions are critical applications such as parasite detection, contamination screening, authentication. Among these, microRNAs have emerged promising candidates due to their deep conservation, near‐hierarchical evolution, stability. I here review the suitability of taxonomic also phylogenetic show how careful annotation efforts establishment curated microRNA gene database MirGeneDB tools like MirMachine revitalized research. These advancements enable accurate studies, highlighting microRNAs' potential in resolving long‐standing questions relationships extending ancient DNA environmental RNA analysis. Future research must focus on expanding complements across all Metazoa further improving methodologies.

Language: Английский

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Future-proofing environmental DNA and trait-based predictions of food webs

BioScience, Journal Year: 2023, Volume and Issue: 73(12), P. 862 - 878

Published: Nov. 1, 2023

Abstract Food webs represent trophic interactions within ecosystems. Matching traits of consumers and resources helps infer food-web properties. Environmental (e)DNA, commonly used for detecting species occurrences, is rarely in trait-matching studies because abundance estimates descriptions relevant are generally missing. We synthesized recent literature on inferences with eDNA trait matching to identify challenges opportunities coupled eDNA–trait recording schemes. Our case study shows how coupling data collection improves the ability characterize greater numbers food across multiple scales ranging from spatiotemporal variation. Future-proofing sets requires new or compilation existing at that detect current future changes

Language: Английский

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New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review

Environmental Science and Pollution Research, Journal Year: 2024, Volume and Issue: 31(8), P. 11406 - 11427

Published: Jan. 6, 2024

Language: Английский

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Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(2)

Published: Feb. 1, 2025

ABSTRACT While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non‐invasive, precise way of estimating wild animal's age. DNA methylation from tissue (tDNA) was recently proposed as method overcome these issues showed more accurate results than telomere‐length‐based assessments. Here, we used environmental (eDNA) the first time template estimation, focusing on larval phase (10–24 days post‐hatch) cultured Dicentrarchus labrax (seabass), species major economic conservation interest. Using third‐generation sequencing, were able directly detect various modification types (e.g., cytosine adenosine in all contexts) across whole genome using amplification‐free nanopore sequencing. However, sites only present mitogenome, which could be specific feature eDNA or consequence better protection within mitochondria. By considering qualitative quantitative about according an objective model selection framework, our epigenetic clock reached cross‐validated accuracy 2.6 (Median Absolute Error). Such performances are higher those previous clocks, notably adult seabass even when scaling MAE range, linked dynamic epigenome during early life stages. Overall, pilot study proposes new determine potential simultaneous assessments, although robust validation preliminary along with methodological developments needed before field applications can envisaged.

Language: Английский

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Inferring Species Interactions From Co‐occurrence Networks With Environmental DNA Metabarcoding Data in a Coastal Marine Food Web

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

Published: March 4, 2025

ABSTRACT A good understanding of biotic interactions is necessary to accurately predict the vulnerability ecosystems climate change. Recently, co‐occurrence networks built from environmental DNA (eDNA) metabarcoding data have arisen as a tool explore interspecific in ecological communities exposed different human and pressures. Such can identify environmentally driven relationships microbial eukaryotic communities, but whether inferred co‐occurrences robustly represent remains unclear. Here, we tackle this challenge compare spatio‐temporal variability structure complexity food webs, using 60 eDNA samples covering vertebrates other eukaryotes North Sea coastal ecosystem. We topological characteristics highly connected species across spatial temporal subsets evaluate variance community composition structure. find consistent trends eDNA‐derived webs that support some ability for detect real processes, despite trophic forming minority significant co‐occurrences. The lack detected may result complexities, such generalist predators having flexible or behavioural partitioning, inability distinguish age class with being by non‐trophic abiotic interactions. infer interactions, further work needed assess their power reliably differentiate interaction types overcome methodological limitations, detection uncertainties, which could influence ecosystem complexity.

Language: Английский

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