tombRaider– improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion DOI Creative Commons
Gert‐Jan Jeunen, Kristen Fernandes, Eddy Dowle

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 26, 2024

ABSTRACT Environmental DNA metabarcoding has revolutionized ecological surveys of natural systems. By amplifying and sequencing small gene fragments from environmental samples containing complex mixtures, scientists are now capable exploring biodiversity patterns across the tree life in a time-efficient cost-effective manner. However, accuracy species haplotype identification can be compromised by sequence artefacts pseudogenes. Despite various strategies developed over years, effective removal remains challenging inconsistent data reporting standards hinder reproducibility eDNA experiments. To address these issues, we introduce tombRaider , an open-source command line software program ( https://github.com/gjeunen/tombRaider ) R package https://github.com/gjeunen/tombRaider_R to remove pseudogenes post clustering denoising. features modular algorithm evaluating multiple criteria, including similarity, co-occurrence patterns, taxonomic assignment, presence stop codons. We validated using published sets, mock invertebrate communities, air zoo, salmon haplotypes aquatic eDNA. Our results demonstrate that effectively removed higher proportion while retaining authentic sequences, thus enhancing reliability eDNA-derived diversity metrics. This user-friendly not only improves quality studies, but also contributes standardised practices, aspect currently lacking this emerging research field.

Язык: Английский

Estimation of Species Abundance Based on the Number of Segregating Sites Using Environmental DNA (eDNA) DOI Open Access
Qiaoyun Ai, Hao Yuan, Ying Wang

и другие.

Molecular Ecology Resources, Год журнала: 2025, Номер unknown

Опубликована: Фев. 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

Язык: Английский

Процитировано

2
A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light, and temperature DOI Creative Commons
Austin M. Guthrie, Christine E. Cooper, Philip W. Bateman

и другие.

Environmental DNA, Год журнала: 2024, Номер 6(4)

Опубликована: Июль 1, 2024

Abstract Environmental DNA (eDNA) degradation influences the effectiveness of eDNA‐based biodiversity monitoring, but factors that determine rate decay eDNA in terrestrial environments are poorly understood. We assessed persistence vertebrate from a mock community created with soil zoo enclosures holding 10 target species different taxonomic classes (reptiles, birds, and mammals) biomass (little penguin giraffe). examined detection rates resulting metabarcoding, as well relative concentrations via qPCR, samples over eight time points (0–12 weeks), during exposure to three ambient temperatures (10, 25, 40°C) levels ultraviolet B (UV‐B) radiation (0%, 50%, 100% intensity). recorded considerable variation detectability between species, independent temperature, UV‐B effects. Quantitative polymerase chain reaction (PCR) indicated for all temperature UV treatments, although it was still possible detect some after 12 weeks. Degradation were lowest high presumably due reducing bacterial metabolism. The investigated did not influence decay. Our results indicate can persist under range longer than expected. Sheltered sites minimal radiation, which have previously been considered ideal collection, may be optimal cases microbial A better understanding is needed enhance accuracy metabarcoding surveying communities.

Язык: Английский

Процитировано

7
Monitoring terrestrial rewilding with environmental DNA metabarcoding: a systematic review of current trends and recommendations DOI Creative Commons

Clare Cowgill,

James Gilbert, Ian Convery

и другие.

Frontiers in Conservation Science, Год журнала: 2025, Номер 5

Опубликована: Янв. 2, 2025

Introduction Rewilding, the facilitation of self-sustaining and resilient ecosystems by restoring natural processes, is an increasingly popular conservation approach potential solution to biodiversity climate crises. Outcomes rewilding can be unpredictable, monitoring essential determine whether are recovering. Metabarcoding, particularly environmental DNA (eDNA), revolutionizing could play important role in understanding impacts but has mostly been applied within aquatic systems. Methods This systematic review focuses on applications eDNA metabarcoding terrestrial monitoring, with additional insights from bulk ingested DNA. We examine publication trends, choice sampling substrate focal taxa, investigate how well performs compared other methods (e.g. camera trapping). Results Terrestrial represented a small proportion total papers, forests most studied system, soil water substrates, vertebrates targeted taxa. Most studies focused measuring species richness, few included analyzes functional diversity. Greater richness was found when using multiple took this approach. Metabarcoding did not consistently outperform terms number vertebrate taxa detected, likely influenced marker, habitat. Discussion Our findings indicate that metabarcoding, eDNA, key rewilding, further ground- truthing needed establish appropriate experimental pipelines for target system interest. Systematic Review Registration https://osf.io/38w9q/?view_only=47fdab224a7a43d298eccbe578f1fcf0 , identifier 38w9q.

Язык: Английский

Процитировано

1
From Water to Land: A Review on the Applications of Environmental DNA and Invertebrate‐Derived DNA for Monitoring Terrestrial and Semi‐Aquatic Mammals DOI
Holly A. Broadhurst, Naiara Guimarães Sales,

Robert Raynor

и другие.

Mammal Review, Год журнала: 2025, Номер unknown

Опубликована: Май 5, 2025

ABSTRACT Terrestrial and semi‐aquatic mammals are facing increasing threats globally, highlighting the need for reliable data on species' occurrence, distribution, abundance effective conservation efforts. However, obtaining robust information over broad spatial temporal scales remains a significant challenge. Environmental DNA (eDNA) invertebrate‐derived (iDNA) applications have emerged as powerful surveying methods, with potential to revolutionise ecological monitoring by improving species detections providing better insights into mammalian distribution diversity. While eDNA relies genetic material shed their surroundings, iDNA leverages from invertebrates that interact mammals. Both approaches offer cost‐effective means obtain records community diversity metrics. This review explores global of e/iDNA terrestrial By comprehensive overview applications, sampling design, challenges, prospects, this serves guide researchers conservationists seeking use evaluating current state identifies challenges milestones be addressed these methods become practical method scale. It highlights further research enhance sensitivity reliability detections, standardisation methodologies, validation through comparison traditional methods. sheds light valuable tools aiding mammal inspiring future advancements in field.

Язык: Английский

Процитировано

1
Metazoan diversity in Chilean hypersaline lakes unveiled by environmental DNA DOI Creative Commons
Mattia Saccò, Matthew A. Campbell, Pablo Aguilar

и другие.

Frontiers in Ecology and Evolution, Год журнала: 2025, Номер 13

Опубликована: Янв. 31, 2025

Saline and hypersaline wetlands are biodiversity hotspots for metazoans such as aquatic invertebrates wading birds. However, the survival of these habitats their biota is increasingly threatened by a combination pressures from climate change extractive processes. With goal improving conservation efforts in ecosystems, this study tests use eDNA methods metazoan biomonitoring. We employed multi-assay approach utilizing three genetic markers—12S rRNA, 18S COI —to analyze sediment water. Samples were collected lakes Northern Chile: Salar de Atacama (Laguna Puilar), Pujsa, Tara. outputs also compared with results generated macroinvertebrate assessments using kick-nets. Our analyses revealed total 21 22 taxa across water, respectively. The highest diversity was found Tara (15 within 13 water). design detected range resident different status, spanning rotifers to endangered snails, amphipods flamingos. Macroinvertebrate data via kick-net surveys further validated most biodiverse system. Compared net-based assessments, analysis allowed more refined taxonomic assignments copepods ostracods, while certain Ephydridae or Hirudinea not through molecular tests. Overall, provides evidence that an effective tool elucidate fine scale assemblages can refine lakes.

Язык: Английский

Процитировано

0
A Novel Approach for Pollen Identification and Quantification Using Hybrid Capture‐Based DNA Metabarcoding DOI Creative Commons
Dona Kireta, Kor‐jent van Dijk, Stephen Crotty

и другие.

Ecology and Evolution, Год журнала: 2025, Номер 15(4)

Опубликована: Апрель 1, 2025

ABSTRACT Pollen identification (ID) and quantification is important in many fields, including pollination ecology agricultural sciences, efforts to explore optimal molecular methods for identifying low concentrations of DNA from plant mixtures are increasing, but quantifying mixture proportions remains challenging. Traditional pollen ID using microscopy time‐consuming, requires expertise has limited accuracy throughput. Molecular barcoding approaches being explored offer improved The common approach, amplicon sequencing, employs PCR amplification isolate barcodes, introduces significant bias, impairing downstream quantification. We apply a novel hybrid capture approach artificial improve upon current taxon methods. method randomly fragments uses RNA baits which allows duplicate removal, reducing bias. Four reference databases were used A restricted matK database containing only species yielded sequence highly correlated with input proportions, demonstrating the potential usefulness metabarcoding mixtures. Identification power was further tested two libraries constructed publicly available sequences: plastid barcode RefSeq complete chloroplast references. Single barcode‐based did not consistently resolve or genus level. performed better qualitatively had coverage (relative here) introduced issues. At family level, both comparable qualitative results, quantitatively. Whilst developed here tremendous potential, choice expansion one most factors allowing quantitative full set genomic regions screened by this method.

Язык: Английский

Процитировано

0
Estimation of Species Abundance Based on the Number of Segregating Sites using Environmental DNA (eDNA) DOI Creative Commons
Qiaoyun Ai, Hao Yuan, Ying Wang

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 20, 2024

Abstract The advance of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. Although most studies focus on detections, some recent explored the potential using eDNA concentration to quantify abundance. However, differential individual contribution samples could easily obscure concentration-species abundance relationship. We propose number segregating sites as a proxy for estimating Since reflects genetic diversity population, which is less sensitive than concentration. examined relationship between silico, vitro, situ two brackish goby species, Acanthogobius hasta Tridentiger bifasciatus . Analyses simulated data vitro with mixed from known individuals showed strong correlation (R 2 > 0.9; P < 0.01). Results experiment further validated = 0.70, 0.01), such was not affected by biotic factors, including body size feeding behavior (P 0.05). cross-validation test also that predicted bias variability Overall, correlates stronger provides better estimate This advancement can significantly enhance quantitative capabilities technology.

Язык: Английский

Процитировано

2
Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes DOI Creative Commons
Peter A. Seeber,

L Batke,

Yury Dvornikov

и другие.

eLife, Год журнала: 2024, Номер 12

Опубликована: Март 15, 2024

Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions late survival extinct species. However, translocation and lateral inflow in can potentially distort stratigraphic signal DNA. Using three different approaches on two short sediment cores Yamal peninsula, West Siberia, with ages spanning only hundreds years, we detect identified mitochondrial genomes multiple mammoth woolly rhinoceros individuals—both species that have been thousands years mainland. The occurrence clearly identifiable aeDNA Pleistocene megafauna (e.g. >400 K reads one core) throughout these subsurface cores, along specificities sedimentology dating, confirm processes acting regional scales, such as extensive permafrost thawing, influence record should be accounted paleoecology.

Язык: Английский

Процитировано

1
Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes DOI Creative Commons
Peter A. Seeber,

L Batke,

Yury Dvornikov

и другие.

eLife, Год журнала: 2023, Номер 12

Опубликована: Сен. 1, 2023

Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions late survival extinct species. However, translocation and lateral inflow in can potentially distort stratigraphic signal DNA. Using three different approaches on two short sediment cores Yamal peninsula, West Siberia, with ages spanning only hundreds years, we detect identified mitochondrial genomes multiple mammoth woolly rhinoceros individuals-both species that have been thousands years mainland. The occurrence clearly identifiable aeDNA Pleistocene megafauna (e.g. >400 K reads one core) throughout these subsurface cores, along specificities sedimentology dating, confirm processes acting regional scales, such as extensive permafrost thawing, influence record should be accounted paleoecology.

Язык: Английский

Процитировано

2
tombRaider– improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion DOI Creative Commons
Gert‐Jan Jeunen, Kristen Fernandes, Eddy Dowle

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 26, 2024

ABSTRACT Environmental DNA metabarcoding has revolutionized ecological surveys of natural systems. By amplifying and sequencing small gene fragments from environmental samples containing complex mixtures, scientists are now capable exploring biodiversity patterns across the tree life in a time-efficient cost-effective manner. However, accuracy species haplotype identification can be compromised by sequence artefacts pseudogenes. Despite various strategies developed over years, effective removal remains challenging inconsistent data reporting standards hinder reproducibility eDNA experiments. To address these issues, we introduce tombRaider , an open-source command line software program ( https://github.com/gjeunen/tombRaider ) R package https://github.com/gjeunen/tombRaider_R to remove pseudogenes post clustering denoising. features modular algorithm evaluating multiple criteria, including similarity, co-occurrence patterns, taxonomic assignment, presence stop codons. We validated using published sets, mock invertebrate communities, air zoo, salmon haplotypes aquatic eDNA. Our results demonstrate that effectively removed higher proportion while retaining authentic sequences, thus enhancing reliability eDNA-derived diversity metrics. This user-friendly not only improves quality studies, but also contributes standardised practices, aspect currently lacking this emerging research field.

Язык: Английский

Процитировано

0