Taxonomic Blind Spots: A Limitation of Environmental DNA Metabarcoding‐Based Detection for Canadian Freshwater Fishes DOI Creative Commons
Kevin C. Morey,

Erika Myler,

Robert Hanner

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(6)

Published: Nov. 1, 2024

ABSTRACT With increasing utilization of eDNA metabarcoding for fish community assessment, it is critical to identify, address, and communicate its capabilities limitations. One limitation great concern the reliability taxonomic coverage. Taxonomic blind spots, defined as consistent false negatives specific taxa despite known presence, reduce corroboration with conventional surveys can limit uptake biomonitoring. These spots result from gaps in reference sequence libraries, issues resolution, inefficient binding universal primers DNA certain species, ineffective collection during sampling eDNA. To explore this, a multiproject empirical dataset was compiled analyzed evaluate coverage subset Canadian freshwater fishes using standardized workflow two genetic markers: 12S MiFish‐U Vertebrate COI. The consists species lists generated by surveys, paired historical records. In total, 59 across 15 families were evaluated which approximately 40% unable be consistently detected either marker because spot. COI markers also differed kinds most frequently observed, exhibiting more resolution unclassified spots. Additionally, silico primer testing exhibited inconsistent predictions amplification when multiple software packages, suggesting need further vitro analysis troubleshoot primer‐related This study highlights impact these on studies fishes. limitations imposed should addressed future optimization efforts sees broader acceptance an applied method

Language: Английский

Metabarcoding advances agricultural invertebrate biomonitoring by enhancing resolution, increasing throughput and facilitating network inference DOI Creative Commons
Ben S. J. Hawthorne, Jordan P. Cuff, Larissa Collins

et al.

Agricultural and Forest Entomology, Journal Year: 2024, Volume and Issue: unknown

Published: May 8, 2024

Abstract Biomonitoring of agriculturally important insects is increasingly vital given our need to understand: (a) the severity impacts by pests and pathogens on crop yield health (b) impact environmental change land management insects, in line with sustainable development global conservation targets. Traditional entomological traps remain an part biomonitoring toolbox, but sample processing laborious introduces latency, accuracy can be variable. The integration molecular techniques such as DNA metabarcoding into insect has gained increasing attention, advantages doing so, kind data this generate, how easily effectively analyses integrated diverse types currently used remains relatively unclear. In review, we examine combining a range conventional unconventional sampling advance way that useful researchers practitioners. We highlight some key challenges mitigate them, using examples its different methods from literature (e.g., interception, pitfall sticky traps) demonstrate efficacy suitability. discuss infer ecological networks, emphasizing importance framework for understanding species interactions ecosystem functioning more effective descriptive biomonitoring. Finally, future advances are highlighted, alongside recommendations best practice both new experienced invertebrate metabarcoding.

Language: Английский

Citations

5
Monitoring terrestrial rewilding with environmental DNA metabarcoding: a systematic review of current trends and recommendations DOI Creative Commons

Clare Cowgill,

James Gilbert, Ian Convery

et al.

Frontiers in Conservation Science, Journal Year: 2025, Volume and Issue: 5

Published: Jan. 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.

Language: Английский

Citations

0
Environmental DNA integrity index is sensitive for species biomass estimation in freshwater DOI
Qinyu Ge,

Yanyan Piao,

Zhihui Li

et al.

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 966, P. 178734 - 178734

Published: Feb. 1, 2025

Language: Английский

Citations

0
Building a DNA barcode reference collection of Hymenoptera in New Zealand DOI Creative Commons
Darren Ward

Biodiversity Data Journal, Journal Year: 2024, Volume and Issue: 12

Published: Sept. 26, 2024

Molecular tools used for the identification of species are heavily reliant on reference DNA sequences and taxonomic annotation. Despite this, there large gaps in availability many groups different parts globe. Here, a barcode library Hymenoptera New Zealand is presented, based COI region 3,145 assigned to 837 BINs which represent 231 genera 236 species. This study provides approximately 25% 42% Zealand. However, when combined with previously deposited BOLD (a further 170 genera), barcodes available 73% Hymenopteran genera. To increase coverage, future efforts need focus predominantly taxa from seven families (Encyrtidae, Pteromalidae s.l., Mymaridae, Eulophidae, Diapriidae, Braconidae Platygastridae). database facilitates DNA-based use both revisions biodiversity monitoring.

Language: Английский

Citations

1
Taxonomic Blind Spots: A Limitation of Environmental DNA Metabarcoding‐Based Detection for Canadian Freshwater Fishes DOI Creative Commons
Kevin C. Morey,

Erika Myler,

Robert Hanner

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(6)

Published: Nov. 1, 2024

ABSTRACT With increasing utilization of eDNA metabarcoding for fish community assessment, it is critical to identify, address, and communicate its capabilities limitations. One limitation great concern the reliability taxonomic coverage. Taxonomic blind spots, defined as consistent false negatives specific taxa despite known presence, reduce corroboration with conventional surveys can limit uptake biomonitoring. These spots result from gaps in reference sequence libraries, issues resolution, inefficient binding universal primers DNA certain species, ineffective collection during sampling eDNA. To explore this, a multiproject empirical dataset was compiled analyzed evaluate coverage subset Canadian freshwater fishes using standardized workflow two genetic markers: 12S MiFish‐U Vertebrate COI. The consists species lists generated by surveys, paired historical records. In total, 59 across 15 families were evaluated which approximately 40% unable be consistently detected either marker because spot. COI markers also differed kinds most frequently observed, exhibiting more resolution unclassified spots. Additionally, silico primer testing exhibited inconsistent predictions amplification when multiple software packages, suggesting need further vitro analysis troubleshoot primer‐related This study highlights impact these on studies fishes. limitations imposed should addressed future optimization efforts sees broader acceptance an applied method

Language: Английский

Citations

0