A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies DOI Creative Commons
Philipp E. Bayer, Adam Bennett, Georgia Nester

et al.

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

Published: April 17, 2025

ABSTRACT Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and plethora of bioinformatic approaches are eDNA‐based community composition analysis. Simulation studies careful evaluation taxonomic classifiers essential to establish reliable benchmarks improve the accuracy reproducibility findings. Here we present comprehensive nine exploring three mitochondrial markers (12S rDNA, 16S rDNA COI) in Australian vertebrates. Curated reference databases exclusion database tests were simulate diverse species compositions, including positive control two negative datasets. Using these simulated datasets ranging from 36 302 marker genes, able identify between 19% 89% using markers. We show that MMSeqs2 Metabuli generally outperform BLAST with 10% 11% higher F1 scores 12S markers, respectively, Naive Bayes Classifiers such as Mothur sequence‐based except COI by 11%. Database reveal less susceptible false positives compared Kraken2 default parameters. Based on findings, recommend classification vertebrates given its ability species‐level assignments while reducing number positives. Our work contributes establishment best practices biodiversity analysis ultimately increase reliability monitoring context conservation.

Language: Английский

A systematic review on environmental DNA (eDNA) Science: An eco-friendly survey method for conservation and restoration of fragile ecosystems DOI Creative Commons
Ashish Sahu, Mahender Singh, Adnan Amin

et al.

Ecological Indicators, Journal Year: 2025, Volume and Issue: 173, P. 113441 - 113441

Published: April 1, 2025

Language: Английский

Citations

0
A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies DOI Creative Commons
Philipp E. Bayer, Adam Bennett, Georgia Nester

et al.

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

Published: April 17, 2025

ABSTRACT Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and plethora of bioinformatic approaches are eDNA‐based community composition analysis. Simulation studies careful evaluation taxonomic classifiers essential to establish reliable benchmarks improve the accuracy reproducibility findings. Here we present comprehensive nine exploring three mitochondrial markers (12S rDNA, 16S rDNA COI) in Australian vertebrates. Curated reference databases exclusion database tests were simulate diverse species compositions, including positive control two negative datasets. Using these simulated datasets ranging from 36 302 marker genes, able identify between 19% 89% using markers. We show that MMSeqs2 Metabuli generally outperform BLAST with 10% 11% higher F1 scores 12S markers, respectively, Naive Bayes Classifiers such as Mothur sequence‐based except COI by 11%. Database reveal less susceptible false positives compared Kraken2 default parameters. Based on findings, recommend classification vertebrates given its ability species‐level assignments while reducing number positives. Our work contributes establishment best practices biodiversity analysis ultimately increase reliability monitoring context conservation.

Language: Английский

Citations

0