Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

@article{Deiner2017EnvironmentalDM,
  title={Environmental DNA metabarcoding: Transforming how we survey animal and plant communities},
  author={Kristy Deiner and Holly M. Bik and Elvira M{\"a}chler and Mathew Seymour and Ana{\"i}s Lacoursi{\`e}re-Roussel and Florian Altermatt and Simon Creer and Iliana Bista and David M. Lodge and Natasha de Vere and Michael E. Pfrender and Louis Bernatchez},
  journal={Molecular Ecology},
  year={2017},
  volume={26},
  pages={5872 - 5895}
}
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review… 

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Validating environmental DNA metabarcoding for marine fishes in diverse ecosystems using a public aquarium

Environmental DNA metabarcoding has been widely touted as a powerful tool for monitoring biodiversity in marine ecosystems. However, this method still requires thorough validation and standardization

Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods

TLDR
To detect fish communities in backwater lakes, the performance of eDNA metabarcoding with the use of 1 L surface water sampling is similar to that of capturing methods, and environmental factors that can cause PCR inhibition, should be considered in eDNA applications.

Fast processing of environmental DNA metabarcoding sequence data using convolutional neural networks

TLDR
This work investigated whether convolutional neural networks (CNN) can optimize the processing of short eDNA sequences and found that the taxonomic assignments from the CNN were comparable to those of OBITools, with high correlation levels and a similar match to the regional fish fauna.

Application of Environmental DNA Metabarcoding for Predicting Anthropogenic Pollution in Rivers.

TLDR
This study gives a novel approach to predicting the pollution status of rivers by eDNA data by observing that the relative abundance of indicative OTUs was significantly correlated with nutrient levels, and could be used to predict the nutrient status up to 79% accuracy on testing data sets.

Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

TLDR
In freshwater systems with fewer than 100 species, eDNA metabarcoding detected more species than conventional methods; however, more studies are needed in these environments to better evaluate relative performance.

Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches

Accurate quantification of biodiversity can be demanding and expensive. Although environmental DNA (eDNA) metabarcoding can facilitate biodiversity assessments through non‐invasive, cost‐efficient

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

TLDR
It is concluded that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.
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