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Is qualitative and quantitative metabarcoding of dung fauna biodiversity feasible?


Blanckenhorn, Wolf U; Rohner, Patrick T; Bernasconi, Marco V; Haugstetter, Johannes; Buser, Andres (2016). Is qualitative and quantitative metabarcoding of dung fauna biodiversity feasible? Environmental Toxicology and Chemistry / Setac, 35(8):1970-1977.

Abstract

In biodiversity assessments, especially of small-bodied organisms for which taxonomic expertise is lacking, identification by genetic barcoding may be a cost-effective and efficient alternative to traditional identification of species by morphology, ecology, and behavior. The authors tested the feasibility and accuracy of such an approach using dung insects of practical relevance in ecotoxicological assessments of veterinary pharmaceutical residues in the environment. They produced 8 known mixtures that varied in absolute and relative composition of small-bodied and large-bodied species to see whether mitochondrial cytochrome c oxidase subunit 1 barcoding picks up all species qualitatively and quantitatively. As demonstrated before in other contexts, such metabarcoding of large numbers of dung insect specimens is principally possible using next-generation sequencing. The authors recovered most species in a sample (low type I error), at minimum permitting analysis of species richness. They obtained even quantitative responses reflecting the body size of the species, although the number of specimens was not well detected. The latter is problematic when calculating diversity indices. Nevertheless, the method yielded too many closely related false positives (type II error), thus generally overestimating species diversity and richness. These errors can be reduced by refining methods and data filtering, although this requires bioinformatics expertise often unavailable where such research is carried out. Identification by barcoding foremost hinges on a good reference database, which does not yet exist for dung organisms but would be worth developing for practical applications.

Abstract

In biodiversity assessments, especially of small-bodied organisms for which taxonomic expertise is lacking, identification by genetic barcoding may be a cost-effective and efficient alternative to traditional identification of species by morphology, ecology, and behavior. The authors tested the feasibility and accuracy of such an approach using dung insects of practical relevance in ecotoxicological assessments of veterinary pharmaceutical residues in the environment. They produced 8 known mixtures that varied in absolute and relative composition of small-bodied and large-bodied species to see whether mitochondrial cytochrome c oxidase subunit 1 barcoding picks up all species qualitatively and quantitatively. As demonstrated before in other contexts, such metabarcoding of large numbers of dung insect specimens is principally possible using next-generation sequencing. The authors recovered most species in a sample (low type I error), at minimum permitting analysis of species richness. They obtained even quantitative responses reflecting the body size of the species, although the number of specimens was not well detected. The latter is problematic when calculating diversity indices. Nevertheless, the method yielded too many closely related false positives (type II error), thus generally overestimating species diversity and richness. These errors can be reduced by refining methods and data filtering, although this requires bioinformatics expertise often unavailable where such research is carried out. Identification by barcoding foremost hinges on a good reference database, which does not yet exist for dung organisms but would be worth developing for practical applications.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Language:English
Date:2016
Deposited On:10 Oct 2016 13:18
Last Modified:10 Oct 2016 13:19
Publisher:Society of Environmental Toxicology and Chemistry
ISSN:0730-7268
Publisher DOI:https://doi.org/10.1002/etc.3275
PubMed ID:26450644

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