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Evaluating next-generation sequencing (NGS) methods for routine monitoring of wild bees: metabarcoding, mitogenomics or NGS barcoding

Gueuning, Morgan and Ganser, Dominik and Blaser, Simon and Albrecht, Matthias and Knop, Eva and Praz, Christophe and Frey, Juerg E.. (2019) Evaluating next-generation sequencing (NGS) methods for routine monitoring of wild bees: metabarcoding, mitogenomics or NGS barcoding. Molecular ecology resources, 19 (4). pp. 847-862.

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Abstract

Implementing cost-effective monitoring programs for wild bees remains challenging due to the high costs of sampling and specimen identification. To reduce costs, next-generation sequencing (NGS)-based methods have lately been suggested as alternatives to morphology-based identifications. To provide a comprehensive presentation of the advantages and weaknesses of different NGS-based identification methods, we assessed three of the most promising ones, namely metabarcoding, mitogenomics and NGS barcoding. Using a regular monitoring data set (723 specimens identified using morphology), we found that NGS barcoding performed best for both species presence/absence and abundance data, producing only few false positives (3.4%) and no false negatives. In contrast, the proportion of false positives and false negatives was higher using metabarcoding and mitogenomics. Although strong correlations were found between biomass and read numbers, abundance estimates significantly skewed the communities' composition in these two techniques. NGS barcoding recovered the same ecological patterns as morphology. Ecological conclusions based on metabarcoding and mitogenomics were similar to those based on morphology when using presence/absence data, but different when using abundance data. In terms of workload and cost, we show that metabarcoding and NGS barcoding can compete with morphology, but not mitogenomics which was consistently more expensive. Based on these results, we advocate that NGS barcoding is currently the seemliest NGS method for monitoring of wild bees. Furthermore, this method has the advantage of potentially linking DNA sequences with preserved voucher specimens, which enable morphological re-examination and will thus produce verifiable records which can be fed into faunistic databases.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Epidemiology and Public Health (EPH) > Health Interventions > Vector Control (Müller)
UniBasel Contributors:Blaser, Simon
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Wiley
ISSN:1471-8286
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
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Last Modified:10 Jul 2019 13:49
Deposited On:10 Jul 2019 13:47

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