SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes

Ji, Yinqiu, Huotari, Tea, Roslin, Tomas, Schmidt, Niels Martin, Wang, Jiaxin, Yu, Douglas W. and Ovaskainen, Otso (2020) SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes. Molecular Ecology Resources, 20 (1). pp. 256-267. ISSN 1755-098X

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Abstract

The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental-sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.

Item Type: Article
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 05 Aug 2019 09:30
Last Modified: 12 Jul 2020 23:53
URI: https://ueaeprints.uea.ac.uk/id/eprint/71876
DOI: 10.1111/1755-0998.13057

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