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

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 R-2 = .93, mitogenomes R-2 = .95) and a high repeatability across environmental-sample replicates (barcodes R-2 = .94, mitogenomes R-2 = .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.

Keywords

Araneae; Arthropoda; biomonitoring; COI internal standard; community composition; DNA barcoding; insecta; metagenomics; mitogenomes; mitogenomics

Published in

Molecular Ecology Resources
2020, Volume: 20, number: 1, pages: 256-267 Publisher: WILEY

SLU Authors

• Roslin, Tomas

  • Department of Ecology, Swedish University of Agricultural Sciences
    
  • University of Helsinki

Sustainable Development Goals

SDG15 Life on land


UKÄ Subject classification

Ecology
Biochemistry and Molecular Biology


Publication identifier

DOI: https://doi.org/10.1111/1755-0998.13057

Permanent link to this page (URI)

https://res.slu.se/id/publ/101387