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

• Published in: Molecular Ecology Resources
• Main Authors: Ji, Yinqiu, Huotari, Tea, Roslin, Tomas, Schmidt, Niels Martin, Wang, Jiaxin, Yu, Douglas W., Ovaskainen, Otso
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2020
• Subjects: Arctic
• Online Access: https://ueaeprints.uea.ac.uk/id/eprint/71876/; https://ueaeprints.uea.ac.uk/id/eprint/71876/1/Accepted_Manuscript.pdf; https://doi.org/10.1111/1755-0998.13057

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.