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
• Other Authors: National Natural Science Foundation of China, Academy of Finland, Jane ja Aatos Erkon Säätiö, Miljøstyrelsen, University of East Anglia
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2019
• Subjects: Arctic
• Online Access: http://dx.doi.org/10.1111/1755-0998.13057; https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13057; https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13057

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.