SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
Cite this dataset
Ji, Yinqiu et al. (2019). SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes [Dataset]. Dryad. https://doi.org/10.5061/dryad.r105t1f
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.
Usage notes
Funding
National Natural Science Foundation of China, Award: 31400470
National Natural Science Foundation of China, Award: 31500305
National Natural Science Foundation of China, Award: 31670536
National Natural Science Foundation of China, Award: 41661144002
Academy of Finland, Award: 276909
Academy of Finland, Award: 284601
Academy of Finland, Award: 285803
Academy of Finland, Award: 309571
Jane and Aatos Erkko Foundation
Environmental Protection Agency
University of East Anglia