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

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.