cc-zeroJi, YinqiuHuotari, TeaRoslin, TomasSchmidt, Niels MartinWang, JiaxinYu, Douglas W.Ovaskainen, Otso2025-03-242019-08-132019-08-13https://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/9492The 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.OpenSpilogona novaesibiriaeGonarcticus arcticusbiomonitoringMitogenomesHelophilus lapponicusSpilogona almqvistiiAraneaePeleteria aeneaHelophilus groenlandicusCOI internal standardDrymeia segnismitogenomicsSpilogona micansSpilogona megastomaScathophaga apicalisLimnophora groenlandicaPardosa glacialisZaphne occidentalisParasyrphus tarsatusEutrichota tunicataPlatycheirus groenlandicusSyrphus torvusMetagenomicsLophosceles minimusSpilogona monacanthaHoloceneScathophaga nigripalpisGeneticsEcology, Evolution, Behavior and SystematicsBiotechnologydataset