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

dc.contributor.affiliationKunming Institute of Zoology - Ji, Yinqiu
dc.contributor.affiliationUniversity of Helsinki - Huotari, Tea
dc.contributor.affiliationUniversity of Helsinki - Roslin, Tomas
dc.contributor.affiliationArctic Research Centre - Schmidt, Niels Martin
dc.contributor.affiliationKunming Institute of Zoology - Wang, Jiaxin
dc.contributor.affiliationKunming Institute of Zoology - Yu, Douglas W.
dc.contributor.affiliationUniversity of Helsinki - Ovaskainen, Otso
dc.contributor.authorJi, Yinqiu
dc.contributor.authorHuotari, Tea
dc.contributor.authorRoslin, Tomas
dc.contributor.authorSchmidt, Niels Martin
dc.contributor.authorWang, Jiaxin
dc.contributor.authorYu, Douglas W.
dc.contributor.authorOvaskainen, Otso
dc.coverage.spatialArctic
dc.coverage.spatialGreenland
dc.date.accessioned2025-03-24T15:15:02Z
dc.date.issued2019-08-13
dc.date.issued2019-08-13
dc.descriptionThe 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.
dc.identifierhttps://doi.org/10.5061/dryad.r105t1f
dc.identifier.urihttps://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/9492
dc.rightsOpen
dc.rights.licensecc-zero
dc.subjectSpilogona novaesibiriae
dc.subjectGonarcticus arcticus
dc.subjectbiomonitoring
dc.subjectMitogenomes
dc.subjectHelophilus lapponicus
dc.subjectSpilogona almqvistii
dc.subjectAraneae
dc.subjectPeleteria aenea
dc.subjectHelophilus groenlandicus
dc.subjectCOI internal standard
dc.subjectDrymeia segnis
dc.subjectmitogenomics
dc.subjectSpilogona micans
dc.subjectSpilogona megastoma
dc.subjectScathophaga apicalis
dc.subjectLimnophora groenlandica
dc.subjectPardosa glacialis
dc.subjectZaphne occidentalis
dc.subjectParasyrphus tarsatus
dc.subjectEutrichota tunicata
dc.subjectPlatycheirus groenlandicus
dc.subjectSyrphus torvus
dc.subjectMetagenomics
dc.subjectLophosceles minimus
dc.subjectSpilogona monacantha
dc.subjectHolocene
dc.subjectScathophaga nigripalpis
dc.subjectGenetics
dc.subjectEcology, Evolution, Behavior and Systematics
dc.subjectBiotechnology
dc.titleSPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
dc.typedataset
dc.typedataset
Zenodo


: