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

• Main Authors: Ji, Yinqiu, Huotari, Tea, Roslin, Tomas, Schmidt, Niels Martin, Wang, Jiaxin, Yu, Douglas W., Ovaskainen, Otso
• Format: Dataset
• Language: unknown
• Published: 2019
• Subjects: Spilogona novaesibiriae; Gonarcticus arcticus; biomonitoring; Mitogenomes; Helophilus lapponicus; Spilogona almqvistii; Araneae; Peleteria aenea; Helophilus groenlandicus; COI internal standard; Drymeia segnis; mitogenomics; Spilogona micans; Spilogona megastoma; Scathophaga apicalis; Limnophora groenlandica; Pardosa glacialis; Zaphne occidentalis; Parasyrphus tarsatus; Eutrichota tunicata; Platycheirus groenlandicus; Syrphus torvus; Metagenomics; Lophosceles minimus; Spilogona monacantha; Holocene; Scathophaga nigripalpis; Genetics; Ecology; Evolution; Behavior and Systematics; Biotechnology; Arctic
• Online Access: https://zenodo.org/record/5006501; https://doi.org/10.5061/dryad.r105t1f

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. ArcDyn_tutorial_20190126.tar.gz Text S6. How to run Step 4 (bioinformatics) of the SPIKEPIPE pipeline. Here we describe how to the user may apply SPIKEPIPE pipeline to a subset of the data used in this paper, henceforth called ArcDyn tutorial. To install the ArcDyn tutorial, download and untar the 4.9 GB tutorial file (ArcDyn_tutorial_20190126.tar.gz) to the root directory. Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31400470Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31500305Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31670536Funding provided by: National Natural Science Foundation of ChinaCrossref ...