Dryad
Published August 13, 2019 | Version v1
Dataset Open

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

Creators

  • 1. Kunming Institute of Zoology
  • 2. University of Helsinki
  • 3. Arctic Research Centre

Description

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.

Notes

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 China
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809
Award Number: 31400470

Funding provided by: National Natural Science Foundation of China
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809
Award Number: 31500305

Funding provided by: National Natural Science Foundation of China
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809
Award Number: 31670536

Funding provided by: National Natural Science Foundation of China
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809
Award Number: 41661144002

Funding provided by: Academy of Finland
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002341
Award Number: 276909

Funding provided by: Academy of Finland
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002341
Award Number: 284601

Funding provided by: Academy of Finland
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002341
Award Number: 285803

Funding provided by: Academy of Finland
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002341
Award Number: 309571

Funding provided by: Jane ja Aatos Erkon Säätiö
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100004012
Award Number:

Funding provided by: Miljøstyrelsen
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100007036
Award Number:

Funding provided by: University of East Anglia
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000736
Award Number:

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