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:...
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ftzenodo:oai:zenodo.org:5006501 2023-09-05T13:17:51+02:00 SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes Ji, Yinqiu Huotari, Tea Roslin, Tomas Schmidt, Niels Martin Wang, Jiaxin Yu, Douglas W. Ovaskainen, Otso 2019-08-13 https://zenodo.org/record/5006501 https://doi.org/10.5061/dryad.r105t1f unknown https://zenodo.org/communities/dryad https://zenodo.org/record/5006501 https://doi.org/10.5061/dryad.r105t1f oai:zenodo.org:5006501 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode 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 info:eu-repo/semantics/other dataset 2019 ftzenodo https://doi.org/10.5061/dryad.r105t1f 2023-08-22T22:58:39Z 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 ... Dataset Arctic Zenodo Arctic |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
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 |
spellingShingle |
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 Ji, Yinqiu Huotari, Tea Roslin, Tomas Schmidt, Niels Martin Wang, Jiaxin Yu, Douglas W. Ovaskainen, Otso SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes |
topic_facet |
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 |
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. 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 ... |
format |
Dataset |
author |
Ji, Yinqiu Huotari, Tea Roslin, Tomas Schmidt, Niels Martin Wang, Jiaxin Yu, Douglas W. Ovaskainen, Otso |
author_facet |
Ji, Yinqiu Huotari, Tea Roslin, Tomas Schmidt, Niels Martin Wang, Jiaxin Yu, Douglas W. Ovaskainen, Otso |
author_sort |
Ji, Yinqiu |
title |
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes |
title_short |
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes |
title_full |
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes |
title_fullStr |
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes |
title_full_unstemmed |
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes |
title_sort |
spikepipe: a metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using dna barcodes or mitogenomes |
publishDate |
2019 |
url |
https://zenodo.org/record/5006501 https://doi.org/10.5061/dryad.r105t1f |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
https://zenodo.org/communities/dryad https://zenodo.org/record/5006501 https://doi.org/10.5061/dryad.r105t1f oai:zenodo.org:5006501 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.r105t1f |
_version_ |
1776198857840918528 |