SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
Abstract 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...
Published in: | Molecular Ecology Resources |
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Online Access: | http://dx.doi.org/10.1111/1755-0998.13057 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13057 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13057 |
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crwiley:10.1111/1755-0998.13057 2024-06-02T08:02:11+00:00 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 National Natural Science Foundation of China Academy of Finland Jane ja Aatos Erkon Säätiö Miljøstyrelsen University of East Anglia 2019 http://dx.doi.org/10.1111/1755-0998.13057 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13057 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13057 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology Resources volume 20, issue 1, page 256-267 ISSN 1755-098X 1755-0998 journal-article 2019 crwiley https://doi.org/10.1111/1755-0998.13057 2024-05-06T07:02:04Z Abstract 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 R 2 = .93, mitogenomes R 2 = .95) and a high repeatability across environmental‐sample replicates (barcodes R 2 = .94, mitogenomes R 2 = .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. Article in Journal/Newspaper Arctic Wiley Online Library Arctic Molecular Ecology Resources 20 1 256 267 |
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Wiley Online Library |
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crwiley |
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English |
description |
Abstract 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 R 2 = .93, mitogenomes R 2 = .95) and a high repeatability across environmental‐sample replicates (barcodes R 2 = .94, mitogenomes R 2 = .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. |
author2 |
National Natural Science Foundation of China Academy of Finland Jane ja Aatos Erkon Säätiö Miljøstyrelsen University of East Anglia |
format |
Article in Journal/Newspaper |
author |
Ji, Yinqiu Huotari, Tea Roslin, Tomas Schmidt, Niels Martin Wang, Jiaxin Yu, Douglas W. Ovaskainen, Otso |
spellingShingle |
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 |
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 |
publisher |
Wiley |
publishDate |
2019 |
url |
http://dx.doi.org/10.1111/1755-0998.13057 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13057 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13057 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Molecular Ecology Resources volume 20, issue 1, page 256-267 ISSN 1755-098X 1755-0998 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/1755-0998.13057 |
container_title |
Molecular Ecology Resources |
container_volume |
20 |
container_issue |
1 |
container_start_page |
256 |
op_container_end_page |
267 |
_version_ |
1800746679796760576 |