Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility
DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote...
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ftdryad:oai:v1.datadryad.org:10255/dryad.48498 2023-05-15T17:57:27+02:00 Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility Porter, Teresita M. Golding, G. Brian King, Christine Froese, Duane Zazula, Grant Poinar, Hendrik N. 2013-04-26T16:09:54Z http://hdl.handle.net/10255/dryad.48498 https://doi.org/10.5061/dryad.4m7d1 unknown doi:10.5061/dryad.4m7d1/1 doi:10.5061/dryad.4m7d1/2 doi:10.5061/dryad.4m7d1/3 doi:10.5061/dryad.4m7d1/4 doi:10.5061/dryad.4m7d1/5 doi:10.5061/dryad.4m7d1/6 doi:10.1111/1755-0998.12124 PMID:23694692 doi:10.5061/dryad.4m7d1 Porter TM, Golding GB, King C, Froese D, Zazula G, Poinar HN (2013) Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Molecular Ecology Resources 13(5): 798–810. http://hdl.handle.net/10255/dryad.48498 ancient DNA contamination reproducibility barcoding Beringia amplicon pyrosequencing Article 2013 ftdryad https://doi.org/10.5061/dryad.4m7d1 https://doi.org/10.5061/dryad.4m7d1/1 https://doi.org/10.5061/dryad.4m7d1/2 https://doi.org/10.5061/dryad.4m7d1/3 https://doi.org/10.5061/dryad.4m7d1/4 https://doi.org/10.5061/dryad.4m7d1/5 https://doi.org/1 2020-01-01T15:01:04Z DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1 and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, sequenced control reactions were used to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance and taxonomic diversity from the 12S, 16S and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the chi-squared metric was used; however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil vs. read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present-day Yukon. Article in Journal/Newspaper permafrost Beringia Yukon Dryad Digital Repository (Duke University) Yukon |
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Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
ancient DNA contamination reproducibility barcoding Beringia amplicon pyrosequencing |
spellingShingle |
ancient DNA contamination reproducibility barcoding Beringia amplicon pyrosequencing Porter, Teresita M. Golding, G. Brian King, Christine Froese, Duane Zazula, Grant Poinar, Hendrik N. Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility |
topic_facet |
ancient DNA contamination reproducibility barcoding Beringia amplicon pyrosequencing |
description |
DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1 and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, sequenced control reactions were used to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance and taxonomic diversity from the 12S, 16S and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the chi-squared metric was used; however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil vs. read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present-day Yukon. |
format |
Article in Journal/Newspaper |
author |
Porter, Teresita M. Golding, G. Brian King, Christine Froese, Duane Zazula, Grant Poinar, Hendrik N. |
author_facet |
Porter, Teresita M. Golding, G. Brian King, Christine Froese, Duane Zazula, Grant Poinar, Hendrik N. |
author_sort |
Porter, Teresita M. |
title |
Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility |
title_short |
Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility |
title_full |
Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility |
title_fullStr |
Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility |
title_full_unstemmed |
Data from: Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility |
title_sort |
data from: amplicon pyrosequencing late pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility |
publishDate |
2013 |
url |
http://hdl.handle.net/10255/dryad.48498 https://doi.org/10.5061/dryad.4m7d1 |
geographic |
Yukon |
geographic_facet |
Yukon |
genre |
permafrost Beringia Yukon |
genre_facet |
permafrost Beringia Yukon |
op_relation |
doi:10.5061/dryad.4m7d1/1 doi:10.5061/dryad.4m7d1/2 doi:10.5061/dryad.4m7d1/3 doi:10.5061/dryad.4m7d1/4 doi:10.5061/dryad.4m7d1/5 doi:10.5061/dryad.4m7d1/6 doi:10.1111/1755-0998.12124 PMID:23694692 doi:10.5061/dryad.4m7d1 Porter TM, Golding GB, King C, Froese D, Zazula G, Poinar HN (2013) Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Molecular Ecology Resources 13(5): 798–810. http://hdl.handle.net/10255/dryad.48498 |
op_doi |
https://doi.org/10.5061/dryad.4m7d1 https://doi.org/10.5061/dryad.4m7d1/1 https://doi.org/10.5061/dryad.4m7d1/2 https://doi.org/10.5061/dryad.4m7d1/3 https://doi.org/10.5061/dryad.4m7d1/4 https://doi.org/10.5061/dryad.4m7d1/5 https://doi.org/1 |
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1766165882428456960 |