DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species.
Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, represe...
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ftdoajarticles:oai:doaj.org/article:9eef0f0431784fe598ddec45153b8156 2023-05-15T14:28:58+02:00 DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. Jeffery M Saarela Paul C Sokoloff Lynn J Gillespie Laurie L Consaul Roger D Bull 2013-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0077982 https://doaj.org/article/9eef0f0431784fe598ddec45153b8156 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC3865322?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0077982 https://doaj.org/article/9eef0f0431784fe598ddec45153b8156 PLoS ONE, Vol 8, Iss 10, p e77982 (2013) Medicine R Science Q article 2013 ftdoajarticles https://doi.org/10.1371/journal.pone.0077982 2022-12-31T04:49:37Z Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species. Article in Journal/Newspaper Arctic Archipelago Arctic Canadian Arctic Archipelago Saxifraga oppositifolia Directory of Open Access Journals: DOAJ Articles Arctic Canadian Arctic Archipelago PLoS ONE 8 10 e77982 |
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ftdoajarticles |
language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Jeffery M Saarela Paul C Sokoloff Lynn J Gillespie Laurie L Consaul Roger D Bull DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. |
topic_facet |
Medicine R Science Q |
description |
Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species. |
format |
Article in Journal/Newspaper |
author |
Jeffery M Saarela Paul C Sokoloff Lynn J Gillespie Laurie L Consaul Roger D Bull |
author_facet |
Jeffery M Saarela Paul C Sokoloff Lynn J Gillespie Laurie L Consaul Roger D Bull |
author_sort |
Jeffery M Saarela |
title |
DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. |
title_short |
DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. |
title_full |
DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. |
title_fullStr |
DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. |
title_full_unstemmed |
DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. |
title_sort |
dna barcoding the canadian arctic flora: core plastid barcodes (rbcl + matk) for 490 vascular plant species. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2013 |
url |
https://doi.org/10.1371/journal.pone.0077982 https://doaj.org/article/9eef0f0431784fe598ddec45153b8156 |
geographic |
Arctic Canadian Arctic Archipelago |
geographic_facet |
Arctic Canadian Arctic Archipelago |
genre |
Arctic Archipelago Arctic Canadian Arctic Archipelago Saxifraga oppositifolia |
genre_facet |
Arctic Archipelago Arctic Canadian Arctic Archipelago Saxifraga oppositifolia |
op_source |
PLoS ONE, Vol 8, Iss 10, p e77982 (2013) |
op_relation |
http://europepmc.org/articles/PMC3865322?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0077982 https://doaj.org/article/9eef0f0431784fe598ddec45153b8156 |
op_doi |
https://doi.org/10.1371/journal.pone.0077982 |
container_title |
PLoS ONE |
container_volume |
8 |
container_issue |
10 |
container_start_page |
e77982 |
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1766303083559649280 |