Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada.
Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geo...
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ftdoajarticles:oai:doaj.org/article:72622e1104e248308a4dd0414f6d21cd 2023-05-15T15:14:27+02:00 Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. Thomas W A Braukmann Maria L Kuzmina Jesse Sills Evgeny V Zakharov Paul D N Hebert 2017-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0169515 https://doaj.org/article/72622e1104e248308a4dd0414f6d21cd EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC5224991?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0169515 https://doaj.org/article/72622e1104e248308a4dd0414f6d21cd PLoS ONE, Vol 12, Iss 1, p e0169515 (2017) Medicine R Science Q article 2017 ftdoajarticles https://doi.org/10.1371/journal.pone.0169515 2022-12-31T10:46:05Z Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Canada PLOS ONE 12 1 e0169515 |
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op_collection_id |
ftdoajarticles |
language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Thomas W A Braukmann Maria L Kuzmina Jesse Sills Evgeny V Zakharov Paul D N Hebert Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. |
topic_facet |
Medicine R Science Q |
description |
Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest. |
format |
Article in Journal/Newspaper |
author |
Thomas W A Braukmann Maria L Kuzmina Jesse Sills Evgeny V Zakharov Paul D N Hebert |
author_facet |
Thomas W A Braukmann Maria L Kuzmina Jesse Sills Evgeny V Zakharov Paul D N Hebert |
author_sort |
Thomas W A Braukmann |
title |
Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. |
title_short |
Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. |
title_full |
Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. |
title_fullStr |
Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. |
title_full_unstemmed |
Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada. |
title_sort |
testing the efficacy of dna barcodes for identifying the vascular plants of canada. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2017 |
url |
https://doi.org/10.1371/journal.pone.0169515 https://doaj.org/article/72622e1104e248308a4dd0414f6d21cd |
geographic |
Arctic Canada |
geographic_facet |
Arctic Canada |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS ONE, Vol 12, Iss 1, p e0169515 (2017) |
op_relation |
http://europepmc.org/articles/PMC5224991?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0169515 https://doaj.org/article/72622e1104e248308a4dd0414f6d21cd |
op_doi |
https://doi.org/10.1371/journal.pone.0169515 |
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PLOS ONE |
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12 |
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1 |
container_start_page |
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