DNA barcoding of recently diverged species: relative performance of matching methods.

Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of rec...

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Autores principales:	Robin van Velzen, Emanuel Weitschek, Giovanni Felici, Freek T Bakker
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/07f8f4a910dc4d1ba625ed2f67f02953
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spelling	oai:doaj.org-article:07f8f4a910dc4d1ba625ed2f67f029532021-11-18T07:30:01ZDNA barcoding of recently diverged species: relative performance of matching methods.1932-620310.1371/journal.pone.0030490https://doaj.org/article/07f8f4a910dc4d1ba625ed2f67f029532012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22272356/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.Robin van VelzenEmanuel WeitschekGiovanni FeliciFreek T BakkerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 1, p e30490 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Robin van Velzen Emanuel Weitschek Giovanni Felici Freek T Bakker DNA barcoding of recently diverged species: relative performance of matching methods.
description	Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.
format	article
author	Robin van Velzen Emanuel Weitschek Giovanni Felici Freek T Bakker
author_facet	Robin van Velzen Emanuel Weitschek Giovanni Felici Freek T Bakker
author_sort	Robin van Velzen
title	DNA barcoding of recently diverged species: relative performance of matching methods.
title_short	DNA barcoding of recently diverged species: relative performance of matching methods.
title_full	DNA barcoding of recently diverged species: relative performance of matching methods.
title_fullStr	DNA barcoding of recently diverged species: relative performance of matching methods.
title_full_unstemmed	DNA barcoding of recently diverged species: relative performance of matching methods.
title_sort	dna barcoding of recently diverged species: relative performance of matching methods.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/07f8f4a910dc4d1ba625ed2f67f02953
work_keys_str_mv	AT robinvanvelzen dnabarcodingofrecentlydivergedspeciesrelativeperformanceofmatchingmethods AT emanuelweitschek dnabarcodingofrecentlydivergedspeciesrelativeperformanceofmatchingmethods AT giovannifelici dnabarcodingofrecentlydivergedspeciesrelativeperformanceofmatchingmethods AT freektbakker dnabarcodingofrecentlydivergedspeciesrelativeperformanceofmatchingmethods
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DNA barcoding of recently diverged species: relative performance of matching methods.

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