Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.

<h4>Background</h4>DNA barcoding has recently been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. Two broad methods (distance and monophyly-based methods) have been used. One method is based on degree of DNA sequence variation within and...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Shanmei Zou, Qi Li, Lingfeng Kong, Hong Yu, Xiaodong Zheng
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e3ff7fc9f2184688adbb812abf267c66
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:e3ff7fc9f2184688adbb812abf267c66
record_format	dspace
spelling	oai:doaj.org-article:e3ff7fc9f2184688adbb812abf267c662021-11-18T07:35:51ZComparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.1932-620310.1371/journal.pone.0026619https://doaj.org/article/e3ff7fc9f2184688adbb812abf267c662011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22039517/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>DNA barcoding has recently been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. Two broad methods (distance and monophyly-based methods) have been used. One method is based on degree of DNA sequence variation within and between species while another method requires the recovery of species as discrete clades (monophyly) on a phylogenetic tree. Nevertheless, some issues complicate the use of both methods. A recently applied new technique, the character-based DNA barcode method, however, characterizes species through a unique combination of diagnostic characters.<h4>Methodology/principal findings</h4>Here we analyzed 108 COI and 102 16S rDNA sequences of 40 species of Neogastropoda from a wide phylogenetic range to assess the performance of distance, monophyly and character-based methods of DNA barcoding. The distance-based method for both COI and 16S rDNA genes performed poorly in terms of species identification. Obvious overlap between intraspecific and interspecific divergences for both genes was found. The "10× rule" threshold resulted in lumping about half of distinct species for both genes. The neighbour-joining phylogenetic tree of COI could distinguish all species studied. However, the 16S rDNA tree could not distinguish some closely related species. In contrast, the character-based barcode method for both genes successfully identified 100% of the neogastropod species included, and performed well in discriminating neogastropod genera.<h4>Conclusions/significance</h4>This present study demonstrates the effectiveness of the character-based barcoding method for species identification in different taxonomic levels, especially for discriminating the closely related species. While distance and monophyly-based methods commonly use COI as the ideal gene for barcoding, the character-based approach can perform well for species identification using relatively conserved gene markers (e.g., 16S rDNA in this study). Nevertheless, distance and monophyly-based methods, especially the monophyly-based method, can still be used to flag species.Shanmei ZouQi LiLingfeng KongHong YuXiaodong ZhengPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 10, p e26619 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shanmei Zou Qi Li Lingfeng Kong Hong Yu Xiaodong Zheng Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.
description	<h4>Background</h4>DNA barcoding has recently been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. Two broad methods (distance and monophyly-based methods) have been used. One method is based on degree of DNA sequence variation within and between species while another method requires the recovery of species as discrete clades (monophyly) on a phylogenetic tree. Nevertheless, some issues complicate the use of both methods. A recently applied new technique, the character-based DNA barcode method, however, characterizes species through a unique combination of diagnostic characters.<h4>Methodology/principal findings</h4>Here we analyzed 108 COI and 102 16S rDNA sequences of 40 species of Neogastropoda from a wide phylogenetic range to assess the performance of distance, monophyly and character-based methods of DNA barcoding. The distance-based method for both COI and 16S rDNA genes performed poorly in terms of species identification. Obvious overlap between intraspecific and interspecific divergences for both genes was found. The "10× rule" threshold resulted in lumping about half of distinct species for both genes. The neighbour-joining phylogenetic tree of COI could distinguish all species studied. However, the 16S rDNA tree could not distinguish some closely related species. In contrast, the character-based barcode method for both genes successfully identified 100% of the neogastropod species included, and performed well in discriminating neogastropod genera.<h4>Conclusions/significance</h4>This present study demonstrates the effectiveness of the character-based barcoding method for species identification in different taxonomic levels, especially for discriminating the closely related species. While distance and monophyly-based methods commonly use COI as the ideal gene for barcoding, the character-based approach can perform well for species identification using relatively conserved gene markers (e.g., 16S rDNA in this study). Nevertheless, distance and monophyly-based methods, especially the monophyly-based method, can still be used to flag species.
format	article
author	Shanmei Zou Qi Li Lingfeng Kong Hong Yu Xiaodong Zheng
author_facet	Shanmei Zou Qi Li Lingfeng Kong Hong Yu Xiaodong Zheng
author_sort	Shanmei Zou
title	Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.
title_short	Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.
title_full	Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.
title_fullStr	Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.
title_full_unstemmed	Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.
title_sort	comparing the usefulness of distance, monophyly and character-based dna barcoding methods in species identification: a case study of neogastropoda.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/e3ff7fc9f2184688adbb812abf267c66
work_keys_str_mv	AT shanmeizou comparingtheusefulnessofdistancemonophylyandcharacterbaseddnabarcodingmethodsinspeciesidentificationacasestudyofneogastropoda AT qili comparingtheusefulnessofdistancemonophylyandcharacterbaseddnabarcodingmethodsinspeciesidentificationacasestudyofneogastropoda AT lingfengkong comparingtheusefulnessofdistancemonophylyandcharacterbaseddnabarcodingmethodsinspeciesidentificationacasestudyofneogastropoda AT hongyu comparingtheusefulnessofdistancemonophylyandcharacterbaseddnabarcodingmethodsinspeciesidentificationacasestudyofneogastropoda AT xiaodongzheng comparingtheusefulnessofdistancemonophylyandcharacterbaseddnabarcodingmethodsinspeciesidentificationacasestudyofneogastropoda
_version_	1718423256572100608

Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda.

Ejemplares similares