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Citation for Study 15265

Citation title: "DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China".

Study name: "DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China".

This study is part of submission 15265 (Status: Published).

Citation

Li J., Zheng X., Cai Y., Liu S., Zhang X., Yang M., Yue B., & Li J. 2014. DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China. Molecular Ecology Resources, .

Authors

• Li J. (submitter) 8615882474902
• Zheng X.
• Cai Y.
• Liu S.
• Zhang X.
• Yang M.
• Yue B.
• Li J.

Abstract

Identification of rodents is very difficult mainly due to high similarities in morphology and their controversial taxonomy. In this study, a 645 bp or 648 bp sequence of mitochondrial cytochrome oxidase subunit I (COI) was used as a DNA barcode to identify the Murinae and Arvicolinae species distributed in China, and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31species; 11 genera) from Murinae and 130 sequences (23 species; 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyze the datasets. There was no obvious barcode gap in the two subfamilies. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees (NJ, BI, MP, and ML) exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high nodal support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision and the inferences of other analytic results. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius, and E. hintoni, and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.

Keywords

DNA barcoding; COI; Murinae; Arvicolinae; species identification

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S15265
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref22806,
  	 author = {Jing  Li and Xin  Zheng and Yansen  Cai and Shaoying  Liu and Xiuyue  Zhang and Min  Yang and Bisong  Yue and Jing  Li},
  	 title = {DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China},
  	 year = {2014},
  	 keywords = {DNA barcoding; COI; Murinae; Arvicolinae; species identification},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Ecology Resources},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Identification of rodents is very difficult mainly due to high similarities in morphology and their controversial taxonomy. In this study, a 645 bp or 648 bp sequence of mitochondrial cytochrome oxidase subunit I (COI) was used as a DNA barcode to identify the Murinae and Arvicolinae species distributed in China, and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31species; 11 genera) from Murinae and 130 sequences (23 species; 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyze the datasets. There was no obvious barcode gap in the two subfamilies. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees (NJ, BI, MP, and ML) exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high nodal support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision and the inferences of other analytic results. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius, and E. hintoni, and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework. }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 22806
  AU  - Li,Jing 
  AU  - Zheng,Xin 
  AU  - Cai,Yansen 
  AU  - Liu,Shaoying 
  AU  - Zhang,Xiuyue 
  AU  - Yang,Min 
  AU  - Yue,Bisong 
  AU  - Li,Jing 
  T1  - DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China
  PY  - 2014
  KW  - DNA barcoding; COI; Murinae; Arvicolinae; species identification
  UR  - http://dx.doi.org/
  N2  - Identification of rodents is very difficult mainly due to high similarities in morphology and their controversial taxonomy. In this study, a 645 bp or 648 bp sequence of mitochondrial cytochrome oxidase subunit I (COI) was used as a DNA barcode to identify the Murinae and Arvicolinae species distributed in China, and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31species; 11 genera) from Murinae and 130 sequences (23 species; 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyze the datasets. There was no obvious barcode gap in the two subfamilies. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees (NJ, BI, MP, and ML) exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high nodal support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision and the inferences of other analytic results. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius, and E. hintoni, and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework. 
  L3  - 
  JF  - Molecular Ecology Resources
  VL  - 
  IS  - 
  ER  -