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Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals

Arong Luo12, Aibing Zhang3, Simon YW Ho4, Weijun Xu5, Yanzhou Zhang1, Weifeng Shi6, Stephen L Cameron7* and Chaodong Zhu1*

Author Affiliations

1 Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China

2 Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China

3 College of Life Sciences, Capital Normal University, Beijing 100048, PR China

4 School of Biological Sciences, University of Sydney, Sydney NSW 2006, Australia

5 Zhongbei College, Nanjing Normal University, Nanjing 210046, PR China

6 UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland

7 Australian National Insect Collection, CSIRO Entomology, Canberra ACT 2601, Australia

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BMC Genomics 2011, 12:84  doi:10.1186/1471-2164-12-84

Published: 28 January 2011



A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagnose and delimit species. However, there is no compelling a priori reason for the exclusive focus on this region, and it has been shown that it performs poorly for certain animal groups. To explore alternative mitochondrial barcoding regions, we compared the efficacy of the universal CO1 barcoding region with the other mitochondrial protein-coding genes in eutherian mammals. Four criteria were used for this comparison: the number of recovered species, sequence variability within and between species, resolution to taxonomic levels above that of species, and the degree of mutational saturation.


Based on 1,179 mitochondrial genomes of eutherians, we found that the universal CO1 barcoding region is a good representative of mitochondrial genes as a whole because the high species-recovery rate (> 90%) was similar to that of other mitochondrial genes, and there were no significant differences in intra- or interspecific variability among genes. However, an overlap between intra- and interspecific variability was still problematic for all mitochondrial genes. Our results also demonstrated that any choice of mitochondrial gene for DNA barcoding failed to offer significant resolution at higher taxonomic levels.


We suggest that the CO1 barcoding region, the universal DNA barcode, is preferred among the mitochondrial protein-coding genes as a molecular diagnostic at least for eutherian species identification. Nevertheless, DNA barcoding with this marker may still be problematic for certain eutherian taxa and our approach can be used to test potential barcoding loci for such groups.