DNA barcoding based on a standardized region of 648 base pairs of mitochondrial DNA sequences from Cytochrome C Oxidase 1 (COX1) is proposed for animal species identification. Recent studies suggested that DNA barcoding has been effective for identifying 94% of bird species. The proposed threshold of 10 times the average intraspecific variation could be used for the identification and delimitation of new species. As a different part of the mitochondrial DNA evolves at various mutation rates, they show a variety of capabilities to distinguish taxa to species level. In order to compare the efficiency of protein-coding genes (PCGs) in birds, the complete genome of 310 birds, including 12 mitochondrial genes (except ND6) and barcoding the region of COX1, were examined. We concentrated on the intra- and inter-specific variations and the degree of mutational saturation as criteria for our evaluations. Some genes like ATP8, ND2 and ND5 showed the greatest divergence in intra- and inter-specific variations. The overlap between intra- and inter-specific variability for all genes is still troublesome. Our results may have been influenced by the sample size because our data were not representative of all bird species. More additional taxa may shed light more on DNA barcoding candidate genes.

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