Analysis of sequence diversity in mitochondrial genes (mtDNA) has contributed tremendously to the understanding of relationships of species in various groups of eukaryotes. Yet, deciding which gene to use to resolve the divergence within a group remains an important issue in phylogenetics. For the goals of species identification in animals, the cytochrome c oxidase subunit 1 (cox1) has been introduced as standard marker. Making use of the difference in intra- and interspecific genetic variation–the DNA barcoding gap- cox1 can be used as a fast and accurate marker for the identification of animal species. We compare the performance of cox1 (2776 sequences, 756 species) in species-identification with that of two other mitochondrial markers, cytochrome b (cob: 4621 sequences, 2087 species) and 16S (708 sequences, 498 species). A wide gap exist between intra- and interspecies divergences for both cox1 and cob genes whereas no such gap is seen for 16S, indicating that rRNA genes are less suitable for species delimitation in DNA barcoding. This study confirms that DNA barcoding allows accurate identification of species and as such DNA barcoding may have an important role in increasing our understanding of comparative ornithology.

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