Figure 4

A NJ haplotype tree obtained by 50% consensus rule using 117 variable sites within the sequenced portion of the D-loop, with their corresponding haplotypes generated from the 146 haplotypes of 855 birds. Different haplotypes are color-coded based on the group they belong to (See methods section for grouping details) as indicated. Filled structures indicate haplotypes consisting of all birds of the same group (e.g. Indian RJF-pink colored), while open structures indicate the presence of at least one bird of a specified/color-coded group that also contains birds belonging to other groups (e.g. Indian RJF containing domestic birds). Different sub-species of G. gallus form only two clusters, one of G. g. bankiva and others containing all other sub-species. The cluster of G. gallus sub-species, however also contained another species of Gallus, namely G. lafayettei. Identical sequences are shown as dots in comparison with H_11. A specific mutation found in 96% of G. g. murghi is shown in bold and red color and the corresponding nucleotide is underlined in H_11. This position corresponds to the nucleotide number 360 (where there is 'C') in the complete mitochondrial genome sequence of G. gallus (Acc. No. NC_001323). The color-coding used is represented below the figure.