Figure 4

RT-based phylogenetic analyses. (A) Simplified phylogenetic relationship of modern bird lineage. Bayesian estimates of the divergence times (in million years, Myr) are based on mitochondrial gene data [68, 91]. (B) Protein identity scores of avian Ovex1 RT fragments. The 133-amino-acid sequences of the RT fragments obtained by PCR from turkey, guinea fowl and duck were aligned with the homologous regions of chicken and zebra finch (Gag-Pol residues 768 to 900). The corresponding sequence of SpeV was added for comparison. The alignment, performed with ClustalW2, is shown in additional file 7 (Figure S8, Alignment of Ovex1 RT and homologous sequences). (C) Relationship of the five Ovex1 RT-fragment sequences. The phylogenetic tree and bootstrap values (1,000 iterations) were calculated by the neighbor-joining (NJ) method [85] using the QuickTree software and the tree drawn with NJplot. Branch lengths are proportional to substitution levels. The scale bar represents 5% divergence. Bootstrap percentages are indicated at the branch forks. (D) RT-based unrooted dendrogram of Ovex1 and representative retroviral elements. The alignment, corresponding to chicken Ovex1 Gag-Pol amino-acid residues 759 to 917, was performed with ClustalW2 with default settings and adjusted manually. It is given in additional file 7 (Figure S8, Alignment of Ovex1 RT and homologous sequences). The relationship and bootstrap values (1,000 iterations) were calculated by the neighbor-joining method with QuickTree and the unrooted dendrogram drawn with NJplot. Abbreviations and database accession numbers are given in Materials and methods. RTs of avian origin are underlined. Branch lengths are proportional to substitution levels. The scale bar represents 10% divergence. Bootstrap percentages are indicated at the branch forks when at least equal to 50%.