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Figure 3 | Retrovirology

Figure 3

From: Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates

Figure 3

Phylogenetic relationship of ELVgv to other retroviruses. (A) Phylogeny of ELVgv and other retroviruses, based on alignment of RT amino acid sequences (Additional file 4 contains the alignment in FASTA format and the full names of the retroviruses). The alignment was generated in MEGA5 software [15] using the MUSCLE algorithm [16]. The ML tree was constructed in MEGA5 software, using the rtREV amino acid substitution matrix [17], Nearest-Neighbor-Interchange ML heuristic method and otherwise default parameters. Support for ML tree was assessed by 1,000 nonparametric bootstrap replicates. Bayesian analysis was run for 200,000 steps, sampling every 1,000 steps and discarding first 25% of the trees. Average standard deviation of split frequencies converged during 10,000 steps bellow 0.001. The amino acid model F81 in program MrBayes was used [18]. The support values are indicated above the branches (percent Bootstrap scores/Bayesian posterior probabilities). The ELVgv position is highlighted in bold and underlined. The names of the retrovirus genera are shown on the right. (B) Phylogenetic relationship of ELVgv to other exogenous and endogenous lentiviruses. The analysis was based on alignment including 2,350 most conserved nucleotides of gag-pol from 31 lentiviruses (used also in Gilbert et al. [5]), together with ELVmpf [6],[8], and ELVgv from this work (alignment available in Additional file 5). The alignment was generated in MEGA5 program [15] using the MUSCLE algorithm [16]. The ML analysis was performed using MEGA5 program under Tamura-Nei model, Nearest-Neighbor-Interchange ML heuristic method and otherwise default parameters. Bootstrap supports (percent out of 1,000 replicates) are shown. Grey lines designate groups of exogenous lentiviruses. The endogenous lentiviruses are denoted by black dots. Scale bars indicate number of substitutions (amino acid or nucleotide) per site.

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