Fig. 2.

Phylogenetic tree of retrovirus species currently listed in the ICTV taxonomy. The tree was constructed for representative members of family Retroviridae using multiple sequence alignments spanning conserved regions of the reverse transcriptase (RT) coding region of pol (domains 1–7), which is highly refractory to mutation. The RT alignment was constrained to the coordinate space of a master reference sequence (SFVpsc), with alignment columns selected based on this reference. The phylogeny was reconstructed using the maximum-likelihood method in RAxML, applying the RTrev model of amino acid substitution, selected using JModelTest. The tree is rooted on a consensus sequence for members of the subfamily Spumaretrovirinae. Asterisks indicate bootstrap support (1000 replicates) ≥ 70% for genus-level relationships and above. The scale bar represents the evolutionary distance in substitutions per site. Note that several retrovirus species listed in Table 1 are missing from the tree due to a lack of specific sequence information for the RT gene. Also note that some retroviruses are recombinants of members of different genera. For instance, Mason-Pfizer monkey virus (species Betaretrovirus maspfimon) and squirrel monkey retrovirus (species Betaretrovirus squmon) have acquired a gammaretrovirus env gene