Fig. 1

Evolutionary analysis of all known HML-2 proviruses. The phylogeny was inferred using the Maximum Likelihood method and Tamura-Nei (1993) model [26] of nucleotide substitutions and the tree with the highest log likelihood is shown. Highlighted in green are proviruses that appeared in literature after the publication of Subramanian list and are therefore missing from both the list and the phylogenetic analyses conducted by the authors [12]. For the sake of correctness of the alignment on which the phylogenetic tree was based, we split the 7p22.1 locus that contained two tandem proviral integrations sharing an LTR in the middle, into 7p22.1a and 7p22.1b. The shared LTR was used in 7p22.1a alignment entry as the 3’LTR and in 7p22.1b as the 5’LTR. Although proviruses 8p22 and 17p13.1 are capable of being aligned, are incorporated in all HML-2 lists cited in the main text, including the Subramanian list, and are also recognised by RepeatMasker as HML-2 elements, they are found to be distant in sequence, resembling an outgroup, hence Subramanian et al. [12] suggested them presumably being members of a group of proviruses that are a close cousin to HML-2, which they termed HML-11. We found that a similar divergence is observed for provirus 1q21.3, which is possibly also a close relative of HML-2 proviruses. Scale bar at the bottom represents genetic change