Phylogeny of provirus LTR sequences. Bayesian inference trees were generated using 5' and 3' LTRs of HML-2 provirus elements in the human genome. LTR sequences of less than 250 bases in length were not included, as they limited capacity to detect phylogenetic relationships among LTR sequences. Sequences are color-coded according to distinctive LTR subgroup features (see Methods). LTR5Hs sequences are shown in (A), with 5B and 5A sequences added to serve as a reference. LTR5A (B) and LTR5B (C) are similarly displayed. Open diamonds indicate recombinant proviruses, and duplications are grouped using colored bars. Posterior probability values > 70 are shown for the best tree rooted on 5A and 5B (A), 5Hs (B), and 5B and 5Hs (C).