Fig. 4

Evolution of HERV-K HML-2 Xq21.33 in Africa. Evolutionary relationships of taxa. The evolutionary history was inferred using the Neighbor-Joining method [34]. The optimal tree with the sum of branch length = 0.00263695 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [35]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method [37] and are in the units of the number of base substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 1). This analysis involved 42 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. All ambiguous positions were removed for each sequence pair (pairwise deletion option). There were a total of 3044 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [36]. The tree is rooted to the known Xq21.33 HERV-K HML-2 sequence (Accession no. KU054272.1). NB: Nigerian BrC, NoB: Nigerian No BrC, AAP: African American PCa, P: Pygmy, GB: Ghanaian BrC, DT22: African BrC cell line. The left side of the tree would indicate a first genetic drift (T > C) event and at the right side the three show two small protruded branches that indicate gene conversion events