Figure 2: Phylogenetic analyses of the ZR59 sequence.
From: An African HIV-1 sequence from 1959 and implications for the origin of the epidemic
ZR59 branched off the D clade near the B/D/F root in all analyses. The taxa are labelled with the year of sampling of a given sequence, or with ‘<’ and the year of the primary publication if the year of sampling was not specified. The analyses included the following reference sequences and their GenBank accession numbers: A 92, 92RW020 (U08794); A 85, U455 (M62320); B 91, 91HT652 (U08443); B 83, LAI (X01762); B 86, JRFL (U63632); H, the internal control for this study sampled in 1994; Man, the Manchester sailor sequence7 (U23487); C 92, 92BR025 (U09132); C 93, 93MW965 (U08455); D <89, NDK (M27323); D <87, Z6 (K03458); D 93, 92ZR001 (U27419); E 90, CM240 (U54771); E 93, 93TH966 (U08456); F 93, 93BR020 (U27401); F 93, 93BR029 (U27413); G <94, LBV217 (U09664); G 92, 92UG975 (U22010); outlier group 91, VAU (X80020); and outlier group <92, MVP5180 (L20571). The same set of input taxa was used for the weighted-parsimony and maximum-likelihood trees, except that H was included in the maximum-likelihood tree only. A larger set of taxa was used for the neighbour-joining tree. The scale for branch lengths is comparable for the maximum-likelihood and neighbour-joining trees. For the weighted-parsimony tree, the branch lengths are not directly comparable to the branch lengths of the other two trees, but the branching pattern substantiates the pattern obtained by the other two methods.
