TABLE 2.
Phylogenetic support for the clustering of the six major PLV lineages in five putative recombinant fragments
| Fragmenta | Monophyletic cladeb | Percentage of bootstrap/jackknife support for:
|
P value for MLc | |
|---|---|---|---|---|
| Neighbor-joining tree (1,000 replicates) | Fitch-Margoliash tree (1,000 replicates) | |||
| PLV_REC1 | (SIVlhoest, SIVcol, SIVcpz) | 81.2/80.2 | 90.8/90.2 | <0.001 |
| (SIVsmm, SIVagm) | 68.7/68.7 | 86.9/90.5 | >0.1 | |
| PLV_REC2 | (SIVsyk, SIVsmm) | 89.8/87.9 | 89.0/88.5 | <0.001 |
| (SIVcol, SIVlhoest) | 74.8/79.2 | 76.4/78.1 | 0.002 | |
| (SIVagm, [SIVcol, SIVlhoest]) | 52.6/50.5 | 54.2/52.3 | <0.001 | |
| PLV_REC3 | (SIVcol, SIVagm, SIVsmm) | <50/50 | <50/50 | 0.007 |
| (SIVcpz, SIVlhoest) | <50/50 | <50/50 | 0.029 | |
| PLV_REC4 | (SIVsyk, SIVcol) | 88.3/88.1 | 88.4/88.0 | 0.01 |
| (SIVcpz, SIVagm) | <50/50 | <50/50 | <0.001 | |
| PLV_REC5 | (SIVcol, SIVcpz) | 56.9/56.3 | 55.9/57.9 | 0.02 |
| (SIVagm, SIVsmm) | 98.3/98.0 | 98.5/98.1 | <0.001 | |
| (SIVlhoest, [SIVagm, SIVsmm]) | 83.6/84.8 | 82.2/83.9 | <0.001 | |
a
Putative recombinant fragments inferred from the results of the bootscanning analyses (Fig. 3). See the text for more details.
b
Monophyletic clades are indicated between parentheses (Newick notation). Only clades significantly supported by at least one of the phylogenetic methods used are reported.
c
P value of the zero-branch-length test for the maximum-likelihood tree (P values of >0.05 are not significant).