TABLE 3.
Likelihood mapping analysis of the 4,845 possible groups of four sequences (quartets) for the putative recombinant fragments according to the SIVgsn-99CM71 genome identified on the bootscan analysis
| Fragment | Nucleotide positionsa | Gene region | Phylogenetic signalb (%) | Assignmentc |
|---|---|---|---|---|
| I | 455-2754 (1,250) | gag-pol | 95.4 | SIVsyk |
| II | 2755-3330 (380) | pol | 84.2 | N.A. |
| III | 3331-4101 (500) | pol | 92.1 | N.A. |
| IV | 4102-4536 (290) | pol | 78.3 | N.A. |
| V | 4537-5464 (360) | pol-vif | 72.9 | N.A. |
| VI | 6147-6761 (280) | env | 76.7 | N.A. |
| VII | 6762-7076 (189) | env | 81.4 | N.A. |
| VIII | 7077-7454 (160) | env | 70.8 | N.A. |
| IX | 7455-8360 (544) | env | 90.7 | SIVcpz |
| X | 8361-9255 (316) | env-nef | 70.7 | N.A. |
The number of nucleotides effectively used in the phylogenetic analysis after excluding gaps and third codon positions from the alignment is given in parentheses. The putative recombinant breakpoints were inferred from the bootscanning profile in Fig. 4.
Values indicate the percentage of quartets that are compatible with tree-like phylogeny (phylogenetic signal) in the likelihood maps obtained with Tree-Puzzle (37). Values of >90% are in boldface. Only first plus second codon positions were used in the likelihood mapping analysis because the third positions of each gene are always saturated (see Table 2).
Deduced from the bootscan analysis. N.A., not assignable.