Summary of analysis of five population data sets
| Locus | mtDNA, control region | mtDNA, D-loop | Envelope gene | SAT1, capsid protein | Vermillion nuclear gene |
|---|---|---|---|---|---|
| Number of sequences | 71 | 21 | 35 | 31 | 20 |
| Alignment length | 764 | 369 | 2874 | 431 | 2160 |
| Organism | Human | Grant's gazelle | HIV1, subtype B | Foot and mouth disease virus | D. melanogaster |
| Population | African | Nairobi | American, years 1986–1990 | Southern Africa | Kenya and Zimbabwe |
| Outgroup | Chimpanzee | Grant's gazelle, Tsavo population | HIV1, subtype D, African sample, 1986 | Sat1 sequence from Uganda | D. simulans |
| Average number of nucleotide differences | 15 | 15 | 184 | 87 | 27.2 |
| R SD | 10.8 | 3 | 19 | 8.9 | 8.3 |
| R ST | 2.62 | 2.25 | 3.62 | 2.67 | 2.88 |
| R BD | 0.05 | 0.79 | 0.89 | 0.38 | 0.41 |
| R PT | 0.37 | 0.57 | 0.29 | 0.49 | 0.47 |
| Rate heterogeneity α | 0.13 | 0.15 | 0.27 | 0.35 | 0.04 |
| Tajima's D | –1.27 | –0.59 | –1.92 | –0.33 | –0.48 |
| ρ | 43.3 | 34.8 | 623 | 127.3 | 259 |
| Reference | Vigilant et al. (1991) | Arctander et al. (1996) | Korber et al. (1998) | A. D. S. Bastos (personal communication) | Begun and Aquadro (1995) |
Data sets were aligned with ClustalX. The aligned sequences were then run through DNAdist and Fitch of PHYLIP (Felsenstein 1995) using the designated outgroup to root the tree. Substitution model used was HKY85. Tajima's D and ρ based on Hey and Wakeley's (1997) method was calculated using SITES (Hey and Wakeley 1997). Rate heterogeneity was calculated using PAML 2.0g (Yang 1999), using the tree topology suggested from Fitch.