Summary of analysis of five population data sets

LocusmtDNA, control regionmtDNA, D-loopEnvelope geneSAT1, capsid proteinVermillion nuclear gene
Number of sequences7121353120
Alignment length76436928744312160
OrganismHumanGrant's gazelleHIV1, subtype BFoot and mouth disease virus D. melanogaster
PopulationAfricanNairobiAmerican, years 1986–1990Southern AfricaKenya and Zimbabwe
OutgroupChimpanzeeGrant's gazelle, Tsavo populationHIV1, subtype D, African sample, 1986Sat1 sequence from Uganda D. simulans
Average number of nucleotide differences15151848727.2
R SD 10.83198.98.3
R ST 2.622.253.622.672.88
R BD 0.050.790.890.380.41
R PT 0.370.570.290.490.47
Rate heterogeneity α0.
Tajima's D–1.27–0.59–1.92–0.33–0.48
ρ 43.334.8623127.3259
ReferenceVigilant 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.