Table 2.

Bayesian estimates of mean time to the most common ancestor, mean nucleotide substitution rates, and percentage lineages at selected time periods for HIV-1C pol in Zimbabwe.

	Expo-strict clock	Expo-relaxed clock	BSP-strict clock	BSP-relaxed clock
tMRCA	1973.638	1974.078	1971.831	1972.035
95% HPD lower	1977.702	1978.246	1977.487	1978.175
95% HPD upper	1969.578	1969.371	1965.799	1965.062
Subst. rate	0.002068	0.00206	0.002186	0.002192
95% HPD lower	0.001729	0.001664	0.001834	0.001791
95% HPD upper	0.00241	0.002456	0.002555	0.002597
% Strains in 1975	1.861	1.861	1.406	1.406
95% HPD lower	0.565	0.565	0.565	0.565
95% HPD upper	5.65	5.65	2.26	2.26
% Strains in 1980	20.7	20.7	10.1	10.1
95% HPD lower	1.695	1.695	1.13	1.13
95% HPD upper	47.5	47.5	31.6	31.6
% Strains in 1985	82.9	82.9	81.3	81.3
95% HPD lower	63.8	63.8	55.4	55.4
95% HPD upper	96.6	96.6	98.3	98.3
% Strains in 1990	98.5	98.5	97.8	97.8
95% HPD lower	97.7	97.7	96	96
95% HPD upper	99.4	99.4	98.3	98.3

The table contains the mean time to the most recent common ancestor (tMRCA), the estimated mean substitution rate (nucleotide substitutions/site/year), and the median percentage of strains present at selected time periods for clade HIV-1C in Zimbabwe. Percentage strains represent the proportion of strains sampled in 2006 estimated to have existed at 5-year time intervals throughout the epidemic period in Zimbabwe. The 95% lower and upper highest posterior density (HPD) intervals are shown. The tMRCA and substitution rate estimates were calculated using BEAST under exponential (Expo) and Bayesian skyline plot (BSP) demographic growth models assuming both a strict and relaxed molecular clock. Lineage estimations were calculated from the posterior distribution of Bayesian trees using TreeStat.