Table 3. Estimated percentage lineages through time for the four different southern African data sets.

Time	Southern Africa Percentage Linages Through Time
	gag p24 full-length + old sequence				pol full-length + old sequence
	Mean	Median	Upper	Lower	Mean	Median	Upper	Lower
2010	100	100	100	100	100	100	100	100
2005	100	100	100	100	100	100	100	100
2000	99.76	99.73	100	99.47	99.66	99.73	100	99.47
1995	99.27	99.2	99.47	98.67	99.42	99.47	99.47	99.2
1990	98.57	98.67	99.47	97.6	98.43	98.4	99.2	97.33
1985	95.89	96.27	98.4	91.2	91.77	91.98	95.99	86.1
1980	61.29	61.07	77.87	46.93	54.3	54.28	66.58	41.98
1975	23.57	22.93	37.33	12.53	9.39	9.09	16.31	4.28
1970	8.46	7.47	18.67	2.93	1.62	1.6	2.67	0.8
1965	2.47	2.4	5.33	0.8	0.75	0.8	1.07	0.53
	South Africa Percentage Linages Through Time
2010	100	100	100	100	100	100	100	100
2005	100	100	100	100	100	100	100	100
2000	97.35	99.89	100	98.32	99.84	100	100	99.41
1995	96.75	95.09	98.61	97.16	99.23	99.41	99.71	98.24
1990	94.52	93.13	98.32	90.78	96.94	97.36	99.41	91.79
1985	70.23	70.69	90.49	42.34	72.03	73.9	91.5	42.82
1980	31.2	27.77	70.19	8.12	32	29.03	70.97	8.21
1975	8.98	6.45	32.19	1.45	9.21	6.74	32.55	1.47
1970	2.2	1.4	8.41	0.58	2.26	1.47	8.5	0.59
1965	0.55	0.35	2.1	0.15	0.56	0.37	2.13	0.15

These estimates were derived from non-parametric runs under a relaxed molecular clock assumption and an estimated substitution rate.