Table 2.

Evolutionary History of Central and Western Chimpanzees, Estimated Using PPP and IMa3.

Subspecies	Analysis	Parametera	Estimateb	95% Confidence Interval
Pan troglodytes troglodytes	IM	N	33,640	24,26054,601
	PPP, IMa3	N	59,911	51,74371,509
Pan troglodytes verus	IM	N	9,187	6,33314,196
	PPP, IMa3	N	9,270	8,37210,414
Ancestor	IM	N	6,303	61417,092
	PPP, IMa3	N	7,474	5,922-9,107
	IM	t	758,504	495,003-1,390,904
	PPP, IMa3	t	740,662	668,662-829,212
P. t. t. $\to$P t. v.	IM	m	6.83E–08	1.07E–07
				1.25E–05
	PPP, IMa3	m	1.89E–06	3.79E–06
				3.01E–07
	IM	2Nm	0.00126	—
	PPP, IMa3	2Nm	0.03314	—
P. t. v. $\to$P. t. t.	IM	m	7.79E–06	2.40E–06
				1.93E–05
	PPP, IMa3	m	2.63E–06	4.47E–06
				9.56E–07
	IM	2Nm	0.5243	—
	PPP, IMa3	2Nm	0.2995	—

^aEstimates for intervals for population size (N), splitting time (t in years), migration rate (m per gene copy per generation), and population migration rates (2Nm) scaled by the geometric mean of mutation rates. IM (Hey and Nielsen 2004) results were obtained from the first IM analysis of P. t. troglodytes and P. t. verus (Won and Hey 2005), which used 48 hand curated loci and the original IM program (Hey and Nielsen 2004).

^bMaximum likelihood estimates. To convert primary parameter estimates, which are scaled by the geometric means of mutation rates, we used the geometric mean of locus-wide mutation rates per year, assuming a per year rate of 1.2e-8 per base (Scally and Durbin 2012) and 24.5 years per generation (Langergraber et al. 2012). For the 48 loci in the original IM study, the value was 2.65654E–07 per year, whereas the corresponding rate was 9.97486e–07 for the longer loci sampled using PPP.