TABLE 2.

Inferred bottleneck parameters for the CEU data set

	Schaffner hotspot modela		Empirical hotspot modelb
Parameter	MLE	95% C.I.	MLE	95% C.I.
Ncur	10,000	9,315–10,665	10,000	9,440–11,454
Nmid/Ncur	0.055	0.052–0.064	0.05	0.042–0.066
Nanc/Ncur	0.8	0.70–?c	0.8	0.66–0.97
tcur	1,100	1,017–1,140	1,200	1,086–1,437
tmid	400	360–475	300	260–552

MLEs and ∼95% C.I.'s from the profile-likelihood curves for the five-parameter bottleneck model are shown.

^aThe hotspot model is similar to that described by Schaffner et al. (2005) (see methods).

^bThe hotspot model is based directly on the LDhat genetic map.

^cWe did not estimate an upper boundary on the C.I. since the profile-likelihood surface for N_anc/N_cur is relatively flat from 0.8 to 1.0 and we did not consider points >1.0 (Figure S11).