Table 2.

Type I error rates of the cross-population extended haplotype-based homozygosity score test (xp-EHHST).

Demographic model	Sample size n	ρ	Nominal level			Sample size n	ρ	Nominal level
			α=0.05	α=0.01	α=0.001			α=0.05	α=0.01	α=0.001
Population structure	100	1.5	0.0388	0.0116	0.0016	60	1.5	0.0468	0.0116	0.0016
		3	0.0316	0.0056	0.0008		3	0.0324	0.0084	0.0012
		6	0.0244	0.0045	0.0000		6	0.0232	0.0044	0.0004
		9	0.0164	0.0028	0.0000		9	0.0228	0.0052	0.0004
Population expansion	100	1.5	0.0432	0.0080	0.0008	60	1.5	0.0352	0.0056	0.0012
		3	0.0352	0.0052	0.0008		3	0.0264	0.0064	0.0012
		6	0.0252	0.0036	0.0004		6	0.0224	0.0048	0.0008
		9	0.0228	0.0052	0.0008		9	0.0148	0.0024	0.0000
Population bottleneck 150/300	100	1.5	0.0768	0.0184	0.0028	60	1.5	0.0732	0.0236	0.0056
		3	0.0420	0.0092	0.0012		3	0.0500	0.0116	0.0012
		6	0.0296	0.0052	0.0008		6	0.0324	0.0080	0.0012
		9	0.0264	0.0032	0.0004		9	0.0240	0.0048	0.0004
Population bottleneck 250/500	100	1.5	0.0692	0.0192	0.0028	60	1.5	0.0724	0.0184	0.0024
		3	0.0380	0.0068	0.0008		3	0.0404	0.0084	0.0012
		6	0.0340	0.0064	0.0008		6	0.0336	0.0056	0.0004
		9	0.0272	0.0028	0.0004		9	0.0292	0.0076	0.0004

All results were based on 2,500 simulations using software ms [10], and a genomic region of 101 SNPs was simulated