Table 1.

Type I error rates for CADM simulations with nucleotide sequences matrices simulated on independently-generated additive trees under a GTR + Γ + I model of evolution.

		Number of IM
n	L	2	3	4	5	10
10	1000	0.052	0.047	0.042	0.049	0.046
		(0.038, 0.066)	(0.034, 0.060)	(0.030, 0.054)	(0.036, 0.062)	(0.033, 0.059)
	5000	0.050	0.050	0.038	0.046	0.046
		(0.036, 0.064)	(0.036, 0.064)	(0.026, 0.050)	(0.033, 0.059)	(0.033, 0.059)
	10 000	0.049	0.048	0.046	0.046	0.047
		(0.036, 0.062)	(0.035, 0.061)	(0.033, 0.059)	(0.033, 0.059)	(0.034, 0.060)
	20 000	0.047	0.047	0.039	0.045	0.043
		(0.034, 0.060)	(0.034, 0.060)	(0.027, 0.051)	(0.032, 0.058)	(0.030, 0.056)
25	1000	0.054	0.056	0.054	0.056	0.04
		(0.040, 0.068)	(0.042, 0.070)	(0.040, 0.068)	(0.042, 0.070)	(0.028, 0.052)
	5000	0.053	0.048	0.046	0.05	0.042
		(0.039, 0.070)	(0.035, 0.061)	(0.033, 0.059)	(0.036, 0.064)	(0.030, 0.054)
	10 000	0.046	0.054	0.05	0.049	0.050
		(0.033, 0.059)	(0.040, 0.068)	(0.036, 0.064)	(0.036, 0.062)	(0.036, 0.064)
	20 000	0.043	0.050	0.054	0.047	0.040
		(0.030, 0.056)	(0.036, 0.064)	(0.040, 0.068)	(0.034, 0.060)	(0.028, 0.052)
50	1000	0.048	0.062	0.059	0.050	0.049
		(0.035, 0.061)	(0.047, 0.077)	(0.044, 0.074)	(0.036, 0.064)	(0.036, 0.062)
	5000	0.056	0.049	0.055	0.053	0.050*
		(0.042, 0.070)	(0.036, 0.062)	(0.041, 0.069)	(0.039, 0.070)	(0.007, 0.093)
	10 000	0.041	0.048	0.053	0.051	0.050*
		(0.029, 0.053)	(0.035, 0.061)	(0.039, 0.067)	(0.037, 0.065)	(0.007, 0.093)
	20 000	0.050	0.053	0.050	0.056	0.060*
		(0.036, 0.064)	(0.039, 0.067)	(0.036, 0.064)	(0.042, 0.070)	(0.012, 0.107)
100	1000	0.051	0.042	0.040	0.044	0.030*
		(0.037, 0.065)	(0.030, 0.054)	(0.028, 0.052)	(0.031, 0.057)	(-0.004,0.064)
	5000	0.066	0.040*	0.030*	0.050*	0.060*
		(0.051, 0.081)	(0.001, 0.079)	(-0.004,0.064)	(0.007, 0.093)	(0.013, 0.107)
	10 000	0.030*	0.060*	0.070*	0.050*	0.040*
		(-0.004,0.064)	(0.013, 0.107)	(0.019, 0.120)	(0.007, 0.093)	(0.001, 0.079)
	20 000	0.060*	0.050*	0.040*	0.060*	0.070*
		(0.013, 0.107)	(0.007, 0.093)	(0.001, 0.079)	(0.013, 0.107)	(0.019, 0.120)

Rejection rate are given at a significance level of 0.05, with 95% confidence intervals in parentheses. Calculated from 1000 replicates, except for cells with * (100 replicates). IM = incongruent matrix, n = number of taxa, L = nucleotide sequence length.