Table 3.

Percentage of false positives splitting one species into two by bpp with posterior more than or equal to 95% in data simulated using tree 2, with three sequences sampled from each population

Nuclear Loci	Method	$A_{\text{1}}{A}_{\text{2}}$	$B_{\text{1}}{B}_{\text{2}}$	$C_{\text{1}}{C}_{\text{2}}$	$D_{\text{1}}{D}_{\text{2}}$
Low-mutation rate
1 locus	RAxML	0.007	0.009	0.003	0.011
	*beast	0.053	0.057	0.058	0.064
5 loci	RAxML	0.004	0.006	0.006	0.002
	*beast	0.006	0.005	0.009	0.006
High-mutation rate
1 locus	RAxML	0.030	0.036	0.030	0.030
	*beast	0.043	0.037	0.040	0.036
5 loci	RAxML	0.001	0.001	0.002	0.002
	*beast	0.000	0.000	0.001	0.000

See note to Table 2.