Table 5.

Median and quartiles (in parentheses) of posterior probabilities for splitting the specified clades by bpp in data simulated using tree 2, with three sequences per population

Nuclear Loci	Method	$A_{\text{1}}{A}_{\text{2}}$	$B_{\text{1}}{B}_{\text{2}}$	$C_{\text{1}}{C}_{\text{2}}$	$D_{\text{1}}{D}_{\text{2}}$	AB	CD
Low-mutation rate
1 locus	RAxML	0.268	0.275	0.266	0.257	0.986	0.988
		(0.138, 0.427)	(0.144, 0.446)	(0.127, 0.418)	(0.140, 0.443)	(0.896, 0.999)	(0.916, 0.999)
	*beast	0.289	0.260	0.291	0.270	0.993	0.993
		(0.146, 0.504)	(0.136, 0.464)	(0.145, 0.503)	(0.136, 0.488)	(0.925, 1.000)	(0.916, 1.000)
5 loci	RAxML	0.106	0.107	0.110	0.109	1.000	1.000
		(0.062, 0.218)	(0.061, 0.215)	(0.062, 0.221)	(0.064, 0.207)	(1.000, 1.000)	(1.000, 1.000)
	*beast	0.113	0.110	0.112	0.107	1.000	1.000
		(0.062, 0.201)	(0.062, 0.219)	(0.063, 0.234)	(0.062, 0.204)	(1.000, 1.000)	(1.000, 1.000)
High-mutation rate
1 locus	RAxML	0.034	0.040	0.036	0.037	1.000	1.000
		(0.016, 0.133)	(0.018, 0.113)	(0.017, 0.120)	(0.018, 0.118)	(0.992, 1.000)	(0.992, 1.000)
	*beast	0.036	0.032	0.040	0.038	1.000	1.000
		(0.018, 0.504)	(0.015, 0.464)	(0.018, 0.503)	(0.018, 0.488)	(0.990, 1.000)	(0.991, 1.000)
5 loci	RAxML	0.004	0.005	0.005	0.004	1.000	1.000
		(0.002, 0.012)	(0.002, 0.011)	(0.002, 0.012)	(0.002, 0.010)	(1.000, 1.000)	(1.000, 1.000)
	*beast	0.004	0.005	0.004	0.005	1.000	1.000
		(0.002, 0.010)	(0.002, 0.012)	(0.002, 0.011)	(0.002, 0.011)	(1.000, 1.000)	(1.000, 1.000)

Notes: The probability for splitting clade ABCD (the root) is 1 in every replicate data set.