TABLE 3.

Average number of recombination events per locus and the average proportion of loci with no recombination (in parentheses)

Tree	$\rho$	$S=2$		$S=8$
		$\theta =0.0025$	$\theta =0.01$	$\theta =0.0025$	$\theta =0.01$
A01 analysis
Tree B (Figure 1a)	0.05	0.7 (0.49)	0.7 (0.48)	0.9 (0.42)	0.9 (0.41)
	0.5	7.2 (0.00)	7.2 (0.00)	8.7 (0.00)	8.7 (0.00)
	5	67.6 (0.00)	67.8 (0.00)	80.5 (0.00)	80.6 (0.00)
Tree U (Figure 1b)	0.05	0.7 (0.49)	0.7 (0.49)	0.9 (0.43)	0.9 (0.42)
	0.5	7.1 (0.00)	7.1 (0.00)	8.5 (0.00)	8.6 (0.00)
	5	66.5 (0.00)	66.4 (0.00)	79.3 (0.00)	79.5 (0.00)
A11 analysis
Shallow (Figure 2a)	0.05	0.5 (0.63)	0.5 (0.63)	0.6 (0.57)	0.6 (0.57)
	0.5	4.7 (0.01)	4.7 (0.01)	5.7 (0.00)	5.7 (0.00)
	5	45.2 (0.00)	45.1 (0.00)	53.9 (0.00)	53.6 (0.00)
Deep (Figure 2b)	0.05	0.2 (0.85)	0.2 (0.85)	0.3 (0.78)	0.3 (0.78)
	0.5	1.6 (0.00)	1.6 (0.00)	2.5 (0.09)	2.5 (0.09)
	5	15.8 (0.00)	15.9 (0.00)	24.6 (0.00)	24.5 (0.00)
A00 analysis
Tree B (Figure 3a)	0.05	0.6 (0.54)	0.6 (0.54)	0.8 (0.46)	0.8 (0.46)
	0.5	6.2 (0.00)	6.2 (0.00)	7.8 (0.00)	7.7 (0.00)
	5	58.8 (0.00)	58.8 (0.00)	72.4 (0.00)	72.4 (0.00)
Tree U (Figure 3b)	0.05	0.6 (0.57)	0.6 (0.56)	0.7 (0.49)	0.7 (0.48)
	0.5	5.7 (0.00)	5.7 (0.00)	7.2 (0.00)	7.3 (0.00)
	5	54.3 (0.00)	54.1 (0.00)	67.9 (0.00)	67.9 (0.00)

The results are averages over the 100 replicate data sets of $L$ = 160 loci. The expected number of recombinations increases with the number of sequences ($S$) and is proportional to the recombination rate ($\rho$), but independent of the mutation rate ($\theta$).