Table 1. Comparison of SNP counts in data sets.

Θ	Length of DNA	Median no. SNPs in 100 generated trees	Mean no. SNPs in 100 generated trees	Mean % SNPs with more than two alleles
0.1	500	215	212.8	12.34
0.01	5,000	260	268.6	1.21
0.001	50,000	268	290.1	0.13

For each Θ-value, 100 trees were generated, each with 148 tips. DNA was simulated for the sequence length given. Sequence lengths were chosen to recover a similar number of SNPs for each Θ-value. Watterson’s estimator predicts 278.6 SNPs for each of these data sets.