Table 4. Estimated proportions of deleterious, neutral, and advantageous nonsynonymous mutations in simulated data sets when the distribution of fitnesses is bimodal for a 4096-taxon tree with increasing total tree height.

	Tree height
	0.01171875			0.75			48
Penalty	p−	p0	p+	p−	p0	p+	p−	p0	p+
True	0.598	0.397	0.004	0.598	0.397	0.004	0.598	0.397	0.004
No penalty (λ = 0)	0.850	0.149	0.000	0.687	0.308	0.004	0.599	0.396	0.004
Normal
σ = 1000	0.850	0.150	0.000	0.687	0.308	0.005	0.600	0.396	0.004
σ = 100	0.850	0.150	0.001	0.687	0.309	0.005	0.600	0.396	0.004
σ = 10	0.813	0.181	0.006	0.680	0.314	0.006	0.600	0.396	0.004
Dirichlet
α = 0.01	0.774	0.216	0.010	0.677	0.317	0.006	0.600	0.396	0.004
α = 0.1	0.390	0.599	0.011	0.581	0.410	0.008	0.599	0.396	0.004
α = 1.0	0.053	0.947	0.000	0.370	0.623	0.007	0.597	0.398	0.005