FIG. 2.

Frequency with which common substitution models are not rejected by (a) GC tests and (b) PPSs for 25 empirical data sets. Simple models such as JC, which assumes equal base frequencies and substitution rates, normally cannot be rejected as long as they incorporate a proportion of invariable sites (I), Γ-distributed rates (Γ), or a combination of the two (I + Γ). Assessed models include JC, F81, which assumes unequal base frequencies and equal substitution rates, K2P, which incorporates equal base frequencies and separate transition and transversion rates, HKY, which assumes unequal base frequencies and separate transition and transversion rates, K3P, which incorporates equal base frequencies, two transversion rates, and equal transition rates, K3Puf with unequal base frequencies, Tamura–Nei, which assumes unequal base frequencies, one transversion rate, and independent transition rates, TrNef with equal base frequencies, transitional (TIM), which incorporates unequal base frequencies, two transversion, and independent transition rates, TIMef with equal base frequencies, transversional (TVM), which incorporates unequal base frequencies, independent transversion rates, and one transition rate, TVMef with equal base frequencies, symmetrical (SYM), which assumes equal base frequencies and independent substitution rates, and GTR, which incorporates unequal base frequencies and independent substitution rates. Overall, PPSs failed to reject somewhat simpler models than the GC test.