Table 1. Positive selection in the TRIM5α gene.

Data set	-2(ln λ)	df	P value	dN/dS	Proportion of sites, %
All primates
M0 vs. M3 (k = 3)	217.94	4	P < 0.0001	2.4, 7.2	33, 4
M1 vs. M2	109.88	2	P < 0.0001	4.5	16
M7 vs. M8	109.50	2	P < 0.0001	4.2	18
Hominids + OWMs
M0 vs. M3 (k = 3)	57.42	4	P < 0.0001	1.8, 17	57, 2
M1 vs. M2	39.16	2	P < 0.0001	10	4
M7 vs. M8	40.21	2	P < 0.0001	10	4

We used likelihood ratio tests to determine whether any codon positions were associated with dN/dS significantly > 1 and hence possibly subject to positive Darwinian selection. Neutral models (M0, M1, and M7) were compared to selection models (M2 and M8), which allow a proportion of codons for which dN/dS exceeds 1, or models for heterogeneity of dN/dS among sites (M3). As indicated by the P values, all analyses find very strong evidence for the selection model. Note that in M3, two classes of sites are permitted to have dN/dS > 1. Also indicated are the proportion of codons that were found to have dN/dS > 1, with the associated dN/dS values shown. Analyses using the f61 model of codon frequencies are shown, but similar results were obtained by using the f3×4 frequency model (full paml results are available in Appendix 1).