Table 1.

Likelihood ratio tests for positive selection in Apobec3DE

Treea	Codon modelb	M1 vs M2c	M7 vs M8d	Chimpanzee-bonobo ancestore
A (h [g {c, b}])	F3 × 4	P < 0.001	P < 0.001	P < 0.05
	F61	P < 0.001	P < 0.001	P < 0.05
B (g [h {c, b}])	F3 × 4	P < 0.001	P < 0.001	P < 0.05
	F61	P < 0.001	P < 0.001	P < 0.05

^aTree A was obtained with Apobec3DE gene sequences. In tree A, human Apobec3DE (h) is an outgroup to gorilla (g), chimpanzee (c), and bonobo (b) Apobec3DE. Tree B follows species phylogeny. In tree B, gorilla Apobec3DE is an outgroup to human, chimpanzee, and bonobo Apobec3DE.

^bTwo different models of codon frequencies (F3 × 4 and F61) were used for analyses.

^cLikelihood ratio tests were performed by comparing model 1 (two-state, dN/dS > 1 disallowed) to model 2 (two-state, dN/dS > 1 allowed). P values of <0.05 indicate that a model of selection (M2) provides a better fit of the data.

^dLikelihood ratio tests were performed by comparing model 7 (beta distribution, dN/dS > 1 disallowed) to model 8 (beta distribution, dN/dS > 1 allowed). P values of <0.05 indicate that a model of selection (M8) provides a better fit of the data.

^eLikelihood ratio tests were performed by comparing a model where dN/dS = 1 to a model where dN/dS > 1 for the chimpanzee-bonobo ancestor. P values of <0.05 indicate that a model of selection (dN/dS > 1) provides a better fit of the data.