The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals

Table 1 Evidence for positive selection in the artiodactyl Z domains.

Z domain^a	Codon frequency model^b	Comparison of null and positive selection models^c	Significance	Tree length^d	dN/dS (%)^e
Z1	F61	M1–M2	p = 0.01	2.6	2.5 (50)
		M7–M8	p = 0.01	2.6	2.5 (50)
	F3 × 4	M1–M2	p = 0.04	3.9	3.9 (28)
		M7–M8	p = 0.02	3.9	3.9 (33)
Z2	F61	M1-M2	p = 0.005	2.4	2.3 (46)
		M7–M8	p = 0.004	2.4	2.3 (45)
	F3 × 4	M1–M2	p = 0.3	3.0	1.7 (27)
		M7–M8	p = 0.04	3.0	1.7 (33)
Z3	F61	M1–M2	p < 0.001	2.4	4.5 (30)
		M7–M8	p < 0.001	2.4	4.4 (31)
	F3 × 4	M1–M2	p < 0.001	3.1	5.8 (22)
		M7–M8	p < 0.001	3.1	5.7 (23)

^aOnly the sequences of Z domain-encoding exons were used in these analyses (see Table S1 for GenBank accessions).
^bTwo different codon frequency models were used to minimize potentially artificial results.
^cLikelihood ratio tests were done to compare the null models M1 and M7 to each positive selection model M2 and M8, respectively, using PAML NsSites.
^dTree length provides a measure of nucleotide substitutions per codon along all combined phylogenetic branches.
^eThe percentage of all codons influenced by positive selection is indicated in parentheses.

ISSN: 1471-2199