. 2012 Jun;86(11):6350–6353. doi: 10.1128/JVI.00311-12

Table 1.

Positive selection of bat ACE2 codons 1 to 358

ω_o and codon model^a	Model comparison^b						dN/dS value (% of codons)^c	Residues under positive selection^d
	M1a vs M2a		M7 vs M8		M8a vs M8
	2ΔlnL	P value	2ΔlnL	P value	2ΔlnL	P value
0.4, f61	52.7	P < 0.0001	56.5	P < 0.0001	52.8	P < 0.0001	4.3 (11)	Q24^*, T27^, K31^, H34^, M82^, L91^, T92, N159^, V212, D213^, D216^, E231^, S280, V298, A301, E329
0.4, f3 × 4	56.3	P < 0.0001	56.4	P < 0.0001	56.1	P < 0.0001	4.3 (11)	Q24^*, T27^, K31^, H34^, M82^, L91^, T92, N159^, V212^, D213^, D216^, E231^, S280, V298^*, A301, E329
1.6, f61	52.7	P < 0.0001	56.3	P < 0.0001	52.8	P < 0.0001	4.3 (11)	Q24^*, T27^, K31^, H34^, M82^, L91^, T92, N159^, V212, D213^, D216^, E231^, S280, V298, A301, E329
1.6, f3 × 4	56.3	P < 0.0001	56.4	P < 0.0001	56.1	P < 0.0001	4.3 (11)	Q24^*, T27^, K31^, H34^, M82^, L91^, T92, N159^, V212^, D213^, D216^, E231^, S280, V298^*, A301, E329

Initial seed value for ω (dN/dS) and model of codon frequency (f61 or f3 × 4).

Twice the difference in the natural logs of the likelihoods (2ΔlnL) of the two models being compared. This value is used in a likelihood ratio test along with the degrees of freedom. In all cases (M1a versus M2a, M7 versus M8, and M8a versus M8), a model that allows positive selection is compared to a null model. The P value indicates the confidence with which the null model can be rejected.

dN/dS value of the class of codons evolving under positive selection in M8 and the percentage of codons falling in that class.

Residues corresponding to codons assigned to the class with a dN/dS ratio of >1 in M8 (P > 0.90 by naive empirical Bayes [NEB]). Coordinates correspond to the human protein, although the human sequence was not used in this analysis. Bat numerical coordinates are identical with the exception of three species with single codon insertions or deletions (see alignment in Fig. S1 in the supplemental material).

, P > 0.95;

^**

, P > 0.99. Three additional codons were identified in the analysis of the full-length gene (see Table S2 in the supplemental material).