Table 1. Evolutionary rate analysis under various substitution models.

Substitution model	Model description	Evolutionary rate, substitutions per year per site	MRCA of subtype A
Nucleotide	Complete homogeneity	1.53 × 10-3 ± 4.70 × 10-4	1940 ± 15.85
	Different rates	1.40 × 10-3 ± 4.43 × 10-4	1940 ± 15.90
	Different rates and frequencies	1.36 × 10-3 ± 4.61 × 10-4	1939 ± 17.50
	Different rates, frequencies, and κ1 and κ2	1.39 × 10-3 ± 5.12 × 10-4	1939 ± 18.92
	Different rates, frequencies, κ1 and κ2, and γ	1.37 × 10-3 ± 4.40 × 10-4	1939 ± 16.36
Codon	Single dN/dS among sites	4.89 × 10-3 ± 1.52 × 10-3*	1940 ± 15.89
	Discrete distribution of dN/dS among sites	5.07 × 10-3 ± 1.30 × 10-3*	1941 ± 12.75

The model description for the nucleotide substitution models refers to the parameter heterogeneity allowed between the gag and env parts of the concatenated alignment. The only model that fitted the data significantly better was the one allowing for different rates between the genes (P < 0.05), which was the model used in all further estimates. For the codon substitution models, the model descriptions specify the dN/dS among sites. Substitution rates and dates for the MRCA of HIV-2 subtype A were estimated under the SRDT constraint.

^*Under codon substitution models the rates are expressed in number of substitutions per year per codon site and therefore are not directly comparable to the nucleotide substitution rates under nucleotide substitution models.