Fit of model of subdivision to HIV-1 subtypes A and B

Subtype/gene–ln L for panmixis–ln L for subdivisionLikelihood ratio (Λ) τ Embedded Image
A env0.9310.6190.3123.2 × 1060.8680.76
A gag0.2740.0940.1801.32 × 1070.7491.0
B env1.1091.1090.0007.5 × 1081.612.8
B gag0.1860.1170.0692.4 × 1061.911.1

The log likelihoods for the fit of the panmictic and subdivided population dynamic models to the gag and env alignments from subtypes A and B, together with parameter estimates for the latter model. The likelihood ratio of the subdivided to the panmictic model is given and can be seen to be less than the ½ χ2-critical value in all cases. Parameters estimated are the current real-time effective deme size, Nτ, the growth rate of the demes, λ, and the migration rate M.