Integration times estimated from independent LTR substitution rates and phylogenies, compared with MCMC estimations.

Integration time estimates in million years ago (Mya) for the 10 LTR loci using independent LTR rates and several phylogenetic inference methods. For the HKY and GTR substitution models, the genetic distance between LTRs was calculated using the Maximum Composite Likelihood method in MEGA 4.0. MCMC 95% confidence interval of the first node age calculated using a 25000 sample analysis after an initial 50000 sample stabilization run. A sample every 100 from the analysis was taken to build the Bayesian estimation. Three separate runs were made and all values for node ages were congruent (data not shown).