We know the city where HIV first emerged
Simian AIDS was discovered after human AIDS. How do they know the jump didn't occur in reverse?<p>Here is the first report of simian AIDS:
"Examination of the species-specific annual mortality rates of macaques at the center during the previous 4 yr showed a significant increase in deaths in 1980 and 1981"
<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393899/" rel="nofollow">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393899/</a><p>Also, it is convenient they do not share the mcmc traces. Based on these settings I bet they were ugly:<p>>"For each data set, at least 3 MCMC chains of 250 million steps were computed. Parameters and trees were sampled every 50,000th step. Samples were combined with LogCombiner (77) and between 10 to 30% of each MCMC chain was discarded as burn-in. MCMC mixing was diagnosed using visual trace inspection and calculation of effective sample sizes in Tracer (77). We report the posterior mean and 95% Bayesian credible intervals for evolutionary parameters."<p><a href="http://dx.doi.org/10.1126/science.1256739" rel="nofollow">http://dx.doi.org/10.1126/science.1256739</a><p>Another thing, they write:<p>"Our estimated location of pandemic origin explains the observation that Kinshasa exhibits more contemporary HIV-1 genetic diversity than anywhere else"<p>This is totally circular. As shown in their figure S2, they used genetic diversity in a region as an indication of earlier presence.