The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates
Figure 2
Maximum clade credibility tree for pol.
Both tips and internal branches are colored according to the patient in which the viral lineages are hypothesized to reside (cfr. legend on the left). For branches that cross a transmission interval, the part up to the interval is assigned to the source patients. For posterior support values for each node, we refer to Figure S2. The transmission intervals are represented by the grey boxes. Dashed red circles indicate the topological and coalescent incongruences. For the CD coalescent event, the posterior marginal density of the tMRCA estimate is plotted over the corresponding node in greyshade. Only a lower limit of the transmission interval is known for the A
B transmission. For transmissions B
C, F
G, C
E, C
L and E
K the most recent boundary of the transmission interval (almost) equals the first sampling date.