Figure 1.
Idealized caricatures of virus phylogenies that show the effects of changes in viral population size.
Figure 2.
Idealized caricatures of virus phylogenies that show the effects of population structure.
Red and blue circles represent spatial locations from which viral samples were isolated.
Figure 3.
Idealized caricatures of virus phylogenies that show the effects of immune escape.
Figure 4.
A gene genealogy illustrating internode intervals.
Figure 5.
Phylogenetic tree of the HA1 region of the HA gene of influenza A (H3N2) from viruses sampled between 1968 and 2002.
Table 1.
Estimated annual growth rates of Ne for early HIV sub-epidemics.
Figure 6.
Between-host and within-host HIV phylogenies.
Sequences were downloaded from the LANL HIV sequence database (http://www.hiv.lanl.gov/content/sequence/HIV/SI_alignments/set1.html). Neighbor-joining trees were estimated from Alignment1, and the within host tree is based on data from patient 2. Trees were re-rooted using Path-o-gen using known sample dates (http://tree.bio.ed.ac.uk/software/pathogen/).