Additional file 3: Figure S9. of Quantifying predictors for the spatial diffusion of avian influenza virus in China

(A to F) Bayesian MCC phylogenies of 6 internal segments of 320 Chinese AIV sequences labelled with sequence names on tips and Bayesian posterior probability on nodes. (A) PB2; (B) PB1; (C) PA; (D) NP; (E) M; (F) NS. (ZIP 523 kb

Additional file 2: Figure S1. of Quantifying predictors for the spatial diffusion of avian influenza virus in China

Host distribution of 320 Chinese AIV sequences in Traditional Region, Economic Region, Economic Divided zone, and China Agro-Ecological Region types. Figure S2. Distributions of 320 Chinese AIV sequences in the sampled time, host order, subtype and sampled provinces. Figure S3. Influence of the sampling scheme on the phylogeographic reconstruction. Figure S4. PB1 tree mapping with region traits. Figure S5. PA tree mapping with region traits. Figure S6. NP tree mapping with region traits. Figure S7. M tree mapping with region traits. Figure S8. NS tree mapping with region traits. (PDF 864 kb

Maximum likelihood and Bayesian phylogenetic trees

Tree files named as “RAxML_PB2.tre” et al. are maximum likelihood (ML) trees of six internal segments (PB2, PB1, PA, NP, M and NS) composed of the same 2343 North America AIV strains, which were reconstructed using RAxML v7.04. In each ML tree, the Mexico H7N3 strains are colored in red, and the lineage in which H7N3 Mexico fell is colored in blue; Tree files named as “HA.mcc.tre” et al. are temporally structured maximum clade credibility (mcc) time-scaled phylogenetic trees of all eight segments, which were generated using Beast V 1.7.3 and annotated with ancestral state changes (A: host order; B: host species; C: flyway; D: state/province; E: subtype) recovered from the discrete trait analyses. In each mcc tree, the branches are colored according to the trait state in the tree nodes. All tree files can be visualized in FigTree V 1.4.0

Summary statistics from HIV gene genealogies versus the fraction of transmissions attributable to early/acute infection.

<p>The threshold TMRCA was five years before the most recent sample. Sample size and distribution of samples over time was matched to the Detroit MSM phylogeny.</p

Excess clustering and excess co-clustering of virus from patients with early/acute infections.

<p>Left: The mean CD4 cell count (top) and frequency of ambiguous sites (bottom) versus the threshold TMRCA used to form clusters. Middle: The assortativity coefficient, a measure of similarity of co-clustered taxa, versus the treshold TMRCA used to form clusters. Assortativity of CD4 is at top, and frequency of ambiguous sites is bottom. Right: The size of each matrix element is proportional to number of co-clusterings between taxa categorized by CD4 (top, ) or quartile of frequency of ambiguous sites (bottom). The color represents the extent to which the count of co-clusterings exceeds the expectation if clusters were forming at random. The color scale (far right) shows strong assortativity within quartiles. The vertical red bar represents the threshold which was used to create clusters and the matrix derived from the set of clusters. This threshold corresponds to the maximum of the assortativity coefficient for the derived matrix.</p

Epidemiological parameters.

<p>Epidemiological parameters.</p

Two simulated epidemics and the deterministic approximations for the prevalent number of early and late infections and the ancestor functions (the number of lineages over time).

<p>The x-axis gives the time since the beginning of the epidemic, or equivalently, the threshold TMRCA used to calculate the number of lineages over time. Green describes the simulated number of late infections. Blue describes the simulated number of early infections. Dots show the simulated ancestor function for the number of lineages that correspond to late infections. And x's show the simulated ancestor function for lineages in early infection. Dashed lines show the prediction of the deterministic coalescent. The top row shows results for a sample taken at 15 years following the initial infections, and the bottom shows results for a sample at 30 years. The right column shows results for a sample fractions of 20%, and the left column for a census of prevalent infections(100%).</p