AICM estimates for the fit of different models with reduced number of transitions.

a<p>The names of the 11 models (Flyway model and Ran1-10) in the comparison test: Model1 is the non-reversible BSSVS model without between flyway transitions (Flyway); Ran1-10 are models in which the same number of transitions has been switched off, chosen at random (Ran1-10).</p>b<p>The estimated AICM score of the posterior: lower values of marginal likelihood indicate a better fit to the data. The model with the best performance is indicated in bold.</p>c<p>The standard error of AICM estimated using 1000 bootstrap replicates.</p>d<p>Differences of models are shown in the matrix being composed by column 4 to 13. In each row of the matrix, the positive value in a cell represented the support for one model (in column 1) over the other (the column title). A difference of AICM = 10 is considered a strong preference for one model over another.</p><p>AICM estimates for the fit of different models with reduced number of transitions.</p

Phylogenies of the H7 and N3 segments of all available North American AIV.

<p>A: HA. Sequences in grey are from before 1990; the clade colored blue is composed of H7N2 AIV isolated from a single surveillance in poultry in New York; the clade colored pink was selected for time-scaled phylogenetic analysis. B: NA tree. The uncoloured sequences are from before 2000; the AIV clade in pink was selected for time-scaled phylogenetic analysis.</p

Inferred host transmission networks of Mexican outbreak AIV.

<p>A: Host order. Node labels in the nodes are host orders identified following the abbreviations used in the colored phylogenetic trees (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone-0107330-g002" target="_blank">Figure 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s002" target="_blank">Figures S2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s003" target="_blank">S3</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s004" target="_blank">S4</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s005" target="_blank">S5</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s006" target="_blank">S6</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s007" target="_blank">S7</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s008" target="_blank">S8</a>): wild birds of the order Anseriformes (ans-wild); wild birds of the order Charadriiformes (cha-wild); wild birds of the order Passeriformes (pas-wild); domestic birds of the order Galliformes and Mexico H7N3 outbreak in the order Galliformes (gal-domestic-Mexico). Arrows show the direction of transmission between two host orders; the arrow weight and the number above each arrow indicates the per capita transmission rate. Node size reflects the number of AIV for each host order (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s012" target="_blank">Table S1</a>). Line colours indicate the overall Bayes Factor test support for epidemiological linkage between host orders, Red lines indicate statistical support with BF>100 (very strong support), dark pink lines indicate support with 30Table S3). Line colours indicate the overall Bayes Factor test support for epidemiological linkage between host species, Red lines indicate statistical support with BF>100 (very strong support), dark pink lines indicate support with 30</p

Time of the most recent common ancestors for the Mexico H7N3 virus.

a<p>Time of the most recent common ancestors (TMRCA) of each segment of the novel Mexico H7N3 virus are represented in the order of date/month/year. The values in parentheses represent the 95% HPD intervals.</p>b<p>The strains are identified are those most closely related to the outbreak strains in each tree phylogeny in this study.</p><p>Time of the most recent common ancestors for the Mexico H7N3 virus.</p

AICM estimates for the fit of different discrete trait models.

a<p>The names of the 8 models (Mod1-8) in the comparison test.</p>b<p>The estimated AICM score of the posterior: lower values of marginal likelihood indicate a better fit to the data. The model with the best performance is indicated in bold.</p>c<p>The standard error of the AICM estimated using 1000 bootstrap replicates.</p>d<p>The AICM comparisons are shown in the matrix composed of columns 4 to 11. In each row of the matrix, the positive value in a cell represents the support for one model (in column 1) over the other (indicated in the column titles). A difference of AICM = 10 is considered to indicate a strong preference for one model over another.</p><p>AICM estimates for the fit of different discrete trait models.</p

Maximum clade credibility (MCC) phylogenies for the HA segment.

<p>Branches are coloured according to the 4 discrete traits (host order, host species, flyway and location) on internal nodes. Mexican outbreak strains are highlighted with pink. A: Host order. Five host orders are labelled on HA tree: wild birds of the order Anseriformes (ans-wild); wild birds of the order Charadriiformes (cha-wild); wild birds of the order Passeriformes (pas-wild); domestic birds of the order Galliformes and Mexico H7N3 outbreak in the order Galliformes (gal-domestic-Mexico). B: Host species. Wild Anseriformes are classified into the five main species and a group comprising the other rarer species of Anseriformes in this study: mallard (Anas platyrhynchos), northern pintail (Anasacuta), northern shoveller, blue-winged teal, green-winged teal and other Anseriformes (other ans); The order Galliformes are shown as “outbreak” (the H7N3 Mexico outbreak) and “other_gal”; The other orders are shown as: Charadriiformes (cha) and Galliformes (gal), Gruiformes (gru) and Passeriformes (pas). C: Flyway. Four specific North American flyways are labelled on the HA tree: the Atlantic, Mississippi, Central, and Pacific. D: State. 22 states and provinces of the viral sample locations are labelled on the HA tree. The original MCC tree files with all taxa names are deposited in Dryad (doi:10.5061/dryad.j5bf8), and trees for the other 7 segments without taxa names can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s002" target="_blank">Figure S2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s003" target="_blank">S3</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s004" target="_blank">S4</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s005" target="_blank">S5</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s006" target="_blank">S6</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s007" target="_blank">S7</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s008" target="_blank">S8</a>.</p

Inferred phylogeographic transmission networks of Mexican outbreak AIV.

<p>A: Flyway. AIV transmission among 4 N. American flyways with links to the Mexican outbreak strains. Arrows show the direction of transmission between two flyways; arrow weight and the number above each arrow indicates the per capita transmission rate. Node size reflects the number of AIV for each flyway (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s017" target="_blank">Table S6</a>). B: Location. AIV transmission among states/provinces in North America and Jalisco (the Mexican state where the outbreak strains were isolated). Arrows show the direction of transmission between the two states; the arrow weight and the number above each arrow indicates the per capita transmission rate. Node size reflects the number of AIV for each flyway (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s016" target="_blank">Table S5</a>).</p

Spatial diffusion of AIV segments of the Mexico outbreak AIV.

<p>The first three panels represent three segments separately (A: HA, B: NA, C: PB2) and D represents the spatial transmission of all 8 segments jointly. The plotted lines represent the branches of the MCC trees for different segments, distinguished by color; the size of each circle represents the number of lineages with that location state. The map source for this figure was OpenStreetMap (<a href="http://www.openstreetmap.org/" target="_blank">http://www.openstreetmap.org/</a>). The spatial diffusions of other five segments (PB1, PA NP, M and NS) on the map are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107330#pone.0107330.s009" target="_blank">Figure S9</a>.</p

Geographical distribution of the JEV sequences included in this study according to climate of collection.

<p>The coloring of the chart corresponds to the map and shows the relative proportions of viral sequences sampled from each climate according to genotype. The estimated dates (95% HPD interval) and location for the MRCA of JEV, as well as its five genotypes are also shown.</p

Climate Bayesian MCC phylogeny of the JEV sequences.

<p>GI-V are represented to the right of the tree. Branch tips correspond to the date of collection of each of the virus isolates from which JEV sequence information was derived. Branch lengths correspond to lengths of time (in years), as measured by the scale underneath the tree. Terminal branches are colored according to the sampling location of the taxon at the tip, while internal braches are colored according to the most probable location of their child node. The branch colors correspond to those used in the map and legend. The numbers to the upper-left of the nodes correspond to the country phylogeographic analysis date presented in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002411#pntd-0002411-t003" target="_blank">Table 3</a> and the numbers to the lower-left of the nodes are posterior probability values.</p