XML for input into BEAST with increasing temporal sampling range

XML were created in BEAUti v1.5.4 for analysis in BEAST v1.7.4, as described in Hedge et al. 2013 (Drummond & Rambaut, 2007, Drummond et al. 2012). Each file specifies the EpiFlu accession numbers of the segments concatenated into the whole-genome sequences and used as input data for the analysis (http://platform.gisaid.org/). Each file is labelled with the name of the last month during which sequences included in the analysis were sampled and the growth modelled employed. For example, June.exp.xml comprises EpiFlu accession numbers of sequences sampled from the start of the pandemic until June 2009 and specifies the use of an exponential growth model. Details of the substitution, clock and coalescent models are provided along with the priors placed on the model parameters. An additional block implementing the estimation of the marginal likelihood of the model using path-sampling is given after the Markov chain Monte Carlo (MCMC) block (Baele et al. 2012)

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

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

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

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

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