Bayesian codon substitution modeling to identify sources of pathogen evolutionary rate variation

Figures 1-4 as published in <i>Microbial Genomics</i> in the following article: 'Bayesian codon substitution modeling to identify sources of pathogen evolutionary rate variation' [10.1099/mgen.0.000057

Supplementary BEAST XML files for our paper 'Bayesian codon substitution modeling to identify sources of pathogen evolutionary rate variation'.

BEAST XML files containing the data and the selected models needed to recreate the results we present in Figures 1 through 4 of our paper

XML

BEAST XML files used for the data analysis

Heterogeneity in evolutionary rates of host-associated bat rabies viruses.

<p>Median substitutions per site per year in the 3^rd codon position of the nucleoprotein gene for estimates generated by the HPM (filled circles) and ILMs (open circles). Colors and dashed gray lines distinguish bat genera as indicated below the x-axis. Credible intervals denote the 95% highest posterior density interval on evolutionary rate.</p

BEAST XML input files used for the data analysis

BEAST XML input files used for the data analysi

BEAST XML input files used for the data analysis

BEAST XML input files used for the data analysi

SupplementEpochModel

Supplementary Infromatio

Predictors of viral evolutionary rate from the Bayesian hierarchical phylogenetic model.

<p>(A) Effect sizes (<i>β</i>) on a log scale for each predictor were conditioned on the inclusion of that term in the model (i.e., <i>β</i> | <i>δ</i> = 1). Climatic region, coloniality, seasonal inactivity and long distance migration were categorical variables. Horizontal lines are the 95% highest posterior density intervals on conditional effect sizes and squares (median effect sizes) are proportional to effect sizes. (B) Violin plot showing the effect of climatic region on viral evolutionary rate. White points, black boxes and whiskers indicate the median, inter-quartile range and the total range of values for that group, respectively. The gray shading shows the probability density of evolutionary rate at different values.</p

Evolutionary lability of viral substitution rates in the rabies virus phylogeny.

<p>(A) Bayesian phylogenetic tree of bat rabies viruses with viral lineage names and climatic regions denoted in black (TE: temperate; ST: subtropical; TR: tropical). Host-associated lineages are condensed to triangles connecting the most recent common ancestor to the sampled branches. Lineages are colored along a blue (slowest) to red (fastest) continuum according to evolutionary rate in CP₃ using estimates from the Independent Lineage Models (ILMs). Bayesian posterior support values (>0.70) are given above branches to the lineage level only. All colored lineages received Bayesian posterior support values of ≥0.91. (B) Frequency histogram of expected values of Blomberg's <i>K</i> from 5000 random assignments of substitution rates estimated from the ILM to lineages. Dashed lines indicate 95% bounds of the null distribution and diamonds denote the median values of <i>K</i> for the randomized rate model, RRM (gray), the ILMs (blue), and the HPM (red).</p

Supplementary Figure S3

Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference