Lengths of dsRNA segments, encoded putative proteins, 5' and 3' non coding regions (NCR) and G+C content of ORUV, LEBV and CGLV.

<p>Lengths of dsRNA segments, encoded putative proteins, 5' and 3' non coding regions (NCR) and G+C content of ORUV, LEBV and CGLV.</p

Maximum likelihood trees showing phylogenetic comparisons of the aa sequences of VP1 of ORUV, LEBV and CGLV, aligned with those of other <i>Orbivirus</i> species.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086392#pone-0086392-g001" target="_blank">Figure 1</a> is an ML amino acid tree, respectively, both depicting the three groups of orbiviruses (i-<i>Culicoides</i>−/sandfly-borne, ii- mosquito-borne and iii- tick-borne) as separate clusters. The polymerase of Banna virus (genus <i>Seadornavirus</i>, family <i>Reoviridae</i>: a 12-segmented mosquito-borne dsRNA virus) used as outgroup. This figure shows the root to be located between the tick/tick-borne orbiviruses and the insect-borne orbiviruses. LEBV, ORUV and CGLV all cluster among <i>Culicoides</i>-borne orbiviruses. The scale bar represents the number of substitutions per site.</p

Phylogenetic tree containing results of the discrete state model.

<p>Maximum clade credibility phylogeny for YFV under the discrete state transition model. Legend color indicates highest probability state transition for annotated node.</p

Bayesian skyline demographic analysis for the prM/E alignment.

<p>Plot is a trace of the effective population size over time of the YFV alignment, using a Bayesian skyline model. Mean population size (black line) is displayed with upper and lower bounds of the 95% HPD interval (blue and purple lines). Constant value of the trace between years 1940 and 2010 is indicative of stability in the estimated viral population during that time.</p

Correspondence between Lebombo virus (LEBV) and Great Island virus (GIV: a tick-borne orbivirus), Bluetongue virus (BTV: a typical <i>Culicoides</i>-borne orbivirus), St Croix River virus (SCRV: a tick-borne orbivirus belonging to a distinct species) and Yunnan orbivirus (YUOV) a mosquito-borne orbivirus.

<p>The functions and abbreviations (shown in parentheses) used to indicate these roles are from the <i>Reoviridae</i> chapter in the ninth taxonomy report of the ICTV <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086392#pone.0086392-Attoui1" target="_blank">[1]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086392#pone.0086392-Mertens1" target="_blank">[2]</a>. NF: Non-functional, NSI: no significant identity.</p

Maximum likelihood trees showing phylogenetic comparisons of the nucleotide sequences of the genome segment encoding the VP7(T13) proteins of ORUV, LEBV and CGLV, aligned with those of other <i>Orbivirus</i> species.

<p>The nucleic acid sequences were aligned based on the profile of aa alignments generating a codon to codon alignment, showing the three groups of orbiviruses (i-<i>Culicoides</i>−/sandfly-borne, ii- mosquito-borne and iii- tick-borne) as separate clusters. LEBV, ORUV and CGLV all cluster among <i>Culicoides</i>-borne orbiviruses. The scale bar represents the number of substitutions per site.</p

Divergence estimates for major lineages.

<p>The table contains estimates of divergence times, in decimal calendar years CE, for mean heights of significant nodes in the Bayesian phylogeny. HPD intervals and posterior node probability are included. These results were obtained using a constant population demographic prior and relaxed, lognormally-distributed clock.</p

Bayes factors for state transitions, comparing significance output for uncorrected vs. distance-penalized connections.

*<p> <b>Transition pair significance for indicator value criteria was not maintained between the uncorrected and distance-penalized model.</b></p><p>Significant reversible state transitions for BSSVS test for Bayes factors greater than 3 and indicator value greater than .50. Table shows a comparison between factor values obtained with an uncorrected model, and a set obtained by imposing an increasing linear distance penalty on computed distance between states. Under distance penalty, significance was reduced below indicator value criterion for indicated transition pairs.</p

Map of supported state transitions for Bayesian Stochastic Search Variable Test (BSSVS).

<p>Colored lines represent the transitions that were statistically supported in the inferred phylogeny, using an uncorrected model. Significance was assessed for state transitions resulting in a Bayes factor greater than 5 and BSSVS indicator value greater than .50.</p

Linear relationships linking the largest genetic distances between tick-borne, mosquito-borne or <i>Culicoides</i>-borne orbiviruses and time of divergence for vectors.

<p>The largest genetic distance within a group of orbiviruses (tick-borne, mosquito-borne or <i>Culicoides</i>-borne) is plotted against the date of separation of vector groups (ticks, mosquitoes or midges). A linear relationship is depicted for both the VP1(Pol) and the T2 (correlation coefficient R²>0.99), and is less obvious in the T13 protein (R² = 0.9311).</p