Sampling scales for acute RNA viruses and the associated phylodynamic processes that viral genome sequence data and host sampling can elucidate.

<p>Sampling scales for acute RNA viruses and the associated phylodynamic processes that viral genome sequence data and host sampling can elucidate.</p

Past and future viral biocontrols of vertebrate pest species.

<p>A limited number of viruses have been used to control invasive vertebrate pests on a global scale: (i) Feline panleukopenia virus against cats on Marion Island (magnified on the map in grey), (ii) MYXV against rabbits in Europe and Australia, and (iii) RHDV in Australia and New Zealand. Despite some initial success, classical swine fever virus proved to be an unsuccessful biocontrol against wild boar on the Channel Islands in California (the islands are magnified, with the two islands affected, Santa Cruz and Santa Rosa, shown in grey). Safety testing is currently underway for the possible release of KHV against carp in Australia. Abbreviations: KHV koi herpesvirus, MYXV myxoma virus, RHDV rabbit haemorrhagic disease virus.</p

Fluctuating genetic diversity of influenza A virus.

<p>The figure shows a Bayesian skyline plot of changing levels of genetic diversity through time for the HA gene (165 sequences) of A/H3N2 virus sampled from the state of New York, US, during the period 2001–2003. The <i>y</i>-axes depict relative genetic diversity (<i>N</i>_e<i>t</i>, where <i>N</i>_e is the effective population size, and <i>t</i> the generation time from infected host to infected host), which can be considered a measure of effective population size under strictly neutral evolution. Peaks of genetic diversity, reflecting the seasonal occurrence of influenza, are clearly visible. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000505#pcbi.1000505-Rambaut1" target="_blank">[30]</a> for a more detailed analysis.</p

Relative node depths of incongruences between host and virus phylogenies showing the median and 25^th and 75^th percentiles (boxplots) as well as the raw data.

<p>A relative node depth close to 0 can be interpreted as the occurrence of host-switching events at the tips of the phylogenetic tree, whereas a relative node depth close to 1 suggests host-switching events at the root of the phylogenetic tree. A range of DNA (blue) and RNA (yellow) virus families are shown. For ease of interpretation virus families are ranked as in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006215#ppat.1006215.g002" target="_blank">Fig 2</a>.</p

Tanglegrams of rooted phylogenetic trees for each virus family.

<p>Host trees were rooted first following their known phylogenetic history, with virus trees then rooted based on the host tree. The ‘untangle’ function was used to maximize the congruence between the host and virus phylogenies. Lines that connect the host (left) with its virus (right) are colored according to the host type (dark blue: mammals; light green: birds; light blue: reptiles and amphibians; red: fish; pink: invertebrates; dark green: plants). Phylogenies with the individual tip labels visible are shown in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006215#ppat.1006215.s001" target="_blank">S1 Fig</a>.</p

Summary of the virus data used in this study.

<p>The best-fit amino acid substitution models were selected according to the Bayesian Information Criterion.</p

Tanglegrams of phylogenetic trees created using simulated data.

<p>Lines connect the virus with its respective host. Hence, if viruses and hosts have congruent phylogenies—indicative of strong virus-host co-divergence—then there will obviously be more horizontal than diagonal lines. Panel (A) illustrates a perfectly matched topology between virus and host trees and thus the nPH85 = 0. Panel (B) exemplifies an entirely mismatched topology between virus and host trees, where the nPH85 = 1. Data from viruses in nature will fall between these two extremes. Panels (C) and (D) illustrate two examples where the host trees have one incongruent node. Panel (C) corresponds to a shallower section of the tree than in panel (D), but the two nPH85 are the same, such that the position of the incongruence does not produce a systematic bias. Panel (E) elucidates the relationship between the nPH85 distance and the number of incongruent nodes between a pair of simulated trees with 100 tips.</p

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families - Fig 5

<p><b>(A)</b> Reconciliation analysis of each virus family using Jane [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006215#ppat.1006215.ref015" target="_blank">15</a>]. Boxplots illustrate the range of the proportion of possible events. The ‘event costs’ associated with incongruences between trees were conservative towards co-divergence and defined here as: 0 for co-divergence, 1 for duplication, 1 for host-jumping and 1 for extinction. Virus families are ranked in order of highest mean co-divergence to lowest mean co-divergence. Abbreviations on the x-axis are as follows: ‘Co-div’ = co-divergence, ‘Dup’ = duplication, ‘HJ’ = host-jumping, ‘Ext’ = extinction. <b>(B)</b> Reconciliation of the <i>Hepadnaviridae</i> phylogeny with that of their vertebrate hosts, again utilizing the co-phylogenetic method implemented in Jane [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006215#ppat.1006215.ref015" target="_blank">15</a>]. The figure illustrates all possible co-divergence, extinction and host-jumping events (no lineage duplication events were reconstructed in this case).</p

Overall normalized topological distance between two unrooted phylogenetic trees for each virus family by normalizing the Penny and Hendy [14] metric (i.e. nPH85).

<p>A range of DNA (blue) and RNA (yellow) virus families are shown. If nPH85 = 0, it is indicative of virus-host co-divergence, while nPH85 = 1 suggests frequent cross-species transmission (red). For ease of interpretation virus families are ranked by descending frequency of cross-species transmission.</p

Rabies_ALL_SPECIES_G.FULL.DATED

Alignment of Rabies virus G gene sequences used in the work in nexus forma