Summary1. We present an R package, GGTREE, which provides programmable visualization and annotation of phylogenetic trees. 2. GGTREE can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other R packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of BEAST, EPA, HYPHY, PAML, PHYLODOG, PPLACER, R8S, RAXML and REVBAYES software, and allows using these data to annotate the tree. 3. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. 4. A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. 5. The package GGTREE is released under the ARTISTIC-2.0 LICENSE. The source code and documents are freely available through BIOCONDUCTOR (http://www.bioconductor.org/packages/ggtree).

may not be possible to achieve, as virus replicates in the upper respiratory tract even in the presence of specific antibodies, similarly to other respiratory viruses. Because dromedary camels do not show severe clinical signs upon MERS-CoV infection, vaccination of dromedaries should primarily aim to reduce virus excretion to prevent virus spreading. Young dromedaries excrete more infectious MERS-CoV than adults (8, 15, 16), so young animals should be vaccinated first. Our results reveal that MVA-S vaccination of young dromedary camels may significantly reduce infectious MERS-CoV excreted from the nose. Two major advantages of the orthopoxvirus-based vector used in our study include its capacity to induce protective immunity in the presence of preexisting (e.g., maternal) antibodies (32) and the observation that MVA-specific antibodies cross-neutralize camelpox virus, revealing the potential dual use of this candidate MERS-CoV vaccine in dromedaries. Dromedary camels vaccinated with conventional vaccinia virus showed no clinical signs upon challenge with camelpox virus, whereas control animals developed typical symptoms of generalized camelpox (33). The MVA-S vectored vaccine may also be tested for protection of humans at risk, such as health care workers and people in regular contact with camels.

Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data. It can also map and visualize associated external data on phylogenies with two general methods. Method 1 allows external data to be mapped on the tree structure and used as visual characteristic in tree and data visualization. Method 2 plots the data with the tree side by side using different geometric functions after reordering the data based on the tree structure. These two methods integrate data with phylogeny for further exploration and comparison in the evolutionary biology context.

Type 2 (or North American-like) porcine reproductive and respiratory syndrome virus (PRRSV) was first recorded in 1987 in the United States and now occurs in most commercial swine industries throughout the world. In this study, we investigated the epidemiological and evolutionary behaviors of type 2 PRRSV. Based on phylogenetic analyses of 8,624 ORF5 sequences, we described a comprehensive picture of the diversity of type 2 PRRSVs and systematically classified all available sequences into lineages and sublineages, including a number of previously undescribed lineages. With the rapid growth of sequence deposition into the databases, it would be technically difficult for veterinary researchers to genotype their sequences by reanalyzing all sequences in the databases. To this end, a set of reference sequences was established based on our classification system, which represents the principal diversity of all available sequences and can readily be used for further genotyping studies. In addition, we further investigated the demographic histories of these lineages and sublineages by using Bayesian coalescence analyses, providing evolutionary insights into several important epidemiological events of type 2 PRRSV. Moreover, by using a phylogeographic approach, we were able to estimate the transmission frequencies between the pig-producing states in the United States and identified several states as the major sources of viral spread, i.e., "transmission centers." In summary, this study represents the most extensive phylogenetic analyses of type 2 PRRSV to date, providing a basis for future genotyping studies and dissecting the epidemiology of type 2 PRRSV from phylogenetic perspectives.Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important virus which infects swine and causes reproductive failure in sows and respiratory problems in growing pigs. As a member of the Arteriviridae family (15,47,59,66), PRRSV has a positive-sense RNA genome of approximately 15 kb that carries eight overlapping open reading frames (ORFs), designated ORFs 1a, 1b, and 2 to 7 (15, 47). Among these ORFs, ORF5, encoding the major envelope glycoprotein, is an ideal candidate for phylogenetic tree construction, because it exhibits marked genetic variation within its relatively short length.PRRSV can be classified into two genotypes: type 1 (EUlike), comprising mainly European strains and represented by the prototype strain Lelystad (75); and type 2 (NA-like), comprising mainly North American strains and represented by the prototype strain VR-2332 (14). Although clinical diseases are similar following infections with these viruses, they differ significantly in terms of antigenic properties (18, 74) and genetic content (42,48,51). This has sparked hot debates on the evolutionary history and divergence time of these two genotypes (24,25,29,58), but no substantial consensus has been reached.Classification and epidemiology of type 2 PRRSV. Clinical disease due to type 2 PRRSV was first recorded in 1987 in the United Stat...