Using maximum likelihood, we constr

Using maximum likelihood, we constructed phylogenetic treesbased on each of the following gene sequences: DNA polymerase(Figure 1), E1a (13S mRNA analog encoded, Figure S1), preterminal protein (pTP, Figure S2), hexon (Figure S3), penton base(Figure S4), protease (Figure S5), ssDNA-binding protein (DBP,Figure S6), and fiber (Figure S7). Overall, these trees wereconcordant with several notable exceptions. For one, species Dbranching in E1a and hexon is discordant as compared to theother proteins studied. Also, the phylogeny of the highly divergentfiber protein is distinctive and possibly reflective of differences inreceptor usage (CD46 for species B as opposed to CoxsackieAdenovirus Receptor for the others; species D fibers are known toadditionally bind sialic acid). The phylogeny of species A and F,and their relationship to the macaque isolates is highly discordantfor the different proteins. The cynomolgus isolates, SAdV-49 andSAdV-50, for example, are closely associated with species A in E1abut are either closer to species F or are divergent for the otherproteins. Internally within clades, discordance is also sometimesnoted in species B and E and may be indicative of intra-speciesrecombination. We used the polymerase tree (Figure 1) as areference phylogeny throughout the manuscript. Overall, thephylogeny of the viral sequences reflects the host species fromwhich the viruses were isolated. All viruses from great apes andhumans except species A and F viruses form a monophyleticgroup, whereas adenoviruses infecting tree shrew, macaques, andbovines (not shown) fall outside this group [29]. The macaquederived viruses SAdV-49 and SAdV-50 were positioned in apreviously uncharacterized clade, yet certain genes have closeresemblance to the same genes in species A and F adenoviruses.SAdV-48, another macaque-derived virus that we isolated, wasmore closely related to SAdV-3 and SAdV-6, both previouslyisolated from rhesus macaques (see Figure 1 and Figures S1, S2,S3, S4, S5, S6 and S7). The viruses isolated from great apessegregated into distinct clades within the larger groups of speciesB, C and E viruses. Human-derived viruses formed separate subclades from ape-derived viruses in each of these viral species.Reconstructed phylogenies consistently place D viruses in amonophyletic group with B, C, and E viruses but we did notidentify any simian viruses belonging to species D. Thephylogenies consistently place human A and F viruses in distinctand somewhat distant clades from all other human viruses. In fact,the A and F viruses are more closely related to macaque strainsthan they are to all other human viruses