Figure 3
Maximum likelihood trees of (a) coat protein (JTT + G 4 model) and (b) replication associated protein (RtRev + G 4 model) amino acid sequences of ECSV (isolate ECSV [Za-Gre3-g257-2007]) and 40 other viruses representing the broadest breadth of currently sampled geminivirus diversity. Whereas the CP tree is unrooted, the Rep tree was rooted using the translated "master" rep sequence of Faba bean necrotic yellows virus (FBNYV; in grey). Viruses that are clearly members of the currently established geminivirus genera, Begomovirus, Topocuvirus, Curtovirus and Mastrevirus are indicated in green, orange, blue and pink respectively. Branches of the tree marked with filled circles were present in 90 or more maximum likelihood tree bootstrap replicates (performed in PHYML)and more than 99% of constructed trees from alignments sampled during the statistical alignment process (performed in STATALIGN). Open circles represent branches supported by 70 or more percent of the maximum likelihood tree bootstrap replicates and 95 or more percent of trees constructed during statistical alignment. Branches were collapsed if they were not supported in the consensus trees of either the maximum likelihood bootstrap replicates or the statistical alignment process. Branches were also collapsed if they were supported in less than either 50% of the bootstrap replicates or 90% of the trees generated during the statistical alignment.