File:OPSR.Roni.Fig4.v2.png

English: Roniviridae. Maximum Likelihood phylogenetic tree inferred in MEGA 7.0 (Kumar et al., 2016) from an amino acid sequence alignment of the concatenated replicase domains in ORF1b of 16 viruses assigned to the three assigned families of arthropod nidoviruses (Mesoniviridae, Euroniviridae and Roniviridae). The amino acid sequences were aligned in ClustalW and then adjusted manually to reflect predicted conserved motifs in seven identified structural domains (NiRAN, RdRP, ZBD, HEL1, ExoN, N-MT and O-MT) (Saberi et al., 2018). The evolutionary relationships were inferred by using the WAG + frequency model of amino acid substitution (Whelan and Goldman 2001) with sub-tree pruning and re-grafting (SPR) branch-swapping. The initial tree for the heuristic search was obtained automatically by applying the neighbour-joining algorithm to a matrix of pairwise distances estimated using a JTT model (Jones et al., 1992), and then selecting the topology with superior log likelihood value. The tree with the highest log likelihood (-28990.5) is shown. Numbers at nodes indicate the bootstrap support where this was > 70%. The scale bar indicates 0.5 substitutions per site.