Origins and Evolution of the Global RNA Virome

Yuri I. Wolf; Darius Kazlauskas; Jaime Iranzo; Adriana LucÍa-Sanz; Jens H. Kuhn; Mart Krupovic; Valerian V. Dolja; Eugene V. Koonin

To resolve the structure of the global relationships, up to five representatives from each 891 cluster were selected using the within-cluster trees to ensure the diversity of the selected 892 sequences. This procedure resulted in a set of 228 virus RdRps and 10 RTs. The alignments of 893 the selected sequences were extracted from the master alignment and filtered for sites containing 894 more than 50% of gaps. A ML phylogenetic tree was reconstructed for the resulting alignment 895 using PhyML (48) (Le Gascuel [LG] evolutionary model with gamma-distributed site rates and 896 empirical amino acid frequencies; aBayes support values). Another form of branch support, 897 bootstrap support by transfer (BOOSTER) phylogenetic bootstrap (130), was also used to assess 898 the reliability of the major tree divisions. Alternatively, the same RdRp alignment was used as 899 the input for ML phylogenetic analysis using RAxML (LG evolutionary model with gamma-900 distributed site rates and empirical amino acid frequencies). 901