MOESM1 of Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates

Bruno Ghersi, Hongwei Jia, Pakorn Aiewsakun, Aris Katzourakis, Patricia Mendoza, Daniel Bausch, Matthew Kasper, Joel Montgomery, William Switzer
2016 Figshare  
Additional file 1: Figure S1. Co-speciation history of New World monkeys (NWM) and simian foamy viruses (SFVs). A consensus NWM tree (left) estimated from a cytochrome-B nucleotide alignment (156 sequences, 618 nt) is compared to a consensus NWM SFV tree (right) estimated from a polymerase nucleotide alignment (80 sequences, 412 nt). Both trees were constructed under the Bayesian phylogenetic framework by using MrBayes 3.2.1 [38], and molecular clocks were not imposed. The host tree was rooted
more » ... st tree was rooted according to the tree in [30]. The FV tree was rooted with ape and Old World monkey SFVs. The 'backbone' polymerase sequences in the SFV tree are labelled with '#'. The scale bars are in the units of substitutions per site, and numbers on nodes are posterior probabilities. Grey lines indicate SFV-host associations. SFVs without associating hosts are labelled in grey, and were excluded from the phylogenetic reconciliation analysis. Thick branches are co-diverging branches used in the SFV-host divergence correlation analysis, labelled with roman numerals (I-XVI), referring to dots in Fig. 4C. See Supplementary Table S1 for a complete list of species codes used in the study.
doi:10.6084/m9.figshare.c.3624296_d1.v1 fatcat:ejt2vgsujnadxmf3wvbojt5yde