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Fig. 3 | Retrovirology

Fig. 3

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

Fig. 3

Co-speciation history of New World monkeys (NWM) and simian foamy viruses (SFVs). a A consensus Bayesian phylogeny of NWM hosts, estimated from an alignment of cytochrome B nucleotide sequences (156 sequences, 618 nt) by using MrBayes 3.2.1 [38]. The tree was rooted according to the phylogeny in [30]. b A consensus Bayesian phylogeny of NWM FVs, estimated from an alignment of polymerase nucleotide sequences (74 sequences, 412 nt), and rooted using six ape and Old World monkey SFVs. ‘Backbone’ sequences are indicated with ‘hash’. ‘Cxa F15 Brazil’ (written in blue and indicated with an asterisk ‘*’) was isolated from a Cebus xanthosternos monkey in Brazil, but was found to be placed well within the clade of Ateles SFVs. The roots of the trees are indicated by grey triangles. Numbers on nodes are posterior probability node supports. The scale bars are in the units of substitutions per site. The comprehensive SFV and host trees are shown in Additional file 1: Figure S1. c Competing models for the co-evolutionary histories of NWM SFVs (red) and their hosts (blue) at the level of species inferred by Jane v4 [39]. The directions of transmissions are indicated by red arrows. Small arrows indicate cross-species transmissions, and large arrows indicate cross-genus transmissions. The red transparent bars show the uncertainty of the cross-species transmission timing. Four co-speciation events at the genus level are indicated by solid red squares, and those at the species level are indicated by solid red circles. Note that, the trees are not scaled to time. d The distributions of the number of co-speciation events expected to occur by chance, estimated by using random tip mapping method implemented in Jane v4 [39] (sample size = 500); d1 genus level; d2 species level, conservative tree collapsing method; d3 species level, overall; and d4 all sequences. The dotted line indicates the actual observed number of co-speciation events inferred by Jane v4 [39]. See Additional file 2: Table S1 for a complete list of species codes used in the study; PFV is primate foamy virus which is the new name given to HFV (human foamy virus)

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