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. 2020 Jan 12;6(1):vez057. doi: 10.1093/ve/vez057

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© The Author(s) 2020. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — FV phylogenies estimated from the Gag (top left), Pol (top right), and Env (bottom left) proteins, and the phylogeny of the vertebrate hosts (bottom right). FV phylogenies were estimated under the Bayesian phylogenetic framework by using MrBayes 3.2.6 (Ronquist et al. 2012), and were summarised by using the 50 per cent majority rule. Their scale bars are in the units of amino acid substitutions per site. Thin branches are those leading to endogenous FVs, some portion of which may represent neutral evolution. Thick branches are those leading to exogenous FVs, representing pure virus evolution. The outgroups are those with the curve dotted branches. Arabic numerals on nodes are Bayesian posterior probability clade support values. The host phylogeny (see Supplementary Table S2 for virus–host association) was estimated elsewhere (Bininda-Emonds et al. 2007; Stone et al. 2010; Perelman et al. 2011; Jones et al. 2013; dos Reis et al. 2015), and its scale bar is in units of millions of years. Arabic numerals on nodes are diversification dates in units of millions of years, also estimated elsewhere (Supplementary Table S3). Both common and scientific names of the hosts are shown. FV phylogenies were compared with the host phylogeny to identify co-speciation events, labelled with Roman numerals. Only those with ≥75 per cent clade support were considered. Nodes that are labelled with the same Roman numeral are those corresponding to the same co-speciation event. Those labelled with ‘*’ are co-speciation events identified based on topology comparison, but previous studies suggested that they were likely cross-species transmission events. The avian and serpentine FVs reported in this study as well as their hosts are written in bold. Branches and names of the viruses and their hosts are colour coded: orange, apes; red, Old World monkeys; magenta, New World monkeys; purple, prosimians; navy, laurasiatherians; blue, xenarthrans; cyan, afrotherians; green, reptiles; lime, birds; olive, amphibians; brown, lobe-finned fish; and black, ray-finned fish.