Fig 1.
Phylogenetic relationship of non-avian/mammalian vertebrate ERVs, representative mammalian and avian ERVs, and exogenous retroviruses.
The phylogenetic tree was reconstructed based on the RT protein and by using a maximum likelihood method. The numbers near the selected nodes indicate the aBayes branch supports. Selected retroviruses are labelled near the corresponding external nodes. The hollow circles indicate exogenous retroviruses, whereas the filled circles indicate ERVs. The root was inferred by using Cer1-6 retrotransposons as outgroups. For virus abbreviation, see S1 Table. For lineage I to IV with asterisks, we performed host-retrovirus co-phylogenetic tests in Fig 3 and Table 1.
Fig 2.
The distribution of major retroviral clades in vertebrates.
The left panel shows the phylogenetic relationship among major vertebrate groups. The numbers near the vertebrates indicate the numbers of genomes used in this study. The top-right panel shows the phylogenetic relationship among the five major retroviral groups. XRV and ERV stand for exogenous and endogenous retrovirus, respectively. α, β, γ, δ, ε, Lenti-, and Spuma- represent Alpharetrovirus, Betaretrovirus, Gammaretrovirus, Deltaretrovirus, Epsilonretrovirus, Lentivirus, and Spumavirus, respectively. I, II, and III represent class I, II, and III ERVs. The filled circles indicate the presence of ERVs.
Fig 3.
The host-retrovirus co-phylogenetic relationship in non-avian/mammalian vertebrates.
(A) to (D) correspond to lineages I to IV with asterisks in Fig 1. For (A) to (D), the left and right panels represent retrovirus and host phylogenies, respectively. The dash lines indicate host-retrovirus association. Retroviruses of fishes, amphibians, and reptiles are labeled in blue, orange, and purple, respectively.
Table 1.
Host-virus phylogeny congruence test for retroviruses.
Fig 4.
Transmission network of retroviruses among major vertebrate lineages.
The gray lines represent the phylogenetic relationship among major vertebrate groups. The pink lines indicate retroviruses from two vertebrate groups share common ancestry at terminal nodes, which represent transmission events between hosts without known direction. The numbers show the frequencies of the corresponding transmission events.
Fig 5.
Retroviral transmission modes at the land-water interface.
The blue boxes indicate aquatic environments. (A) Scenario where retroviruses underwent water-to-land transition simultaneously with the conquest of land by their tetrapod hosts. (B) Scenario where tetrapod retroviruses independently originated by cross-species transmissions from fishes to tetrapods after the origin of tetrapods.