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.