Figure 2

Bel/Pao, Retroviridae and Caulimoviridae phylogenies. A) Inferred NJ tree of Bel/Pao LTR retroelements based on pol. This tree divides Bel/Pao LTR retroelements into five clades collected in three branches, named 1, 2 and 3 (red, black and blue, respectively). B) Inferred NJ tree of caulimoviruses based on pol. The tree is consistent with the six Caulimoviridae genera proposed by ICTV [34] but divides them into four classes depicted in red, black, blue and green. C) Inferred NJ tree of Retroviridae retroviruses based on pol. This tree shows three classes, namely, 1, 2 and 3 (red, black and blue, respectively), which can be divided into seven genera consistent with ICTV [34]. The tree also includes a taxon representative of ERV-L Class 3 elements as well as a fish retrovirus - SnRV - with unclear location but occupying a place within Class 1 in the LTR retroelement common phylogeny (Additional File 1). For more information, see the section "Sequences" under Methods.