Figure 1.

Phylogenetic analyses. A)Ty3/Gypsy and Retroviridae phylogeny inferred based on the concatenated analysis of both gag and pol polyproteins. This tree is robust as gag and pol signals complement and correct each other. It also supports with significant bootstrap values the 2 groups of LTR retroelements and all their accepted lineages (clades, genera and classes). An extended version of this tree facilitating names, lineages, hosts, and Genbank accessions of all retroelement taxa used is provided as the Additional file 1 accompanying this paper (see the Section "Sequences and databases" in Methods). Decomposition of gag-pol tree and analysis of its two components separately, reveals similar phylogenetic signal but conflicting evolutionary perspectives. B) The phylogenetic signal of the pol polyprotein is robust and therefore responsible for the current known taxonomy and classification of Ty3/Gypsy and Retroviridae LTR retroelements into lineages. C) The gag signal supports the clades, genera and classes described in each group, but does not supports the 2 groups. Gag tree outlines an alternative scenario that may relate each Retroviridae class with one or more Ty3/Gypsy lineages.