Has anyone ever tried doing phylogenetic reconstructions that included viral transcripts? Where do they come from? Have viral molecules ever been imputed to have contributed to evolution of species within the 3-domains of life (apart from the presence of epitopes)?
Yes. Some viruses came from eubacteria, some from archaebacteria, and some from eukaryotes. Most have some genes from one source and some from another, for example a polymerase derived from a transposable element and an envelope derived from some other source. So the short answer is that viruses are sort of scattered all over the tree of life, there was no single point source or common ancestor of all viruses.
Viruses in eubacteria (called phages) were some of the first tools used in studying evolution and genes. They very often carry genes from one species or lineage of bacteria to another (horizontal gene transfer) an thus contribute greatly to bacterial evolution. Retroviruses have been co-evolving with vertebrates for hundreds of millions of years (see attached paper) and have contributed to vertebrate evolution in several different ways.
Thanks, this is interesting. So the ssRNA viruses evolved completely independently from the dsDNA ones or has someone shown otherwise?
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