I've just come across a most excellent article by the Genetic Literacy Project. In it, Nicholas Staropoli notes that a proportion of the human genome actually has viral origins.
This might sound a bit strange – after all, we tend to think of viruses as our enemies (smallpox, measles, and the human papilloma virus come to mind). But, as Staropoli notes, there are a lot of what are called 'endogenous retroviruses' (ERVs) – or their remains – tucked away in our genome. (An ERV has the ability to write its own genes into the host's DNA.) And he links to a study that draws this conclusion:
We conservatively estimate that viruses have driven close to 30% of all adaptive amino acid changes in the part of the human proteome conserved within mammals. Our results suggest that viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes.
Carl Zimmer writes about one such example in his blog The Loom: it seems that a gene that's crucial in the development of the placenta (that intimate connection between a foetus and its mother) is viral in origin. In fact, one gene encoding the protein syncytin is found in primates – but carnivores have a quite different form of the gene, while rabbits have a different form again, and mice yet another!
This is a very complex evolutionary story indeed. And so you could do much worse than read the two articles, by Staropolis and Zimmer, in their entirety.