Retroviruses, immune responses, and vertebrate evolution

Last year's New Yorker piece on retroviral inserts in the human genome made some of my readers curious -- could such retroviral DNA be involved in recent human evolution? I think it's fair to say that I've been asked about retroviruses almost as much as about blue eyes -- and that's saying a lot!

Matt McIntosh has written a nice short piece describing what we know about retroviral genes and placental mammal evolution:

A significant chunk of our DNA had its origins as retroviral DNA. Most of these are now inactive, but a tiny portion actually appear to still code proteins. It's been found in mice, sheep and humans (and presumably generalizes to all placental mammals) that a particular kind of endogenous retrovirus is highly expressed in the outermost layer of the blastocyst (see e.g. Venables et al. 1995 for the human example). Furthermore, when you inhibit the expression of these genes the result is uniform spontaneous abortion immediately following implantation (Dunlap et al. 2006).
Most retroviruses are immunosuppressive, the most infamous example being HIV. Connecting the dots, it's quite plausible that these particular ancient retroviruses have been recruited into the mammalian genome and serve as local immunosuppressors in the uterus during development. In fact, we already know that syncytin, a protein crucial in placenta formation, is the product of a retroviral gene (Knerr et al. 2004), so there's nothing at all far-fetched about this.

If all this pans out, it stands as one of the most important cases of lateral gene transfer in eukaryotic evolution, with early mammals possibly accreting genes from many different viral lineages. As McIntosh points out, these genes are not acting as viruses now; they are imports into our genome -- just like most ancestral mitochondrial proteins are now nuclear genes. McIntosh ends with a short list of retroviral-origin genes that may be active during human development.