This paper, by Clément Gilbert, Cédric Feschotte is quite cool. In it they describe their work on "Paleovirology" where they look for viruses than have "endogenized" by inserting into the genome of some host species. This endogenization is important in particular when the endogenous form becomes inactive and thus, in essence, trapped in the genome. This in turn is important because many viruses evolve so rapidly when they are "free" that it is very hard to reconstruct their ancient history through comparative analysis. But the endogenized viruses serve in essence as a molecular "fossil record" that aids in the comparison and phylogenetic analysis of various families of viruses. As we get more and more genomes, this searching for and analysis of endogenous viruses will get much better.
Anyway, in the paper they report on endogenous viruses in the Zebra Finch genome that are in the Hepadnaviridae family. Here is their summary:
Paleovirology is the study of ancient viruses and the way they have shaped the innate immune system of their hosts over millions of years. One way to reconstruct the deep evolution of viruses is to search for viral sequences “fossilized” at different evolutionary time points in the genome of their hosts. Besides retroviruses, few virus families are known to have deposited molecular relics in their host's genomes. Here we report on the discovery of multiple fragments of viruses belonging to the Hepadnaviridae family (which includes the human hepatitis B viruses) fossilized in the genome of the zebra finch. We show that some of these fragments infiltrated the germline genome of passerine birds more than 19 million years ago, which implies that hepadnaviruses are much older than previously thought. Based on this age, we can infer a long-term avian hepadnavirus substitution rate, which is a 1,000-fold slower than all short-term substitution rates calculated based on extant hepadnavirus sequences. These results call for a reevaluation of the long-term evolution of Hepadnaviridae, and indicate that some exogenous hepadnaviruses may still be circulating today in various passerine birds.
|Figure 4. Summary of the evolutionary scenario inferred in this study.|
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- Ancient Bird Virus « Life « Science Today: Beyond the Headlines
Gilbert, C., & Feschotte, C. (2010). Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses PLoS Biology, 8 (9) DOI: 10.1371/journal.pbio.1000495