Carl Zimmer has a terrific blog post on the subject of endogenous retroviruses (ERVs) that should be mandatory reading for anyone who still denies common descent. ERVs are viruses that get inserted into the genomes of other organisms and are inherited by the descendants of that organism. He writes:
Scientists can identify viruses lurking in our genome (known as endogenous retroviruses) by their distinctive DNA. A fully-functioning retrovirus sequence contains three genes--one for copying DNA, one for a shell, and one for escaping and invading cells. These genes are flanked by a series of repeating DNA, which allow viruses to be inserted or snipped out of their host's genome. The human genome carries full-fledged retroviruses, as well as viruses in various state of decay. Scientists have identified 98,000 of these viruses, along with about 150,000 fragments of defunct viruses. All told, they make up 8 percent of the human genome. In many cases, the virus genes have disappeared altogether, leaving behind flanking repeats, which have been duplicated to millions of copies that take up about 40 percent of the genome...Some of these endogenous retroviruses are only found in some people and not others. They must have invaded someone's genome and then spread to his or her descendants, but have not yet spread throug our entire species. Others appear to be ubiquitous--meaning that they are ancient passengers that had already spread throughout an ancestral population.
He then goes on to discuss how the ERVs provide clear evidence of common descent because we can compare the ERVs shared by humans with other species, build a phylogenetic tree based upon the shared sequences, and use it as a check against the phylogenetic trees based upon anatomical and molecular data (a phylogenetic tree is a graphic description of ancestral relationships - we are genetically and anatomically closer to, say, chimpanzees than we are to dogs and closer to dogs than we are to chickens and closer to chickens than we are to salmon - because the last common ancestor between chimps and humans lived more recently than the last common ancestor between dogs and humans, chickens and humans or salmon and humans).
Now, if you really don't enjoy reading about evidence that you are related to a chimpanzee, now's the time to close your browser window. Because now I must write about the endogenous retroviruses in chimpanzees, macaques, and other primates. It turns out that most of the viruses we carry can also be found in these other species. Our retroviruses can be grouped into families. They carry the same families. Our retroviruses usually appear in the same position in the genome, no matter whose genome you look at. Many of theirs are in the same place. These are all the sorts of evidence you'd expect if retroviruses had been carried down from distant primate ancestors.
This is incredibly powerful evidence, the kind of evidence that can only be explained by common descent and not by any sort of design or special creation. Why on earth would the designer place retrovirus sequences into the genome in such a precise manner that they clearly mimic common descent if common descent was false? The only possible explanation would be ad hoc at best, downright absurd at worst. That's why creationists avoid this subject like, well, a virus.
Update: For more information, see Doug Theobald's FAQ on evidence for comment descent. He shows a basic primate phylogenetic tree based on retroviruses that demonstrates how shared ERV sequences can be mapped into nested heirarchies that confirm common ancestry. This technique can also be used to trace ancestral relationships in other ways. For example, as Theobald points out, if you want to know whether large felines (lions, tigers, etc) evolved from smaller cats (like jungle wildcats and domesticated cats) or vice versa, you just look at the shared ERVs. You find that the smaller felines all share a common ERV sequence that they don't share with the larger felines. That tells you your relative splitting off point, that the common ancestor of those smaller cats is more recent than their common ancestor with the larger cats.
I wrote a little bit about this a year ago. The most interesting hypothesis is this: The Viruses That Make Us: A Role For Endogenous Retrovirus In The Evolution Of Placental Species.
Have you read Greg Bear's "Darwin's Radio" and "Darwin's Children"? Those are based on the ERV hypothesis, which sounded so fantastic I had to dig through the real scientific lietarure and was amazed to find how little Bear had to tweak the facts to get a cool SF premise for his books.
There was an interesting article in Scientific American within the last year (I believe it was the last six months) that described how more than a few of the modifications to the human genome apparently were induced by viruses. Which leads me to believe that not all of the potential vectors for modifications have yet been discovered.
One of the most fascinating things about ERVs is that, because they are inserted into the genome, they can later be coopted for something useful. I doubt it happens often, but it apparently does happen. This, in fact, is a good way that new information gets inserted into the genome.
Despite how much the Endogenous Retroviruses have been talked about here and elsewhere, no mention on Uncommon Pissant. Achooo!
This is seriously undeniable stuff. I mean, beyond knowing where the two ape chromosomes came together to form our chromosome 2. Beyond the whale sequences, the theraspids... here we have molecular fossils that leave only one explanation.