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. As a point of comparison, our "own" genes--in other words, those that encode proteins that make up our bodies and allow our bodies live--make up only about one percent of the genome.The viruses themselves can change over time, leading to different variants in different individuals that can be compared to reconstruct the lineage of the virus, and reconstruct the older versions of the virus (as was done with the 1918 influenza virus).
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.
Unfortunately for creationists, this also works across species--and human beings share retroviruses in their genome with chimpanzees, macaques, and other primates. Zimmer again:
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. A particular retrovirus is not identical from one host primate to the next, but you wouldn't expect that. Once each host lineage branched off, the viruses could acquire mutations. But the different versions of these retroviruses are still similar enough that scientists can reconstruct the DNA of original virus that infected some long-gone primate.I recommend reading Zimmer's entire article, "The Sixty-Million-Year Virus," as well as Doug Theobald's "29+ Evidences for Macroevolution: the Scientific Case for Common Descent" FAQ at the talkorigins.org website (the evidence of endogenous retroviruses is item #5 in Part 4 of the FAQ).
Anybody who denies common ancestry of life on this planet does so only by disregarding the evidence.