In a new study, Evan Eichler and colleagues scanned finished chimpanzee genome sequence for endogenous retroviral elements, and found one (called PTERV1) that does not occur in humans. Searching the genomes of a subset of apes and monkeys revealed that the retrovirus had integrated into the germline of African great apes and Old World monkeys—but did not infect humans and Asian apes (orangutan, siamang, and gibbon). This undermines the notion that an ancient infection invaded an ancestral primate lineage, since great apes (including humans) share a common ancestor with Old World monkeys.
Eichler and colleagues found over 100 copies of PTERV1 in each African ape (chimp and gorilla) and Old World monkey (baboon and macaque) species. The authors compared the sites of viral integration in each of these primates and found that few if any of these insertion sites were shared among the primates. It appears therefore that the sequences have not been conserved from a common ancestor, but are specific to each lineage.
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030126
"It appears therefore that the sequences have not been conserved from a common ancestor, but are specific to each lineage."
What would the specific lineage be?
Eichler and colleagues found over 100 copies of PTERV1 in each African ape (chimp and gorilla) and Old World monkey (baboon and macaque) species. The authors compared the sites of viral integration in each of these primates and found that few if any of these insertion sites were shared among the primates. It appears therefore that the sequences have not been conserved from a common ancestor, but are specific to each lineage.
The ERVs that are the smoking gun of common descent do have identical insertion points in the genomes of different species. That is their significance. Further, those ERV's have become slowly corrupted by copying errors since their original insertion. Such copying errors occur at a known rate (approximately, being random), so by reckoning backwards we can identify the point at which each species-split occurred. The ERVs being talked about in your cited article aren't of the same type. Ichneumon probably knows a lot more about this, so I'm pinging him in in case he wants to add any more detail.