The answer is simple, and creationists pointed it out long ago:
The assumption behind using ERVs to determine phylogeny is flawed. It assumes: (1) that ERVs are non-adaptive (at least by default), and (2) that they don't have site-specific integration. The issue can be easily solved if ERVs have a functional role in the ecosystem, binding to certain positions in the genome for specific adaptive purposes. The similarity between humand and chimp retroviruses is because, having similar genomes exposed to similar retroviruses, we had similar integrations.
One of the biggest problems of neo-Darwinism in biology is that it has a default assumption of "nonadaptivity". Thus, transposons, retroviruses, pseudogenes, introns, and any number of other dynamic elements of the genome were viewed by Darwinists as "junk", just because Darwinism requires there to be a lot of leftover junk hanging around. The idea that these could be holistic, functional systems never seems to occur to them. The idea that cells could have system architectures is antithetical to Darwinism, despite the fact that this is precisely what microbiology shows.
If the cell is instead viewed as an adaptive system, then most of the arguments for common ancestry fall away, simply because much of what is assumed to be due to common ancestry might also be due to common environment, common change mechanisms, common design, and the like.
As Simon Conway Morris put it:
"For what it is worth my own belief is that metazoans are indeed monophyletic, but to my mind the argument is not yet won. More importantly, the question of biological constraint, the prevalence of convergence and the inevitability of polyphyly are not only interconnected topics, but also unjustly neglected. In part I suggest this is because of the atomistic emphasis now given to biology, as well as an obsession with cladistic methodology, which although freely acknowledges homoplasy regards it as an irritating diversion rather than a profoundly interesting problem in its own right."
You should read the recent papers by coauthors Shapiro and Sternberg about genome organization. They present the basic case for holistic organization of genomes, rather than the atomistic view of Darwinists.
"If I understand correctly, this would mean that the human-chimp split is closer than anyone thought to the split from gorillas."
So you admit it wasn't something that would falsify the theory of evolution. And, likewise, finding a rabbit in the Cambrian would mean either, (a) we put forward some hypothetical geological event that put it there, or (b) we just move the origin of mammals back in time. It wouldn't falsify the theory of evolution, because contrary to what evolutionists want you to think, evolution is an assumption, not a conclusion.
Actually, it appears to falsify one aspect of common descent: that there was a speciation event that split off gorillas, and then, in the other branch, human and the two chimp species split in an undeteremined order.
Instead, it shows that there was gene flow between the (proto-) chimp and gorilla populations after the proto-humans had branched off. IE, the speciation wasn't yet complete, IE, like I said, the splits were closer together in time.
Very interseting result.
Especially in light of all the ERVs that nest
So the Asian apes should have things in common with each other that aren't shared with African ones?
[musing out loud...]
There are a few thousand ERVs in our genome. We split from the other apes maybe 5-6 million years ago. So that's one ERV getting fixed every few millenia.
If I get a retrovirus in my germ cells (tesitcles), this confers some kind of advantage?!
Are there any known examples of advantageous (retro)viral infections?
RWP, Ichy: You all know anything about this? Thanks