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Genes contain fossilized retroviral insertions. What this means is that, sometime in the past, a virus got its genetic material tangled up in a gene at a particular location. To make a long story short, critters with the same insertion will be related (the odds of it happening exactly the same way twice are astronomical). Using these retroviral insertions, researchers have been able to clarify some aspects of the tree of life and to confirm others.

I understand that you made a quick summary for the sake of brevity in your post, but I think you are jumping the gun a little bit drawing conclusions from retroviral insertion points -- at least at this time. You are making assumptions that the source viruses do not assert an insertion point bias, that the source viruses endogenous markers do not wane and cannot be re-introduced exogenously, and that the source viruses are not capable of zoonosis or other cross-species transmission. Without these assumptions, there is no guarantee that the "critters ... will be related". Here is an interesting study that speaks to some of these issues, if you are interested. Note that this is not a creationist or ID'ist study -- it speaks only to a better understanding of evolution and raises questions regarding the validity of those assumptions from an evolutionist point of view. The bottom line is that the jury is still out on what information can be inferred from retroviral insertions within genomes. We are still in the data collection phase and I'd not hasten to insult a dissenting interpretation of that data until more is known.

The paper is on lineage specific retroviral insertions in the genus pan (chimps and bonobos). As far as I can tell, it has nothing to do with tracing the overall tree of life using fossil retroviral insertions within the genome.

Now, I could be wrong because I'm a computer geek, not a working biologist. That's why I've pinged someone with a lot more experience in this than me when it comes to reading these things.