My initial instincts were that you were a desperate lawyer picking at the only issue with any traction at all.
At best, the information you presented appeared to conflict with Ichneumon's. And my initial instinct was that even assuming ERVs inserted at a single site, the evidence still showed common ancestry.
But even the insertion pattern found in primates and humans made no sense vs. your point. If ERVs always inserted at the same point, then the species distribution of ERVs would be random vs. the species divergence. And/or all related species would have all "hot spots" in their genomes occupied by ERVs.
I was giving you plenty of benefit of the doubt on this, even though I wasn't convinced on your point from the beginning.
Isn't the key here that tallhappy is speaking only about "functional integrations"?
It would seem to me, trusting my initial reaction, that it is the functional location that is nonrandom, rather than the distribution of integrations.
Yes. This is the case. Repeating elements corespond to regions of high gene density. Some chromosomes have uneven gene desnity distributions and some are evenly distributed. Repeating element patterns follow gene density patterns. If integration were purely random an even distribution independent of gene desnity would be seen.
One idea on this is that retroviral integration needs areas of gene activity. The active regions will have increased regions of unwound chromatin which allows the insertion event to take place.