Once every 5,000 years for 5,000,000 years is 1,000 infections getting fixed in the genome. Not obviously impossible. What's "preservation"?
And you can't say that your data 'exactly matches the phylogenetic tree'. The 'tree' doesn't exist.
Huh?
The 'forks' are all imaginary and all of the bushy leaves haven't been sequenced.
OK, I should have said that the tree of presence/absence of genetic markers is always a subtree of the already-known phylogenetic tree.
But the trees produced by the different genetic markers are always consistent with each other and with the phylogenetic tree.
Always? Depends on your definition of 'consistent', I'm sure. Quite a move away from 'exactly matches the phylogenetic tree' already. I'm sure we will find out once we see just how 'consistent' they are.
Preservation is preservation across all speciation events since the mythical infection-to-fixation event. No losses at all? Ever? Exact matches?
And there are 'thousands' of human ERV's, not 1 thousand. Those are tremendous substitution costs for random, inactive retroviral infections.
Credulity. Simple credulity.