Therefore, its presence in such a wide variety of mammals (apes, elephants, humans, etc.), and the improbability that each species of mammal caught the virus separately, indicates a common ancestor, right?
Nothing to do with common ancestry.
It is evidence that there are pieces of the genome that can be replaced without altering the nature of the organism.
It is evidence for the existence of DNA that serves no functional purpose.
A retrovirus uses RNA. It attaches to a cell, dumps its genetic information into the nucleus and reprograms the cell to manufacture more of itself. It can (Not always) do this in such a way that the cell still performs it's original function. (For instance, making spermatozoa) It a case like that, the sperm now have large chunks of their DNA altered yet can still function as sperm. You now have DNA that still works to make mammal X (Let's say a human) with no difference in the result, even though a large chunk of DNA has changed.
That is evidence for "Junk DNA" (Not necessarily the only cause of it, however.) Note that I said evidence and not proof.
It can also be a cause of mutation when it changes DNA that is important. Most mutations lead to dead babies. Some lead to other changes that are possibly cosmetic or less important or even beneficial.
This is also not the only cause of mutations, obviously. Anything that breaks or recombines DNA can cause them. Diet, radiation, age, whatever.
Evidence for 'Junk DNA" is only going to build over time, because it's easy to test. Take a rat or whatever with junk DNA, remove the questionable DNA (And replace it with null proteins) and clone it. Make a bunch of clones from different rats.
If they turn out to be normal rats and you can breed them over several generations and they stay rats, you've found yourself a chain of Junk DNA.
This sort of thing is happening as we speak.
What I fully expect to see is that religious types starting to say things like "Retroviruses are like the hammer and chisel that Gawd uses to create life." or "Gawd had to fill all the gaps where man lost his perfection after the original sin with
something.", when they get backed into a corner about Junk DNA as evidence accumulates.
But none of this really matters. It's about repeatably testable, non-anecdotal evidence for the existence of supernatural agencies.