When retroviruses insert into the host genome it is random. Think of randomly flipping through a dictionary and putting your finger on a random word. That is how retroviruses insert into the 3 billion base human haploid genome.
If you had two people randomly flip through a massive Oxford English dictionary and randomly put their finger on a word, how many times out of 100 do you think they would land on the same word? Probably not once, right? The same for ERV's. The chances that two separate infections will result in the same insertion at the same base is extremely low. Therefore, when we find two genomes with the same ERV at the same base in each genome we know that it is from a single insertion in a common ancestor.
What do we find with humans and chimps. Out of the 200,000 ERV's in the human genome, more than 99% of them are found at the same base in the chimp genome. This tells us that humans and chimps share a common ancestor.
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