No, you don’t understand, and it’s going to be difficult to explain.
Let’s say that the word HIPXPOPOXTAMUS was a gene – the "X"s represent introns. When a gene retrotransposes (i.e., makes a copy of itself to some other place in the genome), two things happen: First, any “introns” (i.e., junk stuck in the middle of a gene) get erased – so, in this case, the copy of HIPXPOPOXTAMUS becomes HIPPOPOTAMUS. Second, the new copy has a trailing “A”-tail attached to it – so, the final form of the copy is HIPPOPOTAMUSAAAAA.
Basically, what this means is that if you find a “clean” gene with a trailing “A”-tail, you know it’s a copy and not an original. Now, keep in mind that these copies can wind up being inserted anywhere in the genome, and the probability that two copy events in two different species will put copies in the exact same places in the genome of each species is incredibly small. It’s really just not going to happen. The truth is, if you see a copy located in the same place in the genomes of two different species, the only way that copy could have gotten there in both genomes is if (1) both species were descended from a common ancestor species and (2) the copy event actually took place in the common ancestor species, and was transmitted down to both descendant groups once they split off from each other.
The long and short of it, then, is that humans and chimpanzees have plenty of copies of genes located in the exact same places in their genomes. This simply could not happen if humans and chimpanzees had totally separate lineages. The only way this could happen – the way it did happen – is that the copy events all took place in a common ancestor species that later split up into humans and chimpanzees.
–Mike