First a little background - a retrotransposon is basically a little chunk of DNA which can 'copy-paste' itself throughout a genome. The insertion of the 'paste' is generally regarded as homoplasy free for some retrotransposons, which basically means random (although there are some insertional prefeances at times, which is why I added the leniant probability below).
Basically, then, the probability that any retrotransposon inserts in a specific location along a genome is 1 in however many places it can insert - many, many millions in terms of human and chimp genomes.
The reasoning comes about because when looking at the two genomes, we see many shared retrotransposons in very specifc shared locations between the human and chimp genomes. This is the spawn of the below test:
By the way I'm doing this here because I really don't have the time to wade through a sea of apologetics excuses. Please, I ask you to be very tough on my maths if it is at all bad.A Simple Mathematical Probability Test –
Let’s try a test. What would it take for all of these shared genetic retrotransposons of a 3 billion base pair genome to come about independently? Let’s give the proposition that they all came about independently a ludicrously lenient probability for two of the same retrotransposons inserting in the same locus – 1 in 10, or 0.1. Realistically, for those elements that are virtually homoplasy free, the probability for even one shared retrotransposon to come about independently of common ancestry is much, much smaller. Now, let’s take the following retroelements as examples –
(100 common retroelements, presented later [trust me, there are more than 100 ])
Taken the simple rule of the multiplication of the probabilities of two unlikely events occurring coincidentally, let’s multiply the 0.1 probability of each event occurring independently of common ancestry and multiply it by the 100 retroelements chosen for analysis. This multiplication gives 0.1^100 which gives us a probability of 0.1^-100 i.e. 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001. This is virtually a probability of zero.
Thanks.