I recently did two analyses into chromosome 2 fusion, which I’ll eventually include in a comprehensive blog post dedicated to the evidence for the fusion when I get around to it.
For now, here’s the summary for those interested.
It’s commonly argued, by Tomkins and other creationists, that two of the primary pieces of evidence for chromosome 2 fusion - the presence of telomeric repeats at the alleged fusion site and the presence of alphoid repeats in the alleged cryptic centromere - are actually very poor evidence because these repeats are in fact found all over the genome, not just in those locations alleged to be related to the fusion event.
They argue that since telomeric repeats and alphoid repeats can be found all over the genome, there’s really nothing special about the sites claimed to represent the fusion site and cryptic centromere. In effect, they’re claiming that “evolutionists” are cherry-picking these sites because they fit the fusion story while ignoring all the other telomeric repeats and alphoid sequences that don’t.
I decided to find out if there was any truth to these claims. Spoiler: there isn’t.
Telomeric repeats are short, just 6bp (TTAGGG and the reverse complement, CCCTAA), so it is obviously true that these can be found throughout the genome, even just by chance. However, it’s also true that there are large chunks of repeats, consisting of tens or hundreds of telomeric repeats, present all over the genome, not just in the telomeric regions. So at first glance, it appears that the creationist claim is true, right? If chunks of hundreds of telomeric repeats are found all over the genome, what makes the alleged 798bp fusion site so special?
The fact that the telomeric repeats in the alleged fusion site are found in a head-to-head arrangement, exactly as expected from a head-to-head fusion.
I’ve done lots of BLATing and BLASTing, and literally the only location in the entire human genome where I can find hits for a sequence consisting of head-to-head telomeric repeats is in the alleged fusion site. In this respect, the alleged fusion site is absolutely unique.
It’s a similar story with the alphoid repeats. These repeats are each 171bp long, and centromeres tend to consist of roughly 10,000-20,000 of these repeats, mostly in one clear block but sometimes with some smaller blocks of repeats closely flanking the main block. (In the diagrams below, I grouped all alphoid repeats within 50kb of each other into a single block, and all alphoid repeats within 6Mb of the annotated centromere as being part of the centromeric block of repeats.)
Searching the human genome for these alphoid repeats, I found that they’re nowhere near as ubiquitous as implied by creationists. Here’s all the repeats representing the centromeres, with the numbers representing the number of repeats in each block, and the dark band represents the location of the centromeres.
There are also a few isolated repeats ranging from 1-15 tandem repeats in the genome, shown below:
After these, the only remaining alphoid repeats are found in two blocks in the genome:
One of them is a large block of 185 repeats that comprises the cryptic centromere, dwarfing the small number of isolated repeats found outside of the centromeres in the previous figure. The other large block of 2011 repeats in chromosome 9 is an exceptional case, where there is a huge block of heterochromatin separating it from its centromere 15Mb away.
The repeats in the cryptic centromere, on the other hand, are 38Mb away from the functional centromere of chromosome 2, so is clearly unique as the largest block of alphoid repeats most distant from a functioning centromere in the entire human genome. Here’s all of the alphoid repeats in a single figure:
So in both cases, telomeric and alphoid repeats, the fusion site and cryptic centromere on chromosome 2 clearly stand out as unique in the human genome, representing the expected signature of fusion that in turn provides compelling evidence for the fusion