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I read this article by Jeffrey Tomkins and Jerry Bergman claiming to debunk chromosome 2 fusion. Is there anything wrong with these conclusions?

" 1.The reputed fusion site is located in a peri-centric region with suppressed recombination and should exhibit a reasonable degree of tandem telomere motif conservation. Instead, the region is highly degenerate—a notable feature reported by a previous investigation.

  1. In a 30 kb region surrounding the fusion site, there exists a paucity of intact telomere motifs (forward and reverse) and very few of them are in tandem or in frame.

  2. Telomere motifs, both forward and reverse (TTAGGG and CCTAAA), populate both sides of the purported fusion site. Forward motifs should only be found on the left side of the fusion site and reverse motifs on the right side

  3. The 798-base core fusion-site sequence is not unique to the purported fusion site, but found throughout the genome with 80% or greater identity internally on nearly every chromosome; indicating that it is some type of ubiquitous higher-order repeat.

  4. No evidence of synteny with chimp for the purported fusion site was found. The 798-base core fusion-site sequence does not align to its predicted orthologous telomeric regions in the chimp genome on chromsomes 2A and 2B.

  5. Queries against the chimp genome with the human alphoid sequences found at the purported cryptic centromere site on human 2qfus produced no homologous hits using two different algorithms (BLAT and BLASTN).

  6. Alphoid sequences at the putative cryptic centromere site are diverse, form three separate sub-groups in alignment analyses, and do not cluster with known functional human centromeric alphoid elements."

I've also heard them say that there has to be a fusion in every living thing that evolved or evolution isn't true. Is that true or not?

The article is here

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You are describing two processes - one of general fusion happening now and then throughout history (which is common) and one of specific fusion, that was supposed to happen at a certain time in human evolution history (which is not sure, but possible). –  jkadlubowska Dec 22 '12 at 10:52
    
@Jeff , could you include the reference to the story you are asking about? –  shigeta Dec 22 '12 at 12:40
    
Thanks! Let me take a crack at this, though @jkadlubowska has it in a nutshell here. –  shigeta Dec 23 '12 at 21:04
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1 Answer

Regarding the Papers referenced above:

If the authors maintain that the evidence at the site of fusion is not clear and that explanations as to how this happened are flawed that is possibly concedable. They would need to do more homework than these papers. The discussion of vestigial centromere sequences and telomere motifs being inverted is interesting, though contrary views have been written up elsewhere. I'm not going to review that evidence as I think its not primary to the question at hand...

I would point out that the centromere and telomere sequences are highly repetitive - they are so repetitive that they are often associated with unreliable sequencing in a typical genome build. While its possible some will be found in future builds of the human genome, such sequences are just as likely to have been excised during mitosis or by mutation. There would be strong selection pressure for them to be excised quickly; having two centromeres on one chromosome would probably be a fatal trait and the same is probably true for telomerase susceptible sequences in the middle of a chromosomal arm is too. A lot has happened at the point of fusion and 150 kB of DNA seems to have included itself which is not from the original Chr 2A or 2B.

I think there is some confusion here: The fusion models examined do not predict the fusion from the local configuration of bases. The main evidence for fusion has always been the fact that the two pieces of human chromosome 2 are nearly identical to chromosomes 2A and 2B of apes - typically 96-98% identical. The genes are almost entirely in the same order, the inter-genic regions are very similar All along the 2A/2B length - millions of bases. The site of fusion ad models for its occurrence is merely confirming what we already - there are two chromosomes somehow stuck together. Since both papers focus on the site of combination and do not adequately address this primary piece of information, they seem to be missing this point.

The chances are infinitesimal that human chr 2 were to resemble those of other primates at random. This is what you say in science when you mean 'impossible'. One simply doesn't see a segment of DNA the size of Chr 2A and 2B being so similar for such a length when we look at rats, dogs, worms or any more distantly related living thing. But for every primate the relationship corresponds to humans the same way. In addition studies show that these highly similar blocks of DNA sit right next to the site of fusion and show a crossover where the fusion probably occurred. Some recent hominids - Neanderthals and Denisovans had the chr 2 fusion as well.

I have to say is that there's always a chance that chromosome 2 fusion did not happen though in my view there's a tremendous amount of evidence that it did. The second most likely explanation is that all the other apes had their chromosome 2 break into 2 pieces at some susceptible site.

I don't quite agree that chromosome 2 fusion is an indispensable or even leading piece of evidence that means that humans and the other primates are interrelated. That question is a different kettle of fish and the relationship between Human chromosome 2 and the chromosomes of other primates is just one contributing point. All the other chromosome sequences in primates are the same, and nearly every gene in human beings is closer to primates than to other animals. If they had not found chromosome 2 fusion in the genome sequences few if anybody would have worried about it.

As to your last question - I don't know if its necessary that chromosomal fusion must occur in every living thing, but it appears that it has. In fact what we see as we look at all the diverse chromosomes being sequenced, is that most chromosomes have been merged or rearranged over and over again. Over long periods of evolutionary time, a typical chromosome looks like a patchwork quilt stitched up from pieces of other chromosomes. These relationships are called synteny, which reaffirm the thesis that all living things came from a single point of origin, if you go back far enough. Really, the fusion point of Chr2 is interesting because its a relatively new event; by picking through the pieces we might find some understanding of something that appears to be a common phenomenon in genome dynamics.

Human Mouse synteny, Human Chr 7

The above image comes from a review of methods to identify syntenic regions. It identifies regions of human chromosome 7 and similar regions of mouse chromosomes, identifying regions on mouse chromosomes 6, 9, 11, and 12 with substantial similarities as well as a little bit of chr 2. Hu chr 7 is 158 million bases long, so even a small band (> 1/1000th of the full length) on this chart means 100,000s of bases.

If all these syntenic relationships are considered together they can construct chromosomal rearrangement events that compare with the phylogenetic tree and typically verify speciation events that separate the two organisms being compared.

Whoops - just found this. Take a look at this Biology.SE question: it refers to Robertsonian translocation where the long arms of several of the chromosomes chr 14, 15, 16, 21 and 22 are known to sometimes fuse, resulting in viability. The answer there is useful - these variants don't tend to produce offspring, but it only takes one time. Its only happened once in the past 5 million years or so. So another point of view there.

That should't discourage the authors from trying again.

All this being said, as a scientific question I'd rather have a discussion like this, based on evidence and facts that anyone can evaluate. The authors did quite a bit of homework and read some of the literature that is out there. This is the right direction some of the creationists are taking here and I personally hope that they keep at it.

If science is to have any merit (or fun) at all, its because any idea can be called into question and be re-evaluated at any time by anyone.

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I'd really like to give you more than just one upvote. –  jkadlubowska Dec 24 '12 at 20:37
    
Thanks for this. Can you tell me, was the fusion of "two chromosomes" actually predicted before it was demonstrated in Chr 2, or was it discovered first and then taken as evidence in support of the lineage? –  Michael Bray Jan 19 at 21:33
    
It was known. When you localize genes in humans and then in chimps the broad idea of a chromosomal fusion is referenced from 1995 on the wikipedia page en.wikipedia.org/wiki/Chromosome_2_(human) –  shigeta Jan 19 at 23:48
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