Chromosome 2 Fusion – The Low Hanging Fruit

Jeffrey Tomkins has written a number of articles in previous years that attempt to cast doubt on the claim that human chromosome 2 is the result of a head-to-head fusion of two ancestral chromosomes.

For the sake of brevity, I will address only a few of the more egregious errors that Dr Tomkins made in his articles; I will address the others when I have the time and the inclination.

Comparative Scale, huh.

In this article Dr Tomkins posts a diagram of the fusion supposedly drawn to scale. The desired effect here is obviously to have people believe that the human chromosome 2 doesn’t align to its chimpanzee counterparts. Here is Dr Tomkins’ diagram:

TomkinsToScale

And here is my diagram:

FusionToScale

The difference is that the PostScript code used to produce my diagram is freely available, and from that you are able to verify the genome coordinates I have used.

Dr Tomkins also claims here that the combined chimpanzee chromosomes are some 10% larger than the human chromosomes. However, according to the most recent chimpanzee assembly – named “panTro4” – the combined length of chimpanzee chromosomes 2A and 2B is 247.5Mbp while human chromosome 2 is 243.2Mbp. This is a difference of only 4.3Mbp, or 1.8%. It should be noted that the centromeres in the chimpanzee assembly are manually placed on the chromosome and are of an arbitrary fixed length of 3Mbp. This introduces some uncertainty in the true length of combined chimpanzee chromosomes. Human centromeres are known to range in length from 0.3Mbp to 5.0Mbp, and if the centromere on chimpanzee chromosome 2B is (in reality) at the lower end of that range, then the size difference would be easily less than 1%.

What should we see at the fusion site?

Tomkins predicts that under the fusion model “thousands of intact TTAGGG motifs in tandem should exist” yet he is fully aware that the function of telomeres is to prevent such fusions in the first place. To expect thousands of intact telomere motifs at the fusion site is to expect that intact telomeres somehow failed.

The most parsimonious explanation is that the telomeres were already missing (or severely shortened) and this allowed the fusion to occur. Lab experiments where components of the telomere nucleoprotein complex have been disabled demonstrate the ease at which head-to-head fusions occur when the telomeres are depleted.

Moteefs y’all

Jeffrey Tomkins says explicitly that forward telomere motifs (‘TTAGGG’) should only be found on the left side of the fusion site, and reverse telomere motifs (‘CCCTAA’) should only be found on the right of the fusion site.

Yet by my calculations, any 6 base pair sequence should occur entirely by chance approximately every 4,096 base pairs (4 ^ 6 = 4,096). Dr Tomkins produced a table showing the breakdown of forward and reverse motifs found both to the left and to the right of the fusion site.

On the RP11-395L14 BAC used by Tomkins, there are 108,569 base pairs to the left of the fusion site. Mathematically, I would expect 26 reverse telomeres to be present while Dr Tomkins expects zero – there are 18. To the right of the fusion site are 68,167 base pairs. I would expect 17 forward telomere motifs, Dr Tomkins expects zero – there are 18.

In your hands

As indicated by the title, these are just the low-hanging fruit; claims made by Tomkins that can be addressed quite easily. Some of the other claims are a little more complex and/or take more time to address. If there is a particular claim that anyone would like me to address, please let me know in the comments.

 

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One thought on “Chromosome 2 Fusion – The Low Hanging Fruit

  1. Great analysis once again man. Two of the more “burning” questions about Tomkins article (as I hate to call it a paper) is his claim that the DDX11L2 gene he claims that is located in the fusion cite is functional with an alternate transcription as long with being “highly expressed”. We have looked into this and found that there is no known transcription for DDX11L2 nor any indication it is highly expressed…as it’s expression across the board in tissues were nominal with a minor exception to the testes. What have you found about these claims?

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