A new article by Jeffrey Tomkins is out: Epigenetic Study Produces ‘Backwards’ Human-Ape Tree. The subject is a paper called “Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes” in the Journal of Human Genetics – it’s open access, but a little dense.
To recap a subject we’ve seen before: various processes, the most famous of which is known as “DNA methylation,” can modify the amount that a gene or other stretch of DNA is expressed and with that its effect. This adds up to what is called epigenetics, a relatively new biological field of investigation. Most epigenetic research has concentrated on what is seen in human cells, but some more recent studies have shown that patterns of methylation are to some extent heritable, and also differ between species. In October of last year Brian Thomas pointed to a study showing differences in methylation in cells in various organs between chimpanzees and humans, and tried to argue that this showed that the two groups could not be related based on the unfounded assumption that methylation patterns could not change – even despite the not-inconsiderable variation observed even within humans.
This study adds gorillas and orangutans into the mix. They included in their paper an illustration of a tree generated from the differences between the patterns observed in each species. Here’s how Tomkins illustrates it (claimed as fair use for criticism) – concentrate first on the tree on the left (his reproduction of the one in the paper) and it’s associated asterixed note:
It’s not immediately obvious what Tomkins has done, aside from rotating and flipping the diagram, but it looks like he disagrees with the length of some (or at least, one) of the branches. Here’s the original tree:
The caption in the paper says that, for their figure, “The length of each vertical branch is proportional to the degree of difference in DNA methylation.” Tomkins has apparently extracted the original data, somehow, and calculated a tree with somewhat differing lengths for what are in his figure the horizontal branches. For all his claims of the original authors “mis-representing” their results here, this particular aspect doesn’t seem to be nearly as important to his claim as the overall structure of the tree.
You see, regardless of how long the branches are represented as or what direction the diagram as a whole is oriented, that’s not the commonly-accepted tree made up of humans and our nearest relatives. For one, chimps and humans should be most closely related to each other, not chimps and gorillas. But what then is that tree? If you remember, Tomkins also included above what he thinks it looks like. Go take another look at it – I’ll wait.
That’s not what we’re looking for either, is it? If we again ignore line length and revert the orientation to the vertical, the overall structure of the tree usually presented is this:
Humans are most closely related to chimps, and then to gorillas and finally to orangutans. On close inspection, the structure is not actually all that different to the tree calculated, with the only difference being the position of the human branch: in the methylation tree we’re out to the side, while we should be deep within the group.
With the true problem identified, we move to the solution, as seen by the authors of the paper – not that they seem to think of it as a problem:
These results suggest that the methylation status changed more rapidly in the human lineage than in the chimpanzee lineage, consistent with the results of Martin et al. [link]
In other words, while the other tree groups have evolved naturally with respect to the methylation patterns investigated, humans have spun off and done their own thing. There is, however, one more wrinkle – Tomkins says:
Orangutans, who supposedly are the least evolved among apes compared to humans, actually had more DNA methylation patterns similar to humans than chimps or gorillas. And if that was not enough, gorillas were the next closest in similarity to humans with chimps falling out last! According to evolutionary predictions, chimps should have been most similar to humans, then gorillas, and lastly orangutans.
Humans should still be most similar to chimps, but it seems that this is not the case. I suspect that the result may be due to the degree of divergence of the human group coupled with the way the tree was calculated, possibly producing something like this, but I don’t know nearly enough about this subject to say. Do any of you have an idea?