The platypus genome, which was published for the first time last week, has proved to be a Whitman’s sampler of biological treats. In case you missed the initial reports, you can check out a good summary from PZ Myers (and also take a look at Ryan Gregory’s take-down of the bad coverage). But today I just happened to come across another treat that, to my knowledge, hadn’t yet been picked out from the box. It’s a paper that came out today in Genome Biology. It concerns a very cool side of evolution that not many people appreciate. Species can evolve when their genes are modified, or when they acquire new ones. But the platypus turns out to be a great example of how species can evolve by losing genes.
When scientists sequencing the platypus genome matched up genes from the platypus to the genes from other mammals, a bunch of genes were missing from the duck-billed creature’s DNA. They were genes for protein-cutting enzymes called proteases. A closer looked revealed that these missing genes were for enzymes made only in the stomach. An even closer look revealed that these genes were not absent altogether, just disabled. Virus-like pieces of DNA had been inserted in the middle of these genes, making it impossible for the cells to make proteins from them. The scientists then looked at other genes for proteins that typically get made in the stomach. Some proteins, for example, create the acidic conditions in the stomach. The genes were broken in the platypus too.
Here’s what makes these losses really weird: Platypuses have lost their stomach. Just about all vertebrates have a stomach, a special, acid-drenched pouch with a number of specialized types of cells for producing digestive enzymes. The stomach of fish is build with the same developmental genes as ours. But for some reason, the platypus stomach has disappeared, leaving just as featureless tube connecting the esophagus to the intestines. Why platypuses would lose their stomachs while almost no other vertebrate has over the past 400 million years is a question I’d love to hear the answer to. (I didn’t even know to ask the question till I read the paper today.) And now scientists have found that stomach genes have performed the same disappearing act. But their remnants leave a sloppy trail of evidence of how this gastric bypass evolved.
May 15th, 2008 at 8:51 pm
Oh, is that ever neat! Thanks for pointing that one out.
Any idea how common this genetic break is? If they’ve lost something as basic as a stomach, their diet must make that a selectively beneficial (or at the very least neutral). If that’s the case we would likely expect to see that same break in other species with similar diets.
Or is it at all possible that the genetic damage came first resulting in a beneficial dietary shift?
May 15th, 2008 at 8:52 pm
Carl — They couldn’t stomach the only foods they had to eat.
May 15th, 2008 at 9:04 pm
Do they not have a stomach because they’re missing the (functional) genes, or did the genes become irrelevant (and finally mutated to the point of not functioning) because they didn’t have a stomach anyway?
Did all the genes mutate somewhat simultaneously, or was there one that started the whole cascade?
May 16th, 2008 at 9:49 am
Oh come on now. We all know that loss of information is not evolution. Right guys?
Oh, right.
May 16th, 2008 at 12:53 pm
That’s wild.
I wonder how they absorb vitamin B12. In humans, gastric intrinsic factor depends on stomach pH to bind B12 properly (which is why people taking antacids have to watch out for B12 deficiency).
A quick BLAST brings up what looks like a pretty good intrinsic factor homolog in the platypus genome, but I’m not used to sequence-gazing in eukaryotes, so I don’t know if it’s likely to be functional or not. If so, it must work at whatever pH the platypus gut is at. That could be useful…
Very cool result. Thanks for the link!
May 16th, 2008 at 3:27 pm
An even closer look revealed that these genes were not absent altogether, just disabled.
These are termed pseudogenes.
May 16th, 2008 at 4:45 pm
This is most curious and a bit startling – how did the platypus community react to news of their loss? In all seriousness – does this development (undevelopment) aid them in any way? I guess they don’t have to stay out of the pool for two hours after eating, my colleague says.
May 17th, 2008 at 8:50 am
The paper is freely available, nicely written and answers some of the questions above.
It seems that stomach reduction occurred in the ancestor of both platypus and equidna.
Michael: The authors found that gastric intrinsic factor is primarily expressed in the pancreas. They also comment that it is also expressed in the pancreas in dogs. Thus, it seems likely that GIF is functional and can work at the pH found in the duodenum.
Eva: They also talk about possible scenarios for the loss of the stomach. One I found interesting is that stomach reduction may have been selected as a defense against parasites, some of which need the acidic pH for infection.
The mechanisms of gene loss are varied, implying that they occurred secondarily to stomach loss. Again, the paper describes several examples clearly and with nice diagrams.
Thanks for another interesting post Karl!
May 17th, 2008 at 11:18 am
Thanks, Arturo! Another mystery solved.
That’s what I get for skimming the paper…
May 17th, 2008 at 6:31 pm
*slaps mr. Benson*
It would be interesting to see if any of the stomach functions have been replaced by other (intestinal?) functions. Perhaps someone can earn a phd on that
May 27th, 2008 at 3:51 pm
Interesting stuff. So the platypus was unable to produce the enzyme that was used to digest in the stomach, the stomach becomes useless and redundant, so they eventually evolve to survive without a stomach at all? My question is how do they digest there food properly without a stomach? do they have “psuedostomach” at the start of the small intestine?