Amylase and human evolution

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Blogging on Peer-Reviewed Research

I made a mistake that was quickly corrected by a correspondent. Yesterday, in writing about copy number variants in human genes, I used the example of the amylase gene on chromosome 1, which exists in variable numbers of copies in human populations, and my offhand remark was that the effect is "nothing that we can detect", but that maybe people with extra copies would be "especially good at breaking down french fries". Well, it turns out that we can detect this, that there was even a very cool study of this enzyme published last year, and that the ability to break down complex starches rapidly may have been a significant factor in human evolution.

So of course I have to tell you all about this now.

Amylase is a digestive enzyme that specifically helps break down complex sugars, like starch, into simpler sugars that can be processed by other enzymes or absorbed by the intestine. You are secreting this enzyme all the time into your saliva, so that as soon as you pop something made of starchy carbohydrates, it's coated with these enzymes that get to work breaking it down. As it's swallowed and enters the stomach and intestine, these enzymes are still busy rendering the starches down into something more manageable for your gut to handle. This is an important function: if you chew starchy foods made from rice, corn, or potatoes, saturating them with the enzyme, blood glucose levels afterwards are measurably higher than if you just swallow the food whole.

As I said yesterday, the amylase gene has another interesting attribute — it seems to be in a hotspot for duplication, and different people have different numbers of copies of the gene. If you just had one copy of the gene per chromosome, your cells would each have a grand total of two copies…but instead, we more typically have 5 to 7, with some people having only 2, and others having 15 or more.

There are a number of ways to count how many copies of the gene there are, but one of the more visually appealing ways is to use fiber FISH (fluorescent in situ hybridization). In this technique, intact DNA is extracted from cells and stretched out, then a probe for the amylase gene that is tagged with a fluorescent label is allowed to bind to the strand, and every place with an amylase gene lights up red. As you can see below, then you can directly count the genes: in this case, the individual at the top has 14 copies of the gene on two chromosomes, the one in the middle has six copies, and the very interesting fellow named Clint at the bottom has only two copies. Clint happens to be a chimpanzee.

fiber_FISH.jpeg
High-resolution fiber FISH validation of AMY1 copy number estimates. Red (~10 kb) and green (~8 kb) probes encompass the entire AMY1 gene and a retrotransposon directly upstream of (and unique to) AMY1, respectively. (a) Japanese individual GM18972 was estimated by qPCR to have 14 (13.73 ± 0.93) diploid AMY1 gene copies, consistent with fiber FISH results showing one allele with ten copies and the other with four copies. (b) Biaka individual GM10472 was estimated by qPCR to have six (6.11 ± 0.17) diploid AMY1 gene copies, consistent with fiber FISH results. (c) The reference chimpanzee (Clint; S006006) was confirmed to have two diploid AMY1 gene copies.

Chimpanzees don't exhibit much copy number variation in the amylase gene, but humans do…how interesting. Could this variation be a reflection of something specific in human evolution? Why, yes.

This work by Perry and others went on to look for patterns in different human populations with different dietary historys, and discovered that there is a correlation: cultures with diets heavy in starch, agricultural populations such as Americans, Europeans, and Japanese, or hunter-gathers who live on many roots and tubers, have a higher average copy number than cultures that depend more on hunting and fishing.

Look at the distributions! Populations with little starch in their diets also have a relatively low copy number of 5.44 amylase genes per individual; we french fry eaters have a higher number of 6.72 amylase genes per individual. The difference is small, and the distributions also overlap significantly (note that some with high starch diets only have 2 copies, and some living on low starch diets have 13 copies), but the difference is measurable and significant. It implies that there may have been some selection for greater copy numbers in cultures with diets high in starchy plants.

amy_copy_number.jpeg
Diet and AMY1 copy number variation. (a) Comparison of qPCR-estimated AMY1 diploid copy number frequency distributions for populations with traditional diets that incorporate many starch-rich foods (high-starch) and populations with traditional diets that include little or no starch (low- starch). (b) Cumulative distribution plot of diploid AMY1 copy number for each of the seven populations in the study.

We can't entirely rule out drift as a possible cause of the difference; while we can see differences in the enzyme levels in saliva, low levels of the enzyme haven't been shown to be directly deleterious to anyone. It is again implied: oral digestion of starches may be an important pathway for taking in energy during episodes of diarrhea, so it could be critical when individuals are experiencing disease-related stress.

It is very suggestive. The fact that it represents a distinct difference between other apes, such as chimpanzees, and ourselves also suggests that it may have had significant evolutionary consequences. Maybe we aren't primarily the biggest-brained apes; we are the Apes Who Eat Roots As Well As Bananas. A core nutritional difference could have played a more significant factor in our early evolution than small differences in brain size, and may have been an enabler of brain expansion.


Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet. 39(10):1256-60.

28 Comments

PZ Myers? A mistake? Stop the presses.

I wonder if Uncommon Descent will have an entry called “Vindication.”

NS

Thanks again for sharing, PZ. Unlike some others (looks directly above), your contributions actually help spread useful information.

I like this type of post that tells me something I had absolutely no idea existed - it can get me practically salivating.

notedscholar said:

I wonder if Uncommon Descent will have an entry called “Vindication.”

Is this a poe or just clueless? But if it is a malicious troll, how stupid do you think your creationist comrades reading this?

Which btw are YEC:ers, not “don’t ask, don’t tell which age” ID creationists - but you had to read the whole material to see that, and of course a troll can’t read that much before being distracted by the blank keyboard with buttons that can be pressed in seemingly random order.

The post confirms the previous one, which describes how AIG distorted actual research into a fallacious description.

So if AIG repent their lies there may be an act of vindicating for actual biologists. And what are the chances for that?

D’oh, bad edit; it was a general comment/first line observation, and “… reading this are”.

notedscholar said: I wonder if Uncommon Descent will have an entry called “Vindication.”

Sadly, no vindication over the fact that amylase gene CNVs in humans actually support evolution, instead of having no effect as PZ originally claimed.

No, they are busy posting about how a sci-fi story explains that articulating the notion of moment requires an articulator. Take that, evolution!

Noscholar wrote:

“PZ Myers? A mistake? Stop the presses. I wonder if Uncommon Descent will have an entry called “Vindication.”

Yea, it took Dembski twelve years to admit his mistake. It took PZ twelve hours. Anyway, he really didn’t make a mistake, he just slightly underestimated the importance of an observation. And of course he corrected himself immediately when he was shown to be even slightly in error. Now if he had published ten books bypassing the peer review process and then refused to admit his error even when it was pointed out to him then maybe UD would have something to crow about, at least if they were the ones doing the correcting.

In any event, this is a perfect example of gene duplication caught in action. Who knows what role the duplicate genes might take on due to mutation and exaptation later in human evolution. Perhaps a study of the evolution of mechanisms regulating levels of gene expression would also prove instructive. We could call it the McDonald’s adaptation.

Thanks for this post - I teach a high school lab in which my students compare the rates at which their individual salivas digest starch. It is, like most high school labs, very general but how nice to be able to follow it up with this research and to relate what they have seen in lab to actual variation, to possible natural selection and to genetics. It’s also interesting to students that scientists actually do research with things like spit.

Now exactly what would my ID lesson plan cover?

Hey guys, NS just made a little joke. Chill.

No, they are busy posting about how a sci-fi story explains that articulating the notion of moment requires an articulator. Take that, evolution!

There’s probaby a joke about magnets and pendulums in there. But I’m not going after it.

Is it just me, or does reading this artivle make we want to eat a big baked potatoe…covered in butter and just a pinch of salt.…

mmmmmmm.…starches.…

I can’t type. I meant “Article” “make me” and “potato.” My mind is definetely elsewhere…

Mmmmm.…Starchy goodness.…

Pete Dunkelberg said:

Hey guys, NS just made a little joke. Chill.

Thank you Mr. Dunkelberg. These academics on this blog are pretty ornery, I have found.

Although they’d be pleased to know that I’ve attacked ID on my own blog, putting to death once and for all silly rumors floating around the blogosphere that I’m a creationist.

NS http://sciencedefeated.wordpress.com/

Now exactly what would my ID lesson plan cover?

Just do what the ID experts do - make it up as you go along. ;)

Henry

On a related note, on CSI last night one of the lines that caught my ear was that humans and chimps share 99.5% (I forget if he said DNA or “genes”). If it’s DNA, there are different ways to count it, and AIUI the “% similarity” comes out to 95 - 98.5, depending on the method. That bothered me because the quote is easy to misrepresent by anti-evolutionists, especially to pretend that the “liberal media” is trying to inflate the similarities. I would have much preferred if line was “humans and chimps share common ancestors from as little as 6 million years ago, which is just a tiny fraction of the history of life on Earth.” While AIG might complain, the DI knows better than to try to refute that.

Henry J Wrote:

Just do what the ID experts do - make it up as you go along. ;)

You gotta admit, they have an almost endless supply of clever ways to say “we don’t need to connect no stinkin’ dots.”

Frank J said:

Henry J Wrote:

Just do what the ID experts do - make it up as you go along. ;)

You gotta admit, they have an almost endless supply of clever ways to say “we don’t need to connect no stinkin’ dots.”

Besides, they don’t need to stoop to our pathetic level of detail.

Just a little niggle; salivary amylase doesn’t really do that much to the overall digestion of starches. Its good for breaking starches down for working in the taste receptors, but its inactivated at low pHs (especially those in a normal stomach). That’s why we have lots produced by the pancreas later in the intestine when the pH gets back up. The study of increased sugar absorption after chewing is more about surface area than about the amylase (though it plays a small role).

Scott Reese said:

Just a little niggle; salivary amylase doesn’t really do that much to the overall digestion of starches. Its good for breaking starches down for working in the taste receptors, but its inactivated at low pHs (especially those in a normal stomach). That’s why we have lots produced by the pancreas later in the intestine when the pH gets back up. The study of increased sugar absorption after chewing is more about surface area than about the amylase (though it plays a small role).

I haven’t read the paper yet (printed it out and it’s sitting on my desk), but I was wondering if the duplicated versions have accumulated mutations giving variants on the amylase enzymes that have shifted their optimal pH.

What a cool story! Thanks for posting this!

I’m a professor at a midwest medical school, and a course director for two first-year medical school courses. I gotta figure out how to use this.

Is there personal consequences too if only 2 or many 15 copies ? Harder to digest starch also without diarrhea if only 2 copies ?

Yes, they won’t let you in the secret entrance or show you the handshake if you fail the saliva test.

Hey, while we’re playing “let’s all shoot down PZ Myers’ mistakes,” can I point out that in the last line where he talks about bananas, he’s forgetting that bananas are also starchy? OK, we’ve come up with sugary “dessert banana” cultivars recently but in evolutionary time bananas have nearly always been starchy. :)

notedscholar said:

PZ Myers? A mistake? Stop the presses.

I wonder if Uncommon Descent will have an entry called “Vindication.”

NS

Yeah, snarf, I just found Jesus.

He was playing in the dirt with a shovel burying fossils and what not. I asked him what he was doing and he started laughing hysterically, saying something about “just eff’ing with ‘em.”

And whodathunkit?! … jesus had a southern draw xD

notedscholar said:

silly rumors

So, or sigh, a poe.

The religion of evolutionism teaches that humans are genetically the same as monkeys and all differences between them are the result of culture. Now we have evidence that humans and monkeys are genetically different after all and America’s archbishop of atheism calls it a confirmation of evolution–what a crock!

Not even close. First of all this is not a religion but rather a fact, humans are about 95% genetically similar. The differences are not just due to culture. As to your ignorance of what evolution did and did not say and the fact that evolution never stated that humans and apes (not monkeys) are genetically the same shows that your are either a troll or an ill informed person. Did I guess right?

Toidel Mahoney said:

The religion of evolutionism teaches that humans are genetically the same as monkeys and all differences between them are the result of culture. Now we have evidence that humans and monkeys are genetically different after all and America’s archbishop of atheism calls it a confirmation of evolution–what a crock!

“religion of evolutionism”?

How can something be a religion when it’s accepted by people of many different religions, as well as being from many different cultures and ethnicity, having different native languages, etc.?

Henry

Henry J said:

“religion of evolutionism”?

How can something be a religion when it’s accepted by people of many different religions, as well as being from many different cultures and ethnicity, having different native languages, etc.?

Henry

Then there’s the little problem of how there are no recognized holypeople, prophets, holy books, holy relics, or defined prayer and rituals of “evolutionism” (sic).

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This page contains a single entry by PZ Myers published on December 11, 2008 11:43 AM.

Evolution Education: Evolution of the Eye Special Issue was the previous entry in this blog.

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