3 February 2008

Detecting natural selection: a pika's tale

ResearchBlogging.orgChoosing a paper for my inaugural "blogging on peer-reviewed research" post was a real no-brainer. Anything that has both my favorite theory (natural selection) and my favorite animal (pika) in the title, and is published in my favourite journal (PLoS ONE), is the peer-reviewed equivalent of a flashing neon arrow.

Equally alluring is that the paper (Yang et al, 2008) offers me the chance to do battle with the the popular misconception that all evolutionary change is brought about by natural selection.

At this point I expect that some of you are scratching your heads and thinking "but isn't Darwin famous for evolution by natural selection?" and a smaller number of you are nodding your heads knowingly.

This post is aimed more towards the head scratchers than the head nodders (though far be it from me to discourage my fellow nodders from reading on and enjoying the sheer scientific pleasure of it all).

So, back to natural selection and why it's not all she wrote. Even the head scratchers will remember that natural selection is the mechanism proposed by Charles Darwin and Alfred Russel Wallace to explain the observable fact that organisms change through time.

Evolution by natural selection as they conceived it, and as we still know it today, is an adaptive process. Adaptive evolution is when 1) a new trait arises in a population because of a random, heritable change (which we now know is caused by a genetic mutation) and 2) the trait confers a non-random reproductive advantage or disadvantage. The end result is that the new trait will be preserved or discarded respectively by the process of natural selection.

For roughly sixty years after the publication of Darwin's On the Origin of Species by Means of Natural Selection in 1859, the scientific (if not wider) community was fairly content with the idea that natural selection was the sole agent of evolutionary change. In the meantime new areas of research bubbled up, not least genetics, and started making people itch for some way to integrate their new understandings in an evolutionary framework. Then, in the 1920's, along came Ronald Fisher, Jack Haldane, Sewall Wright et. al. and their brainchild, the modern evolutionary synthesis. Not only did it unite evolution with genetics but it also introduced a new competitor to natural selection called "genetic drift".

Genetic drift starts out in the same way as natural selection, with a random genetic change occurring in a population of organisms. With genetic drift, though, the change doesn't bestow any particular advantage or disadvantage on the organisms that carry it. Nevertheless, by pure chance (described mathematically in terms of probability), some genetic variants are carried forward (fixed) in the population while others simply fade away. This can cause evolutionary change without having to invoke natural selection.

So, to summarise so far:
Natural selection = random change + non-random (adaptive) selection
Genetic drift = random change + random (neutral) selection

Phew, after that bit of mental exercise, I'm ready for some light entertainment: cue tablas, enter pikas, stage right.

Pikas are...
  1. energetic little denizens of the alpine realm who collect wildflowers and belt out high-pitched warning calls from their prominent perches in the talus.
  2. members of the order Lagomorpha, which also contains rabbits and hares.
  3. indisputably cute.
  4. both harbingers and victims of climate change5.
  5. useful for studying the mechanisms of evolution, in particular detecting adaptive evolution and exploring its genetic and physiological mechanisms (keep reading).
  6. Did I mention cute?
So, pikas are not only cute (did I mention that?) but have also recently made an appearance in PLoS ONE precisely due to their generous participation (it must be acknowledged) in an evolutionary biological study that addresses point 5 above.

Let us all now put ourselves into the shoes of the pika researchers (sigh). Pikas, unlike other lagomorphs, live exclusively in cold, usually high alpine, environments. It seems an obvious thing to immediately start asking questions like "what selective advantage over the other lagomorphs do these animals have that has enabled them to colonise these cold, high places? Is it some kind of cold-tolerance? A dietary adaptation? Resistance to the effects of high altitude?"

In Darwin's day, it would have been just fine to mentally browse this set of questions, but since the modern synthesis, we know we have to be a little bit more careful. The first question we must ask is: do pikas differ (e.g. in appearance, behaviour, habitat) from other lagomorphs because of natural selection, or because of genetic drift? Most of us, of course, are rooting for natural selection so that we can have fun investigating our more advanced questions such as those mentioned above.

But how on earth does one go about separating the natural selection wheat from the genetic drift chaff?

Fortunately for us, some very clever people (Kimura M, 1983; Ohta T, 1992; Yang ZH et al, 2000) figured out that they could do it by taking advantage of a quirk of the genetic code (for an informative and humorous refresher course on the genetic code, I recommend A Somewhat Old, But Capacious Handbag).

Here's how it works: the genetic code translates the four-letter alphabet of nucleotides (the A's T's G's and C's of DNA) into the twenty-letter alphabet of amino acids (the lysines and arginines etc. of protein). Just as our English alphabet of just 26 letters can, by being combined into multi-letter words, encode millions of unique meanings, so can different combinations of the four nucleotide "letters" encode 20 unique amino acid "words".

As it turns out, the dictionary of amino acids is made up entirely of three-letter words, called codons. There are more possible three-letter "spellings" than there are possible amino acid "meanings", though, so most amino acids are encoded by more than one codon.

A happy implication of this for our natural selection vs. genetic drift question is that sometimes when a mutation (spelling error) occurs, the protein (meaning) is changed (a "nonsynonymous substitution"), and sometimes it isn't (a "synonymous substitution"). This means that if a gene is experiencing positive natural selection towards a particular amino acid outcome (a more cold-tolerant version of a protein for example), the ratio (ω) of non-synonymous to synonymous substitutions should be greater than one. Specifically, if...
  • ω = 1, the new mutation is neutral (ho-hum).
  • ω less than 1, the new mutation is deleterious; in other words, there is selection against it (not quite so ho-hum because, though it does not necessarily signal adaptive evolution, it does indicate functional importance of the protein).
  • ω greater than 1, the new mutation is advantageous; in other words, there is selection for it (yippee! adaptive evolution! natural selection!)
Now, back to our pikas (did I mention how cute they are?). In their PLoS ONE paper, Yang and colleagues ask whether the fact that pikas have been able to colonise cold places might be due to positive selection on a gene that regulates energy metabolism, specifically the leptin gene, famous for its role in obesity (Shimizu H et al, 2007). In their words, "Due to the extraordinary environment in which pikas live, and their apparent changes in energy metabolism under cold conditions, we hypothesized that leptin, acting as a cold stress-response protein, plays an important role in the pikas' ecological adaptation to the harsh plateau environment."

To test this hypothesis, they first measured the level of variation in the leptin gene among pikas (cold-adapted) and found that pika leptin had much higher levels of variation than the leptin gene among other lagormorphs (not cold-adapted). But while this result was consistent with adaptive evolution of pika leptin, it did not conclusively rule out neutral evolution (genetic drift).

To take that next step and ask whether the observed high level of variation in pika leptin was due to neutral evolution (genetic drift) or natural selection, they measured the ω ratio in pikas vs. other lagomorphs and found that the increase in leptin variation in pikas was in fact due to differences is non-synonymous, not synonymous, change (P less than 0.05). As Yang et al. put it, "Our study confirmed the previous hypothesis that leptin is a cold stress-response protein and that cold probably is the primary environmental factor for driving the adaptive functional evolution of leptin within the native cold-adapted Ochotona family, contributing to fitness enhancement for the pikas' survival in a stressful environment."

But the last word in this story really has to go to the pika (listen). Translation: let's hear it for leptin!

This post is dedicated to Kimiora Ward, fellow head nodding pika appreciator, whose thesis defense was the single most eloquent and succinct explanation I've ever heard of selection vs. drift.


Yang, J., Wang, Z.L., Zhao, X.Q., Wang, D.P., Qi, D.L., Xu, B.H., Ren, Y.H., Tian, H.F., Bromage, T. (2008). Natural Selection and Adaptive Evolution of Leptin in the Ochotona Family Driven by the Cold Environmental Stress. PLoS ONE, 3(1), e1472. DOI: 10.1371/journal.pone.0001472

Kimura M (1983) The Neutral Theory of Molecular Evolution.; New York: Cambridge University Press. 367 p.

Ohta T
(1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23: 263–286.

Yang ZH, Nielsen R, Goldman N, Pedersen AM
(2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431–449.

Grayson, D. 2005. A brief history of Great Basin pikas. Journal of Biogeography. Volume 32, Number 12, pp. 2103-2111(9)

Shimizu H, Oh-I S, Okada S, et al. 2007. Leptin resistance and obesity. Endocrine Journal 54 (1): 17-26. (pdf)


Richard Carter, FCD said...

Fantastic post pitched at exactly the right level.

Now, if you could just knock out two or three of those every day, I'd really start learning stuff.

Michael Barton, FCD said...

Here's a cute pika:

Adrian Thysse, FCD. said...

Nice first post on peer reviewed scientific research. My 12 year old daughter also loves pikas, and we spent quite some time observing and photographing them up near Angel Glacier in Jasper National Park, Alberta, Canada.

Note that Darwin also recognised sexual selection, even though it is hidden away in the fourth chapter, Natural Selection!

Kevin Z said...

Well Done Karen! A superb post and article to kickstart you entry into peer-reviewed blogging. They are cute... for a vertebrate...

nunatak said...

Adrian, Thanks for your comment. Two reasons I didn't talk about sexual selection in this post: 1) the post was already super long (though that is a cop-out of sorts because surely I could've included some kind of snippy little clause about it) and 2) I happen to agree with Greg Laden that sexual selection is really a subset of natural selection especially if viewed in a neodarwinian context:

Kevin Z said...

I agree with Karen, sexual selection is a population level selective force and its only natural! ;p

Richard Carter, FCD said...

I'm with you chaps re sexual selection: it's just a sub-species of natural selection - but a very interesting sub-species.

Adrian Thysse, FCD. said...

Thanks for the correction and the link to Greg Ladens blog - very helpful.

Sid Leavitt said...

Excellent post, Nunatak. I am a complete layman on this subject, unable to either scratch or nod my head, but I found your exposition interesting, clear and informative.

Thank you.

R N B said...

That was excellent. That was the clearest explanation of the whole "natural selection" versus "genetic drift" argument that I have seen. Real evidence always helps. If only you had been there as a referee between Gould and Dawkins, I think you could have stopped a lot of bloodshed. Sorry that's overdramatic analogy, but that was a really fine exposition of a complex argument to very simple language, everything that "blogging on peer-reviewed research" should be.

I don't agree with you on everything though. There might have been a typo ("in" vs "is"), the explanation of how to use "w" could have been explained more, and I think that the critters are less "cute" and more "fat rat". But still, well done, thanks.

nunatak said...

Wow, thanks for that comment, R N B. You have made my day if not my month and after that, I am most definitely going to keep blogging on peer reviewed research!

Anonymous said...

This article was fun to read and informative. As a head nodder due to my biology class, I enjoyed reading about how natural selection is not the sole reason for change within a population. I enjoyed learning that pika are cute furry animals related to rabbits. Maybe if global warming continues the leptin in the pika species will become less important as a cold stress reliever. Through natural selection due to climate change, maybe the cold adapted leptin gene would become very scarce in the pika species. The article was very enjoyable.