Common ancestry, bottlenecks, and human evolution

Human evolution has been in the news quite a lot recently.

• New genetic data suggest that ancient humans included both Neanderthals and Denisovans, which colonized different parts of the world but subsequently interbred with so-called modern humans and left telltale traces of this history in the genomes of living humans.
• New analysis of current genetic diversity suggests that human population size underwent interesting fluctuations throughout the history of our species, but concludes that the population never dipped below a few thousand reproducing individuals.

Unsurprisingly, these findings have been discussed in the context of Christian views of human origins. In the context of some of these discussions (among Catholics, for example), I have noticed some confusion regarding the implications of common ancestry. I will illustrate the error with a stylized example, then explain why it is an error.

Harmful genes, and sneaky, too: Genetic hitchhiking in the human genome

Genetic hitchhiking is thought to be an inevitable result of strong positive selection in a population. The basic idea is that if a particular gene is strongly selected for (as opposed to selected against), then the chunk of the genome that carries that gene will become very common in the population. The result is a local loss of genetic diversity: all (or nearly all) of the individuals in the population will have that same chunk of genetic information, whereas before the selection process acted, there might have been a lot of variation in that chunk throughout the population. And this means that areas of the human genome that are less variable between people are suspected sites of recent positive selection. Within that chunk, there are potentially many genes and genetic elements that became more common in the population by virtue of their placement near the gene that was actually selected for. Those other genes are the hitchhikers. And it's likely that some hitchhikers are bad news – they're harmful mutations that would normally become rare or extinct in the population, but instead have become common by hitchhiking.

In the last few years, large amounts of genetic information have become available that have enabled biologists to look for evidence of such phenomena in the human genome. Specifically, two major projects have collected genetic data for the purpose of analyzing genetic variation among humans. One project, the International HapMap Project, mapped and quantified sites in the human genome that are known to vary among humans by a single genetic letter. These sites are called single nucleotide polymorphisms, or SNPs (pronounced "snips"). The project has mapped millions of these sites in a group of 270 humans representing various lineages. Another project that has made the news recently is the 1000 Genomes Project, which also seeks to provide a picture of human genetic variation using more people (more than 1000 at present) and slightly different technology. Efforts like these have taken analysis of the human genome to a new level. No longer do we merely wonder what "the" human genome is like – we can begin to learn about how genetic differences give rise to biological differences such as susceptibility to particular diseases.

Mapping fitness: bacteria, mutations, and Seattle

Thinking about fitness landscapes can stimulate detailed discussion and consideration of the meanings and limitations of such metaphors, and my introductory comments at The Panda's Thumb did just that. Most notably, Joe Felsenstein pointed us to the various ways these depictions can be employed, and urged everyone to use caution in interpreting them. All too true, but the goal here is modest: I want to discuss the interesting questions that arise when considering the relationship between genotypes and phenotypes, i.e., how a particular genetic makeup influences fitness, whether the genetic makeup in question is simple or complex, and however fitness is conceived. These questions can take further discussion in all sorts of directions, but there are two that I have in mind in this series. First, I want to point to increasing capacity of scientists in their ability to examine these relationships experimentally. Second, I want to highlight the failure of design creationists to address or even to understand such matters.

Carnival of Evolution 14

Welcome to Quintessence of Dust and to the 14th Edition of the monthly Carnival of Evolution. Thanks for stopping by, and for supporting scientific carnivalia, members of a taxon that seems to be flirting with extinction.

One good reason to visit a carnival: brain stimulation. Brain Stimulant offers some thoughts and speculations on Free Will and the Brain, touching briefly on themes of selection and adaptation, and he doesn't charge as much as the clinic would.

Another good reason: you can bump into real scientists, the kind who actually work on evolution. Ryan Gregory has a day job as an expert on genome evolution, but somehow finds the time to blog at Genomicron. Recent entries there include fascinating pictures of ongoing field work. For this month's carnival, be sure to read two reviews of the ideas of Stephen Jay Gould, focusing on controversial papers by Gould published in 1980 and 1982. You may find that you have been misinformed about Gould's positions, and you'll surely learn more about evolution.

Michael White at Adaptive Complexity is another blogging scientist, and he writes very clearly about parasitic DNA in Selfish Gene Confusion.

David Basanta is a biologist who runs a cool blog called Cancerevo: Evolution and cancer, which is subtitled "Studying cancer as an evolutionary disease." Check it out, and don't miss his recent piece on Stem cells and ecosystems.

Zen Faulkes is a biologist who blogs at Neurodojo. That's cool enough, but the subtitle of that blog is "Train your brain." Hey, this could be a theme for the whole carnival! He recently wrote about a walking bat in New Zealand. Bat evolution...we can't get enough of that. I've written about it myself.

Brains and their origins come up in an extensive discussion of early animal evolution at AK's Rambling Thoughts. The post is The Earliest Eumetazoan Progression.

At The Loom, the peerless Carl Zimmer discusses AIDS in chimps and the relevance of the story to conceptions of scientific progress. AIDS and The Virtues of Slow-Cooked Science is engrossing and important. And John Wilkins discusses some new fossil apes in an excellent recent post at Evolving Thoughts.

John Lynch reviews a new book on Alfred Russell Wallace. Caveat lector. Brian at Laelaps takes us on a historical tour of the work of Florentino Ameghino. Are those elephants or not? Brian's discussion is typically excellent.

At The Spittoon, AnneH discusses new findings concerning both the past and the future of the mammalian Y chromosome.

Hoxful Monsters is a future host of this carnival; Nagraj recently reviewed some recent work on pattern formation in the development of spiders. Wonderful evo-devo stuff.

Someone at Wired wrote some swill about the "10 Worst Evolutionary Designs" which annoyed a few smart bloggers. At Deep-Sea News, Dr. M sets the record straight. The title is self-explanatory: Worst Evolutionary Designs? No! Brilliant Solutions to the Complexity of Nature and Constraints.

Larry Moran at Sandwalk is attending a conference entitled Perspectives on the Tree of Life. He's posted reviews of days one and two so far.

And that's our carnival. Thanks for reading, and on the way out I hope you'll look at my nearly-complete series on Notch and deep homology.

Next month's edition will appear at Southern Fried Science. To submit posts, use the submission form found at the Carnival of Evolution site. And if you like the carnival, help us promote it with a link, and/or consider hosting. More info at the carnival site.

Mendel's Garden, 28th Edition

Hello and welcome to the 28th edition of the genetics blog carnival known as Mendel's Garden, where we celebrate blogging on topics related to anything touching on what Mendel discovered (or thought he discovered).

While reading these interesting and informative pieces, please think about work that should be featured in a future edition and/or blogs (like yours) that would serve well as future hosts.

So do tomato seeds get you excited? No? Oh. Well, they should, if you're at all interested in evolutionary genetics. Michael White at Adaptive Complexity explores some new findings in which evolutionary changes in seed size in tomatoes are explained to a large extent by variation in a single gene, pinpointed through the use of standard genetic crosses. He summarizes the work as "a clear case of natural genetic variation controlling the size of seeds, variation for evolution (or plant breeders) to work on when larger or smaller seed sizes are needed to adapt to a new environment." Not peas, but close. Mendel would be proud.

"Mendel would be proud" happens to be the title of a post by Michael at Ricochet Science, pointing to a new educational site which he hopes will help students and laypersons learn genetics.

Ouroboros describes experiments on an interesting DNA repair enzyme called Ercc1. One might think that deletion of the gene encoding this protein (it controls nucleotide excision repair) would be a Bad Thing, but in fact mice that have been so altered are strikingly cancer-resistant. And there's more, but you'll have to check out the excellent Ouroboros blog (focused on aging and related biology) yourself.

At the Spittoon, Erin introduces her post entitled "Miss Con-GENE-iality" with this teaser: "If Facebook is starting to take over your life, maybe your genes are partly to blame." The subject is heritability of various aspects of social connectedness, and instead of whining "I could quit Facebook anytime I want" just go read about these new genetic analyses of our social behavior.

On a more serious note, Razib at Gene Expression explores the genetics that might underlie the interesting case of Sandra Laing, a woman born to apparently white parents but who appeared to be "of a different race." And in South Africa. For more on the genetics of human appearance, see the Eye on DNA interview with Dr. Tzung-Fu Hsieh, developer of a test for the red hair gene.

Oh, and before you give your credit card number to a personal genomics outfit, spend some time at Genetic Future – Daniel notes when a company is charging too much, and comments on some recent remarks by Francis Collins on the future of "consumer genetics."

Organic transgenic food might sound like an oxymoron, but Anastasia at Genetic Maize explains why it's not and introduces the new word for such methods: orgenic.

Jonathan Eisen at The Tree of Life is recruiting people to help with analysis of metagenomic data. Go there to learn more. I forgot to inquire about salary and benefits.

Back to evolutionary genetics: Todd at Evolutionary Novelties reports on an extraordinary example of evolutionary convergence, involving proteins called opsins which are best known for their roles in vision.

Need more evolution (with genetics)? Go read about pink iguanas at Nothing's Shocking. This should get you thinking about speciation, and that means it's time to read about "speciation genes" at Evolving Thoughts. John's not crazy about the term. What a grouch.

And here's a new twist on the whole "species boundary" concept: Ed at Not Exactly Rocket Science writes about a single gene in glowing bacteria that accounts for the ability of the same bacterial species to colonize (in a mutualistic relationship) two completely different organisms (pinecone fish with glowing "headlights" and squid with a luminous "cloaking device"). Now that's cool.

Let's give the Digital Cuttlefish the last word, at least because the blogosphere recently treated us to intensely disturbing images of cuttlefish meeting violent ends. At that little piece of blogospheric heaven, the Digital Cuttlefish reports on the cuttlefish genome project. It's not what you think – it's better.

Thanks for reading, and look for the next edition of Mendel's Garden the first Sunday in March at Biofortified.

Finches, bah! What about Darwin's tomatoes?

Charles Darwin collected all sorts of cool stuff (like a vampire bat, caught while feeding on his horse) on his journey aboard the Beagle, and it has to be said that he understood little of it until after he got back. The finches that bear his name were identified as such by someone else, and his own bird collections from the Galapagos were nearly worthless due to the fact that he hadn't bothered to label specimens as to their place of origin. It was only upon their correct identification as different species of finch that Darwin realized that the birds represented what we now call an adaptive radiation.

Darwin collected a lot of plant material, too, and much of it was completely new to science. J.D. Hooker was a botanist and contemporary of Darwin, and in 1851 he wrote a little paper, "An Enumeration of the Plants of the Galapagos Archipelago; with Descriptions of those which are new" describing his studies of Darwin's collection. It was more than 100 pages long.

One unique feature of the collection was a pair of species of tomato plant. Like all other species in the archipelago, the Galapagean tomatoes resemble South American species, but are subtly different. More interestingly, the two Galapagean species are highly similar to each other (and reproductively compatible), but occupy separate habitats and exhibit some odd variations, including a striking divergence in leaf shape.

Image from Figure 1 of Kimura et al., cited below. On the left is S. cheesmaniae; on the right is S. galapagense.

How might such a variation arise in evolution? A nice study published in Current Biology two weeks ago provides the interesting answer, and addresses an important question raised by evo-devo theorists. The article is "Natural Variation in Leaf Morphology Results from Mutation of a Novel KNOX Gene," by Seisuke Kimura and colleagues at UC Davis.

Look again at the picture: the leaves pictured on the left are "normal" tomato leaves, as one might see in a Michigan garden or on the South American plants thought to be the ancestors of the Galapagean species. The leaves on the right are significantly more complex. (For lovers of botanical detail, the "normal" leaves are unipinnately compound, while the S. galapagense leaves are three- or four-pinnately compound. For the botanically challenged like me, the leaves on the right are more snowflake-like.)

This trait has long been known to be under the control of a single gene, but the nature of that gene and its effects were unknown before the experiments of Kimura et al. They did some pretty intense genetic mapping, and zeroed in on a rather small piece of the genome. Specifically, they ended up examining a region 1749 base pairs in length. Inside that region, they found exactly one change that could account for the leaf variation: a deletion of a single base pair. One DNA letter, removed from the genome, makes all that difference.

But there's more. That change isn't in the coding region of a gene, meaning that the mutation doesn't affect the structure of any protein. Like the genetic variation that Cretekos et al. studied in their analysis of bat wing development, this is an example of a change in a regulatory region of the DNA, the kind of change that evo-devo theorists have predicted to be fairly common in the evolution of new forms.

The authors showed that the teeny little one-letter change results in a huge increase in the amount of a protein called TKD1. And they did a compelling experiment similar to the one that Cretekos and colleagues did with the bat and the mouse: they took that piece of regulatory DNA (with the one-letter change) and stuck it into a tomato plant, and showed that it could induce a complex-leaf trait all by itself. No change in protein structures, just a one-letter change in a regulatory DNA region. Isn't that cool?

Kimura et al. went on to show that TKD1 reduces the formation of a complex between two other proteins, and their data suggest that the levels of TKD1 constitute a dimmer switch-like (rheostat) control on that complex, which ultimately controls the development of leaf shape.

Now, here's why this result is interesting in the context of evo-devo. A structural mutation in a protein that controls development can result in dramatic changes in form, for sure. But such a mutation will likely alter all of the processes controlled by that protein, resulting in widespread developmental reorganization. (Think "hopeful monster" here.) Evo-devo thinkers assert that regulatory changes are better suited (in general) for the induction of evolutionary changes in form, because such changes can affect isolated developmental processes without affecting the overall development of the organism. In this case, the excess TDK1 protein is able to inhibit the action of a particular complex in particular areas at particular times, without interfering in the functions of those other proteins elsewhere and at other times. Here are the concluding sentences of the paper:

Mutations affecting the expression levels of transcription factors can modify the function of a major developmental regulatory complex in some organs without interfering with its other essential roles in morphogenesis. Such dosage-sensitive interactions may be broadly responsible for evolutionary change and provide a relatively simple mechanism for the generation of natural variation.

I hope you agree that studies like this one and the bat-wing story are inherently interesting. But I hope you also see how sadly foolish it is to disparage evolutionary science as mere mythology, or to pretend to invalidate a century of evolutionary genetic analysis with a few bogus calculations. Scientists are weird enough to think tomato plant leaves on the Galapagos are worth subjecting to detailed genetic analysis, and maybe that means we're a bit on the obsessive side. But come on: we're not stupid.

Article(s) discussed in this post:

KIMURA, S., KOENIG, D., KANG, J., YOONG, F., SINHA, N. (2008). Natural Variation in Leaf Morphology Results from Mutation of a Novel KNOX Gene. Current Biology, 18(9), 672-677. DOI: 10.1016/j.cub.2008.04.008

Mutations, selection, and bacteria

Several weeks ago, a commenter (Donald) asked an interesting question about natural selection and genetic variation, and I promised to address it because I want the issue to be a theme on QoD in the coming months. Here's Donald:

The link below is to a NYT blog where it says that E coli studies have found that there are 100,000 harmful mutations for each single beneficial one. I'm no population geneticist, but this kind of thing does make you wonder how selection could work with that much noise to overcome.

That aside, I have read a little of Ronald Fisher and I recall his mathematical argument that for mutations of very small effect, there was a 50 percent chance that the net effect would be beneficial. This is in "The Genetical Theory of Natural Selection". The mutations with large effects, on the other hand, are almost certainly going to be deleterious.

So are these studies only detecting mutations with large effects, or was Fisher wrong?

The blog article that Donald is citing is at The Wild Side by Olivia Judson, and the figure of 100,000 deleterious mutants for every helpful one is widely referenced.

Donald raises two questions, which I'll rephrase somewhat.

1. How can natural selection lead to adaptation when there is so much interference from harmful mutations?

I think there are at least three misconceptions that are acting together to create this common misunderstanding. First, that widely-cited ratio of harmful to helpful mutations is apparently an overestimate, off by three orders of magnitude, or a factor of 1000. The study that reported this dramatic correction in our understanding of bacterial mutations was published in Science last August, and represents a wonderful case study of the difference between real scientific thinking and the thinking of most design advocates. (Subject of an upcoming post.)

Second, the existence of harmful mutations doesn't necessarily "interfere" with adaptation. Many deleterious mutations will just kill the organism, and that's that. Natural selection does that all the time, and it doesn't get in the way of life in general, so there's no special reason to worry that it will get in the way of adaptation.

But most importantly, I think Donald is a little confused about the material on which natural selection acts, and understandably so. (This error is the centerpiece of Michael Behe's ludicrous recent book The Edge of Evolution.) The mistake seems subtle, but it's gigantic, and I think it arises in part from a semantic shortcut that is often used when explaining selection and adaptation. To see the problem, consider these two alternative descriptions of the process of adaptation.

• Adaptive evolution occurs when natural selection favors certain mutations which are beneficial as opposed to harmful. When new challenges arise, new adaptations arise as new beneficial mutations are generated and selection favors these mutations.
• Adaptive evolution occurs when natural selection favors previously-existing genetic combinations that are more fit than others. When new challenges arise, new adaptations arise as selection favors individuals whose genetic endowments are best suited to the new challenges.

The first description probably sounds more familiar to you than the second one does, but they're quite different, and the second description is far more accurate than the first. The distinction between these two scenarios lies in the implication of the first scenario that new mutations must arise "on demand" or "just in time." Michael Behe's whole silly book is based on calculations that assume that new mutations must be generated, simultaneously, after the introduction of the new challenge. (His main example is the adaptation of the malaria parasite in the face of drugs intended for its destruction.) Those who promulgate this error (intentionally or not) tend to emphasize natural selection acting on mutations, and consequently it's easy to picture a species "mutating around" a challenge or obstacle. (Behe, for example, uses such language repeatedly.)

But that's a mistaken view of the process, and the way to avoid the trap is to picture selection acting on variation, specifically on variation that is always present in any population of organisms. (Populations without significant genetic variation, when confronted with serious challenges, are more likely to illustrate extinction than evolution.) Such variation is continuously generated and therefore continuously present. This is the lesson from studies of the effects of human selection on domesticated species of all kinds: when selection is applied, such populations typically reveal a remarkable propensity for rapid and dramatic change, because they harbor vast resources in the form of genetic diversity. If you carefully attend to this distinction, you will understand Darwinian evolution far better than any ID advocate.

2. Are most large-effect mutations harmful, and many small-effect mutations beneficial, as predicted by Fisher?

Well, first of all, kudos to Donald for reading Fisher. I've been browsing The Genetical Theory of Natural Selection, and it's demanding (but comprehensible). Michael Behe either hasn't read it, or didn't understand it, and in either case is therefore unqualified to write on evolutionary genetics.

Fisher was certainly right that large-effect mutations are almost never beneficial, but it is largely unknown whether very small-effect mutations are frequently beneficial, as he postulated. Theoretical and experimental work in this field has recently accelerated, and the current model is that effects of beneficial mutations are exponentially distributed, such that beneficial mutations are far more likely to be of very small effect than of large effect. This was Allen Orr's proposal, and it has been borne out in some very recent experimental analyses. The most recent, and significant, was the Science paper I mentioned above, in which the authors found that beneficial mutations in bacteria are far more common than previously estimated, but have relatively small effects (individually). Here's an excerpt from their last paragraph:

...our estimate of [the beneficial mutation rate] implies that 1 in 150 newly arising mutations is beneficial and that 1 in 10 fitness-affecting mutations increases the fitness of the individual carrying it. Hence, an enterobacterium has an enormous potential for adaptation and may help explain how antibiotic resistance and virulence evolve so quickly.

That's enough for now. Start with papers by Allen Orr when reading on the genetics of adaption; his historical overview in Nature Reviews Genetics in 2005 is particularly helpful.

Gene duplication: "Not making worse what nature made so clear"

But he that writes of you, if he can tell
That you are you, so dignifies his story,
Let him but copy what in you is writ,
Not making worse what nature made so clear,
And such a counterpart shall fame his wit,
Making his style admired every where.
--Sonnet 84, The Oxford Shakespeare

One of the most common refrains of anti-evolutionists is the claim that evolutionary mechanisms can only degrade what has already come to be. All together now: "No new information!" It's a sad little mantra, an almost religious pronouncement that is made even more annoying by its religious underpinnings, hidden or overt.

But it's a good question: how do new genes come about?

One major source of new genes is gene duplication, which is as conceptually simple as it sounds. It might seem a little odd, and it's not that easy to picture, but the duplication of discrete sections of genetic material is commonplace in genomes. In fact, a significant amount of the genetic variation among individual humans is due to copy number variation, which is variation in the number of copies of particular genes or chunks of genetic material from individual to individual. Genes can be duplicated within a genome via various mechanisms, one of which includes the rare but fascinating occurrence of whole-genome duplication. In any case, it is very clear that gene duplication and subsequent evolution explains the existence of thousands of the most interesting genes in animal genomes.

It should be obvious that gene duplication gives you more genes, but perhaps it's not so clear how this can yield something truly new. For many years, new genes were thought to arise after duplication by a process called neofunctionalization. The basic idea is this: consider a gene A, with a set of functions we'll call F1 and F2. Now suppose the gene is duplicated, so that we now have genes A and B, both capable of carrying out F1 and F2. In neofunctionalization, gene B is free to vary and (potentially) acquire new functions, because gene A is still making sure that F1 and F2 are covered. So the duplication has created an opportunity for a little "experimentation." Most of the time, gene B will be mutated into another piece of genomic debris, a pseudogene with no evident function. (The human genome is riddled with pseudogenes, and that's a story all its own.) Occasionally, though, the tinkering will yield a gene with a new evolutionary trajectory. This model makes good sense and surely accounts for numerous genetic innovations during evolution.

But another model has come to the fore in the last several years, in which the two duplicates seem to "divide and conquer." The process is called subfunctionalization, and the idea is straightforward: gene A covers F1, while gene B covers F2. Straightforward perhaps, but this scenario creates some interesting evolutionary opportunities that aren't immediately obvious. Here in this newest Journal Club, I'll look at another example of the experimental analysis of evolutionary principles and hypotheses, summarizing some recent work that examines subfunctionalization in the laboratory.

In the 11 October issue of Nature, Chris Todd Hittinger and Sean B. Carroll examine an actual example of subfunctionalization in an elegant set of experiments that seeks to re-create the evolutionary changes that occurred after a gene duplication. Specifically, they looked at the events that led to the formation of a new pair of functionally-intertwined genes in yeast. The genes are GAL1 and GAL3, and there are several aspects of this story that make it an ideal system in which to experimentally explore the creation of new genes.

1. GAL1 and GAL3 arose following a whole-genome duplication in an ancestral yeast species about 100 million years ago. The ancestral form of the gene (see Note 1 at the end of this article) is still present in other species of yeast (namely, those that branched off before the duplication event). This means that the authors were able to compare the new genes (meaning GAL1 and GAL3) and their functions to the single ancestral gene and its functions.
2. The genomes of these yeast species have been completely decoded, so that the authors had ready access to the sequences of the genes of interest and any DNA sequences in the neighborhood.
3. Decades of research on yeast have yielded superb tools for the manipulation of the yeast genome. Using these resources, the authors were able to create custom-designed yeast strains in which genes of interest were altered to suit experimental purposes. (Those of us who work in mammalian systems can only dream of being able to do this kind of genetic modification with such ease.)
4. The biochemical functions of GAL1 and GAL3 were already well known.

Hittinger and Carroll capitalized on this excellent set of tools, and added a key component of their own. They needed a way to measure fitness of different strains of yeast, namely strains that had been modified to resemble various ancestral forms. But most typical methods for testing gene function are unsuitable for estimating fitness, which is the relevant issue. The question, in other words, is focused not on the ability of a particular protein to perform a particular function, but on the ability of a particular protein to change the fitness of the organism that expressed it. The authors' solution can only be described as elegant: they assessed fitness of various yeast strains by measuring the outcomes of head-to-head competitions between strains. Their experimental approach, developed by a colleague (see Note 2) employed some very nice genetic tricks and a sophisticated analytical tool called flow cytometry. (Take some time to read about Abbie Smith's research at ERV if you haven't already done so; in her work on HIV, she asks similar questions regarding fitness and uses a very similar approach in seeking answers.)

Why did the authors choose the GAL1-GAL3 system for close scrutiny? The two genes are critical components of a system in yeast that controls the utilization of galactose (a certain sugar) as an energy source. The GAL1 protein is an enzyme that begins the breakdown of galactose; the GAL3 protein controls the induction of the GAL1 protein. When galactose is present, the GAL3 gene is induced, such that GAL3 protein amounts increase by a few fold. The GAL3 protein is in turn a potent inducer of the GAL1 gene: when galactose is present, GAL1 protein levels increase 1000-fold or so. The two proteins are very similar to each other, and both are very similar to the single protein that is found in the genomes of yeasts that never underwent the genome duplication. So this means that the ancestral protein is bifunctional: it must carry out the very different processes of induction and of galactose metabolism. Not surprisingly, situations like this are thought to involve trade-offs which resolve "adaptive conflicts" between the two different functions of the protein. The reasoning is straightforward: mutations that would improve function A might degrade function B, and vice versa. So the protein is not optimized for either function. There is an adaptive conflict between the two functions. The GAL1-GAL3 system clearly involves subfunctionalization following duplication, and because the ancestral gene is available for comparison, the story invites exploration of the notion of adaptive conflict.

Hittinger and Carroll found that there is indeed an adaptive conflict that was resolved by the evolution of GAL1 and GAL3 following the duplication. But the nature of that conflict is not what some might have predicted. Look again at my description of adaptive conflict above. I focused exclusively on the proteins themselves, claiming that the conflict would arise during attempts to optimize two functions in a single protein. But there's another possibility (that need not exclude the first): perhaps the conflict occurs in the regulation of the expression of those proteins. In the case of GAL1 and GAL3, the two different genes can be turned on and off by two different signaling systems. But in the ancestral situation, there's only one gene and therefore fewer opportunities for diversity in the signaling that leads to expression.

The data presented by Hittinger and Carroll suggest that there is not strong adaptive conflict between the two functions of the ancestral protein. If such a conflict existed, we would expect that changes in GAL1 that make it look more like GAL3 (and vice versa) would cause significant decreases in fitness. But that's not what the fitness analysis showed, and the authors inferred that the adaptive conflict must occur in the arena of regulation, and not in the context of actual protein function. The story is complicated, and I'm not convinced that the authors have ruled out adaptive conflict at the level of the structure of the proteins. Nevertheless, their subsequent experiments demonstrate a clear adaptive conflict in the regulation of expression of the different proteins, and an efficient resolution of that conflict in the subfunctionalization of the two genes following duplication. Those results are strengthened by some detailed structural analysis that seems to account for the physical basis of the optimization that occurred during evolution of the GAL1 and GAL3 genes, optimization that occurred in DNA sequences that control the levels of expression of protein.

If you're a little dizzy at this point, relax and let's zoom out to reflect on this article's significance in evolutionary biology, and its relevance for those who are influenced by the claims of anti-evolution commentators.

First, take note that this article is another example of a sophisticated, hypothesis-driven experimental analysis of a central evolutionary concept. Research like this is reported almost daily, though you'd never learn this by reading the work of Reasons To Believe or the fellows of the Discovery Institute. The mis-characterization of evolutionary biology by the creationists of those organizations is a scandal, and as you might already know, my blog's main purpose is to give evangelical Christians an opportunity to explore the science that is being so carefully avoided by those critics. You don't need to understand sign epistasis or the structure of transcription factors to get this take-home message: evolutionary biologists are hard at work solving the problems that some prominent Christian apologists can't or won't even acknowledge. How does gene duplication lead to the formation of genes with new functions? The folks at the Discovery Institute can't even admit that it happens. Over at Reasons To Believe, they don't mention gene duplication all, despite their fascination with "junk DNA." That's from a ministry that claims to have developed a "testable model" to explain scores of questions regarding origins.

This makes me mad. No matter what you think of the age of the earth or the need for creation miracles, you should be upset by Christians who mangle science to serve apologetic ends.

Second, it's important to note that Hittinger and Carroll's paper is not merely a significant contribution to our understanding of subfunctionalization. It's also a salvo, in an apparently intensifying debate within evolutionary biology regarding the kinds of genetic changes that are more likely to drive evolutionary change. Sean Carroll is one of the leading lights in the new field of evolutionary developmental biology, or evo-devo, and one of the tenets of this upstart school is the claim that most of the genetic changes that lead to adaptation -- and especially to changes in form -- occur in regulatory regions of the genome and not in the genes themselves. (More technically: evo-devo advocates like Carroll postulate that changes in form are more likely to arise from mutations in cis-regulatory regions than in protein-coding sequences within genes.) This assertion is hotly contested, as are many of the other basic views of the evo-devo school. The antagonists include some serious evolutionary biologists, Michael Lynch and Jerry Coyne among them. (Lynch is the guy who took the time to explain why Michael Behe's paper on gene duplication was a joke. Coyne co-wrote the book on speciation, literally.)

I'm a developmental biologist, and therefore partial to many of the arguments of evo-devo thinkers. I'm excited about the union of evolutionary and developmental biology, and I do think that many of the new evo-devo ideas are thought-provoking and potentially fruitful. But the debate is riveting and informative, and I find Lynch and Coyne and their talented colleagues to be alarmingly convincing. I'm worried about some of those cool ideas, but I do take some comfort in this thought: any idea that can survive the onslaught of Lynch and Coyne is a hell of a good idea.

It's easy to see how the disputes spawned by the brash (and perhaps rash) evo-devo folks can lead to innovation and discovery, even if many of their proposals are diminished or destroyed in the process. The disagreement is pretty clear-cut, and both sides seem to agree on how to figure out who's right. They'll go to the lab; they'll perform hypothesis-driven experiments; they'll analyze their data; they'll write up their findings; their work will be subjected to peer review. In other words, they'll do real science.
---
Note 1: The ancestral gene itself, of course, isn't available for analysis. The authors are studying the ancestral form of the gene, using a yeast species that never experienced the whole-genome duplication.
Note 2: As Hittinger and Carroll indicate in the acknowledgments, the experimental design was developed by Barry L. Williams, who was a postdoctoral fellow in Carroll's lab and is now on the faculty at Michigan State. And by the way, this little state of Michigan doesn't have much of an economy, but boy are we crawling with gifted evolutionary biologists.

Article(s) discussed in this post: Hittinger, C.T. and Carroll, S.B. (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449:677-681.

They selected teosinte...and got corn. Excellent!

Evolutionary science is so much bigger, so much deeper, so much more interesting than its opponents (understandably) will admit. It's more complicated than Michael Behe or Bill Dembski let on, and yet it's not that hard to follow, for those who are willing to try. The best papers by evolutionary biologists are endlessly fascinating and scientifically superb, and reading them is stimulating and fun.

Yet, as an experimental developmental biologist reading work in evolutionary biology, I often find myself yearning for what we call "the definitive experiment." Molecular biology, for example, can point to a few definitive experiments -- elegant and often simple -- that provided answers to big questions. Sometimes, while examining an excellent evolutionary explanation, I think, "Wouldn't it be great if they could do the experiment?"

Now of course, plenty of evolutionary biology is experimental, and I've reviewed some very good examples of experimental evolutionary science on this blog. But when it comes to selection and the evolution of new structures and functions, the analysis often seems to beg for an experiment, one that is simple to conceive but, typically, impossible to actually pull off -- there's not enough time. The previous Journal Club looked at one way around this limitation: bring the past back to life. Even better, though, would be to find an example of evolutionary change in which the new and old forms are still living, so that one could do the before-and-after comparison. It would look something like this: take a species, subject it to evolutionary influences of some kind until the descendants look significantly different from the ancestors, then compare the genomes (or developmental processes) of the descendant and the ancestor, in hopes of discovering the types of changes at the genetic or developmental level that gave rise to the differences in appearance or function of the organisms. That would be a cool experiment.

In fact, that kind of experiment has been done, more than once. The best example, in my opinion, involves an organism far less sexy than a dinosaur or a finch or a whale: Zea mays, better known as corn (or maize).

Corn is a grass, but a grass that's been so extensively modified genetically that it's barely recognizable (to non-specialists like me) as a member of that family. Wait...genetically modified? Yes, and I'm not talking about the really modern tricks that gave us Bt corn or Roundup Ready corn. In fact, the wonderful stuff they grow in Iowa is quite different from the plants that humans first started to harvest and domesticate in Central America a few millenia ago. Corn as we know it is the result of a major evolutionary transformation, driven by selection at the hands of humans. (I don't find the natural/artificial selection distinction at all useful, since there's no explanatory difference, but you can refer to the selection under consideration here as 'artificial' if it makes you feel better.) The story has been a major topic in evolutionary genetics for decades, but it's largely absent from popular discussions, probably because the Discovery Institute has wisely avoided it. I hope it will soon be clear why you won't find the word 'teosinte' anywhere at discovery.org.

For many years, the origin of corn was a mystery. Like most known crops, it was domesticated 6000-10,000 years ago. But unlike other crops, its wild ancestor was unknown until relatively recently. Why this odd gap in our knowledge? Well, it turns out that corn is shockingly different -- in form, or morphology -- from its closest wild relative, which is a grass called teosinte, still native to southwestern Mexico. In fact, corn and teosinte are so different in appearance that biologists initially considered teosinte to be more closely related to rice than to corn, and even when evidence began to suggest a genetic and evolutionary relationship, the idea was hard to accept. As John Doebley, University of Wisconsin geneticist and expert on corn genetics and evolution, puts it: "The stunning morphological differences between the ears of maize and teosinte seemed to exclude the possibility that teosinte could be the progenitor of maize." (From 2004 Annual Review article, available on the lab website and cited below.)

But it is now clear that teosinte (Balsas teosinte, to be specific) is the direct ancestor of corn. In addition to archaeological evidence, consider:

• The chromosomes of corn and teosinte are nearly indistinguishable at very fine levels of structural detail.
• Analysis using microsatellite DNA (repetitive DNA elements found in most genomes) identified teosinte as the immediate ancestor of corn, and indicated that the divergence occurred 9000 years ago, in agreement with archaeological findings.
• Most importantly, a cross between corn and teosinte yields healthy, fertile offspring. So, amazingly, despite being so different in appearance that biologists initially considered them unrelated, corn and teosinte are clearly members of the same species.

The basic idea, then, is that corn is a domesticated form of teosinte, exhibiting a strikingly distinct form as a result of selection by human farmers. And that means that we have a perfect opportunity to examine the genetic and developmental changes that underlie these "stunning morphological differences." We can do the experiment.

First, have a look at an example of one of the evolutionary changes in teosinte under human selection.

The small ear of corn on the left is a "primitive" ear; the brown thing on the right is an ear from pure teosinte. (Both are about 5 cm long.) The "primitive" ear is similar to archaeological specimens representing the earliest known corn. Image from John Doebley, "The genetics of maize evolution," Annual Review of Genetics 38:37-59, 2004. Article downloaded from Doebley lab website.

The thing on the far left is a teosinte "ear," the far right is our friend corn, and the middle is what you get in a hybrid between the two. Photo by John Doebley; image from Doebley lab website.

The pattern of branching of the overall plant is also strikingly different between corn and teosinte, and you can read much more on the Doebley lab website and in their publications.

When I first heard about this work at the 2006 Annual Meeting of the Society for Developmental Biology, I was astonished at the amount of basic evolutionary biology that was exposed to experimental analysis in this great ongoing experiment. Here are two key examples of the insights and discoveries generated in recent studies of corn evolution.

1. Does the evolution of new features require new, rare, mutations in major genes?

Perhaps this seems like a stupid question to you. Anti-evolution propagandists are eager to create the impression that evolutionary change only occurs when small numbers of wildly improbable mutations somehow manage to help and not hurt a species. And in fact, experimental biology has produced good examples of just such phenomena. But there is at least one other genetic model that has been put forth to explain the evolution of new forms. This view postulates that many major features exhibited by organisms are "threshold" traits, meaning that they are determined by many converging influences which add together and -- once the level of influence exceeds a threshold -- generate the trait. The model predicts that certain invariant (i.e., never-changing) traits would nevertheless exhibit significant genetic variation, since evolutionary selection is acting on the overall trait and not on the individual genetic influences that are added together. Hence the implication that...

...populations contain substantial cryptic genetic variation, which, if reconfigured, could produce a discrete shift in morphology and thereby a novel phenotype. Thus, evolution would not be dependent on rare mutations, but on standing, albeit cryptic, genetic variation.

--from Nick Lauter and John Doebley, "Genetic Variation for Phenotypically Invariant Traits Detected in Teosinte: Implications for the Evolution of Novel Forms," Genetics 160:333-342, 2002.

In that paper, the authors show that several invariant traits (e.g., number of branches at the flower) in teosinte display significant genetic variation. In other words, the traits are the same in every plant, but the genes that generate the traits vary. The variation is 'cryptic' because it's not apparent in basic genetic crosses. But it's there. The authors ask: "How can cryptic genetic variation such as we have detected in teosinte contribute to the evolution of discrete traits?" Two ways: 1) the variation is available to modify or stabilize the effects of large-effect mutations; and 2) variation in multiple genes can be reconfigured such that it adds up to a new threshold effect. Note that the first scenario is clearly applicable to the kind of evolutionary trajectory outlined by Joe Thornton's group and discussed in a previous post. The second scenario is particularly interesting, however, since it addresses an important question about the role of selection. Consider the authors' discussion of this issue:

At first glance, cryptic variation would seem inaccessible to the force of selection since it has no effect on the phenotype. However, if discrete traits are threshold traits, then one can imagine ... that variation ... could be reconfigured such that an individual or population would rise above the threshold and thereby switch the trajectory of development so that a discrete adult phenotype is produced. We find this an attractive model since evolution would not be constrained to “wait” for new major mutations to arise in populations. (Italics are mine; ellipses denote deletion of technical jargon, with apologies to the authors.)

In fact, in a 2004 review article, Doebley is bluntly critical of the assumption that new mutations were required during the evolution of corn, and seems to suggest that this view led researchers significantly astray:

There is an underlying assumption in much of the literature on maize evolution that new mutations were central to the morphological evolution of maize. The word "mutation" is used repeatedly to describe the gene changes involved, and Beadle led an expedition ("mutation hunt") to find these rare alleles. The opposing view, that naturally occurring standing variation in teosinte populations could provide sufficient raw material for maize evolution, was stated clearly for the first time by Iltis in 1983. Although new mutation is likely to have made a contribution, anyone who has worked with teosinte would agree that teosinte populations possess abundant genetic variation. [...] Allowing for cryptic variants and novel phenotypes from new epistatic combinations to arise during domestication, it is easy to imagine that maize was domesticated from teosinte.

--John Doebley, "The genetics of maize evolution." Annual Review of Genetics 38:37-59, 2004.

Compare that discussion, and others like it in the paper I'm quoting, with the yapping about mutations that passes for anti-evolution criticism of evolutionary genetics. I can find no evidence that Michael Behe or any other ID theorist has even attempted to seriously address the importance of genetic variation in populations. I haven't read The Edge of Evolution yet, but I have it right here, and the index suggests that Behe hasn't tried to engage genetics beyond the high school level. There's a good reason why Behe is an object of scorn in evolutionary biology. He wants you to think it's because his critics are mean. No; it's much worse than that.

2. Does evolutionary change ever result from a "gain of information," or does Darwinian evolution merely prune things out?

It would be easy to get the impression from various creationists and ID proponents that mutation and selection can only remove things from a genome. Young-earth creationist commentary on "microevolution" (a yucky term for the now-undeniable fact of genetic change over time) always adds that this kind of change involves NO NEW INFORMATION. (The caps are important, apparently, since caps and/or italics are de rigueur in creationist denialism on this topic.)

Similarly, Michael Behe wants you to think that beneficial (or adaptive) mutations are some kind of near impossibility, and that when they do happen it's almost always because something's been deleted or damaged, with a beneficial outcome.

Studies of evolution in corn and teosinte (and other domesticated plants), not to mention findings like the HIV story on Abbie Smith's now-famous blog, tell a different -- and, of course, more wonderfully interesting -- story. In a minireview on the genetics of crop plant evolution in Science last June, John Doebley notes that most of the mutations that led to major evolutionary innovations occurred in transcription factors, which are proteins that turn other genes on and off. Then this:

Another remarkable feature of this list is that the domesticated alleles of all six genes are functional. If domestication involved the crippling of precisely tuned wild species, one might have expected domestication genes to have null or loss-of-function alleles. Rather, domestication has involved a mix of changes in protein function and gene expression.

In other words, the new genes are not dead or damaged; they're genes that are making proteins with new functions. ('Allele' is just the term for a particular version of a particular gene, and 'null', as you might have guessed, is a version that is utterly functionless, as though the gene were deleted entirely.) Now, if you've even flipped through The Origin of Species, you might not be surprised by Doebley's conclusion:

Given that the cultivated allele of not one of these six domestication genes is a null, a more appropriate model than "crippling" seems to be adaptation to a novel ecological niche -- the cultivated field. Tinkering and not disassembling is the order of the day in domestication as in natural evolution, and Darwin's use of domestication as a proxy for evolution under natural selection was, not surprisingly, right on the mark.

The change from teosinte to corn happened in about a thousand years. That's fast evolution. Apply selection to a varying population, and you get new functions, new proteins, new genes, completely new organisms. Fast.

So in summary, we can do the experiment. And we've done the experiment. ('We' being John Doebley and his many able colleagues.) And we've learned a lot about evolution and development. Now if we can just get people to read it. Then they'll know more about evolution, and about God's world, and about the trustworthiness of the anti-evolution propaganda machines that are exploiting the credulity of evangelical Christians.