Tag: natural selection

Scientists again see natural selection in real time

June 8, 2009 • 3:32 pm

In WEIT, I describe several studies showing that natural selection can change species over periods shorter than a human lifetime.  These studies have been important in convincing skeptics (although not creationists, who will never be convinced) that natural selection is more than just a speculation, but a force that can really mold animal behaviors, appearances, and reproductive traits in real time.  The most famous of these, of course, is the work of Peter and Rosemary Grant on a species of Darwin’s finch.  Their work showed that individuals’ beak and body characteristics could change over a single generation when an El Niño event changed the finch’s food.  (See The Beak of the Finch, by Jon Weiner, for a popular account of the Grants’ work.)

Now a group of researchers from Canada and the US have reported natural selection acting in guppies, molding their reproductive behavior over a period of only 8 years: roughly 13-26 guppy generations.  This work is based on the observation that in Trinidad, the common guppy (Poecilia reticulata) lives in streams both above and below waterfalls.  The guppy’s downstream predators cannot migrate past the waterfall barriers, so upstream guppies experience different environments from downstream guppies. In other words, downstream populations have to deal with much stronger predation.

This leads to some evolutionary predictions.  The body of evolutionary theory called “life history theory” predicts that when an animal species experiences higher predation, it should evolve a different reproductive strategy.  In short, guppies harassed by predators should reproduce earlier than un-predated guppies, for the greater your chance of being chomped, the less likely you are to leave offspring if you delay reproduction. Second, fish that experience less predation should produce larger embryos, since they have the luxury of delaying reproduction and because larger embryos make the newly hatched fish more competitive.  Finally, low-predation fish should have fewer offspring in each bout of reproduction, for it is to their advantage to spread their given lifetime allotment of reproductive effort over a longer time.

In 1996, some of these authors introduced guppies from downstream, high-predation populations into uninhabited upstream, above-waterfall areas. Eight years later, in 2004, they took samples from both ancestral and derived populations to see if any differences in life history had evolved.  And they did — in the predicted direction.  Upstream guppies had fewer but larger embryos than downstream guppies, as well as a small reproductive allotment (egg mass as a proportion of body mass).  Mark-recapture experiments on adults also showed that, when tested in the upstream environment, upstream-evolved guppies had higher survival than their downstream ancestors.

The analysis is arcane, but the results are clear:  guppies have changed their life histories in an adaptive way in only eight years.  This certainly reflects the action of natural selection, since previous studies have found similar results for life history, and also for color. (Guppies introduced to a low-predation regime evolve brighter colors in males; brightly colored males are favored everywhere by sexual selection but become disadvantageous in high-predator environments since they are more likely to be spotted and eaten.)

In toto, the guppy work is as powerful a body of evidence for selection, if not more so, than the work on finches.  This is not to denigrate the finch study, which is brilliant.  That work, however, was an uncontrolled “natural experiment” that affected two characters (bill and body size), while the guppy work has involved many groups of investigators doing controlled introductions — and all finding the predicted evolutionary changes in many characters.  Birds, of course, are more charismatic, but the humble guppy has a lot to show us about evolution.

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S. P. Gordon et al. 2009.  Adaptive changes in life history and survival following a new guppy introduction.  The American Naturalist, Volume 174, pp. 34-45.

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More on Dick Lewontin and WEIT: what’s the deal with natural selection?

May 12, 2009 • 6:58 am

Several days ago I called attention to Richard Lewontin’s review of WEIT and several other books in The New York Review of Books.  In it, Dick (excuse the informality, but he was my Ph.D advisor) praises the book but takes me to task for implying that the evidence for natural selection is as strong as the evidence for evolutionary change per se:

Where he is less successful, as all other commentators have been, is in his insistence that the evidence for natural selection as the driving force of evolution is of the same inferential strength as the evidence that evolution has occurred. So, for example, he gives the game away by writing that when we examine a sequence of changes in the fossil record, we can

“determine whether the sequences of changes at least conform to a step-by-step adaptive process. And in every case, we can find at least a feasible Darwinian explanation.”

But to say that some example is not falsification of a theory because we can always “find” (invent) a feasible explanation says more about the flexibility of the theory and the ingenuity of its supporters than it says about physical nature. Indeed in his later discussion of theories of behavioral evolution he becomes appropriately skeptical when he writes that

“imaginative reconstructions of how things might have evolved are not science; they are stories.”

While this is a perfectly good argument against those who claim that there are things that are so complex that evolutionary biology cannot explain them, it allows evolutionary “theory” to fall back into the category of being reasonable but not an incontrovertible material fact.

There is, of course, nothing that Coyne can do about the situation. There are different modes of “knowing,” and we “know” that evolution has, in fact, occurred in a stronger sense than we “know” that some sequence of evolutionary change has been the result of natural selection. Despite these misgivings, it is the case that Coyne’s book is the best general explication of evolution that I know of and deserves its success as a best seller.

This “critique” has been picked up by several bloggers (see below), and I want to respond in a bit more detail.

First of all, yes, it’s true that the evidence for natural selection as the cause of most evolutionary change in the past is not as strong as the evidence that evolutionary change occurred.  It cannot be otherwise.  We can see evolution happening in the fossil record, but it is infinitely harder to parse out the causes of that change.   We weren’t around when it occurred, so we must rely on inference.  This difficulty is one reason why it took biologists much longer to accept natural selection than to accept evolution.   But to say that the evidence for selection is weaker than for evolution does not mean that the evidence for natural selection is weak, a conclusion I fear that creationists will extract from Lewontin’s comment.

Here is why selection still seems the best hypothesis for the origin of adaptive features of organisms.

1.  It is the only scientific theory, among all of those that have been adumbrated, that currently makes sense.  Failed explanations include teleology, intelligent design, and Lamarckism.  Some of these were once valid scientific alternatives to natural selection, but have failed either because they are untestable or because they were testable and shown to be wrong. If Lewontin and others want to say that some process other than selection is responsible for the limbs of tetrapods, the fins of whales, and the white color of polar bears, they must say what they envision.  Yes, Lewontin and Gould showed that many things for which we can concoct adaptive stories may be “spandrels” — nonadaptive traits hitchhiking on other adaptations — but this does not mean, as Lewontin seems to imply, that selection may not play a major role in creating adaptations.

2.  In cases where we can actually investigate whether selection is responsible for an adaptive change in a species, it is.  I give several examples in WEIT, including coat colors in mice and the famous work of Rosemary and Peter Grant on Darwin’s finches. And of course there are those dozens of cases of antibiotic resistance in bacteria, insecticide resistance in arthropods, and herbicide resistance in weeds.  In bacteria, for instance, we can show that the genetic variation for resistance preexisted in the population and not invoked by the selective agent, precisely as the theory of natural selection posits.

3.   In tests where we envision that selection was responsible for an adaptation, we can do laboratory tests to see if the adaptation at least gives a fitness advantage to those individuals possessing it.  One example of this is the Browers’ work on Batesian mimicry in the viceroy butterfly.  It was shown that exposure to a toxic monarch made naive bluejays sick, and that later these bluejays avoided the nontoxic viceroys, giving a survial advantage to mimics.  This is precisely what has to happen for that mimicry to evolve by natural selection.  Likewise with color in guppies:  brightly colored guppies get eaten more often in Trinidadian streams than do their duller confreres.  This explains why guppies are less colorful in predator-filled streams.

4.  The prerequisites for selection — the heritability of traits, the fact that there is competition between individuals, and that there are fitness differences between individuals with different traits — have all been demonstrated in living organisms in nature.  If few traits showed any heritable genetic variation, we’d be justified in rejecting selection as a major cause of evolution. Guppy coloration is heritable.

5.   Even in ancient species we can test the likelihood that selection caused evolutionary change.  Horses lost their toes right about the time when the forests were disappearing on the Great Plains.  We know that hooves are more effective adaptations for running in open grassland than are multi-toed feet. Likewise, horse teeth become higher and more robust precisely when silicon-rich grasses were replacing the leafy forests.  We know that herbivores need higher and more robust teeth to deal with grass. It is a good inference that the appearance of grassland was the selective factor promoting the loss of horse toes and the change in horse teeth.

6.  As discussed in previous posts, selection as we envision it has certainly been adequate to explain the evolution of complex adaptations like the eye, and in geologically reasonable periods of time.  Therefore it remains a viable hypothesis for adaptive change. This didn’t have to be the way it turned out.

What about my supposed double standard about accepting natural selection for many traits but being skeptical when it comes to evolutionary psychology?  This is a reasonable tactic for one important reason: we have many more alternative theories for the appearance of human behavioral traits than we do for morphological adaptations in other species.  How many alternative theories do we have for the appearance of flippers in proto-whales, or for the movement of their nasal passages to the top of their heads?  In contrast, there are many alternative theories for the appearance of traits like human rape, depression, music, art, religion, etc.  Blowholes aren’t likely to be spandrels; the appearance of music and poetry might well be.  Humans have culture and rationality to a degree possessed by no other animal, and can learn many things not permitted in species having smaller (or no) brains.   That’s why we need to be more cautious about imputing selection to human behaviors than to blowholes.

Now I think Dick did have a point: I should have pointed out (though I might have; I can’t remember!) that it is a lot easier to come up with evidence for evolution than for selection.  But I think Lewontin’s own anti-selectionist biases are intruding here. As I mentioned in an earlier post on ideological grounds neither he nor Gould were ever very strong promoters of selection. I’m not sure what the connection is between selection and politics (it may be the misuse of selectionism that Gould and Lewontin saw among sociobiologists), but neither of these chaps were avid promoters of selection.  They preferred to emphasize other processes, including pleiotropy, spandrels, genetic drift and the like. I think this was a deliberate strategy.

Over on EvolutionBlog, Jason Rosenhouse analyzes Dick’s review and has some good comments:

I don’t understand what it means to say that “natural selection is the driving force of evolution.” Given Lewontin’s past writing (most notably his spandrels paper with Stephen Jay Gould) I would guess that his point is that some biologists are too quick to attribute some anatomical feature of some organism to the prolonged working of natural selection.

That may be true, but when we are talking about adaptations the evidence for natural selection seems to me to be very strong. For one thing, it is the only natural mechanism known that can account for complex structures (like bird wings or vertebrate blood clotting systems). For another, every complex structure studied to date shows clear evidence of being a cobbled together Rube Goldberg machine, which is exactly what we would expect if they were crafted by natural selection.

On top of this, biologists routinely use adaptive reasoning to generate testable hypotheses about the creatures they are studying. Lewontin would know better than I whether biologists engaging in flights of fancy is a genuine problem in the field, but it is undeniable that “the adaptationist program” has yielded great dividends over the years . . .

. . In fairness, I think Stephen Jay Gould was pretty clear on this point [the ubiquity and importance of selection] in several of his essays. I compiled some of his statements on the matter in this essay. But I share Coyne’s frustration. I’ve never really understood what it is exactly that anti-selectionists are complaining about. If they agree that complex adapations arise as the result of gradual accretion mediated by natural selection, then I fail to see how they are really so different from people like Richard Dawkins or Daniel Dennett (two people often described as being beknighted uber-selectionists). If they do not agree then I would like to hear their proposed alternative mechanism.

Now I have great affection for Lewontin (as all of his students say, “I love that man”), but I would like to see him make an explicit statement about what aspects of nature he imputes to natural selection.  We’re not just talking about rape, male domination, and music here, but coat colors, physiology, feathers, gills, flowers, toxins, and the like.  Like Jason, I think the anti-selectionists have gone way, way overboard, and have thrown out the baby with the bathwater.  (These people also include the “structuralists,” and those who attribute adaptations to the self-organizing properties of biological matter.)

Dick Lewontin reviews Brown, Gibson, Darwin, and Coyne in the NYRB

May 8, 2009 • 11:00 am

Richard Lewontin (who, I confess, was my Ph.D. advisor at Harvard) reviewed WEIT and three other books in the latest New York Review of Books (Janet Browne’s Darwin’s Origin of Species: A Biography, James Costa’s The Annotated Origin,  Greg Gibson’s  It Takes a Genome: How a Clash between Our Genes and Modern Life is Making Us Sick.)

As usual, Dick’s intellectual energy (and immense knowledge) takes him far beyond the bounds of the books under review. He traces Darwin and Wallace’s theory back to the socioeconomic climate of Victorian England, explores the hagiography of Darwin, and takes on the hegeomony of selection (this harkens back to his and Steve Gould’s famous –and explicitly antiselectionist — paper, The Spandrels of San Marco).  He does disagree somewhat with how I dealt with selection in WEIT:

The scientific community has the definite sense of being embattled and one of its responses is to use the two hundredth anniversary of the birth of its apostle of truth about the material basis of evolution and the 150th anniversary of the appearance of his gospel to carry on the struggle against obscurantism. Jerry Coyne’s Why Evolution Is True is intended as a weapon in that struggle.

Coyne is an evolutionary biologist who, like his former student H. Allen Orr, has been a leader in our understanding of the genetic changes that occur when species are formed. His primary object in writing this book is to present the incontrovertible evidence that evolution is a physical fact of the history of life on earth. In referring to the theory of evolution he makes it clear that we do not mean the weak sense of “theory,” an ingenious tentative mental construct that might or might not be objectively true, but the strong sense of a coherent set of true assertions about physical reality. In this he is entirely successful.

Where he is less successful, as all other commentators have been, is in his insistence that the evidence for natural selection as the driving force of evolution is of the same inferential strength as the evidence that evolution has occurred. So, for example, he gives the game away by writing that when we examine a sequence of changes in the fossil record, we can “determine whether the sequences of changes at least conform to a step-by-step adaptive process. And in every case, we can find at least a feasible Darwinian explanation.”But to say that some example is not falsification of a theory because we can always “find” (invent) a feasible explanation says more about the flexibility of the theory and the ingenuity of its supporters than it says about physical nature. Indeed in his later discussion of theories of behavioral evolution he becomes appropriately skeptical when he writes that “imaginative reconstructions of how things might have evolved are not science; they are stories.”  While this is a perfectly good argument against those who claim that there are things that are so complex that evolutionary biology cannot explain them, it allows evolutionary “theory” to fall back into the category of being reasonable but not an incontrovertible material fact.

There is, of course, nothing that Coyne can do about the situation. There are different modes of “knowing,” and we “know” that evolution has, in fact, occurred in a stronger sense than we “know” that some sequence of evolutionary change has been the result of natural selection. Despite these misgivings, it is the case that Coyne’s book is the best general explication of evolution that I know of and deserves its success as a best seller.

I have to say that Dick has indeed hit on a tricky issue in compiling the evidence for evolution.  While natural selection is the only reasonable explanation for the evolution of adaptations, we cannot in most cases do more than adduce its plausibility.  Direct demonstrations are rare (note to creationists: this is only because they’re HARD TO DO, so don’t take this out of context), and demonstrations in the past nearly impossible.  And I should have talked more about this in WEIT (although we have discussed it on this website).  But I can’t help but sense Dick’s own anti-selectionist views here:  views that may stem from seeing others support preconceived biases by invoking soft adaptationism , and views that were of course instrumental in Lewontin and Gould’s battle against sociobiology in the 1970s.   When I was at Harvard with Dick and Steve, it was almost as though selection was a forbidden topic — just once I would have liked either of them to have admitted openly, “Yes, of course selection is the only plausible explanation for adaptations.”  In their fight against unthinking adaptationism, they nearly threw the baby out with the bathwater.

Nevertheless, Dick has a point.  But I’m glad he that he seems to have liked the book.  As one friend wrote me today:

An interesting piece.  Lewontin certainly can’t be accused of lobbing his old student a batting-practice pitch!  Even so, I see that he was careful to supply a line that would serve perfectly in an ad: “Coyne’s book is the best general explication of evolution that I know of and deserves its success as a best seller.”

Oh, and for those who didn’t see this before, Dick turned 80 this year.

Recent natural selection in human populations

April 6, 2009 • 10:18 am

A bunch of high-powered genomics people have just come out with a paper in Genome Research surveying the human genome for recent signs of natural selection (which you can assess by looking at the patterns of DNA variation around various genes).  You can get the original paper (reference and abstract below) here as a pdf file, or read a story about it in the April 2 New York Times.  The survey was based on DNA data from 938 people from 53 populations, making this the most extensive survey of selection in human groups to date.

I’m leaving shortly (see post below by Matthew Cobb, my replacement), but just a few conclusions from this survey:

1.  Geographically adjacent populations tend to have similar histories of selection: Europe, Central Asia, and the Middle East tend to share their genetic complements compared to populations elsewhere in the world.  This presumably reflects the history of migration and intermarriage between the former three areas.

2.  Genes that seem indubitably under selection include not only loci involved in pigmentation, but some loci of unknown function (e.g., the gene called C21orf34, which resides on our 21st chromosome).  As I note in WEIT, human skin pigmentation is one of the few “racial” traits whose difference between human populations is pretty clearly connected with natural selection.  We previously had a good “intuitive” explanation for this difference (in sunnier climes, darker pigmentation is selected to prevent melanomas, while in northern, less sunny areas, the skin becomes less pigmented to allow production of vitamin D), but now we have more direct evidence from looking at the genes that themselves produce pigment.  However, most of the differences in appearance between groups don’t have an evolutionary explanation so far: they may have changed via sexual selection. Note that in the chart below, the SLC genes are pigmentation alleles, with a pretty strong signal of selection in Europe, the Middle East, and Asia.

3.  A gene that is a risk factor for diabetes and celiac disase also shows signs of being positively selected in some populations.  Why?  Perhaps because, as the authors theorize, the “risk allele” is involved in some other, positively selected trait, or perhaps it is genetically linked to such traits by being nearby on the chromosome.

4.  As mentioned in an earlier post, a pygmy and nearby non-pygmy African population differ in their insulin growth factor genes, which may have been selected to have alleles for smaller height in pygmies. (See earlier post for possible reasons for this).  These data come from only two populations, however, and it would be interesting to see if pygmy populations in Southeast Asia and South America have similar forms of the IGF gene.

Note that much of this selection has to be fairly recent, since populations outside of Africa have differentiated only within the last 60,000-100,000 years.

02visuals_graph600-1

This chart shows the sites along the genome (listed at the left) at which natural selection has occurred in the genome of eight regional groups (shown at top). These are 1) Biaka pygmies, 2) Bantu-speaking Africans, 3) Western Europeans, 4) Middle Easterners, 5) South Asians (people of Pakistan and India),

6) East Asians, 7) Oceanians and 8. Native Americans. The colored bars show the degree of selection at each site, with yellow denoting a signal of clear but moderate statistical significance and red denoting high statistical significance. (Photo and caption courtesy of The New York Times)

Signals of recent positive selection in a worldwide sample of human populations

Abstract: Genome-wide scans for recent positive selection in humans have yielded insight into the mechanisms underlying the extensive phenotypic diversity in our species, but have focused on a limited number of populations. Here, we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel. We refine the geographic distributions of known selective sweeps, and find extensive overlap between these distributions for populations in the same continental region but limited overlap between populations outside these groupings. We present several examples of previously unrecognized candidate targets of selection, including signals at a number of genes in the NRG–ERBB4 developmental pathway in non-African populations. Analysis of recently identified genes involved in complex diseases suggests that there has been selection on loci involved in susceptibility to type II diabetes. Finally, we search for local adaptation between geographically close populations, and highlight several examples.

Joseph K. Pickrell et al., Genome Res. May 2009 ; published ahead of print March 23, 2009,

Coat color in wolves

March 6, 2009 • 11:08 am

by Greg Mayer

An alert reader has directed my attention to an interesting paper on coat color in wolves (abstract only without subscription) in today’s issue of Science by Tovi Anderson of Stanford and 14 colleagues from the US, Canada, Italy, and Sweden. Coat color in wolves is a polygenic trait affected by age, but Anderson and her colleagues show that black color in young wolves is associated with a 3 base-pair deletion in a gene called CBD103, and that there is a habitat correlation with the frequency of this color: black wolves live in the forests, gray (or white) wolves on the tundra.  This would be very interesting on its own, but Anderson et al. go further.  By careful phylogenetic analyses, they show that the gene for black color has entered North American wolves, and coyotes and Italian wolves as well, by hybridization with domestic dogs; and that the gene has been subject to recent positive natural selection (shown by low variability in the part of the chromosome immediately surrounding the gene, indicating what is known as a “selective sweep”).  Thus, a correlation between habitat and coat color that is suggestive of adaptation, is shown to be based on heritable variation undergoing natural selection.

The sort of combined field and lab study done by Anderson et al., using classical genetics (they have pedigrees of the wild wolves!), ecology, and now molecular genetics, is among the kind of work that first attracted me to evolutionary biology, and is known as ecological genetics. This field of study, pioneered by the great British geneticist E.B. Ford, was once characterized by the great American geneticist Dick Lewontin as carrying on the British “genteel upper-middle-class tradition of fascination with snails and butterflies”; I’m glad the fascination has moved to some of the colonies and beyond, and been extended to wolves, coyotes, and dogs.

Genes for surviving after reproduction

February 3, 2009 • 1:03 pm

An alert reader has written me about a statement I made in WEIT:

You write that “a gene that knocks you off after reproductive age incurs no evolutionary disadvantage.” And you go on to say that selection would not favour genes that helped survival after reproduction has finished. “One example would be a gene that helps human females survive after the menopause.” I understand and accept this point. But could there be an exception (in theory) as follows? If women were giving birth right up to menopause, they would need to survive after menopause to bring up their last children. Also, if a woman who survived post-menopause helped her daughter to bring up her grandchildren and had the effect of improving the survival rate of those grandchildren, wouldn’t her “live longer genes” then get passed on?

The reader is absolutely right–I glossed over the nuances of this idea in the interest of space, and probably shouldn’t have.  Indeed, a woman will be selected to live until all the benefits she can confer upon her children (the most important being maternal care) have already been bestowed, and that means staying alive until she has brought up all her offspring.  To the extent that children are grown and independent before menopause, selection will be very small against a gene that bumps mom off.  That is, of course, unless she can help her grandchildren grow up, for in that case she is still contributing to the survival of her own genes in her offspring’s offspring.  So there are exceptions to what I said.  Let me then rephrase my statement to say that “a gene that knocks you off after you’ve made all possible contributions to rearing related individuals incurs no evolutionary disadvantage.”

More evidence of selection in action

January 26, 2009 • 4:59 pm

I’m going to try to post fairly frequent updates about new observations and experiments in evolutionary biology that are relevant to my book.  Here’s the first.

Two weeks ago, in an article in The New York Times, Cornelia Dean summarized a recent article in The Proceedings of the National Academy of Sciences about how inadvertant selection by humans has led to evolutionary change.  (The original article, by C. T. Darimont et al., can be found here.)  Darimont et al. showed that in 29 species for which long-term data exist—species ranging from fish to caribou—human harvesting has led to extraordinarily large genetic changes in size at reproductive maturity and age at which reproduction begins.  Actually, these changes were predictable from evolutionary theory, which tells us that if we selectively remove from nature the biggest fish or the largest sheep, we  leave  behind those individuals who reproduce at a smaller size, and those will be the the ones who contribute their genes to the next generation.  This will eventually cause the observed evolutionary changes in age of maturity and body size at maturity.

What is remarkable is the speed of this evolutionary change: it is far faster than normal rates of evolution produced by “natural” (i.e., non-human-based) natural selecction (for example, the changes in beak size in Galapagos finches during periods of drought), and faster even than observed rates of evolution produced by other cases of human-caused selection.  These cases supplement and extend the examples of human-caused evolution described in my book, but also add a new dimension because in these new cases selection was inadvertent–people were not trying to change the population, they were just catching the biggest fish and shooting the most desirable rams.  It thus differs from deliberate artificial selection such as that involved in dog breeding. It proves yet again that if there is genetic variation for a trait and selection operates on that trait, evolution will follow.