There is a new paper, just coming out in Proceedings of the National Academy of Sciences, that explores the idea that humans have undergone an increased rate of evolution over the last several tens of thousands of years.

Blogging on Peer-Reviewed ResearchBy an increased rate of evolution, the authors mean an increased rate of adaptive change in the genome. By recent times, the authors mean various things, depending on which part of the analysis you examine, and depending on what is meant by “increased.” … In other words, the timing of an event that is not really an event (but rather a change in rate of something) is hard to specify. The time scale we are talking about here is several tens of thousands of years.

The authors accredit the major cause of the increase in rate of evolutionary change to an increase in population size during the last 50,000 years, but also point out that the biggest change in the rate of population increase would have been with the origin of agriculture subsequent to about 10,000 years ago. This partly underscores the difficulty of talking about vague (in time and space) events, but it also points out a potential problem with the analysis.

But before I delve into what I think is wrong with the analysis, let’s make clear what they are saying, and point out what is probably very valid and important.

Essentially, evolutionary change, and the amount of evolutionary change that happens in a population, begins with mutation (happening at a certain rate) and continues through either random processes that cause a mutation to become more or less common over short to medium time scales. If the mutation is deleterious, it disappears quickly, and when looking at long time scales, we expect to see very few deleterious mutations that are old. If the mutation is neutral (does not have an effect one way or the other) then we expect to see the mutation become more common over time, then less common, them more common, in a kind of random walk. If there are two different forms (alleles) of a gene (the original one and a mutation) and both have the same adaptive effects (in other words, the mutation was neutral) then we expect these two alleles to increase and decrease in relation to each other randomly, and eventually, one of the mutations will accidentally bump into “zero” and disappear, leaving the other represented at 100%. Any neutral mutation that arises will by definition start off at a very low percentage, and therefore, the new mutation is usually the one that bumps into zero first, thus disappearing.

Geneticists have done a lot of work with modeling the math of change over time in frequencies of alleles that are either deleterious or neutral. The neutral part is pretty easy, because that is simple probability. The deleterious side of this is a little more difficult because “deleterious” is a quantitative and qualitative thing … just how deleterious is a particular allele? On the other hand, it is pretty easy to insert a deleterious allele in a population of laboratory critters (bacteria, mice, etc.) and see what happens. Therefore, the statistical models that predict the behavior of deleterious mutations over time are embedded in a good sense of reality, and as a result are pretty good too.

So, when studying genetics of populations, geneticists have the ability to predict what the genetic variation should look like given the null conditions of a particular mutation rate, a particular population size and structure over time, and no positive selection. The distribution and nature … distribution both in the genome and across a population … of genetic variants (alleles) should look a certain way, and when they don’t, you are probably looking at postitive (adaptive) selection.

I will leave it to others who know more about the statistics of population genetics than I do to evaluate the research presented in this paper. Here, in fact, I will rely on the authority of some pretty bad-ass population geneticist and evolutionary scientists who wrote the paper. Nonetheless, I eagerly await a critical analysis by my colleagues.

Going on the assumption that this research is OK, or at least, if flawed, not utterly wrong, there are two conclusions of special interest. One of these conclusions supports ideas that have already been suggested about human evolution, but in a new way, with new and more precise information, and the other contradicts a commonly held belief that those of us who think about these things a lot have long known to be a fallacy.

First, the rate of human evolution is higher now, and has been higher for tens of thousands of years, than the rate of evolution is expected to be for, say, a typical ape, and higher than we believe it may have been previous to, say, 50,000 years ago. In other words, higher than expectations, with this increase being relatively recent.

Yea! We evolve fast! Good for us. Of course, just remember that the ultimate outcome of evolution so far seems to be extinction, at least this has been the case for most species, so don’t you get all full of yourself, human!

The other conclusion is this: Yes, you hear all the time that “culture overrides biology” or similar sentiments. Well, yes it can, but it is also very often not true, and I can think of many examples of culture very much NOT overriding biology. Well, this study, indicating that as the range, intensity, and ubiquity of various cultural adaptation (read: technology of all sorts from agriculture to cell phones) increases over time, so does the rate of genetic evolution. We are probably adapting to our culture. Makes sense.

Here is what I do not like about the paper. The researchers make some seriously important assumptions about population size and change in human population over time. In so doing, they model population as an ever increasing value. There is no part of their model that has a population crash. This is based on a number of papers that are individually potentially weak in this area, as well as, I think, a general assumption that archaeologists and others often make about the past. I’ve written and given talks about this phenomenon in the past, but apparently my wisdom has not yet been understood (damn them!)… We tend to make the assumption that changes we see happening today, in a certain direction, always happened in that direction in the past. We also tend to make the assumption that a given feature of human endeavor… writing, agriculture, whatever, is tied by an unbroken line to an origin evinced in some record (or assumption) in the past. Both of these assumptions are invalid, yet powerful in shaping our view of prehistory and history.

Indeed, the idea that agriculture was invented once (in each of the several areas in which it was invented) and continued to the present is an assumption that has not been tested. How do we know agriculture was not invented a few times over the last 100,000 years, but fell totally out of use in many areas?

This one-wayness and simplicity imposed on the past very much applies, inappropriately, to the population model used in this paper. The authors are very well aware of population crashes and bottlenecks, but probably do not adequately take them into account in this work. If you go into the archaeological record and look at the Last Glacial Maximum, it is actually pretty hard to find evidence of people living anywhere but a few locations, for instance. (That was about 18,000 years ago.) The assumption of a steady increase is unfounded.

Nonetheless, I liked the paper. Look for it to be widely cited and frequently abused, like all good papers.


Hawks, John Hawks, Eric T. Wang, Gregory M. Cochran‡ Henry C. Harpending, and Robert K. Moyzis. (2007) Recent acceleration of human adaptive evolution. Proceedings of the National Academy of Sciences. Forthcoming. PNAS.

Comments

  1. #1 Colugo
    December 10, 2007

    Based on a science news article, it appears to be an important paper. However, in their remarks some authors have indulged in speculation beyond what the data supports.

    http://tinyurl.com/24zhkg

    “We aren’t the same as people even 1,000 or 2,000 years ago,” [Harpending] says, which may explain, for example, part of the difference between Viking invaders and their peaceful Swedish descendants. “The dogma has been these are cultural fluctuations, but almost any temperament trait you look at is under strong genetic influence.”

    That’s just hand-waving.

    Harpending: “Human races are evolving away from each other. Genes are evolving fast in Europe, Asia and Africa, but almost all of these are unique to their continent of origin. We are getting less alike, not merging into a single, mixed humanity.”

    Well, I doubt it. Who were the source populations?

    “Han Chinese, Japanese, Africa’s Yoruba tribe and northern Europeans”

    What if they had used the genes of Brazilians, African-Americans, and Madagascar natives? Would they still be able to conclude that the human species is diverging?

    The increased rate of evolution is an interesting finding that contradicts Stephen Jay Gould’s argument that human evolution is slowing or even at a standstill.

    I’ll have more to say after I read the paper in PNAS.

  2. #2 Greg Laden
    December 10, 2007

    There is absolutely nothing in this paper that supports this kind of suggestion, even though, yes, it is being made. I suspect from Harpending’s perspective, this is a way of sneaking some views on race that he appears to hold past the peer review process. Rather shameful.

  3. #3 razib
    December 10, 2007

    that contradicts Stephen Jay Gould’s argument that human evolution is slowing or even at a standstill.

    where is this argument? what is its general shape?

  4. #4 pkiwi
    December 10, 2007

    I like your point Greg about population changes affecting frequency. Bottlenecks are where you expect to see selection pressures. I presume that the sort of changes in the last 10-20,000 years or so are like lactose-tolerance in agricultural communities becomes mighty useful if you are short of food.

    Without reading the paper, the defintion of evolutionary change above looks a bit loose. Genetic variation and drift? Sure that should increase as a subject of population size, generally. But evolutionary change? Doesn’t that require some selection pressure. I think Gould’s argument was along the lines that there wasn’t definitive selection pressures you could identify.

  5. #5 Colugo
    December 10, 2007

    Razib:

    I don’t have the cites at the moment, but if I recall correctly Gould argued that since punctuated change requires a small isolated population driven by drift (the Mayr model), then because human population is so large and mixed we should expect stasis. The only way that evolution is going to produce markedly different humans, he argued, was if humanity goes into space.

  6. #6 razib
    December 10, 2007

    colugo, ok, sounds like a garbled form of adaptive landscape. in any case, i don’t think we need to take dogmatic sides in the wright-fisher debates. agricultural geneticists validate both models to some extent. i don’t think much of the idea of large populations resulting in stasis though, i’m with fisher on this one. meta-population dynamics are probably more important than fisher thought though. also, in terms of humans it looks like gould simply is wrong, population expansions seem to have come mostly from the regions with the largest ambient hominid groups (africa).

  7. #7 Greg Laden
    December 10, 2007

    Forget about Gould. Nothing he said was relevant here.

    Evolutionary change simply means change in allele frequency over time, and that can be with our without selection. The paper at hand asserts that among the different kinds of evolutionary change, there looks like more selection than there should be, and that this is kind of blossoming over the last several tens of thousands of years.

  8. #8 Colugo
    December 10, 2007

    How might Harpending’s “unofficial” assertions jibe with the paper’s “official,” explicit argument?

    “In our view, the rapid cultural evolution during the Late Pleistocene created vastly more opportunities for further genetic change, not fewer, as new avenues emerged for communication, social interactions, and creativity.”

    That sounds like genes related to cognitive ability and possibly temperament.

    And what was going on immediately following the Late Pleistocene?

    “Demographic growth intensifed during the Holocene, as domestication centers in the Near East, Egypt and China underwent expansions commencing by 10,000 – 8000 years ago. From these centers, population growth spread into Europe, North Africa, South and Southeast Asia, and Australasia during the succeeding 6000 years. … Despite the possible early appearance of annual cereal collection and cattle husbandry in North Africa, subsaharan Africa has no archaeological evidence for agriculture before 4000 years ago. … As a consequence, some 2500 years ago the population of Subsaharan Africa was likely fewer than 7 million people, compared to European, West Asian, East Asian, and South
    Asian populations approaching or in excess of 30 million each”

    Interesting.

  9. #9 Colugo
    December 10, 2007

    I structured my first post badly; I should have mentioned human evolutionary stasis vs rapid evolution before criticizing speculations (by Harpending, outside of the paper) that go beyond the data of the paper. I didn’t mean to include that with the things I thought were unsupported speculation: rapid evolution in temperament and racial divergence.

  10. #10 razib
    December 11, 2007

    the racial divergence part, the logic is pretty simple: recently selected variants are the ones less likely to span these three groups. additionally, with simultaneous population expansions each group might develop endogenous responses to the same pressures that differ, and their different variants can’t cross and sweep across populations because the selection coefficients aren’t as high once you have a competitive variant already at high frequency. if we are in a transient and there’s a lot more substitution recently then that means that older sweeps which went across the whole species are less frequent so you’re seeing divergence on new salient traits. to be short about it, northern european, east asian and african physical phenotypes as we imagine them are all probably holocene creations.

  11. #11 JL
    December 11, 2007

    According to USA Today, John Hawks said “Blue eyes are new.” How is that determined?

  12. #12 Richard Parker
    December 11, 2007

    Colugo – Are you by any chance related to my old friends here?
    http://www.coconutstudio.com/Shoreline%20Mammals.htm#Kago

  13. #13 razib
    December 11, 2007

    According to USA Today, John Hawks said “Blue eyes are new.” How is that determined?

    the gene responsible for 3/4 of the variation in blue vs. non-blue eye colors in europeans, OCA2, has been subject to recent selection. it seems to have started to rise in frequency in the last 10-5 thousand years.

  14. #14 Jim Thomerson
    December 11, 2007

    A fuzzy comment: there was an article in the newspaper sometime back which contrasted us today with our ancestors at the time of the Civil War. Presented data on a number of parameters which are strikingly different between then and now. Made the comment that this was the highest rate of evolutionary change ever known for humans. Probably correct if you think in terms of change in phenotypes. Only one I remember is change in onset of puberty, which is much earlier now than when I was a kid.

  15. #15 Greg Laden
    December 11, 2007

    JL: On blue eyes, what he (razib) said.

    However, there is an assumption that everyone had brown eyes until fairly recently that is also partly derived from Euros having non-brown eyes. What is not taken into account is the frequency of blue eyes in non-european groups, for which we probably don’t actually know the genetics (Pygmies often have blue eyes, for example).

  16. #16 Colugo
    December 11, 2007

    AAPA 2007 abstracts:

    Understanding human races: the retreat of neutralism.
    Henry Harpending

    “Discussion and debate about human races has been dominated for decades by neutral theory and statistics. Since this literature never posed a real question, it has never produced an answer. Lewontin’s 1972 paper with its claim that a value of 1/8 of a statistic like Fst is “small” and that this means that human race differences are insignificant is a staple of our textbooks. … An appropriate comparison shows that human are more, not less, differentiated than other large mammal species. … It appears that there is a lot of ongoing evolution in our species and the loci under strong selection on different continents only partially overlap. Human race differences may be increasing rapidly.”

    Acceleration of adaptive evolution in modern humans.
    J. Hawks and G. Cochran

    “… A constellation of features in the face and cranial vault, notably including endocranial volume, changed globally during this time period and documents common patterns of selection in different regions. Holocene changes were similar in pattern and chronologically faster than those at the archaic-modern transition, which themselves were rapid compared to earlier hominid evolution. In genomic and craniometric terms, the origin of modern humans was a minor event compared to more recent evolutionary changes.”

    Interesting:

    http://tinyurl.com/2n37dt

    “Dr Hawks said the value of most genetic changes, including many in the brain, remained a mystery. Some could involve personality, or help our brains be “more perceptive”".

    Richard Parker, to answer your question: Yes, I like flying lemurs, the sister clade to us primates.

  17. #17 razib
    December 12, 2007

    for which we probably don’t actually know the genetics (Pygmies often have blue eyes, for example).

    hey greg, wuz your source on this? it is literature, or do you know from personal exp?

  18. #18 razib
    December 12, 2007

    and pygmy = african pygmy right? not the “negritos” of southeast asia.

  19. #19 Greg Laden
    December 12, 2007

    R: Yex, eastern Pygmies (Efe). I have lived amongst them.

  20. #20 David Harmon
    December 12, 2007

    Isn’t the transition period within the error bars for our development of speech/culture? Assuming that was pushed hard for its immediate advantage, it makes sense that we’re still trying to adapt to the implications of that major change.

  21. #21 Greg Laden
    December 12, 2007

    If you take the three or four major classes of theory regarding origin of language, the error bars get way,way big. So the answer is a definitive maybe.

  22. #22 henry harpending
    December 14, 2007

    It is interesting that no one in the blogworld seems to have put together our remarks about plausible evolutionary rates with Greg Clark’s “Farewell to Alms.” His suggestion that genetic change in England (and by implication much of Europe I think) made a new kind of human is exactly what we say can happen.

    Clark is not committed to the idea of genetic change, but we do know that everything anyone looks at is moderately heritable (Bailey’s rule). Given that, it is hard to believe that the demographics of medieval England did _not_ lead to big genetic changes.

    Henry

  23. #23 Danniel Soares
    December 14, 2007

    I haven’t read the paper and not even most of the bloggin around it yet, but I have a few doubts. Is really safe to assume that this acceleration that looks adaptive is really adaptive?

    It’s a sort of common sense that evolution is slowing down for humans due to technology, agriculture, medicine and etc, but that’s actually valid only for adaptive evolution, not neutral, which would actually speed up (in absolute numbers, even though the rates would still pretty much constant). Natural selection not only gradually ceases to filter or benefit mutations as drastically as before, but at the same time artificial changes in the environment allow the population to grow larger than previously possible (more food available, more group protection, more protection from climate, etc), further increasing the total genetic variability.

    The funny thing is that natural selection is not actually something that can ever speed up evolution in a certain way, but only reduces the relative speed from the maximum potential of evolution, which would be the mutation rate undisturbed. That’s why neutral evolution is faster than natural selection.

    Even when natural selection is really fast, when some selective factor actively kills most of the population that lacks some adaptive trait, then unavoidably it will cause a bottleneck effect, a huge difference in relative genetic frequencies, that is not a product of selection per se, that is, most of the evolution that happened was a only a byproduct of natural selection, but not adaptive in itself.

    So I think that it’s unavoidable to conclude that the distinction between exceptionally rapid positive selection and neutral evolution is reasonably expected to be really blurry, since both are essentially approximations of the full mutation rate potential. Can we really discern it from statistics alone, without pointing how the specific genes differ adaptively between each other?

    The closest thing that was done in the blogosphere was to point those old examples of lactose tolerance and similar things. But it think that it is not something that settles the whole thing, allows us to accept that populations today differ more adaptively from each other than H. sapiens from 5 000 years ago differed from H. neanderthalensis (if I correctly recall the statement), it’s just an example of a few that things that we know that happened.

    I think that statistics alone can be very tricky under this specific scenario, where, intuitively, the selective pressures are reasonably expected to do decrease. To me seems that, despite of the increase of genetic variability that arises as raw material for potential NS, the potential for actual NS is reasonably rare in our species.

    No, that’s not some anthropocentrist humans-aren’t-just-other-animal type of argument – we’re the most generalist animal species on the Earth. Human’s most important adaptation is a specialization in being the ultimate generalist.

    Does not appeals much to me the idea that people that were a bit more genetically potentially stronger, or even more intelligent, would have had more children and grandchildren than the others. So I think that, despite of increased variation, it would most likely be things that arose from mutations and just were not harmful enough to be eliminated by NS, not traits that were significantly promoted by NS in detriment of older versions.

    I think that the immunologic variation would be the more likely targets of actual selection, since vaccines and things like that are very recent and restricted, and since large populations are also a fertile terrain for epidemics. And some other few uninteresting stuff, things that wouldn’t make much of a great news report, less interesting than those things of lactose tolerance and the different susceptibility to alcoholic beverage (which has something to do with body size also, if I’m not mistaken. At least for women, that’s the proposed mechanism, I think.)

    And by the way. It was (and still is, sometimes) commonly said that human populations differ more within each other than between each other, even today. I think this statement has or had some empirical basis, rather than being theoretical alone (since intuitively one would more likely expect the opposite). So, that’s wrong, or both affirmations don’t necessarily contradict each other? We may differ more from each other (or was it from people of 5 000 years ago?) than people from 5 000 years ago differed from neanderthals, and yet we have more differences within populations than between populations?

  24. #24 Colugo
    December 15, 2007

    The relationship of the PNAS paper to Clark’s thesis (as well as some others) did occur to me. I, too, have been surprised that there has been so little discussion of the implications of the paper for recent human evolution in cognitive abilities and temperament. Perhaps you could elaborate on this topic for us.

  25. #25 Colugo
    December 15, 2007

    Also, Dr. Harpending, perhaps you could discuss how recent adaptive human evolution relates to phenomena such as D4 dopamine receptor allelic variation,

    http://www.pnas.org/cgi/content/full/99/1/10

    changes in the size and shape of the cranial vault since the Upper Paleolithic, cultural change, and reproductive strategy.

  26. #26 Greg Laden
    December 15, 2007

    Henry! Great to hear from you.

    I’m sure the Middle Ages, as well as WW II and the Plague and lots of other things have left their mark on Europe. Many, many people who live in Europe today came to Europe after these events (depending) and there’s been a lot of other gene flow. Many people from Europe, who’s ancestry was affected by these events, have gone elsewhere to bring their accelerated genetic novelty to places like Australia and Peru and so on.

    I think there are two BIG errors being made here. One is making up shit. Just because one finds (possible) statistical evidence of increased evolution (and I think you probably have that right) does not mean that any idea that happens to fall out of someone’s head (or other body part) is worthy of exposing to the press as an obvious conclusion. You should know better than to assume that the press will not take and run with whatever you feed them. Go test your hypotheses and then come back with something interesting.

    The second big mistake is equating the concept of bounded, fairly static races with an expanding dynamically changing population with increasing rather than decreasing degrees of interaction. I’m not sure who’s been saying that (as supported by your paper) but it’s been around.

  27. #27 Greg Laden
    December 15, 2007

    (Oh, and henry, I assume people were not making the connection between your paper and Clark is because we think there might be some hope for the geneticists, but we know clark, and his neo-social darwinism is a crock of shit. Right?

  28. #28 Colugo
    December 15, 2007

    Greg, I don’t think these kinds of implications (which I do not agree with) are just in the comments to the press. It’s in the paper itself.

    Consider this passage:

    “In our view, the rapid cultural evolution during the Late Pleistocene created vastly more opportunities for further genetic change, not fewer, as new avenues emerged for communication, social interactions, and creativity.”

    …in light of the history of differential population sizes of Africa, Europe, and Asia and differential adoption of agriculture.

    But on the subject of statements to the press:
    http://tinyurl.com/2n37dt

    “”We are more different genetically from people living 5000 years ago than they were from Neanderthals,” said Professor Hawks. “In the last 40,000 years humans have changed as much as they did in the previous 2 million years. …

    Dr Hawks said the value of most genetic changes, including many in the brain, remained a mystery. Some could involve personality, or help our brains be “more perceptive”.”

  29. #29 Henry Harpending
    December 15, 2007

    Everyone has their undies in a bunch about our remarks about evolutionary rate. One audience that was not the least perturbed by these remarks has been agricultural geneticists, who know all about evolutionary rates. They all just said “of course”.

    The so-called “breeders’ equation” is a workhorse of evolutionary biology as well as quantitative genetics. It is taught in AgSci 101. It says the response to selection is the product of the additive heritability and the selective differential. So if the parents are on average 1/10 of a standard deviation higher than the rest of the population on trait x, and if the heritability were 40% (which is a good generic guess for almost anything anyone has ever measured) then the change per generation would be .04 standard deviations. After 20 generations, say 500 years, the change would be .8 standard deviations. This really does mean that a whole lot of evolution can happen real fast over time scales of millenia.

    What on earth is controversial about this??

    And what are Greg Clark’s eugenics proposals?

    Henry

  30. #30 henry harpending
    December 16, 2007

    Oops, sorry, I misread you about Clark–you spoke of his “social darwinism” rather than his “eugenics.”

    I don’t see anything unusual or remarkable about what he says. Greg you remember very well the cottage industry of the 1970s and 1980s showing that wealthy people had higher fitness here, there, and everywhere. How could that process fail to have genetic consequences? It must have, and Clark finally is laying out a hypothesis about what those consequences were.

    Can you propose a scenario in which the differential reproduction would have had no evolutionary effect?

    Henry

  31. #31 Greg Laden
    December 16, 2007

    Henry: You need to demonstrate that the differential reproduction is linked to a heritable trait.

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    January 12, 2008

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