Natural selection in our species during the last two millennia

October 18, 2016 • 11:30 am

A question I’m always asked in popular lectures on evolution is this: “Are humans still evolving?” The answer I give is “Yes, but we have good evidence for such evolution in only a handful of traits: evolution of earlier reproductive maturity in females, later menopause, and selection for reduced blood pressure and a few other traits related to heart disease.” That is based on longitudinal studies of human health over decades, observing changes in these traits and presumed estimates of the genetic basis of their variation.

Now, however, we can, by DNA sequencing, look at DNA directly, and with some fancy statistical footwork, get an idea of which genes have changed in frequency so fast that they must have been due to positive natural selection. That’s the subject of a new paper in Science by Yair Field et al. (reference and free download below).  The authors conclude that several traits, including lactose tolerance, hair and eye color, and parts of the immune system, as well as height, have evolved within the last 2,000 years.

A short primer on how they did it. The authors looked at 3,915 sequenced genomes in the UK population trying to find evidence of recent selection. How does that work? Well, if a rare allele suddenly becomes favorable, it will rise quickly to high frequencies, dragging along with it the DNA in regions adjacent to the selected sites (recombination wouldn’t have time to separate the selected site from adjacent sites on the chromosomes, since recombination is rare between closely spaced bits of DNA). This means that a region of the genome around a recently selected bit of DNA would be genetically depauperate compared to the same stretch of DNA that isn’t around a selected nucleotide.  Then, if you look at variable DNA sites in that region, where more than one base pair is segregating at a single site, regions around a selected site would have fewer such “singletons” because they’d be genetically homogenous. And that, in turn, would mean that in regions near selected bits of the DNA, the distance between “singleton” (variable) sites would be larger than in alleles not subject to recent positive selection, since selected forms of genes would be linked to fewer variable singletons.

The authors figured out the statistics of the distribution of the inter-singleton-site distance in the sequenced genomes compared to alternative “alleles”, looking for those regions that showed significantly longer inter-singleton distances around a site that differed between forms of a gene, and thus a site that might have been subject to selection. That indicates that, with all probability, the target site between the singleton DNA bases rose to high frequency fairly recently.

How recently? The authors say that their method is best at detecting selection events (“sweeps”) in the last 2,000 years (about 75 or fewer generations). What did they find? Here’s some figures showing those genes (and traits) whose statistics indicate they were subject to selection during roughly the last two millennia.

Lactase persistence: the gene for digesting lactose, lactase, is usually turned off at weaning. In “pastoral” populations—those that keep sheep, goats or cows and drink their milk—there’s strong selection (a roughly 10% reproductive advantage) to keep the gene turned on, giving you a rich source of nutrients. And that gene shows recent signs of selection (see the longer distance between singletons around the A/A “lactase persistence” allele compared to the alternative heterozygote [G/A] and non-persistent [G/G] form). We knew this in fact from other data over the past decade, but it’s reassuring to see it with these authors’ statistics:


Genes associated with pigmentation. Although the loci for skin color, presumably subject to selection for light skin in northerly climates, didn’t show a significant signal of selection, other genes associated with pigmentation, like blond hair, freckling, blue eyes, and so on, did. The four dark boxes are highly statistically significant, and if you combine all the data, the probability that this association is due to chance is miniscule: 0.000000003. Lighter pigmentation was selectively favored in the British sample. There are several theories of how such selection works, but I won’t go into them now.

screen-shot-2016-10-18-at-10-37-06-amGenes for becoming taller. Here’s a plot of the distance between singletons for height increasing alleles (combined across several genes thought to be involved in height) compared to alternative alleles that make you shorter. Although the displacement of the graphs looks minor, the probability that the distributional difference occurred by chance is 0.000000000001.


The Major Histocompatibility region, involved in the immune system, is subject to “balancing selection”, with individuals having two forms of a gene deriving a selective advantage, presumably because they have a more responsive immune system. This, too, inhibits recombination around each selected allele, increasing the inter-singleton distance. This locus also shows highly significant differences from other regions.

Other genes. Finally, there is a host of other genes that give suggestions of having been recently selected: genes or “polygenic” (several-gene) traits. The traits or genes with the purple dots show significantly longer inter-singleton distances, but the authors are a bit less willing (except for height in both sexes) to say these genes and traits were subject to selection because there’s a problem of population structure (non-random mating across the entire group) that could make these differences appear more significant than they are. But here’s the figure just to show you what might have been selected (the pluses and minuses show the direction of evolutionary change).


The upshot: In the last 2,000 years, there’s good evidence that lactase persistence and lighter pigmentation have been positively selected in the British sample of genes, that the MHC complex has been under balancing selection, and that the UK population  has been selected to get taller (you can devise your own explanations for that). Along with the putatively selected traits in the figure just above, this considerably expands the list of characters that have been selected in our species in recent centuries. Anybody who claims that human evolution has stopped is simply talking nonsense.


Field, Y., E. A. Boyle, N. Telis, Z. Gao, K. J. Gaulton, D. Golan, L. Yengo, G. Rocheleau, P. Froguel, M. I. McCarthy, and J. K. Pritchard. 2016. Detection of human adaptation during the past 2000 years. Science. Published online, 13 OCT 2016, DOI: 10.1126/science.aag0776

58 thoughts on “Natural selection in our species during the last two millennia

  1. I’m happy the fair skinned are reproducing since we’re told how yucky we look (happened to me as recently as a month ago by a total stranger) so often, you’d think we’d never see any action.

      1. My favourite companion on Doctor Who is Martha because of her spunk in telling the Doctor to call her and leaving him. But, I always liked Amy because she was pale but still wore skirts with bare legs!

    1. Diana, I hope you applied serious pressure to damage the generative capacity (a ‘reverse Trump’) of this oafish stranger

    2. That stranger was definitely weird!

      As for the fair-skinned phenotype, maybe you have read rants by European white racists about how it would soon disappear under the influence of non-European immigration.
      I think that if these racists want to portray a scary future, there are more suitable things to fear. With the persistent inability of Europeans to take care of themselves, and the increasing reluctance of Americans to babysit them, I can imagine a collapse in Europe comparable to the Fall of Rome. Then, health care as we know it will disappear, nutrition will deteriorate, fair skin in northern regions will become as advantageous as it was 2,000 years ago, and natural selection will enforce it.

  2. I don’t doubt that human evolution continues, but I can’t help wondering if the premise of Idiocracy could actually come true due to the environment we’ve created for ourselves no longer favoring intelligence as a contributor to survival and reproduction.

    1. Incidentally, if you browse the Trivia section of the Idiocracy write-up on IMDB you’ll find this:

      “Upon its initial release, writers Mike Judge and Etan Cohen insisted that they did not intend for the film to be a satire of modern life. However, the writers changed their tune over a decade later. Due to a particularly contentious and unpopular presidential campaign season in 2016 and social developments in the United States, Judge and Cohen admitted on social media that they fear that portions of their film are coming to fruition.”

      1. There’s a Cracked video on Youtube that makes the case that the society in Idiocracy is utopian compared to ours. They know they are stupid, and they are trying to fix that.

        In any case, I think stupidity is largely learned, rather than genetic, so we don’t really need to fear a Marching Morons scenario.

  3. I don’t see any practical advantage of being taller unless you’re a basketball or football player. It seems that many (most?) women prefer taller men, so could it be sexual selection at work? Or perhaps women don’t really prefer taller men, but rather prefer a man that is taller than them. But isn’t it also true that tallness is a byproduct of better nutrition? Evolution presents many puzzles.

    1. I suppose that being taller brings more absolute strength, while being shorter is advantageous when resources are scarce.

      It is true that women – at least the ones I know, myself included – prefer a man who is taller than them. But not too tall! Actually, I guess that until very recently (and in the Third World, even now) guys too tall for you were hazardous for your health/life, because an infant with size determined partly by the father’s genes had to pass through a pelvis with size determined entirely by the mother’s genes.

    2. Being taller provides greater reach, which I believe can be (but is not always) a significant advantage in one-on-one combat.


      In the last 2,000 years, there’s good evidence that lactase persistence and lighter pigmentation have been positively selected in the British sample of genes

      The pigmentation issue seems easy; the British isles were subject to multiple invasions from Scandinavians, Danes, etc.

      A bigger question is probably why this pigmentation continued to spread after direct invasions and rapine stopped. Though even in the last few hundred years, I guess there may be social selection for marrying rich and high status colonialists over others.

    1. I think it is. And it is often bizarre. Men seek a combination of almost incompatible traits (such as “slim body, large breasts”) while women fall for individuals such as career and war criminal Arkan:

      “Željko Ražnatović fathered nine children by five different women” (Wikipedia).

  4. I know it’s in the weakly supported portion but how could increasing infant head circumference be selected/favored? When choosing a mate you don’t know what the offspring will look like. Perhaps it’s because of improved medical support that helps both mother and big headed baby survive a difficult delivery and therefore pass on the pumpkin-head genes. There are limitations to how large an infants head can be for vaginal birth. Is the increasing hip size apparently seen in women a response to the infant head increase? This is complex and fascinating stuff.

    If I were a woman, a tiny skull would be near the top of my mate selection criteria. If that logic held for all women, Jay Leno would die a virgin.

    1. Medical intervention might be too modern to show much evolutionary effect.

      It would seem to make more sense from the mothers’ point of view to chose a mate with a small head since that would reduce the chances of death during childbirth and hence increase the chance to have more children.

      Male reproductive strategies might differ. From the male POV the longer the child develops in the womb the better, hence the placenta, which is coded for by DNA inherited from the father.

    2. If that logic held for all women, within a few generations our brains would be too small to understand that logic.

      1. Maybe. But my point is that the pigmentation and lactase persistence changes, the most conspicuous examples, reflect continuing adaption to latitude and dairy farming, which is concentrated in Europeans. This would give a misleading view of selection pressures on humans overall.

    1. Using the same SDS method:

      Global shared natural selection for increased stature in recent human history

      “In agreement with earlier studies, we find that selection for increased height has recently elevated in Northern Europe. However, surprisingly, we find that all examined populations, independently across continents (Africa, East Asia and Europe), had experienced detectible selection for taller stature.”

      The East Asians are Han, Japanese, Dai, Kinh Vietnamese. Other Europeans are Finns, Italian, French, Spanish.

      This is over 7,000 years though. Not 2,000. We shall need the Chinese 10K Genomes to check that timescale out.

  5. Fascinating. Now I do not have time to parse the technical details right now, and perhaps b/c of that I am left with the possibility that some of these could be due to strong genetic drift from fluctuations in population size. How can one tell the difference between expansion of a locus in a regional population due to selection versus expansion of a locus due to a bottleneck effect or the founder effect in that region?

  6. It’s always interesting to read about examples of positive selection in humans. However, the vast majority of changes in the frequency of alleles is due to random genetic drift acting on nearly neutral alleles.

    Of course humans are still evolving. You can’t stop random genetic drift. Our species is always evolving even if there’s no selection.

    1. Assuming by “thing” you mean “population”, then it might be the case to the extent that selection keeps the gene pool from changing significantly. Like coelacanths, perhaps?

      1. I should maybe re-phrase the question so as not to get into specific rare species and so forth. Is there any evidence that normal living animals or plants have stopped evolving (changing in any way genetically? I mean, the question, are humans still evolving would require a yes answer unless great evidence would prove otherwise.

        1. Not only is there no evidence, it’s theoretically impossible unless the entire genome is under constant, invariant, and fairly strong stabilizing selection. If any least bit of the genome is close enough to neutral for drift to occur, it will.

      2. Coelacanths and a few other species are often used as examples of ‘living fossils’. But coelacanths they have visibly changed over the past 70 million years. It is likely that they have also changed in ways that are not easily visible, since everything changes.

        1. Everything changes, but not everything changes at the same rate. Selective pressures can work to make populations change rapidly. But they may also work to maintain a “feature set” by reducing variation. At least that is my understanding for why certain creatures exhibit great stability over long periods of time.

  7. Mr Coyne, Have you read the 10000 Year Explosion by Gregory Cochran & Henry Harpending? I was impressed by it until I got to the section about Ashkenazi Jews and found it taking a bizarre turn.

  8. Is this really ‘natural selection?’ If human sexual selection/decision is the prime mover (which seems like it could be argued for fairer skin and tallness; maybe not so much for lactase gene) isn’t this more akin to ‘artificial selection’ or ‘selective breeding’?

    1. Sexual selection isn’t selective breeding in the same sense as, say, eugenics is. When we choose an attractive mate, we’re (usually) not doing it with the deliberate intention of creating offspring with specific attributes.

      But even if we were, it would still be natural selection in the broadest sense. That is, genes that help organisms succeed are selected for, even when human preferences form part of the selective landscape.

      1. Seems with this line of reasoning one could portray humanity’s effect on environment and resulting selection (eugenics, hunting animals to extinction, global warming contribution etc) as ‘natural selection’ at least in the broadest sense?

        1. Well, I suspect that mass extinction (whatever the cause) involves a large component of luck as well as selection.

          But apart from that, sure: when an invasive species colonizes a new environment, it creates new selection pressures to which native species must adapt or die. I don’t see why we should call that process something other than natural selection when the invasive species happens to be us.

          Calling it natural doesn’t mean it’s ethically justified, if that’s what you’re getting at.

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