How big was the human population bottleneck? Another staple of theology refuted.

A new paper in Nature by Heng Li and Richard Durbin contains estimates of the “effective population size” of our ancestors at different points in evolutionary time. (Effective population size isn’t the same as census size, as it reflects things like unequal sex ratios—unlikely in our ancestors—or variation in family size, but it’s probably not too far off.)  These are the best estimates of our demographic history to date, as they rest on fewer assumptions than previous methods, and have been validated by computer simulation studies.  They bear not only on what happened when early humans were in Africa and then left Africa, but also on our recurrent discussion of the scientific evidence that absolutely rebuts the Adam and Eve story.

The data come from “coalescent” models—estimates of the time in the past at which two copies of genes from different people, or from the same person, last shared a common ancestral gene form. From these models, data on genetic differences within individuals (i.e., between the two copies of each non-sex-chromosome gene that everyone carries), and estimates of ancestral generation times (25 years in this paper) and mutation rates (rates of change at individual DNA bases), you can work out what the population size of our ancestors was at different times in the past.

The authors made their model from complete genome sequences of six individuals: two Europeans, a Korean, a Chinese, and two Yoruba (a west African group). The figure below pretty much tells the tale: it gives effective population size (on the Y axis) at different times in our species’ history (the X axis shows time before the present on a log scale). The estimates from each individual are represented by different-colored lines, and the key gives the ethnicity of each person.  These data are from “autosomes” (those chromosomes that are not sex chromosomes), but DNA data from sex chromosomes gives pretty much the same result.

The first thing you see is obvious: our ancestors went through two different phases of population “bottlenecking” (constriction): one occurred about three million years ago, when a large population declined to around 10,000 individuals. The authors note that while this may reflect population size decline associated with the origin of hominins after our split with the lineage that produced modern chimps, they also say that this could be an artifact of ancient genetic polymorphisms maintained by natural selection.

The second bottleneck is the one of interest, for it’s the one associated with a reduced population size as humans left Africa.  For the Chinese, Korean, and European genomes, effective population size fell from about 13,500 (at 150,000 years ago) to about 1200 between 20,000 and 40,000 years ago.  Now this is the effective population size, almost certainly an underestimate of census size, but that only makes the problem worse: we never went through a bottleneck of anything near two individuals, as the Biblical Adam-and-Eve story suggests.  This, of course, means that theologians have to scramble to save that story, turning it, as always, into a “metaphor”.  (In science, a falsified hypothesis gets tossed on the scrap heap; in religion, a falsified hypothesis becomes a metaphor.)  And it also suggests that Jesus died for that metaphor.

But enough of Biblical exegesis.  While the bottleneck for non-European populations was probably associated with a group leaving Africa and subsequently colonizing the world, we also see a somewhat less severe bottleneck in the African samples: from about 16,100 people about 100,000-150,000 years ago to 5,700 about 50,000 years ago.  It’s not clear why the populations in Africa bottlenecked as well.

Finally, we also see the population recover in size, with a huge increase  in all populations beginning roughly 20,000 years ago.  This clearly reflects population growth in both Africa and in areas colonized from Africa as humans expanded around the globe.

There are two other interesting points:

  • All the data clearly show that all modern humans,  African and non-African alike, descend from one “homogeneous ancestral population in the last 100,000 years, with subsequent minor admixture out of Africa from Neanderthals.”  This goes against earlier theories that there is a much older divide separating West African from non-African populations.
  • Also contrary to earlier assumptions that after Homo sapiens left Africa (ca. 60,000 years ago) there was little interbreeding between African and non-African populations, the new data show that genetic interchange between these populations continued up until 20,0000-40,000 years ago.  This conclusion, though, is provisional because it depends on estimates of mutation rates which are necessarily indirect.

The upshot and the lesson for the science/religion debates: we now have a pretty good estimate of how many ancestors our own species had at various times in the past, all the way back to near when we diverged from the lineage leading to modern chimps.  And the lesson for theology is the usual: science has shown that scripture is wrong, so yet another Biblical “truth” becomes a metaphor.

Science continues to invalidate the claims of faith.  First special creation went by the board, so theologians—at least the rational ones—were forced to show that of course God would have used evolution to fulfill his Big Plan to Produce Humans.  Now Adam and Eve have also become metaphors, leading to all kinds of humorous theological speculations about who were humanity’s parents and what, exactly, was the nature of their Original Sin.  Next on the agenda are morality and free will, staples of religious doctrine but items that are starting to be explained purely by science.  We now see morality as having a purely secular origin, perhaps involving evolution; and we don’t really have the freedom of choice envisioned by many faiths.

All of this shows that science is dominant to religion, for when they clash, as they inevitably must, “sophisticated” theologians must frantically revise their doctrines to comport with scientific truth.  And they hate that. This innate recognition of the precedence of science over faith is, I think, one reason why so many religious people and faitheists are picking at science, claiming that the methodology of science is based just as strongly on faith as are the “truths” of religion.  But if that were the case, why does religion inevitably bow before science?

________

Li, H. and R. Durbin.  2011. Inference of human population history from individual whole-genome sequences.  Nature 475:493-497.

48 Comments

  1. Frank
    Posted September 18, 2011 at 7:35 am | Permalink

    “But if that were so, why does religion inevitably bow before science?”

    Because, deep down, the religious apologists and science critics KNOW that science is not a faith-based enterprise after all. They take that philosophical stance lately out of desperation. If religious leaders and defenders claim the Earth is flat for TOO long after it has been proved to be round (approximately!), they know that their members who receive any decent sort of education will start to wonder: “Let’s see, my religion was completely wrong about this particular point, … what ELSE were they wrong about?”

    (Of course the question at the end of Professor Coyne’s post was mainly rhetorical.)

  2. Eddie Janssen
    Posted September 18, 2011 at 7:44 am | Permalink

    And then, there is ofcourse the Flood bottleneck…

    • Achrachno
      Posted September 18, 2011 at 8:38 am | Permalink

      Yes, just 4300 years ago. How could this study possibly have missed that? I can think of one way.

  3. Mattapult
    Posted September 18, 2011 at 7:47 am | Permalink

    The two bottlenecks in the study confirm the two in the Bible: Adam and Eve, and Noah and his family. See, science matches what the Bible says *exactly*

    • Torbjörn Larsson, OM
      Posted September 18, 2011 at 8:17 am | Permalink

      I think that argument passed too many bottles, necked or not.

    • Achrachno
      Posted September 18, 2011 at 8:59 am | Permalink

      The earth was repopulated by 8 survivors from one family that time, apparently Noah and his wife plus 6 children. I don’t remember any mention of inlaws or cousins — but I don’t have a Bible handy.

      The meaningful bottleneck is thus just two people again, since whether children are born before or after the flood should have no effect on their genetic diversity. The children are still only going to get whatever the parents had. Floods don’t cause a lot of mutations, right?

      Just 4300 years ago remember!

      Does Liberty U. have a genetics program?

      • Sili
        Posted September 18, 2011 at 10:44 am | Permalink

        The earth was repopulated by 8 survivors from one family that time, apparently Noah and his wife plus 6 children.

        No. Three sons and their wives.

        • Achrachno
          Posted September 18, 2011 at 12:20 pm | Permalink

          Ah! I shouldn’t work from my dim memory. Thanks, Sili.

          That increases the size of the bottle neck to five people, assuming the wives were unrelated to each other.

    • Circe
      Posted September 18, 2011 at 1:18 pm | Permalink

      There is just the slight problem with the Sumerians, the Indus Valley People and the Mesopotamians, who all vehemently disagree. See this for a report on the anger in Sumeria: http://www.theonion.com/articles/sumerians-look-on-in-confusion-as-god-creates-worl,2879/

  4. Rob
    Posted September 18, 2011 at 8:12 am | Permalink

    Unfortunately, since the project of theology consists entirely of just making stuff up, this new information will have no effect on the dogma.

    Witness Edward Feser’s recent adorable example. NO, no, no silly Professor Coyne, when the bible speaks of human beings it is not referring to those animals with just human bodies, but to those human bodies that at some time in the past a god swooped down and magically injected with a soul. The recent article linked by TOF is just as asinine.

    If a person is willing to go to such ridiculous and elaborate contortions, then all reasonable discourse is impossible. Such a person has disqualified himself from the conversation.

    Facts just do not matter to such people. They will construct ever more layers to their crumbling worldview in order to insulate their deeply held belief.

    It is a sad a pathetic display. But an all too human one.

    • Claimthehighground
      Posted September 18, 2011 at 12:37 pm | Permalink

      And of course, none of us has read enough books about this, in which the theists have clearly set out the proofs which we so ignorantly bypass. ‘Tis a fools game, made up by fools.

    • Kieran
      Posted February 18, 2012 at 7:16 am | Permalink

      As a Catholic I find your statement, along with numerous other statements on this page, annoying due to the pure ignorance that it shows. It was people like you that argued originally that Big bang Theory was not true purely because it was a Catholic priest which created it.

      • Posted February 18, 2012 at 7:46 am | Permalink

        And overwhelmingly atheist scientists who did the math and the observations and concluded that the Big Bang Hypothesis was supported, regardless of the (irrelevant) religious flavor or the proposer.

        Ironically, a group of other Christians are arguing that it could not possibly be true because their unique interpretation of the Bible says it isn’t.

        If the Christian god exists then he is hopelessly inept at getting the meaning and of the message across to his followers.

  5. Torbjörn Larsson, OM
    Posted September 18, 2011 at 8:15 am | Permalink

    And it also suggests that Jesus died for that metaphor.

    Since, as Ben Goren use to remind us the Jesus character is neither historical nor showing the historical footprint he should have, and as Jeffrey Coyne use to remind us the Jesus character is neither natural in life (XY zygote without Y gamete) or in death (zombie), I can only read that as

    “it also suggests that this metaphor died for that metaphor.”

    “Died” metaphorically speaking of course!

    • Posted September 18, 2011 at 10:33 am | Permalink

      Well, no Christian will ever acknowledge that the Jesus story is just a zombie snuff porn fantasy for the simple reason that, in doing so, said person will stop being a Christian (by definition).

      So, you either have Christians who believe in a literal Zombie of Zion who wandered Jerusalem demanding gut gropings but who think various other fantastic bits of the Bible are “metaphor,” or you have non-Christians who’re mature enough to understand that none of it is any more real than Beowulf (and nowhere near as wholesome).

      Cheers,

      b&

      • sls
        Posted March 1, 2013 at 3:15 pm | Permalink

        Actually, I consider myself a Christian, and I believe the bodily resurrection to be ridiculous — why would a spiritual, immortal entity concern itself with flesh that is designed to die? The Virgin Birth falls along that same line.

        I also have always assumed Adam and Eve and the Flood to be silly myths.

        Most of us don’t really buy that whole “literal truth even when it flies in the face of observable fact” crap.

    • Posted September 19, 2011 at 3:27 am | Permalink

      Who is Jeffrey Coyne?
      Is he the real JC?

  6. ChasCPeterson
    Posted September 18, 2011 at 8:50 am | Permalink

    we never went through a bottleneck of anything near two individuals, as the Biblical Adam-and-Eve story suggests.

    I continue to find this line of argument perplexing. That is NOT what the A&E story suggests! It states explicitly that the human species started with a single couple (plus maybe those mystery wives).

    Bottlenecks in an existing species/population are irrelevant to the question of origin.

    To test the A&E narrative, it seems clear to me that what we would need to know is the size of the original allopatric subpopulation that started the separate lineage leading to Homo sapiens. But that should be plural. It could be argued that we would need to look at all of the speciation events that gave rise to our single extant species, i.e. the split of H. sapiens from H. habilis, then the split of the h/s lineage from H. erectus (or whatever), etc. (through the Ancestor’s Tales until we all agreed we were out of ‘human’ territory). Only if it can be shown that all of these initial isolated subpopulations numbered more than two could the A&E story be scientifically tested. And of course we will never know (recover/reconstruct) enough of our own true phylogeny to even count the number of these subpopulations, let alone quantify their sizes.

    Waterloo, athiests!!!!1!!

    [Of course I do not believe in anything like the A&E myth, but I am serious about the--perceived, ny me--irrelevance of Dr. Coyne's oft-repeated argument-from-bottleneck-size.]

    • ChasCPeterson
      Posted September 18, 2011 at 8:56 am | Permalink

      It occurs to me that perhaps the statistical models of gene coalescence applied here could perhaps be extended to include other extant apes? Probably confidence limits get much wider as you extrapolate backward, so it might be tough to make robust conclusions, but it’s maybe worth trying?

    • Posted September 18, 2011 at 10:24 am | Permalink

      But that should be plural. It could be argued that we would need to look at all of the speciation events that gave rise to our single extant species, i.e. the split of H. sapiens from H. habilis, then the split of the h/s lineage from H. erectus (or whatever), etc. (through the Ancestor’s Tales until we all agreed we were out of ‘human’ territory).

      You need to re-read Jerry’s article at the top. This study did exactly that. Specifically:

      The upshot and the lesson for the science/religion debates: we now have a pretty good estimate of how many ancestors our own species had at various times in the past, all the way back to near when we diverged from the lineage leading to modern chimps.

      Cheers,

      b&

    • Posted February 18, 2012 at 7:53 am | Permalink

      You seem to be forgetting the Flood Myth, where the entire human population was reduced to less than than 10 people and then repopulated the entire world in the space of a couple of generations. Even my guppy fish can’t do that.

  7. Bernard Leikind
    Posted September 18, 2011 at 9:37 am | Permalink

    I see the local population minimum around 3 m years ago, and I see the minimum around 20,000 or 30,000 years ago.

    I see three minimums. Why is the broad minimum around 300,000 or 500,000 years ago not worthy of discussion?

    It looks to be at a lower population and to have lasted about as many years as the 3 m year minimum.

    The horizontal axis is logarithmic. Hence the apparently broad minimum around 500,000 years ago and the apparently shorter one at 3 million years ago are roughly the same duration and the same number of generations.

    Each of the older bottlenecks lasted many more generations than the recent one. The logarithmic scale distorts this aspect.

    You refer to the graph as if it had one value, the effective population, but there are six lines. Does each line have its own effective population, which you combine as a single average?

    • Gregory Kusnick
      Posted September 18, 2011 at 11:48 am | Permalink

      Why is the broad minimum around 300,000 or 500,000 years ago not worthy of discussion?

      Perhaps because it’s not of the same depth as the others. The 3 million year minimum goes from off the charts to around 10,000, a decline of 80-90% or more. The 20K minimum for the out-of-Africa group is another 90% drop. By contrast, the 500K minimum represents a decline of maybe 50% from the previous peak.

      As for the six lines, they represent the ancestral populations of six modern individuals. Where the lines converge, they had the same ancestors, hence the same population size.

  8. Posted September 18, 2011 at 9:41 am | Permalink

    Razib Khan discussed the Nature paper here: http://blogs.discovermagazine.com/gnxp/2011/07/what-one-or-more-genomes-can-tell-us/

  9. Posted September 18, 2011 at 9:51 am | Permalink

    Two more links if I may — I can’t find much discussion of the Nature article, which is of course paywalled:

    http://www.sciencedaily.com/releases/2011/09/110907171533.htm

    http://dienekes.blogspot.com/2011/07/human-population-history-from-single.html

  10. Keith
    Posted September 18, 2011 at 10:23 am | Permalink

    Is anyone else having trouble downloading the supplement to this Nature article? My institutional account works for the main article, but I’m interested in the references used for the “true history” data illustrated in Figure 2 (which I assume are in the supplement). Perhaps someone here already knows?

    • Keith
      Posted September 18, 2011 at 12:23 pm | Permalink

      Oh, nevermind. I see it now; these are simulated data, and true history is the control for the bootstrap.

  11. Posted September 18, 2011 at 2:51 pm | Permalink

    ( subscribing )

  12. MadScientist
    Posted September 18, 2011 at 3:15 pm | Permalink

    “… “sophisticated” theologians must frantically revise their doctrines to comport with scientific truth. And they hate that.”

    I wouldn’t say they hate it. This is just another day at work for them; they love playing this game because they think they’re so clever in the way they delude themselves by making up a convoluted story which purports to show how their religion predicted or supported a scientific discovery. They then proceed to pervert the truth – for example, see how the catlick church claims it “supports evolution” but when you ask what they know about evolution you get bizarre statements which have nothing to do with evolution.

  13. ToLo
    Posted September 18, 2011 at 5:21 pm | Permalink

    Please proofread your submissions once at least to catch oddities like the typos in your all important numbers. It would be nice to not have to guess what you mean, and I don’t think you want to offer the least ammo to theologists . . .

  14. JG
    Posted September 18, 2011 at 6:14 pm | Permalink

    I’m just subscribing to comments — seems no way you’re allowed to do this without inserting a comment!

  15. Posted September 18, 2011 at 10:15 pm | Permalink

    You’ll need to go much further back in time to find (chromosomal) Adam and Eve:

    Francisco J. Ayala and Mario Coluzzi
    Colloquium Paper: Systematics and the Origin of Species: Chromosome speciation: Humans, Drosophila, and mosquitoes
    PNAS 2005 102:6535-6542; published online before print April 25, 2005, doi:10.1073/pnas.0501847102
    http://www.pnas.org/content/102/suppl.1/6535.full

    There is more information in the “Speciation” section of the theory here:

    Google Viewer:
    https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxpbnRlbGxpZ2VuY2Vwcm9ncmFtc3xneDo1NWEyNjA2NzZmN2NiNTEx

    MS Word document:
    http://sites.google.com/site/intelligenceprograms/Home/TheoryOfIntelligentDesign.doc

  16. Duane
    Posted September 18, 2011 at 10:46 pm | Permalink

    A question: Is it possible for me (for example) to locate a living individual who’s most recent shared common ancestor with me is 60,000+ years in the past?

    • Bill Gilliland
      Posted September 19, 2011 at 6:48 am | Permalink

      Think about what such an individual would represent, and you should be able to answer your own question — you and 60K would both have family trees that are totally non-overlapping and go back for over 3000 generations.

      About the only place you could find such potential individuals would be pureblood aborigines from places like Australia. A little googling says the first individuals arrived there about 68,000 years ago.

      That is assuming no additional migrants (in either directions) since then.

  17. Posted September 19, 2011 at 5:12 am | Permalink

    But if that were the case, why does religion inevitably bow before science?

    Because Scientific Inquisitors go around accusing dissenters of heresy and strap them to various medieval torture devices until they confess to practicing scientific witchcraft. Science isn’t more valid: it’s just used the principle of “might makes right” to make people think it’s a valid epistemology.

    Oh wait, no. That was Catholicism. And it’s still losing. Never mind.

  18. Posted September 19, 2011 at 8:44 am | Permalink

    Looks like the neutral mutation rate is now believed to be much smaller than what was used in the paper. So all the dates will become older than reported. Biased sex-related demographic events might also play a role. The X chromosome is just different autosomes.

    • JG
      Posted September 19, 2011 at 8:48 am | Permalink

      Looks like the neutral mutation rate is now believed to be much smaller than what was used in the paper.

      Do you have a reference for this? (Interested to read more, not snarking.)

    • derekw
      Posted September 21, 2011 at 8:37 am | Permalink

      Such uncertainty in the mutation rate and even even generational times as being main factors in the ‘coalescent’ models calls into question any dating output. A key impact is obviously any correlation (or de-correlation) between these dates and the understanding of the current hominid fossil record.

  19. Mark Erickson
    Posted September 19, 2011 at 9:31 pm | Permalink

    Nice job: “In science, a falsified hypothesis gets tossed on the scrap heap; in religion, a falsified hypothesis becomes a metaphor.”

    Since you made this pithy statement parenthetically, I assumed you borrowed it from somewhere. But I did a basic Google search (science+religion+metaphor+hypothesis) and I can’t find anything with all those words in a continuous stretch of text.

    So, bravo! For both your wit and originality.

    • Kieran
      Posted February 18, 2012 at 7:24 am | Permalink

      Can you explain to me why Enviromental scientists look for evidence that backs their own theorys rather than look at all evidence and reason, most weather stations are in cities which are warmer than countrysides, different types of weather measurement disagree with rising temps. Also the arrogance shown here makes relgious people dislike your message even more. Insulting people makes it less likely that they will accept you.

  20. Posted September 20, 2011 at 11:45 am | Permalink

    I have to thank you too eveysolara!

    This would certainly move the first bottleneck Jerry mentioned (where the authors of the paper noted a possible artifact) that I’m interested in appearing at 3 mya into the 6 mya region where I would expect it to be (to correlate with other lines of evidence) and going off the chart just prior to that event would make sense where the baseline and/or span rises just before resolution is lost.

    Now I have to wonder what a head to head telomeric fusion that produced some rearrangement of the chromosome territories might produce for sudden genetic change in generations that soon follow, to possibly help resolve the baseline at the far end and explain what the authors of the paper noted may be a possible artifact. With so little known about chromosome speciation it’s probably still an area that needs more research before anyone would know more, but I thought it would be worth mentioning.

    • psybird
      Posted September 25, 2011 at 6:30 am | Permalink

      That chromosomal change has always puzzled me. Presumably it happened only once. But in that case, how did the individual breed with anything nearby, or even with anything at all? Theoretically the offspring should have been human “mules” – sterile.

      • Posted September 25, 2011 at 12:42 pm | Permalink

        Excellent question psybird! Even though it is generally believed that all mules are sterile, that is not always true. And in the case of human chromosome speciation it would not be the result of combining two relatively different genotypes to produce a third, an interspecies. The replicative machinery would only have a fusion to handle, which it is already for the most part adapted for coping with.

        Since I would like to know more about the systems biology of the process as it pertains to human origin that would certainly be a good question for Jerry Coyne to in more detail answer in a future article.

  21. HP
    Posted September 20, 2011 at 2:47 pm | Permalink

    First special creation went by the board…. Now Adam and Eve have also become metaphors…. Next on the agenda are morality and free will….

    You left out the Prime Mover/First Cause of the theological cosmological argument, currently threatened by extinction due to quantum mechanics. (Why should biologists have all the fun?)

  22. BCoppola
    Posted February 6, 2012 at 9:51 am | Permalink

    “Two Europeans, a Korean, a Chinese, and two Yoruba walk into a bar…”

    (sorry)

  23. Chris Watson
    Posted October 26, 2013 at 7:08 am | Permalink

    A couple of things here:

    1) The population bottleneck presents a parallel of the worldwide *Flood* story – worldwide as in anecdotal cultural and historical reports across the Earth – even if taken as an allegory, this fits the model of a larger group that founds the basis of all of humanity today.

    2) The recent comparison of chimp and human DNA in National Geographic (http://bit.ly/Hbhzba) shows that a bottleneck stabilized the genetic diversity of the human race post-bottleneck. That does not preclude a greater diversity and variety beforehand.


6 Trackbacks/Pingbacks

  1. [...] – Jerry Coyne (University of Chicago) [...]

  2. [...] How big was the human population bottleneck? Another staple of theology refuted. (whyevolutionistrue.wordpress.com) [...]

  3. [...] human couple like the fictional Adam and Eve – which is explained in simpler language here). As the PEW forum on religion and public life notes, All but a small number of scientists regard [...]

  4. [...] a population bottleneck of only three couples (Noah doesn’t count, the three sons do) is just not genetically possible. There is also no geologic evidence for a global flood while humans [...]

  5. [...] doesn’t even remotely support that humanity came from two people or eight.  You can look at this article and see how wrong our Christians [...]

  6. [...] any documentation for it.  He has attempted to claim that this article reviewed by Dr. Coyne over at Why Evolution is True doesn’t have anything to do with population bottlenecks.  That’s quite a denial of [...]

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