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Gene Expression Blog

Citation: Racimo, Fernando, et al. "Evidence for archaic adaptive introgression in humans." Nature Reviews Genetics 16.6 (2015): 359-371.

Citation: Racimo, Fernando, et al. “Evidence for archaic adaptive introgression in humans.” Nature Reviews Genetics 16.6 (2015): 359-371.

41ePHetk1dL._SY344_BO1,204,203,200_Nature published a paper recently, New species from Ethiopia further expands Middle Pliocene hominin diversity, which seems to complicate the deep history of the hominin lineage. More precisely, it gets curiouser and curiouser, as the number of human(ish) groups proliferates. Honestly I don’t know well this will hold up, a lot of science seems to fade out. Remember the article in Science, A New Kind of Ancestor: Ardipithecus Unveiled? I’m not totally clear on whether the controversy about this find has resolved. At least we’re at the stage where most people seem to accept that Homo floresiensis was a true hominin lineage, rather than a pathology. (by the way, Carl Zimmer has a good write up on the most recent addition to the human family tree)

Genes are something that is more concrete to me. Nature Reviews Genetics has two pieces of interest in this domain. First, Evidence for archaic adaptive introgression in humans. A close reader of this weblog will find little of surprise; the authors do an excellent job of reducing down the key results of the past five years or so that have issued from the discovery that the ancient whole genome of the Neandertal bears all the hallmarks of having been carried over into some lineages of modern humans. In particular, the authors focus on adaptive alleles and regions through a statistical genomic lens. Second, Svante Paabo has a comment in the same edition, The diverse origins of the human gene pool (ungated), which leans heavily on the previous piece.

51r8Ph-vcaL._SY344_BO1,204,203,200_ Paabo to me seems to finally put to bed some old conflicts which have been roiling the field of paleoanthropogy for decades. I think we’re going to finally see the abating of the rhetorical war between those who promote “Out of Africa” vs. “Multi-regionalism.” The fact is in some ways both viewpoints are worth taking into account. As Paabo, and others, have noted, the former model turns out to likely be correct about the provenance of most recent human ancestry. It is mostly derived from an African or near-to-African (e.g., in the Middle East) population on the time scale of ~100,000 years. But, the latter model’s emphasis on regional evolution and adaptation and gene flow across a meta-population system is also a critical insight in understanding the dynamics of how modern humans came to be.

I do like the fact that Paabo also seems to moving past the idea that genomics will yield the one allele or set of alleles that define what made modern humans so biologically special. I don’t have an opposition to biology as being determinative in our cultural flexibility. But, if anything has been clear in what genomics is telling us about recent human evolutionary history, it’s that it is rather more complicated than we might have imagined. I doubt the uniqueness of the surviving lineage of hominins is going to be any more, or less, subtle in the difficulties of resolution.

I do have one bone to pick with Paabo. He states that:

Adaptation through the acquisition of new mutations is generally a slow process: it is rare for favourable alleles to appear, and these are often lost by chance when they first occur in a single individual or in very few individuals. By contrast, if favourable alleles have emerged in one group, they can spread to other groups relatively rapidly by gene flow. This process, called ‘adaptive introgression’, is well documented in bacteria and plants, and described in some cases in animals but it has not previously been considered an important factor in human adaptation.

The idea of “adaptive introgession” has been something I’ve been thinking about, and talking about, in relation to human evolution since 2006 (Google it). That’s because of the focus that Greg Cochran, Henry Harpending, and John Hawks, put on the topic (all these years later I am also professionally interested in this topic, but that’s for a later post!). Now, it is true that Svante Paabo does not seem to have thought of the issue in much detail. His book Neanderthal Man has no references to “adaptive introgression” according to Google Books. In contrast, 10,000 Year Explosion has 9 mentions of the term.

introgress I will note that the authors of the review paper that Paabo leans on heavily for his comment don’t make this omission where credit is due. They cite both Greg Cochran and John Hawks, with a special laudatory note.

Finally, I want to suggest that to a great extent, Multi-regionalists excepted, the previous consensus in human evolutionary studies tended to overestimate the extinction rate of “archaic” lineages. But, it also underestimated the extinction rate of modern lineages. That is, archaic lineages rooted outside of Africa before ~100,000 years ago may play more of a role in the evolution of our modern lineage than we may have guessed when it comes to both genotype and phenotype. Paabo quotes the standard figures of a few percent for Neandertal ancestry, and ~5 percent of Denisovan among Oceanians. From all I have heard and know this seems about right, but I do wonder if this is actually just a floor. Without ancient genomes I suspect we’d still be debating the possibility of archaic admixture from inferences which only statistical genomicists would have a good grasp of. In 2006 Jeff Wall and Michael Hammer stated that “Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools.” They were basically dead right. Second, the ancient DNA is also yielding the conclusion that many local populations which flourished during the Pleistocene outside of Africa seem not have to left much genetic legacy today in the same regions. We’ll get more clarity on the topology of the human phylogeny in the near future, but it strikes me that it’ll exhibit features which are somewhat at variance with what we’d have expected 10 years ago.

• Category: Science • Tags: Paleoanthropology 


41gl5ENbKZL._SY344_BO1,204,203,200_ Today on Medium I saw a post, Shouldn’t We Fix Poverty Before Migrating to Mars? The substance of the piece is less important to me than the title, because the title expresses a viewpoint common among many. Why look to the heavens when we don’t have heaven here on earth? The first time I heard this sentiment was as a child when I saw Joe Kennedy II express this opinion on the floor of congress in relation to funding to NASA in the 1980s. As something of a space-nerd the sentiment shocked me to my core. Obviously I understood poverty in at least a sensory fashion. I was born in Bangladesh before it was a textile powerhouse and there wasn’t at least the promise of development. But as a nerd it seemed to me that sacrificing knowledge of the world for a full stomach seemed like a false trade-off. Of course I was self-interested. This is what I wanted to be true.

But as it happens, I do believe that it is the truth, and that is because what we know from economic history. The rise of the post-Malthusian consumer economy validates the position that we should have one eye to the heavens above, and another focused on the concerns of the earth. The two are synergistic. What is needed for prosperity in a manner we understand to be prosperity in our day and age are two things. First, increased economic growth through gains in productivity. Second, a lack of concomitant population growth to eat up the gains in productivity. The demographic transition. In other words, get smarter to get wealthier, and don’t divide that wealth between too many children.

410uvoV1qDL._SY344_BO1,204,203,200_ The West, and more precisely Britain, was the first society to break out of the “Malthusian trap,” whereby gains in productivity were eaten up by population growth. This change was not foreseen by the economists of the day. Thinkers such as David Ricardo and Thomas Malthus assumed that the “end of history” was always characterized by a stationary state where population and economic production balanced out so that much of humanity was caught in a condition of immiseration. The irony is that they were flourishing just during the period that Britain was breaking the iron laws of economics as they were understood at the time. What we term the industrial revolution was triggering the rise in gains of wages to unskilled workers that would continue to 1970, and the demographic transition would lead to the emergence of the two-child nuclear family. There are many books which chronicles this change, but one is particularly good for a lay audience is David Warsh’s Knowledge and the Wealth of Nations: A Story of Economic Discovery. It traces the evolution of endogenous growth theory, basically a model which accounts for economic growth by parameters such as innovation and human capital (this problem is not solved by the way). Greg Clark’s A Farewell to Alms and Kenneth Pomeranz’s The Great Divergence as two alternative takes forwarding specific more empirical theses.

41W-0XB-m2L._SY344_BO1,204,203,200_ But let’s think about this in a more high level manner. Compare the Chinese intellectual and political tradition and that of the West. Since the Axial Age there are broad similarities, particularly with the rise of humanistic traditions. But to generalize one might assert that the Chinese tradition has been more pragmatic and concrete, while the Western tradition has allowed for more abstract concepts and considerations. The most otherworldly element of traditional Chinese thought actually turns out to be exogenous, that of Buddhism (the rise of Buddhism coincides with the decline of scientific Daoism and the rise of religious Daoism). After the Tang dynasty Buddhism lost its place at the table of Chinese elites, and the dominant ethos was that of Confucianism, which prioritized proper governance on earth to maintain harmony and order. A key consequence of this was that scholar-officials were fixated on the need for the peasantry, the true productive units of society, to be prosperous and fruitful. The Chinese system was deeply humanistic and civilian in its orientation. It can be argued that the Chinese state and society by the 18th century had reached the stationary state at the “end of history.” Every unit of production was being squeezed that could be squeezed by traditional means agriculture and trade between regions to maximize comparative advantage. They were at the end of the line of economic growth as could be conceived by Adam Smith’s model.

In contrast the West has been subject to less cultural continuity, and was more fragmented. The medieval scholastics, and men such as Baruch Spinoza, reflected a fixation on deep abstraction and a concern with ontology which was marginalized early on in the mainstream of Chinese intellectual thought. Arguably this flight from the pragmatic can be traced back to Pythagoras and the pre-Socratics. Mathematical mysticism continued in Western civilization because of the influence of Plato. Empirical science had its origins with the interests of Aristotle. The fusion of mathematical formalism and empirical methodology in the early modern era wrought a miracle: science. Over time science was turned into the handmaid of technology, and the elixir of innovation emerged from the synthesis.

20130601_FBC699 I assume most people can understand how this ties back to the piece in Medium, and the concern of people about poverty now, rather than future dreams and horizons. But we also have to remember that it is a fact that global poverty is declining. China is a big reason, and the root is not the revival of Confucianism,* but the expansion of technological civilization. The production of iPhones is driving the decline in misery, not redistribution or primary production through agriculture. We already have a map to abolish material misery: growth and demographic transition. It may happen in our age that extreme material want will be a memory, just as slavery is.

SaganPaleBlueDot What drives growth? Innovation. How do we get innovation? By investing in crazy projects whose payoffs we can’t calculate rationally and whose outcomes are not foreseeable. The reality is that Chinese civilization over ~2,000 years was caught in a local optimum of maximizing prosperity in Malthusian conditions. The Chinese sages were wise, but their eyes only saw to the edge of the horizon. The West’s intellectual forebears were less practical, but more diversified. This allowed for it to break out of the trap of fixating on the practical-before-our-nose. Rather, Western thinkers should dream delusional visions of abstraction and imagination. Worlds beyond imagining for the common ken. When you explore more of the parameter space you are likely to find novel optima which you would otherwise never have arrived upon. To some extent this is how evolution may work, with mutation, drift and co-evolution perturbing cozy fitness peaks. More plainly, we can only realize true innovation when we are able to understand that that entails blue sky long-shots into the deep. That is just the empirical and factual trend over the course of history, not a mystical vision.

But these issue are not simply nakedly utilitarian, they’re also normative. If we crush the spirit to explore and unleash a touch of insanity, even in the face of misery, we crush the human spirit. We were the crazy apes who dreamed to cross the vast blue oceans. Only our ancestors settled Oceania and the New World. We do not stay at home. That is not in our nature. For some of us, to explore is part of who we are. Denying that aspect denies a filament of our being.

Addendum: I have noticed and unfortunate trend of some biologists to denigrate space science as a “waste of money.” That goes to show that even among scientists horizons and wonderment can be constrained by narrowness of vision and zero-sum psychology.

* Confucianism is reviving actually in response to prosperity.

• Category: Science • Tags: Space 

Source: Pew

In the culture of science you occasionally run into the sort of person who believes as an apodictic fact that if one is religious one can not by their fact of belief be a good scientist. You encounter this sort of person at all levels of science, and they exhibit a range of variation in terms of the volume of their belief about beliefs of others. I don’t want to exaggerate how much it permeates the culture of science, or at least what I know of it. But, it is a tacit and real thread that runs through the world-views of some individuals. It’s a definite cultural subtext, and one which I don’t encounter often because I’m a rather vanilla atheist. A friend who is now a tenure track faculty in evolutionary biology who happens to be a Christian once told me that his religion came up nearly every day during graduate school! (some of it was hostile, but mostly it was curiosity and incomprehension)

This is on my mind because a very prominent person on genomics Twitter stated yesterday that Francis Collins by the very fact of his evangelical Christianity should not hold the scientific position of authority that he holds (the individual in question was wondering if they could sign a petition to remove him!). The logic was very straightforward: science by its nature conflicts with religion, and those who engage in the sort of cognitive processes which result in religion will be suboptimal in terms of scientific reasoning. As I indicated above the people who promote this viewpoint treat it as a deterministic scientific law. And, importantly there is little reference to cognitive science or survey data to support their propositions. Ten seconds on Google will yield the figure you see above. A substantial proportion of American scientists aver a religious affiliation.

Programming_Perl_4th_Ed_cover Mind you, there are patterns. The data when examined in a more granular fashion suggests that academic scientists are more secular than those in industry, as are the more eminent ones. But it doesn’t take much time to think of great scientists who avowed some sort of religious affiliation. In evolutionary biology R. A. Fisher and Theodosius Dobzhansky affiliated as Christians. The mid-20th century evolutionary biologist David Lack was an Anglican convert. In Reconciling Science and Religion the historian of science Peter J. Bowler outlines a movement in early 20th century Britain to accommodate and assimilate the findings of evolutionary biology to that of mainstream Christianity, so it is entirely unsurprising that Anglicans such as Fisher and Lack were active researchers within evolutionary science.

Outside of evolutionary biology there are two examples which stand out in my mind. Larry Wall, the originator of the Perl language which has had a long history in bioinformatics is an evangelical Protestant Christian. And Donald Knuth, the author of the magisterial series The Art of Computer Programming is a Lutheran.

51-C0feX3uL._SY344_BO1,204,203,200_ My point in reviewing this data, which should be widely known, is to bring some empiricism to this discussion. What do the data say? Not one’s prejudices and intuitions. One response on Twitter was that empiricism precludes faith. That’s the theory about empiricism. The reality is that there are many great empirical scientists who have a religious faith. Any scientist worth their salt who wishes to air hypotheses about the incompatibility of religion and science on an individual level needs to engage with these facts.

To be fair, I don’t think it’s a coincidence that there’s a correlation in the aggregate between secularism and science. But this issue is complex, emerging at the intersection of cognitive science, sociology, and history. These subtleties can’t be waved away airily with a reference to facts that everyone knows which happens to reflect one’s own personal prejudices. That reminds me of things besides science.

Finally, this truth that in the aggregate scientists are a diverse lot even if there tends to be particular patterns of social concentration is a general one. E.g., most scientists are more liberal than not. But a substantial minority are not, with a fraction of those being rather closeted about this. The average scientist, in particular in the academy, is a secular liberal. But the minority are not trivial. We’re in your lab meetings, at your conferences, collecting data for you, and on your committees, reviewing your grant applications.* Because of the nature of the academy outside of religious colleges there is often silence from this minority lest they be pigeon-holed as out of step with the social culture of science. That’s human nature. And scientists can’t escape that, whether they are in the majority, or the minority. For all the talk of logic and empiricism, scientists are all too human in their basic wiring.

* Much of what I say applies to natural science. From the survey data in the academy non-liberals-to-Leftists are almost entirely absent in sociology and a lesser extent in areas of psychology.

• Category: Ideology, Science • Tags: Science, Sociology 

A_Candle_in_the_Dark_by_soraferret Science is a pretty big deal. Science is the foundation for our civilization. Science is the best method we’ve found to map reality, and take us into the unknown on more than whim and prayer. I don’t agree with those who believe that science drained romance from our understanding of the world around us. I don’t agree with those who assert science is just another superstition. I don’t agree with those who assert that science is a tool of oppression by its nature.

With all that stipulated, science has problems. And that’s because it is a human enterprise. Humans are both the root of science’s problems, and, the source of its solutions. Philosophers can think deeply about how science is done, from Karl Popper to Thomas Kuhn, but high level abstraction has little impact on the day to day practice of science. Science today is social. Individuals work in the context of research groups, and then publish and disseminate their findings across the broader community of peers. The social aspect is why genuine scientific productivity on an international scale is so concentrated in a few nations, above and beyond what you might expect from economic development. The per capita gross domestic product difference between Germany and Italy is significant, but it is dwarfed by the yawning scientific productivity chasm between Germany and Italy in any area of science I am personally familiar with. Science exhibits returns to scale. Who you are around makes you smarter in science.

download This is why Twitter has become such a big deal. It’s a way to enable disintermediation; cutting the middlemen and gatekeepers out of the equation, and ratcheting up on the metabolism of discourse so that it is nearly frictionless. About ten years ago some friends of mine disagreed with a scientific paper in PNAS. They were going to write a response, but didn’t think anyone would pay attention, even if PNAS accepted and published it. So they put up a blog post. Today they would probably start responding on Twitter.

This is relevant because of a controversy that recently erupted over disputes about the results of a major paper from a reputable group. Nature has already reported on this, Potential flaws in genomics paper scrutinized on Twitter. Yoav Gilad, a University of Chicago professor, released some critiques of a high-impact PNAS paper from last December, Comparison of the transcriptional landscapes between human and mouse tissues, on Twitter. The critique is now more fully fleshed out in a paper posted at F1000Research. But what has really gotten peoples’ attention is what Mike Snyder, the last author on the mouse-human transcriptional landscape paper, said in response to the way the critiques were delivered:

Michael Snyder, a geneticist at Stanford University in California and co-author of the original paper, stands by his team’s study and its conclusions and says that Gilad broke the “social norms” of science by initially posting the critique on Twitter. Gilad says that he took to social media to highlight his work, which might otherwise have been overlooked.

Obviously there isn’t a book which outlines the social norms of science. These norms have developed and coalesced implicitly, tacitly, over time. And, they change. It’s no surprise that a lot of people on Twitter are taking Gilad’s side in this. Also, many are giving credit to Snyder’s group for releasing the raw data to Gilad for the reanalysis. If Gilad and company are correct then this is another victory for open(ish) data. Derek Lowe has some reasonable thoughts on the details of how this has been playing out in public. I don’t have much to add.*

But, I do wonder how ephemeral the role of Twitter is going to be in the scientific community. After all, Twitter is not a public utility. It’s a public firm which is traded on the stock market and exists to make a profit and return value to its shareholders. There was a time when AOL, or Myspace, were ubiquitous corners of the internet. Though Twitter allows for a level of disintermediation, to some extent it is a stealth intermediary in and of itself.

The social norms of science are evolving, and the rate of change is increasing. I doubt that this generation shall pass into emeritus before the entire edifice of scholarship as we know it, from publishing status quo to the tenure system, is overturned. Snyder put his finger on the fact that Gilad is likely violating the social norms of science, but those were past norms. Scientists are making it up as they go along right now. Genomics in particular, which is a heavily computational field, with many researchers amenable to data sharing, distribution, and reanalysis, is to some extent going to be a guinea pig for other domains. We’re in a time of change, so likely don’t have the clarity we will in a decade or so, when the current maelstrom will have passed and a new equilibrium attained.

* I didn’t pay much attention to the original paper, so I’m having a hard time understanding how the authors didn’t bother to check for batch effects as some are claiming. Finally, I’ve met Mike Snyder, and he’s a very nice person from what I can tell for how big of a deal he is. I hope this resolves without too many hurt feelings and reputations intact on all sides.

• Category: Science • Tags: Science 

Citation: Figure adapted from Lumley, Alyson J., et al. “Sexual selection protects against extinction.” Nature (2015).

9780198503361_200 Sex is a big deal. William Hamilton spent a significant part of his career on the topic, and the second volume of his collected papers, The Narrow Roads of Gene Land, is focused on this issue. Whenever I talk about sex in an evolutionary biological context one thing that always pops up is why males? In other words, why do so many complex organisms have a whole sex which does not bear offspring? Parthenogenetic lineages of organisms where females can reproduce asexually have double the per generation reproductive output as sexual lineages. And yet over evolutionary history it seems clear that in lineages where sexual and asexual species coexist, the latter are always novel derived lineages. In other words, asexual lineages have a high extinction rate. Sex, and more specifically males, must be good for something. What then?

One hypothesis is that males are good for purging genetic load via sexual selection. On a genetic level all individuals carry deleterious mutations, which they pass on to their offspring. But, because of sample variance in transmission, there will be a distribution of outcomes in any given set of offspring. By chance some individuals will exhibit a higher load of deleterious alleles, while others will carry fewer alleles. If this load is correlated to traits which are visible to the opposite sex, then excess load every generation can be purged through reproductive skew. In other words, one might envisage a situation of sexual selection-mutation balance, where de novo mutations introduced every generation are balanced against deleterious alleles purged from the population through selection of more fit males.

330px-Tribolium_castaneumAll good in theory. But is this empirically true? A new paper in Nature suggests it is. At least for the red flour beetle. The paper is titled Sexual selection protects against extinction. Recall that asexual lineages seem to be more likely to go extinct when one examines them with comparative phylogenetic methods (i.e., with in a clade asexual lineages are invariably young in evolutionary time scales, implying that they do not last long).

41SSqWzJIGL._SY344_BO1,204,203,200_ The adapted figure above shows the experimental results which support the proposition that sexual selection purge deleterious alleles. These experiments ran for ~10 years, and consisted of varying primary treatments which differed in terms of intensity of sexual selection in red flour beetles. In panel A you see a comparison between a male and female skewed sex ratios (9:1), red and blue lines respectively. In a male skewed ratio the males are competing for the attention of a few females, and in a female skewed ratio the situation is the reverse. To test for the fitness of the lineages the researchers took the outcomes of long term breeding in these scenarios (fixing the effective population sizes to be comparable) and then forced them to engage in sibling matings. This would “expose” deleterious recessive alleles because of the nature of inbreeding. As is evident above in the female skewed (blue) lineages there is a much quicker extinction rate as inbreeding begins to expose deleterious alleles in the recessive phenotype. In the second set of experiments the authors compared polyandrous (5 males to 1 female) and monogamous lineages. Again, you see that the polyandrous lineages are much more robust to inbreeding, suggesting that sexual selection driving reproductive skew correlated with mutational load is resulting in a lower population wide genetic load.

41czavSUnNL._SY344_BO1,204,203,200_ There are many arguments for why sex persists (though many of them do not seem to directly address the cost of males, since sexuality does not necessarily entail two different sexes where one does not bear offspring or produce eggs). I don’t think that sexual selection needs to be the explanation as such. Additionally, I think there is the problem that extremely skewed sex ratios as is the case above does not seem biologically plausible in many organisms. In big and slow breeding organisms, such as humans, extreme sex ratios are not typically common. It seems unlikely that sex is maintained purely through purging of deleterious alleles via a “good genes” model of sexual selection. But then to truly test this hypothesis it strikes me that some sequencing methodologies could be brought to bear. For example, do individuals with lower load have a higher realized reproductive fitness? This is entirely testable.

Citation: Lumley, Alyson J., et al. “Sexual selection protects against extinction.” Nature (2015).

• Category: Science • Tags: Sex, Sexual Selection 


F5.medium A common model of the range expansion of modern humans out of Africa ~50,000 year ago forces us to conceptualize it is as a tree with successive bifurcations. Each of these bifurcations often is accompanied by a bottleneck in one of the daughter populations, with the sum totality of the demographic events producing a “serial bottleneck” model of the origin of modern human lineages around the world. Though this paradigm has been around in various forms for decades, most influential among geneticists has been the 2005 paper, Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. In the paper the authors show persuasively that heterozygosity declines as a function of distance from Addis Ababa, near the likely point-of-departure out of Africa.

But there’s minor problem with this model. Most extant populations may in fact be compounds of highly diverged late Pleistocene lineages. That is, after an initial serial founder expansion ~50,000 years ago there may have been many local extinctions and admixture events overlaying it. That is the model that Joe Pickrell and David Reich argue for in Towards a new history and geography of human genes informed by ancient DNA. While in a serial founder conceptualization of an out of Africa migration modern populations are the tips of the phylogenetic tree, in the Pickrell and Reich framework they’re syntheses of divergent evolutionary histories. As Towards a new history and geography of human genes informed by ancient DNA shows older genetic techniques and data, not informed by ancient DNA, may not have had the power to differentiate between the serial bottleneck model, and one of reticulation and fusion.

41h+3YmTZRL._SY344_BO1,204,203,200_ It seems likely that the serial founder model has some utility. One can still hold defensibly that everyone outside of Africa, excluding recent admixture from within Sub-Saharan Africa, sits within their own phylogenetic clade. That is, all non-Africans are equally related to Sub-Saharan Africans, because all of them descend from an ancient population of ~1,000 breeding individuals. But, you have populations such as South Asians who are both numerous, and, fusions of two very distinct branches of out of Africa humanity. The stylized model of a tree subject to bifurcations fundamentally misleads in this case.

All this came to mind reading a new preprint that’s on biorxiv, Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes. Theory and intuition should suggest to us that out of Africa populations will have higher genetic load of deleterious mutations than within Africa populations. The reasoning is straightforward: the power of selection to remove deleterious mutations is hampered the smaller the effective population size, as random genetic drift becomes more determinative in generation to generation changes in allele frequency. More formally if 4 N es << 1, where N e is effective population and s is the selection coefficient, then even deleterious alleles behave as if they are neutral. From neutral theory we know that the rate of substitution in this model is simply the rate of mutation. That is, molecular evolution is determined by new mutational input, rather than being constrained or diversified by selection. In small populations which are drift dominated N e can get very small. I’ve seen assertions that the original group of humans who settled North America and South America may have had an effective population in the first generation on the order of ~100. In their history they also had the out of Africa effective population of ~1,000. In addition, there were likely bottlenecks between Berengia and the out of Africa event.

download You can see in the figure above from the preprint that the number of deleterious mutations does seem to increase with further distance from Africa. Their genomic coverage was good, ~80x on the exome. That is, when they found variants that differed from the reference sequence they could be confident that it was not in error. On the other hand their population coverage struck me as less than ideal, though I am willing to accept that their result is probably true (and obvious with finite resources they selected their individuals and populations to be informative). They admit for example in the text that the Mozabite population has higher heterozygosity due to a back-to-Africa migration, which has had successive admixtures of Sub-Saharan ancestry. In addition, it is also rather inbred. Its demographic history bears no correspondence to the serial founder bottleneck model which spans 50 to 15 thousand years (i.e., from the out of Africa to the settlement of the NewWorld). The Pathan and Cambodian populations also are actually the product of Holocene fusions between distinct groups with very different histories. The PSMC results in the bottom left panel can be thought of as collapsing distinct population histories, and, from what I am to understand may then inflate the effective population trajectories of individuals who descend from admixture events.

As one might expect from this sort of title the authors refer back to the 2005 paper that I mention above. I don’t want to belabor this point, as I think the authors’ results are probably robust, and, important, population history aside. But, much of the audience will not know that the serial founder bottleneck model is now being challenged. The 2005 paper has 588 citations as of this writing. The Pickrell and Reich paper, which was published in 2014, has 5 citations. I just want to mention this since it’s a preprint and presumably the authors are taking in any critiques.

When it comes to burden of deleterious mutations in human populations there have been some conflicting results, reviewed in the preprint, about mutational load. The authors argue that results which suggested that non-Africans did not exhibit higher load were subject to a bias which did not have power to detect non-common variants, and also modeled mutations as additive, as opposed to across the full range of dominance (h). It turns out that non-Africans, and those populations which are more drifted, exhibit higher recessive deleterious loads. This is what you would expect intuitively, as you need large populations to purify this class of deleterious alleles (since they are only exposed to selection in homozygotes). This matters when it comes to expectations of the number of recessive diseases one might expect in populations which practice consanguinity. I would, though, have liked to see more typical populations in the mix. For example, instead of just African hunter-gatherers it would be nice to see the Yoruba, as well as Han Chinese, and a northern European population. I doubt it would be very surprising, but it would give one a better baseline.

Finally, I want to note that many ancient DNA results, from “archaics” to modern human Mesolithic hunter-gatherer groups, have very low effective population sizes due to inbreeding. Genetic load may be more important in the history of the human species, especially on the edge of the range in the far north, than we may now understand, because of its tendency to reduce fitness of groups due to the drag of recessive disease.

Citation: Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes, Brenna M. Henn, Laura R Botigue, Stephan Peischl, Isabelle Dupanloup, MikhailLipatov, Brian K Maples, Alicia R Martin, Shaila Musharoff, Howard Cann,Michael Snyder, Laurent Excoffier, Jeffrey Kidd, Carlos D Bustamante,

• Category: Science • Tags: Genomics, Human Genetics 

51QrNyN0KzL._SY344_BO1,204,203,200_ In 2002 I read Stanislas Dehaene’s The Number Sense: How the Mind Creates Mathematics. Though it’s not at the same level as Steven Pinker’s The Language Instinct*, it’s not that far below it. There was a time when I read a fair amount of cognitive neuroscience. Not so much now. So I’m finally trying to get through Reading in the Brain: The New Science of How We Read, again, by Stanislas Dehaene. This is partly an exercise of narcissism, since I want to do what I can to understand myself.

CoverReadingInTheBrain Speaking of which, Bryan Caplan, a big fan of Judith Rich Harris’ The Nurture Assumption, reports that reading is kind of a big deal in developing a child, and impacting their ultimate life outcomes. The effect is modest, but robust. Though also please read Will Ambrosini’s cautionary comments about interpretation of this result.

So what else is going on? I apologize to those whose comments I don’t respond to who are asking me a direct question. Time is finite and it often slips my mind, even though responding to questions is on a “TO-DO”. Also, the new book about Elon Musk, Elon Musk: Tesla, SpaceX, and the Quest for a Fantastic Future, looks interesting. But I doubt the whole of the text is worth purchasing. I care a lot less about Musk’s family background and personal life than I do about his vision for the human race. But really the latter could be outlined on a napkin.

Finally, BAPG XII @Stanford in Palo Alto. May 30th, a Saturday. Looking forward in particular to Michael McLaren’s talk on fitness landscapes.

* The Blank Slate is probably more well known, and Pinker’s most successful book in terms of broad cultural impact. But I think The Language Instinct is his best science book aimed at a general audience.

• Category: Miscellaneous • Tags: Open Thread 

51fQMbh-NnL._SY344_BO1,204,203,200_ A few months ago the anthropologist Pat Shipman published a book, The Invaders: How Humans and Their Dogs Drove Neanderthals to Extinction. I’ve read Shipman before, and because of my interest in domestication it’s been on my radar, but I haven’t gotten around to purchasing it. The major reason is that as I understand it the title is somewhat misleading, in that there’s a lot less in the text on human-dog cooperation than one might think. Which is reasonable, it’s a speculative hypothesis at best.

Perhaps the biggest problem is that there’s no strong evidence that dogs were domesticated or distinct as early as ~35 thousand years ago, when modern humans replaced Neandertals in Europe. This comes up in a very highly rated comment on Amazon in fact. The best genetic work, Genome Sequencing Highlights the Dynamic Early History of Dogs, implies a date of ~15,000 years before the present, at the earliest.

But now it looks like it’s time to update our priors on this. Shipman’s speculative theory, still unlikely in opinion, is no longer extremely unlikely. The reason is ancient DNA. Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds:

The origin of domestic dogs is poorly understood…with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum…conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations…Here, we present a draft genome sequence from a 35,000-year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

gr2_lrg As you can see from the figure to the left the Taymyr sample diverges at about the same time as the common ancestor of wolves and modern dogs. In other words, you have a polytomy. Not only that, but there has been introgression from the Taymyr lineage into particular northern dog populations.

Genetics and genomics are big deals. But at this point I have to point out that archaeologists have really been here the whole time. Archaeologists reported that the Amerindians brought dogs with them over through Berengia. Historians know that the indigenous people had dogs. Yet in 2010 geneticists published, in Nature, Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication, who put the focus on the Middle East and the Neolithic revolution. There was basically no way this really made sense. Then you had a 2011 paper in PLOS ONE, A 33,000-Year-Old Incipient Dog from the Altai Mountains of Siberia: Evidence of the Earliest Domestication Disrupted by the Last Glacial Maximum. Even the authors themselves assumed that this was a “false dawn.” That this dog-like canid probably did not give rise to later dog lineages. But if the results above are correct, then in fact this 33,000 year old individual may actually be part of the extant proto-dog population.

Let’s let this sink in: if the results above hold, then the arrival of modern humans to northern Eurasia may have been coincident with the emergence of a distinct dog lineage. The term “man’s best friend” takes on a whole new meaning. The relationship between man and dog may be nearly as ancient as modern humans as we understand them, that is, populations capable of copious and protean symbolic cultural production which explode out in the archaeological record over the past ~40.000 years. In addition, I also believe we now need to totally reconceptualize how we view the relationship of wolves and dogs. Rather than an ancestral and derived set of populations, whose “species” status is only semantic convenience, they are actually sister clades. The results in this paper confirm other findings that the wolves of North America and Eurasia seem to share a post Last Glacial Maximum origin. Wolves as we understand them today may have emerged simultaneously with dogs, both descending from the melange of canid lineages which flourished during the Pleistocene. There’s a reason that feral dogs, such as dingos, do not “revert” to wolves. The ancestor may not have even been a wolf!

Additionally, the authors also note that the features of the dog which are hallmarks of domestication may themselves be derived within the dog lineage. That is, the separation of the ancestors of dogs and wolves predates the Last Glacial Maximum, ~20,000 years ago. But the evolution of dogs so that they exhibit particular derived traits may have occurred far later in time. In fact, I would hold that perhaps the true story is one of co-evolution between dogs and humans.

The ultimate moral of this true story to me is that many Pleistocene mega-fauna with wide ranges in Eurasia were subject to similar evolutionary dynamics. Extinction of distinct local lineages was the rule, not the exception. Recolonization from populations which dodged extinction was also inevitable. The phylogenetic tree was pruned repeatedly, but tempered somewhat in the ferocity of clipping by admixture and introgression, as branches fused together.

• Category: Science • Tags: Evolution, Human Genetics, Science 


Large-scale recent expansion of European patrilineages shown by population resequencing:

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Looking at this paper, it basically confirms what we know from ancient DNA, and other large scale sequencing projects. Until recently much Y chromosomal phylogenetic analyses were done utilizing highly mutable regions, microsatellites. This had a major upside, in that variation was copious. But, it wasn’t as precise as more slow mutating regions of the genome would have been. But without next generation sequencing the Y chromosome is just hard to work with due to its paucity of SNP variants. So that’s why we’re seeing some gains here.

The relatively homogeneity in Northern Europe in particular is attributed to a few lineages which have gone through “star-like” expansions. That aligns rather well with the idea that the arrival of populations from the steppe was demographically an earthquake.

• Category: Science • Tags: Y Chromosome 


A few years ago a paper was published, Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins, in PNAS, which argued that ancient population structure within Africa might be the reason that non-African populations are genetically closer to Neandertals. The basic logic is simple. If within Africa there was variation in relatedness to Neandertals, and modern non-Africans are derived from the group that was closer to Neandertals, then one might infer that there was recent admixture between the groups even though any connection was very distant in the past. This objection actually popped up immediately when the Neandertal admixture Science paper was published. Over time many people have been convinced by various ingenuous and abstruse arguments.

The problem is that not everyone is a statistical geneticist, nor do they think about these issues very often. When it comes to the media they have to rely on what’s being published in prominent journals. The PNAS paper above has haunted the field in my opinion, because reporters have had to take the researchers at their word, when frankly most statistical geneticists that I know did not find their arguments very persuasive in the first place. Today we have even less reason to believe them. A few hours ago I saw this in my feed from the Genetic Literacy Project, More mystery about Neanderthal and modern humans: How reliable is ancient DNA analysis? The answer is very reliable. There’s no controversy.

The figure at the top of this post is from Genome sequence of a 45,000-year-old modern human from western Siberia. What you see is that the markers diagnostic of Neandertal ancestry are clustered together in segments to a far greater extent in the ancient sample than among modern peoples. This sort of pattern of decaying tract length is a hallmark of pulse admixtures. Each generation recombination breaks apart associations until the tract lengths are very small (or, they are not detectable). There are now at least two ancient samples which show that Neandertal-modern human admixture occurred in the relatively recent past in relation to their own period in comparison to modern individuals. That in itself reduces the probability of ancient structure being the dominant explanation for the Neandertal affinities of non-Africans, as ancient structure would not exhibit this tract length bias. And, this result has the utility of being amenable to common sense comprehension.

• Category: Science • Tags: Neandertal 

Olivia Munn

Olivia Munn

Periodically rather than offering up original thoughts it is needful to engage defensive warfare against pernicious memes. For example, one thesis that is commonly bandied about today is that racial admixture will result in the blending away of all differences, toward a homogeneous beige future without end. This is false. It is false for several reasons, genetic, and sociological. But, it is persistent for ideological reasons.

Here’s the latest instance, Future Humans Will All Look Brazilian, Researcher Says:

Meanwhile, many other physical traits will simply blend together. “Most of the traits that we think of as distinguishing different groups (hair colour, skin colour, hair curliness, facial features, eye shape) are controlled by multiple genes, so they don’t follow a simple dominant/recessive pattern,” McDonald explained. “In those cases, blending will make people look more similar over time.”



The recourse to a blending analogy is unfortunate. Genetics is not a blending process, it is a discrete one, which reconfigures variation every generation. The underlying variation in the form of alleles is maintained, even if the genotype frequencies shift. This insight is implied in the article with talk about recessive phenotypes and nods to Hardy-Weinberg equilibrium. One of the key problems with Charles Darwin’s original theory of evolutionary process is that it did not account for how heritable variation could be maintained. If that variation melted away every generation through blending processes then the world would rapid equilibrate toward homogenization. Roughly half the variation would disappear per generation in an exponential decay process.

41PHSZN6AEL And yet variation remains! Though the phenotypes, the traits, may exhibit blending between parents, the underlying genetic variation is governed by Mendelian dynamics. This is why in populations where alleles for traits like pigmentation segregate in a polymorphic fashion, such as in India, it is not uncommon for complexion to vary within families. Though on the population wide scale there is some tendency toward clustering about the mean, variance remains within a random mating group at equilibrium.

Another major issue is that these discussions too often focus on single traits. When evaluated across loci the variation and range in possibilities due to admixture in fact results in greater diversity than is possible today. Mendel’s law of independent assortment implies that traits and variation will not be co-inherited. Before international travel and migration the possibility of someone with blue eyes, an epicanthic fold, and tightly curled hair, was a theoretical affair. Today there are almost certainly people who exhibit all these traits.

By coincidence these people are likely to be Brazilian, as this is a nation where there are large populations of African, Japanese, and Northern European (German) ancestry. And the example of Brazil itself illustrates empirically why homogenization will not proceed in the manner which intuition tells us. Brazil may be modally a brown nation, but its physical types run the gamut, expressing the underlying genetic variation. Among populations such as the Uygurs, who are fusion of eastern and western streams, individuals arise who reflect in near totality the physical types of only one of their ancestral populations, even if most individuals exhibit configurations in equipoise.

And so it was, and so it will be. The reality is that today is not the age of amalgamation, that age has passed. The most recent work in human genomics actually brings us to the conclusion that in fact most of the “pure” populations we see around us today are fusions of deeply diverged human evolutionary threads. The ancestors of Europeans in the Pleistocene were as differentiated as modern continental races (i.e., Fst on the order of 0.05 to 0.15 depending on the pairwise comparison). The same is true of South Asians, and most other groups you can think of. The “Great Mixing” after the retreat of the ice and collision of peoples may explain why there is so little evidence for hybrid inviability today in cross-racial pairings; it may have been purged from the genomes of modern groups through selection during that period.

The admixture of this age will be but a shadow of the past. The reality is that for centuries into the future huge numbers of people will persist who we might recognize as European, African, and East Asian, in totality of their form and genetic heritage. The amalgamation of the early Holocene probably occurred through the fusion of groups in the early stages of demographic expansion. They were tribal affairs, parochial in their scope, born out of desperation and chaos, even if the consequences were continental in their implications. The clans of yore became the mothers of nations, but those nations are mature and endless in their number now. The existence of Brazil as we understand it is exceptional, the product of racial slavery on a massive scale during a time of tumult. It is the exception, rather than the norm.

Rahul Gandhi

Rahul Gandhi

In the next few decades international elites will no doubt enter into a period of intermarriage as old barriers fall, and new commonalities of class transcend ethnicity. But for the majority of the citizenry of the old nations such considerations will be theoretical. The initial period of synthesis and cross-fertilization will give way to stasis as all those open to the new possibilities of finding mates across old racial categories will have done so. Those who remain, the majority, will be more conservative in their preferences and tastes. The Holocene ushered in races which are extant across the world today through admixture; the anthropocene will usher in the post-national international race of global elite. Rather than twining a few threads of the human lineage, this new population will twist all the threads together in a radical new conformation. And it will be anything but homogeneous and uniform in its expression!

• Category: Race/Ethnicity, Science • Tags: Genetics, Race 


12918295 Sometimes it is useful to enter into the record what you think, even if it is not fully formed, or even not strongly held. After reading a review on mutational load in human populations, which lingered long over demographic inferences of our species’ fluctuations in population size, as well as conversations with Gregory Cochran and Ian Mathieson, I have come to the conclusion that cultural group selection is a very important, perhaps dominant, dynamic in explaining the ubiquity of anatomically modern humans over the past ~50,000 years.

This is not a novel position. A group of evolutionary theorists, most prominently today David Sloan Wilson, have argued for the primacy of group level collective dynamics for human societies which allow for a plausible organismic metaphor in their action and behavior for the past 40 years. Peter Richerson and Robert Boyd have developed an extensive body of theoretical work outlining precise models (see Not by Genes Alone) which extend this framework. Importantly, I want to be careful and qualify that I am being precise when I limit my conjecture to humans, and, cultural phenotypes. For empirical and theoretical reasons I believe that humans may be sui generis.

My intuition here is tied in to what I have stated earlier about Aurignacian populations, and their likely extinction in Europe due to the arrival of Gravettian populations. The ancient DNA results are yielding to the conclusion that the human past has been subject to a great deal of local population replacement. To me this is peculiar, because even in the course of inter-group competition one would expect a fair amount of admixture, as is assumed in a demic ‘wave of advance,’ where populations push forward their range through natural increase. In fact the replacements don’t strike me as typically genetical in their fluctuations. Rather, they’re cultural. Punctuated. Alternating between stasis and rapid switches in state and character. The genetic data may simply be witness to the outcomes of winner-take-all outcomes.

Of course there has long been speculation that the social organizations of anatomically modern humans was the key for why they replaced their cousins. Many of these models though were derived from conjecture, and extrapolation. The new twist for me is that the historical population genetics is now aligning with this possibility. These are real concrete data and results.

• Category: Science • Tags: Human Evolution 

51aBlSPDX8L._SY344_BO1,204,203,200_ I’ve been reading The Making of Modern Japan. Tokugawa Ieyasu is a pretty big deal, and I’ve long been intrigued by him as an individual after reading about him and his contemporaries in the novel Taiko. Also, Japan seems a good way to investigate the possibilities of how one becomes modern without being fully Western.

Stanford is hosting BAPG XII in two weeks. Unless something intervenes I’ll be attending as usual. I also assume that the excessive population genomics tweeting will lose me some followers, as is the norm.

Had a good chat with Iain Mathieson today, as I swung through Berkeley (had Peking duck for lunch and Texas barbecue for dinner!). It’s a good time to be alive and be interested in human evolutionary genomics.

Lots of comments below on my post on Asian Americans and university admissions. I don’t really have a strong opinion as to how admissions should be handled. As usual my sentiment is to make a plea for honesty and candor. But I’m probably being naive and hopeless about it all.

Update: I’m in the third & fourth segments.

• Category: Miscellaneous • Tags: Open Thread 

The Wall Street Journal is reporting on a suit brought by Asian American organizations, Harvard Accused of Bias Against Asian-Americans:

The complaint, filed by a coalition of 64 organizations, says the university has set quotas to keep the numbers of Asian-American students significantly lower than the quality of their applications merits. It cites third-party academic research on the SAT exam showing that Asian-Americans have to score on average about 140 points higher than white students, 270 points higher than Hispanic students and 450 points higher than African-American students to equal their chances of gaining admission to Harvard. The exam is scored on a 2400-point scale.

Ron Unz, among others, has written about this, before. So not a big surprise as to the underlying empirical trends. Liberal commentator and Harvard grad Matt Yglesias has talked about the patterns for years. It’s an open secret. The question is whether anyone cares, and whether the legal system will do anything about.

But let me note something, a lawyer defending Harvard notes:

Robert Iuliano, Harvard’s general counsel, said the school’s admissions policies are “fully compliant with the law.” The school says its admissions process takes into account a variety of factors besides academics, including applicants’ extracurricular activities and leadership qualities.

This is what a leader looks like

This is what a leader looks like

It strikes me as unlikely that Asian American applicants lack extracurricular activities. Though first generation immigrants may come from societies where academic achievement is the summum bonum, they know that in American admissions criteria that non-academic strengths matter. But, you can’t manufacture leadership and charisma. Harvard’s role is to educate and inculcate the leaders of the next generation of Americans. It is the training ground for our natural aristocracy. Can American society actually conceive of a situation where 40% of those leaders are Asian? I doubt it. Asian Americans are not seen as plausible leaders. Especially by the established oligarchs, who would prefer their own offspring to inherit the mantles of power. Asian males in particular exhibit a “penalty” in the dating game. White females perceive them to be sexually impotent (on average), and for better or worse the opinions of white females as to who is a plausible leader in our society is very telling. If American women won’t want have to have sex with them, then why would the broader society see them as creditable leaders?

This is related to something Josh Harkinson at Mother Jones pointed out recently: Asians are far underrepresented in top management in relation to their representation among rank and file workers, especially in technical positions, in Silicon Valley. This is well known. People make all sorts of excuses for this. For example, a large number of the Asians are immigrants to the children of immigrants, who may not have the “social capital” to be successful in management at an American firm.

For me, here’s the upshot: we just need to be honest. Perhaps the cultural skills and dispositions that Asian Americans bring to the labor force are naturally more amenable to technical positions and professions like medicine than they are to management. It may not be as much discrimination, even of the implicit sort, as opposed to the natural sorting of personality types. This is an option we may need to entertain, rather than assuming that it is all invidious discrimination. It does strike me as obvious that Harvard and other Ivy League schools are attempting to racially balance by putting their fingers on the admission knobs in just the perfect manner. Though I’m not particularly happy about this, being transparent and honest would at least allow us to address what’s going on, and wonder whether we should do something about it. The fact is that Asian Americans are doing relatively well, even if their proportion at Harvard is 20% instead of 40%. Do we as a society need to abolish all discrimination by any means necessary? I’d say no.

• Category: Race/Ethnicity • Tags: Asian Americans 

Phylogenetic tree of mtDNA lineages, with 40 K B.P Aurignacian "Fumane 2"

Phylogenetic tree of mtDNA lineages, with 40 K B.P Aurignacian “Fumane 2″

220px-Cro-Magnon A new paper in Science, The makers of the Protoaurignacian and implications for Neandertal extinction, seems to establish definitively that the Aurignacian culture, often identified as the first modern human society within Europe, was in fact of modern humans. The part that is of interest to me is the DNA evidence from this paper. In particular, they got a good quality mtDNA sequence, and put it on a phylogenetic tree with other humans. As you can see, it is clearly within the clade of modern humans, and in particular non-African modern humans. More precisely, this individual is a basal branch of haplogroup R, which is common across western Eurasia, and ancestral to many common lineages. The fact that it’s basal isn’t too surprising, this individual is ~40,000 years in the past. Because of the rapid turnover of mtDNA lineages it isn’t surprising if past lineages have gone extinct in a given region, even if total genome content is passed down.

But, I do want to enter into the record that in concert with rumors I’ve been hearing as well as the broad picture of what ancient DNA is telling us about genetic turnover that I doubt that modern Europeans in any way descend from the Cro-Magnon populations of the first settlement of the continent by moderns. Rather, I’d bet that the “hunter-gatherer” ancestry of the Europeans of today goes no further back than the post-Gravettian cultures, and perhaps later. The genetic makeup of ancient populations seems to have been more complex than we’d have imagined, and there were meta-population dynamics which we’re only getting a good grasp of. With low population densities and a fragmented Pleistocene landscape it strikes me as plausible that Palearctic mammals in particular may be characterized by repeated resettlement of the frontier of the range from core source populations after local extinctions and retrenchments.

• Category: Science • Tags: Paleoanthropology 

51GD7A9F3WL._SY344_BO1,204,203,200_ Recently I reread War Before Civilization: The Myth of the Peaceful Savage, with a particular focus on the transition in Europe during the Mesolithic/Neolithic. Today with ancient DNA we know that in western Europe there were two distinct populations which came together with the arrival of agriculture. One population, which is very similar to modern southern Europeans, was a synthesis of Ice Age indigenes and an intrusive group from the Middle East. The other population, Mesolithic hunter-gatherers, were related to, or in part ancestral to, much of the heritage of modern northern Europeans. An interesting aspect of the division between these two populations is that their genetic distance was very high, on the order of 0.05 to 0.10. Or that between continental races. Additionally, the hunter-gatherers may have been a fearsome sight to behold, large robust people with dark skin and hair and piercing blue eyes. A novelistic treatment of the meeting between hunter and farmer invites itself naturally (Ted Kosmatka?).

WillianGolding_TheInheritors Further back in time you have the meetings between our own lineage and Neandertals and other assorted hominins. No doubt some of the same discordances that characterized the interface of farmer and hunter would have applied in these situations, though even more starkly. I’ve read a fair number of novelistic takes on this “first contact.” Clan of the Cave Bear of course. But also Bjorn Kurten’s Dance of the Tiger. I’m finally getting to reading William Golding’s The Inheritors. And Robert J. Sawyer’s Neanderthal Parallax series, which is a strange twist on the theme, deploys many of the same tropes as prehistorical fantasy despite its science fiction setting.

Orientalism But a major problem with these books is that they turn the Neandertals into reflections of some aspect of our own dreams and nightmares about ourselves. Jean Auel’s Neandertals in Clan of the Cave Bear were patriarchal brutes, as opposed to the matrifocal Cro-Magnons. Ayla’s nemesis Broud is a nightmare inversion of dreamy Jondalar. In contrast Sawyer and Kurten depict Neandertals as a more gentle folk, more or less, in comparison to the rapacity of modern humans (Golding also goes in this direction). This is the same problem that Keeley observes in War Before Civilization, and that Steven Pinker explored in depth in The Blank Slate, though applied to our own species, with Europeans tellingly substituted for modern humans. Against this reference the Other is a noble savage, with different weights to nobility and savagery contingent upon cultural fashion.

cover_passing Contemporary American discourse about social justice is marinated in this intellectual framework, the heir of the age of white supremacy and scientism which crested in the early 20th century. Left-liberals who espouse strident progressive social justice views ascribe regressive practices among non-whites purely to extraneous Western colonial influences, as if non-white peoples were innocents in the garden before the arrival of Europeans, lacking agency for good or will. Whereas a previous generation of white supremacists perceived in the non-Western the inferior and primitive, a modern generation of Westerners sees the authentic and pristine. Though the moral valence differs, the underlying structural framework is invariant. To truly carve nature about its joints in a manner which exhibits appropriate fidelity we need to go beyond this reflex. Hopefully in such a manner we can also begin to probe our own past without fewer illusions which are haunted by the present.

• Category: Ideology • Tags: Human Nature 

By now you are aware that another blogger who happened to be an atheist was killed. The modus operandi is pretty familiar. It looks like there are now “hits” going up against these individuals as a way for Islamic radicals to target an easy to scapegoat minority in Bangladesh. Atheists are now caught in a crossfire between religious nationalists and secularists, a divide which goes back to the Pakistan days. How vulnerable are the atheists? Well:

“The culture of impunity that has spread over the last few years clearly has very damning results,” Arifur Rahman told IHEU after Washiqur Rahman was killed. “… The word ‘Nastik’ (atheist) has been vilified in Bangladesh (and the rest of the Muslim world); they are seen as sub-human, it is OK to kill them.”

All cultures are not the same. In most of the Islamic world sufferance would be enough for many minorities. While craven Leftists wring their hands over insults to Islamic minorities in their midst, Islamic civilization is wrecking havoc upon the liberties of millions. That being said, there is a continuum. Saudi Arabia, Iran, Turkey, Malaysia, and Azerbaijan are not interchangeable. There are some analogies being made to Pakistan right now (like being analogized to Mississippi in the United States this is never good). That’s apposite at this particular moment because 45 Ismaili Muslims have been gunned down in Karachi. It strikes me that Pakistani sectarianism is now proceeding down a Bonhoefferian Niemöllerian gangplank, first dehumanizing non-Muslims, and then progressively narrowing the set acceptable. The nation is on the way to being a literal circular firing squad.

Bangladesh is a different case. I won’t rehash it. I will point out though that when I posted about my own identity, as an atheist of Bangladeshi origin, that when put that on reddit the response by one individual was “Who cares”? Obviously there are many things in Bangladesh that warrant attention, but, targeted killing of a reviled minority is apparently not worth notice by some. Fair enough, I suppose.

But I’m not here to emote and reflect. Rather, what does the data say? The World Values Survey has data from Bangaldesh for 1999 to 2004. One of the questions asks: Politicians who don’t believe in God unfit for public office. It seems a rough gauge for attitudes toward atheists. The results are below.


As you can see Bangladesh is roughly in the middle of the list. Observe the contrast with Pakistan. Hostility toward atheism is the majority position in all likelihood, but protests of people in the face of Islamist terror, as well as the persistence of atheists in Bangladeshi culture, indicates that there is a sufficient groundswell of liberal religious civil society that there’s a shot. In contrast in Pakistan you have a society which is now at total conformity when it comes to toleration for free thought.

Raw data:

Question: “Politicians who don´t believe in God unfit for public office”

Country Agree strongly Agree Neither agree or disagree Disagree Strongly disagree No answer Don’t know
Sweden 1.7 2.3 11.4 36.8 47.3 0 0.4
Spain 1.8 8.7 17 40.2 23.7 0 8.7
South Korea 2.6 6.7 27.3 37.5 15.4 0 10.5
Vietnam 4.5 11.9 16.9 47.4 5.8 0 13.5
Bosnia 5.1 10 30.2 25.5 22.2 0 7
Serbia 8.7 16.2 14 34.7 17.2 0 9.2
Canada 6.6 12 21.8 35.9 21.2 0 2.5
India 14.5 18.2 11.3 26.6 8.1 0 21.3
Chile 14 18.3 10 20.6 31.4 0 5.6
Japan 2.2 5.4 49.6 25.5 14.9 0 2.5
Mexico 14.9 21.5 9.2 27.3 16.2 0 10.9
Macedonia 17.7 14.7 16.8 27.5 16.6 0 6.8
Argentina 13.7 20.5 17 31.1 12.3 0 5.4
Kyrgyzstan 10.5 25 19.1 35.2 9.6 0 0.6
Moldova 11.7 28.9 21 24.1 5 0 9.2
Albania 16.1 24.8 24.7 19.2 7.2 0 8
United States 17.6 20.3 25.8 27.1 8.4 0 0.8
Zimbabwe 14.9 36.4 8.3 31.8 3.6 0 5.1
South Africa 22.9 24.6 19 19.9 7.1 0 6.5
Turkey 28.7 28.2 11.5 16.9 9.1 0.1 5.6
Venezuela 35.5 15.8 15.1 18.8 12.7 0 2.2
Uganda 25.2 36.2 14.3 17 4.3 0 3
Bangladesh 30.2 37 5.2 20 2.3 0 5.3
Puerto Rico 36.5 26.9 11.7 19.3 3.6 0.4 1.5
Tanzania 53.4 11.2 11 13.9 8.1 1 1.4
Philippines 26.8 44.4 14.7 11.9 1.9 0 0.2
Algeria 51.7 20.7 8 8.7 3.3 0 7.6
Jordan 66.6 11.1 2.1 6.8 9.3 0 4.1
Iraq 66.1 15.1 0 5.5 6.9 2.2 4.2
Nigeria 56.8 24.2 7.6 6.8 3.6 0 1
Indonesia 59.4 27.9 1.9 7.2 2 0 1.6
Morocco 72.4 14.2 2.7 4.3 1.2 0 5.1
Egypt 70.1 17.6 2.4 4.9 4.9 0 0
Pakistan 82.4 12.5 4 0.9 0.2 0 0
• Category: Foreign Policy, Ideology • Tags: Bangladesh, Religion 

The_Clan_of_the_Cave_Bear_cover By now you have heard of the recent ancient DNA finding dating from ~40,000 years ago in Southeastern Europe. The individual is a representative of one of the first anatomically modern groups to arrive in Europe…sort of. It exhibits robust characteristics, and may have had some admixture from Neandertals. Now, thanks to ancient DNA, that’s confirmed:

Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts, told the meeting how she and her colleagues had sequenced DNA from a 40,000-year-old jawbone that represents some of the earliest modern-human remains in Europe. They estimate that 5–11% of the bone’s genome is Neanderthal, including large chunks of several chromosomes. (The genetic analysis also shows that the individual was a man). By analysing how lengths of DNA inherited from any one ancestor shorten with each generation, the team estimated that the man had a Neanderthal ancestor in the previous 4–6 generations. (The researchers declined to comment on the work because it has not yet been published in a journal).

Two major points. First, the admixture fraction is way higher than any modern population. This isn’t a fluke. Second, they must be seeing ancestry tract lengths to make this inference. Basically the Neandertal ancestry blocks have been chopped up, but only a finite number of times. This really one-ups talk of “Cherokee great-grandmothers”, that’s for sure.

So what about the earlier results that most of the admixture must have happened in the Middle East? There have been revisions to this model, with many researchers now suggesting that a second pulse might have occurred in eastern Eurasia. But, another possibility is that very little of the ancestry of the first modern Europeans remains in modern Europeans. That is, the later Paleolithic populations of Europe may have replaced the first settlers, just as they in their turn were replaced or assimilated. The landscape of Mesolithic/Neolithic Europe seems demographically complex, so I see no reason not to suspect that the same was the case for the period before the Last Glacial Maximum. There may have been several admixture events with Neandertals, but the “outriders” may have been left no traces in the modern human lineages. It may be that the human “phylogenetic bush” has been extremely pruned many times over, so that most “fossil ancestors” are simply dead ends.

Addendum: As usual, great piece in Nature too.

• Category: Science • Tags: Paleoanthropology 

Screenshot from 2015-05-13 07:47:30 In a review for the new installment of Mad Max Dana Stevens in Slate writes:

The way the world ends, for Miller, is not in overpopulated high-tech megacities slicked with film-noir rain, but in something like the polar opposite. Miller’s nightmare of the future posits the planet as a parched desert landscape against which the world’s few remaining humans scratch out a meager, violent existence, equipped only with the salvaged remains of mid-20th-century technology. It’s that future that, 36 years after Mel Gibson first put the pedal to the metal as Max Rockatansy, is looking more like the one we may be leaving to our own survivors….

I understand this is a movie review, and that line was probably thrown in there for artistic effect. But facts matter, and there is no way that you justify the position that the world is more like that of Mad Max today than 40 years ago. Paul Ehrlich has definitely lost his bet, and even the peak oil worry has abated. The data show that a smaller proportion of the world’s population is undernourished and and poor. The total fertility rate is declining and life expectancy is increasing. Yes, the situation of the middle class in much of the developed world has been in relative stagnation by many metrics, but enormous increases in human well being have occurred throughout what was once termed the Third World.

The Right and Left have particular hobbyhorses. Young people today are more secular and tolerant of sexual diversity in lifestyles, but they are also less sexually promiscuous (we were blogging about this at Gene Expression seven years ago by the way). Similarly, despite worries about income inequality in the developed world, billions are rising out of poverty in places like China and India. Yes. Billions. Though environmental threats exist, the world is healthier and wealthier than it was a generation ago.

It’s not very important that Dana Stevens’ editor didn’t remove a rhetorical flourish which was just factually unfounded (though I it’s insulting to the people of places like the Sahel who suffered through privation a generation ago, and no longer do so). But, it does suggest a mental weakness that these sorts of slips get through, to influence the public, and continue to distort the perceptions of the way the world is. To prepare for the exigencies of the future we need to see the present clearly.

• Category: Ideology • Tags: Environmentalism 

god-is-back Long-time readers of my content know that about 10 years back I used to make fun of a book by two writers for The Economist, God Is Back: How the Global Revival of Faith Is Changing the World. It was a sexy thesis, but really it was meant to appeal to paranoid liberals who were scared, as well as reassure religious conservatives worried about “a secular age.” The basic idea was that religious views and values were ascendant again, not a totally crazy thesis on the face of it. The problem is that the data in some regions were already suggesting major changes in the direction of secularism, in particular in the United States. This change took most people by surprise unless they were looking closely. Samuel Huntington’s last book, Who Are We?, was written unfortunately in the late 1990s just before the release of multiple academic surveys which chronicled the rapid de-Christianization of vast swaths of the American populace. In it Huntington took for granted the thesis that America would become more, not less, Christian, as more Asian Americans converted to Christianity, and the Hispanic Catholic fraction increased (contrary to visible evangelical Asian-American Christians, this is the least religious of America’s ethnic groups, and Hispanics are secularizing very fast).

Even though the data are pretty clear, and were for a long time, people tend not to update. And timing is always an issue. For example, the last major wave of secularization in the USA happened in the late 1960s, before which Time Magazine published Religion: Revival’s Crest in 1963. In the early years of my blog I kept having to remind people of facts when they relied on impressions. In 2009 I corrected The New York Times’ John Tierny, who stated that “As an agnostic myself, I’ve tended to see the European trend as a harbinger of a general move toward secularism as societies become richer and more educated. But you don’t see that trend in the United States, where church attendance is still robust….” I happen to know his email address and I sent him my post. He wasn’t convinced that I was right even then. I bet now he would admit that the data were robust.

PF_15.05.05_RLS2_1_310px I suspect that a new survey from Pew (very large sample sizes) is going to change resistance even from holdouts who don’t want to read the writing on the wall, America’s Changing Religious Landscape. The major “shock result”, which has been prefigured elsewhere, is that huge numbers of younger Americans are not religiously affiliated, and larger fractions are now admitting to being atheists and agnostics. The change over the generations has been enormous, going from a nation that’s over 85 percent Christian, to 70 percent Christian, mostly driven by defection. Before the 1990s religious adherence was a matter of social conformity. Far less today when 25 percent of the population does not have an affiliation, and even less so in regions where religious adherence may even be a subculture, rather than a norm. The fraction of the unaffiliated who are atheists and agnostics is also increasing, suggesting that the taboos around these terms are declining (I doubt I’d get as many shocked expressions saying I’m an atheist today in Red America as I did in the early 1990s).

agcover165.jpg What does this portend for the future? Over 1/3 of those born in the 1980s and 1990s have no religion. These are people who will be retiring in the 2040s and 2050s, the grandparents of that era. The trends, which are not guaranteed, mind you, indicate then that future generations may be even more secular, so that the electorate of that period may be extremely polarized in terms of religious culture (as the fractions of evangelicals is holding its own better than other Protestants and Catholics). This result was already evident in Robert D. Putnam’s American Grace: How Religion Divides and Unites Us, which received far less attention than Bowling Alone. But it was an important finding. Basically, the association of religion and right-wing politics has been having a secularizing effect on non-right wing Americans, and making ostensibly right-wing individuals more religiously identified. In other words, socially binding cross-cutting institutions are unraveling.

I believe this is more important than the coming “white” minority of 2050. The reasons are manifold. In the early 2000s some Democratic strategists saw an emerging majority from the coalition of minorities. On the other side many on the Right feared the rising tides of color, implicitly or explicitly. Nearing the end of the Obama era we now see how this story did not turn out to be so neat, with one of the proponents of demography-as-Democratic-density now recanting. Obviously we need to be cautious about over-reaction. The white Protestant conservative demographic core of the modern Republican party, and American conservatism, is going to decline somewhat over the generations. But the basic thesis that all non-white populations will vote Democratic indefinitely for generations seems unfounded. And definitions matter. Many Americans of mixed backgrounds may be assumed by Left-liberals to take the black tack of hypodescent, but they may actually simply exhibit more flexible self-identities which do not disassociate them so much from the mainstream (people who are visibly white, but have non-white ancestry, do not react well to racism against non-whites for obvious reasons, but neither are they anti-white, and often identify as white).

In an America where racial boundaries are fuzzier and more malleable, the strictness enforced by social-cultural categories in theory may actually be appealing and bracing. This goes to the heart of genetic vs. cultural distance in variation. Genetic variation rapidly diminishes due to the constraints and conditions of biological inheritance. Cultural inheritance is theoretically more powerful and airtight. As the ethno-biological categories melt on the edges, religious-cultural ones may emerge to more fully demarcate various tribal-political coalitions. And this is part of the reason why religion may increase in salience, despite the rapid expansion of a non-religious population. Confessional politics may come to the United States in an explicit fashion with the decline of implicit normative convention.


51KXqRwj+gL._SY344_BO1,204,203,200_ Some of you may wonder as the Americo-centric focus of this post, especially light of another recent Pew survey which highlights religion’s international robustness, The Future of World Religions: Population Growth Projections, 2010-2050 (as well as books I’ve blogged such as The Next Christendom: The Coming of Global Christianity and Shall the Religious Inherit the Earth?). First, international projections are dicier than national ones. More variables are on the move. You can’t predict easily the rapid secularization you saw in Quebec in the 1960s, in the United States in the past 15 years, or, the glimmers of change on the horizon in the Arab world. Second, what happens in the developed world matters more. The huge numbers of African Christians will result in change. But, Catholicism will still be based out of Rome, and intellectual currents out of Western Christianity will likely shape Sub-Saharan African Christianity more than the reverse. Philip Jenkins in his work celebrating African Christianity nonetheless observes that over time indigenous religious traditions begin to align themselves with world-normative practices, often to standards established in Western societies.

• Category: Race/Ethnicity • Tags: Religion 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"