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Citation: Complex History of Admixture between Modern Humans and Neandertals

In 2010 when the Neandertal sequence paper was published the word was that all non-Africans had the same proportion of ancestry from this population, a few percent. Over the past few years researchers have looked closer, and come to the conclusion that that was wrong. In particular, East Asians seem to have ~20 percent greater Neandertal ancestry than Europeans. Why? A simple solution is that there were several admixture events with Neandertals on the way out of Africa as modern humans settled the world. But there are other options, making recourse to standard population genetic theories. So last year in The genomic landscape of Neanderthal ancestry in present-day humans proposed that the higher fraction in East Asians in Neandertals was a function of the weaker efficacy of purifying selection, which removes deleterious alleles from the genetic background, in populations which went through bottlenecks. As you may know, East Asians seem to have gone through more bottlenecks in the out of Africa migration, probably because of several choke points from west to east Eurasia.

Two new papers in The American Journal of Human Genetics seem to suggest that this explanation is unlikely. First, in Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in East Asian than in European Human Populations, the authors use simulation frameworks to suggest that the extent of the bottleneck difference can not account for the difference in ancestry fractions. In other words, there isn’t that much variation in purifying selection. In the second paper the authors explicit test the ‘two pulse’ model vs. the ‘single pulse’ model. To remove the confound of selection they looked at neutral regions, and the difference persisted. Though the authors could not rule out the possibility that Europe received an influx of African-like individuals who reduced the Neandertal fraction in western Eurasian, the three ancestral populations which fused to form Europeans (i.e., hunter-gatherers, first farmers, and the steppe invaders) all had about the same Neandertal fraction. This leaves then the possibility that East Asians received a second dollop of Neandertal ancestry, ergo, the two pulse model.

A few years back Jeff Wall published a paper that showed that the Complete Genomes Gujarati samples were in between the Europeans and East Asians in Neandertal fraction. We know that the “Ancestral South Indian” (AS) fraction of Gujarati ancestry is closer to East Asians than to West Eurasian groups. To me this suggests that the second admixture may have occurred in the eastern zone of the Middle East, seem it seems basal to the eastern lineages of humans.

The topology of the human phylogenetic graph is getting somewhat more complex. But there are diminishing returns. We’re arguing over tenths of a percent now, as opposed to percents. In the near future this book will be probably be closed.

 
• Category: Science • Tags: Neandertals 
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Over the past week or so the perpetual argument about whether we were “superior” to Neandertals or not has cropped up again, thanks to a new paper in PLoS ONE, Neandertal Demise: An Archaeological Analysis of the Modern Human Superiority Complex. In it the authors utilize material remains to infer that no, in fact Neandertals were not “inferior”, and their demise was more a matter of demographic assimilation than competitive exclusion and extinction. To get the “other perspective” in a measured fashion I recommend this interview of Chris Stringer in National Geographic.

The-Dawn-of-Human-Culture As I suggest above this debate has gone back and forth for a long time, and seems subject to fashion as much as empirical results. Ten years ago the Stanford paleoanthropologist Richard Klein published The Dawn of Human Culture, which laid out very cogently the dominant perspective of the time that Neandertals were not humans as we understand humans, and were superseded by a neo-African lineage which was gifted with the bio-behavioral capacity for exceedingly flexible and protean cultural adaptability. Klein’s central conjecture is that ~50,000 years ago a subset of ancient humans in Africa developed the biological capacity for cultural creation on a scale unprecedented before in the hominin lineage. He appealed in a rather hand-wavy fashion to punctuated equilibrium to serve as the basis for what was basically a model of modern human origins out of a single saltation event. Though not perhaps in every exact detail, the broad outlines of Klein’s thesis were accepted as part of the “Out of Africa” canon which had crystallized over the previous 20 years. Modern humans came, they saw, they conquered.

All this changed in 2010 when A Draft Sequence of the Neanderthal Genome was published. Over the past four years the general inference established in this paper, that a few percent of non-African human ancestry derives from Neandertals, seems to have been supported by further publications. At the time I observed, and have continued to see, a trend to humanize Neandertals. After all, they were in part our ancestors, so the previous dehumanization now seems rather uncharitable. Klein and his fellow travelers even hypothesized that Neandertals did not have language, that complex speech may have been the bio-behavioral shift which allowed for the rapid expansion of neo-Africans. Though those who study science and claim that it is strongly shaped by cultural priors tend to become overly enthusiastic about this dynamic, there is some truth in it, and how we view Neandertals does seem subject in part to what we want them to be.

But it’s hard to shake the intuition that there was something special about neo-Africans 50,000 years ago. Stringer lays out the archaeological perspective, what I might term the “Great Leap Forward-lite” model. Complex, elaborate, and protean cultural expression with symbolic connotations seem to have exploded exponentially after the expansion of neo-Africans. That’s hard to deny. It’s easy then to make the leap to assuming that this cultural change was due to a biological change.

My own primary reason to be swayed by the view that neo-Africans were different in some fundamental and biological way is not much informed by archaeology, since I have only a superficial grasp of this field. Rather, it is the fact that it is neo-Africans who crossed the Wallace Line, and ventured into the New World. Hominins, humans of some kind, were present across Eurasia for over one million years, but it took neo-Africans to expand the frontiers of the Homo range almost immediately after they appear on the scene outside of the original contintent. That’s not in dispute at all, and requires no deep and specialized knowledge.

And yet this point does make me think somewhat about what to make of the Polynesians. The ancestors of the Melanesians arrived in “Near Oceania” ~30,000 years ago, and there they stopped. It took 25,000 years for humans to push past the eastern fringes of Melanesia into the vast Pacific, with the arrival of the Austronesian Lapita culture. As you can see on the map above the Austronesian maritime range was incredible, from Madagascar all the way to Easter Island off the coast of Chile. In fact it seems likely that Austronesians were the first settlers of Madagascar, as opposed to Africans from the relatively nearby coast. Using the same logic that informs my perception of Neandertals vs. neo-Africans one might ask if the Austronesians of Taiwan were somehow biologically different from the Melanesians. Perhaps there was a mutation which compelled the Austronesians on their long journey out of Taiwan?

The point here is not to underplay biological differences between Neandertals and neo-Africans. The fact that there seems to be a paucity of Neandertal ancestry on the X chromosome is suggestive of hybrid incompabilities. But, the conclusions one draws from the facts seem to be strongly colored by the model which one already presupposes. As a matter of fact there may be bio-behavioral differences between modern human lineages which explain differences in cultural expression. But obviously these are not so clear in a genetic sense. When we think of differences between Neandertals and neo-Africans it is often as if the traits were disjoint between the two groups. But perhaps it is a much more subtle and nuanced biological difference, which was ratcheted upward and amplified by the flexible nature of human culture. The rise and fall of neo-African cultures themselves exhibits an almost inexplicable waxing and waning. There is no reason it had to be any different in the past.

 
• Category: Science • Tags: Neandertals, Out-of-Africa 
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Citation: Patterns of coding variation in the complete exomes of three Neandertals PNAS 2014; doi:10.1073/pnas.1405138111

Citation: Patterns of coding variation in the complete exomes of three Neandertals
PNAS 2014; doi:10.1073/pnas.1405138111

A new paper in PNAS, Patterns of coding variation in the complete exomes of three Neandertals, reiterates what seems to be an emerging fact about ancient northern Eurasian hominins: they were rather inbred. The chart above illustrates it by focusing on regions of the genome that code for proteins. The ratio of benign to deleterious for Neandertals is obviously not optimal. As noted in the paper the authors suggest that this implies small population sizes which could not purge the deleterious variants through negative selection. The operative dynamic here is that when populations are small, drift becomes very strong relative to selection, and can therefore increase frequencies of mutations which would otherwise be swept out of the genome.

And it is clear from a variety of standard population genetic metrics that these Neandertals, separated geographically by the expanse of all of Eurasia, and distinct over ~20,000 years, would be considered quite inbred if they were examined today. This is curious because it is often stated that humans, our own neo-African lineage, are a relatively homogeneous population which expanded rapidly in size recently. We haven’t had that much time to diverge, and non-Africans tend to have genomes suggestive of bottlenecks in the deep past. And yet looking at these Neandertals, as well the Denisovan individual, modern humans seem a positively genetically variegated lot in comparison. But the authors of the above paper also found something else interesting, the Neandertals were themselves very distinct from each other, more distinct in terms of between population variation than modern human lineages. The main caveat is that the individuals were separated in time by thousands of years, in additional to geography, and the authors don’t seem to have corrected for this aspect of drift (though then they’d have to have an explicit demographic model, which they may not have enough information to construct). Additionally I do wonder if pre-Holocene humans also exhibited the same pattern of high genetic distance over small regions, and that only the demographic expansions and admixtures of the past 10,000 years have produced the reduced F st values that we take for granted as expectations.

Finally, I have to emphasize that looking at hominins on the edge of the human range on the north may not be representative of archaic lineages more broadly. It seems possible that meta-population dynamics characterized by extinctions and expansions, and very low effective population size, were much more normal on the northern fringe of marginal habitation than further south in the core of the hominin range. Imagine taking Amerindians as representative of human variation, as an analogy. Because of the preservation bias in ancient DNA we’ll always over-sample these northern locales, but we should be wary of over-generalizing.

Addendum: I didn’t say much about the functional differences, because I’m not sure that we can say much with the data sets that they had. It is suggestive that they found differences in genes related to skeletal morphology in Neandertals, but that is not surprising. The fact that modern humans may be enriched for differences and evolution in regards to pigmentation seems likely to be a bias of the fact that this area has been well studied in modern humans. Obviously there haven’t been genome-wide associations for this trait in Neandertals, since we don’t have cases and controls (to my knowledge).

 
• Category: Science • Tags: Neandertals 
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Another Neandertal paper in Proceedings of the Royal Society B. But, because there is a delay between when the press is released to talk about it, and when it goes live, I haven’t gotten a look at the primary material. There’s a lot of juicy stuff in this piece at NBC Science though, Brain comparison suggests that Neanderthals lacked social skills. The two scientists giving quotes, Chris Stringer and Robin Dunbar, know their stuff (one of Dunbar’s graduate students also contributed heavily). In case you don’t know Stringer, he is the paleoanthropologist who was most forceful in pushing for the “Out of Africa” model. Dunbar is the popularizer of Dunbar’s number. I’m assuming Stringer brings the anatomy to the game, while Dunbar frames the bigger theoretical picture. Basically the morphology of the cranium implies that Neandertals may have allocated more of their cognitive capacity to vision and coordination, and less to social activities (because there’s not as much room for the latter). This explains how Neandertals could have a larger cranial capacity than modern humans (they did, though so did Ice Age modern humans) but be somewhat less “intelligent” than us (regular readers know I’m not a big fan of scare quotes for intelligence, but in this case I think it’s warranted).

The main problem I have isn’t the conclusion. It’s plausible enough. But the whole framework of understanding the difference between ourselves and Neandertals has changed in the past 10 years. In short, 10 years ago it might be defensible to assert Neandertals were another species. This is not so today. Rather, most of us are Neandertals (in part). When Richard Klein wrote the Dawn of Human Culture the chasm between Neandertals and humans in a phylogenetic sense was large. This made more plausible sharp and crisp differences in traits between the two distinct and separate populations. Now it is harder to maintain that cordon, because it seems likely there was admixture between modern humans and Neandertals. The difference between Neandertals and moderns has now become one of degree, rather than kind. So, for example, the idea that Neandertals were at the far end of the autism spectrum based on some suggestive genes.

Papers will be published and careers will be made positing traits which led to the downfall of Neandertals. But until the phylogenetic origin of our own lineage, and possibly those of sister lineages, becomes more rock solid I think this is not particularly useful. We can’t bring back Neandertals and run experiments, so any hypothesis and inference generation system must be interpreted in light of background assumptions. Currently we are picking up signs of punctuated admixture events, but what if there was more constant gene flow between different human lineages? The behavioral differences may be subtle indeed if the latter occurred.

Why we are not mostly Neandertal is I think more soluble right now than understanding the evolution of language. But I don’t think there’s any problem right now in confidently admitting that we really don’t know a lot of things.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Anthropology, Neandertals 
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A month ago I posted Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology, in response to James Fallows at At 5% Neanderthal, You Are an Outlier. Fallows has now put up a follow up, The Neanderthal Defense Committee Swings Into Action, where he links to my response post. This prompted the original archaeologist in question to reach out to me via email. I am posting the letter, with their permission, below.

Hello!

I’m dropping an email because I followed a link from Fallows to find my email to him highlighted negatively on your blog. I’ve emailed a few times with Mr. Fallows on various topics and had no idea he was going to post that email – he didn’t ask until after it was already up and so, yes you’re right it was a casual dashed off email and confused two different articles (both of which incidentally I have read so please no more comments on what I may or may not have done). Mea Culpa. And you’re right, I’m not a geneticist – I’m not even a lab scientist. However, I know a heck of a lot about archaeology and I work closely with lab scientists including several colleagues who specialise in ancient DNA.

The thing that I’m writing about isn’t a defense of myself (such as I need it) but rather a defense of archaeologists’ right to comment on other, linked fields. The attitude you displayed in that blog post was one my colleagues and I encounter frequently from the people with whom we attempt to collaborate – sometimes it’s a light (but head shaking) critique such as yours, sometimes it’s closer to amused contempt. Archaeology as a discipline is intensively interdisciplinary in a way that other fields are not, so we find ourselves constantly working out of our specific specialty and with colleagues whose knowledge of closely allied fields is far deeper than ours ever will be. Such is the nature of a field that requires us to be historians, philosophers, social theorists, materials scientists and, now, geneticists. You can shake your head and suggest that the archaeologists should stay out of genetics, but without the larger narratives (such as the out of Africa theory – based in large part on the type and presence of ancient human remains, carefully excavated and reassembled) and archaeological contexts which we create and control, respectively, geneticists would not be able to say anything at all about ancient remains.

I, like many of my colleagues, have been excited to see the results of initial work into ancient DNA; but, like many of my colleagues, I am highly skeptical that we have adequate procedures in place to deal with the contamination. Until the 2010 study is replicated a few more times – and as long as numerous studies from various labs continue to emerge showing the problems of contamination – my skepticism will remain. I don’t know if you have ever been around an archaeological excavation, but they are messy places. There are many people involved (from volunteers and local paid diggers to students of various skill levels and ages to directors, land-owners and visitors) with different amounts of knowledge, different amounts of supervision and, invariably, not enough time to do what they’re trying to do. Keeping remains uncontaminated is an enormous struggle – whether for DNA analysis or for the more frequently undertaken C14 dating. Even when collected and stored to the highest standard, and those standards are different on every excavation in every country, many of the samples are so obviously flawed that one is forced to wonder about the less obvious ones.

In writing James Fallows, I was not trying to be a singular authority, but to encourage some skepticism – especially in light of breathless blog posts and newspaper articles. If you think the popular press gets science wrong, become an archaeologist. Every time our field is mentioned in a newspaper, on the internet or in a film, we despair. Unfortunately, this popular presentation of archaeology has seeped so far into the cultural fabric that we’re constantly having to prove that we are more than just treasure hunters, particularly over-qualified ditch diggers or vague historians who don’t bathe often enough.

I’m happy to talk further about genetics (which you’ll have to be patient about), archaeology (which you might need to be a bit patient about) or Neanderthals, but for now, let me finish by encouraging you, in future, when critiquing strangers online to reach out and perhaps try and find out who those strangers are because they might actually have something to say.

With best wishes,

[name redacted]

As I told my correspondent I agree with much of the sentiment above. Rather, the problem in the general sense is that James Fallows should have been cautious about taking the expertise of a non-geneticist for granted when it came to genetics. Second, on the specific issue of contamination, I think Nick Patterson’s comment is the sort whose thrust should convince non-specialists:

(I was an author of both the Green et al (Neandertal) and Reich et al (Denisova) papers) When thinking about contamination it’s important to realise that contamination will look like modern human gene-flow -> archaics. But we find very strong evidence for flow in the reverse direction.

Additionally, remember that Denisovans and Neandertals seem to form a distinct clade in relation to modern humans. I have difficultly understanding how modern contamination would result in this pattern.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Anthropology, Archaeology, Genetics, Neandertals 
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If you have a hard time following all the Neandertal genomics findings from the last few years, and their implications, National Geographic has a really thorough piece up. It’s a good digest of all the news you can use. One thing I would like to add: from what I can tell the probability of the signals of admixture in non-Africans being genuinely Neandertal seem to be increasing as we progress. In other words, you should weight the “other side” (ancient population structure, where some African populations were closer to Neandertals before they left Africa) less than you did in 2010.

Of course one of the more inevitable aspects of the admixture story has been the humanization of Neandertals. I don’t know how I feel about this. Should our own affinity to Neandertals alter our view of their behavior or anatomy? Plenty of behaviorally anatomically modern humans were beastly after all.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Human Evolution, Neandertals 
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John Hawks prompts to reemphasize an aspect of my thinking which has undergone a revolution over the past 10 years. I pointed to it in my post on the Khoe-San. In short, the common anatomically modern human ancestors of Khoe-San and non-Khoe-San may not have been people. Rather, people may have evolved over the past 100-200,000 years ago. Of course the term “people” is not quite as scientific as you might like. In philosophy and law you have debates about “personhood”. Granting the utility of these debates I am basically saying that the common ancestor of Khoe-San and non-Khoe-San may not have been persons, as well understand them. Though, as a person myself, I do think they were persons. At this point I am willing to push the class “person” rather far back in time.

As I suggested earlier there is an implicit assumption that personhood is a shared derived trait of our species. Or at least it is a consensus today that all extant members of H. sapiens are persons. Since Khoe-San are persons, the common ancestor of Khoe-San and non-Khoe-San must also be persons if personhood is a shared derived trait. But, we also know that there are many aspects of realized personhood on a sociological or cultural scale which seem to diminish the further back in time you go. For example, the Oldowan lithic technology persisted for ~1 million years. A common modern conception of persons is that persons in the aggregate are simply never so static. Persons have culture, and culture is protean. Therefore, one might infer from the nature of Oldowan technological torpor that the producers of that technology were not persons.


But there’s a large gap between the decline of the Oldowan and the rise of anatomically modern humans. Where to draw the line? Let’s take a step back about a decade. Here’s an extract from Richard Klein’s excellent Dawn of Human Culture:

Our third and final observation is that the relationship between anatomical and behavioral change shifted abruptly about 50,000 years ago. Before this time, anatomy and behavior appear to have evolved more or less in tandem, very slowly, but after this time anatomy remained relatively stable while behavioral (cultural) change accelerated rapidly. What could explain this better than a neural change that promoted the extraordinary modern human ability to innovate? This is not to say that Neanderthals and their non-modern contemporaries possessed ape-like brains or that they were as biologically and behaviorally primitive as yet earlier humans. It is only to suggest that an acknowledged genetic link between anatomy and behavior in yet earlier people persisted until the emergence of fully modern ones, and that that postulated genetic change 50,000 years ago fostered the uniquely modern ability to adapt to a remarkable range of natural and social circumstances with little or no physiological change.

Arguably, the last key neural change promoted the modern capacity for rapidly spoken phonemic language, or for what anthropologists Duane Quiatt and Richard Milo have called “a fully vocal language, phenmiized, syntactical, and infinitely open and productive.”

The non-moderns were not ape-like, but they were clearly not human-like, if they lacked language as what we understand language to be. Today this view is likely in the minority position, but why? I think the possibility of admixture between these distinct human lineages suggests that the gap between “them” and “us” was not quite as large Klein postulates above. And even then there is a major problem with Klein’s thesis: there was mitochondrial and archaeological evidence even then that the divergence of the Khoe-San and non-Africans far pre-dated the 50,000 year time period alluded to above. Since then the evidence has become even stronger that the divergence of the Khoe-San from other humans, and likely Africans from non-Africans, pre-dates the emergence of “behavioral modernity.”

An implicit assumption that personhood is a shared derived trait from a common human ancestor to me speaks to the same needs and urges which posit a specific ensoulment or creation of humanity from clay. Our minds are not very good at continuities, so we must create distinctive breaks. One moment an animal, and another moment a man! The occasional scientist who speculates that there may be a set of genes which define humanity I think falls into the trap of assuming discontinuity where there is none. There may be no genetic variant necessary or sufficient to being a human. Let me finish by quoting John Hawks, who inspired me to be a bit more explicit in my own line of thinking:

Personally, I think that “cognitive modernity” is a red herring. Today’s people learn some kinds of technical and symbolic complexity that were never present in ancient peoples. Some people living today in Western cultures, despite all our educational efforts, fail to attain levels of technical knowledge that are regular outcomes for the majority of people in the same environment. Human performance varies continuously.

I assert that it is unreasonable to suppose that Neandertals had a “stupid gene”. If so, it should be just as unreasonable to suppose that a “smart gene” could explain the evolution of human cognition during the last 100,000 years. These unrealistic assumptions are widespread, and impede our understanding just as thoroughly as assumptions about the nature of biological species impeded our understanding of Neandertal ancestry of living human populations. Some archaeologists have concluded that Neandertal cognition is an either/or proposition. Some look at Neandertals, find a lack of evidence that they behave identically to later people, and conclude that the Neandertals were therefore unquestionably cognitive inferiors. Others look at Neandertals, find some signs of modern-like behaviors, and conclude that Neandertals were therefore unquestionably our cognitive equals.

Cognition in modern humans varies continuously across many axes of variation. No two humans are cognitively identical in outcomes. Nor can we appeal to “cognitive capacity”, a meaningless abstraction unless we are discussing a particular structured learning environment in which the outcomes are potentially measurable. Will we someday raise a Neandertal in a human society to see whether and how they attain the skills and abilities we consider essential?

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Anthropology, Human Evolution, Neandertals 
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Last August I had a post up, The point mutation which made humanity, which suggested that it may be wrong to conceive of the difference between Neanderthals and the African humans which absorbed and replaced them ~35,000 years ago as a matter of extreme differences at specific genes. I was prompted to this line of thinking by Svante Pääbo‘s admission that he and his colleagues were searching for locations in the modern human genome which differed a great deal from Neanderthals as a way through which we might understand what makes us distinctively human. This sort of method has a long pedigree. Much of the past generation of chimpanzee genetics and now genomics has focused on finding the magic essence which differentiates us from our closest living relatives. Because of our perception of massive phenotypic differences between H. sapiens and Pan troglodytes the 95-99% sequence level identity is thought by some to be perplexing. Therefore models have emerged which appeal to gene regulation and expression, or perhaps other forms of variation such as copy number, to clear up how it can be that chimpanzees and humans differ so much. Setting aside that the perception of difference probably has some anthropocentric bias (i.e., would an alien think that chimpanzees and humans are actually surprisingly different in light of their phylogenetic similarities? I’m not so sure), it doesn’t seem to be unreasonable on the face of it to plumb the depths of the genomes of hominids so as to ascertain the source of their phenotypic differentiation.

But can this model work for differentiating different hominin lineages? Obviously there’s going to be a quantitative difference. The separation between chimpanzees and modern humans is on the order of 5 million years. The separation between Neanderthals and modern humans (or at least the African ancestors of modern humans ~50,000 years B.P.) is on the order of 500,000 years. An order of magnitude difference should make us reconsider, I think, the plausibility of fixed differences between two populations explaining phenotypic differences.

 

Backing up for a moment, why do we think there might be fixed differences between Neanderthals and modern humans? The argument, as outlined in books like The Dawn of Human Culture, is that H. sapiens sapiens is a very special lineage, whose protean cultural flexibility allowed it to sweep of the field of all other hominin sister lineages. The likelihood of some admixture from these “dead end” lineages aside, this rough model seems to stand the test of time. Consider that the Mousterian technology persisted for nearly 300,000 years, while the Oldowan persisted for 1 million! In contrast, our own species seems to switch and improve cultural styles much, much, faster. Behavioral modernity does point to a real phenomenon. The hypothesis of many scholars was that there was a genetic difference which allowed for modern humans to manifest language as we understand it in all its diversity and flexibility. The likelihood of this seems lower now that modern humans and Neanderthals have the same variants of FOXP2, the locus which seems to be correlated to elevated vocal and auditory capabilities across many vertebrate lineages. And, if it is correct that ~2.5% or so of modern human ancestry in Eurasia, and nearly ~10% in Papua, comes from “archaic” lineages, then I think that should reduce our estimates of how different these humans were from the Africans.

Therefore you can posit two stylized scenarios of contrasts between Neanderthals/modern humans and chimpanzees/modern humans. In one model the difference between the two comparisons is fundamentally of degree. Neanderthals and chimpanzees are still disjoint from modern humans. That is, there’s no overlap in the traits. But, Neanderthals are far closer to modern humans, as would be likely expected from the phylogenetic relationship. Another model though is that Neanderthals and modern humans did differ, but there was a great deal of overlap. This is a model with qualitative differences from that of chimpanzees vs. humans. If the second model is correct, and I think with all that we know from the Neanderthal genome project would should take it more seriously, then looking for disjoint pairwise differences in allele frequencies is not the way to go in understanding how the two human lineages diverged in phenotype.

In the second model, where there is a great deal of overlap, there is still a difference in the tails of the distribution. The idea I had in mind with my earlier post was that it is at these tails that the differences between Neanderthals and modern humans will be found when it comes to cultural differences. I think one might wonder where the Michelangelo or a Bachs of the Neanderthals were, but then one has to observe that the vast majority of modern humans are not Michelangelo or a Bachs! One of the primary indications of the transition to behavioral modernity is the proliferation of symbolism. But are we to presume that every member of an ancient Paleolithic tribe was equally capable of creative virtuosity? I think likely not. It could be that in fact the vast majority of “modern humans” are no different from all Neanderthals in the sort of things we might expect to be different across the two lineages. Rather, it may be that a small minority of modern humans crossed a particular threshold at the edge of the distribution of the phenotype, and when that transition was made the world was never the same.


Julius Caesar

I’m not proposing here that the victory of African humans ~50,000 years ago was due to artists. What I’m proposing is that at some point a critical mass of exceptional individuals arose. These individuals were possessed of peculiar characteristics, but instead of these characteristics making them outcasts, the qualities which they possessed were seen by their fellow humans as marks of greatness. In short, they were the children of gods among men.

Or perhaps demons. Men such as Alexander, Napoleon, and Hitler, were possessed of peculiar charisma, but whether they were good or evil is a matter of dispute and perspective. The point is not that they achieved greatness, but that they were the catalysts for a great number of events. As charismatic leaders they took collections of human beings, and turned them to their purpose. Individual humans became more than the sum of their parts, and for moments exhibited almost organismic levels of cohesion. Though the number one predictive variable in who won wars in the pre-modern world is the simple one of numbers, organization and structure also mattered. The Roman legion operating in a Testudo formation could beat off the attacks of more numerous barbarians who were physically more robust on a per person basis because the unit exhibited synergy, and translated cohesion into efficient collection action. This does not occur bottom up, but requires a personality type, a genius, to serve as the nexus or locus.

The model I have in mind then is one where the African humans faced up against their near relations, but not as one against one. Rather, under the guidance of charismatic leaders, Paleolithic megalomaniacs driven by fervid nightmares and irrational dreams, they ground through the many enemies who fought as sums of singulars as a cohesive social machine. It was not because they were superior on a per unit basis, but because they were superior on a per tribe basis, driven by individuals who turned the many to their own ambitions. With the lever of superior social organization the few moved the world, and swept over it. How many insane voyages were their east over the horizon from Sundaland before one tribe finally made landfall in Sahul? How many tribes perished in the ice of the far north, before some finally made it to Beringia? Why did humans look over the horizon, and venture out across the black waters? Perhaps just because they could. This answer is likely confusing and disquieting to many alive today, and perhaps it was disquieting to the more reasonable and level-headed “archaics” who were confronted with the zealous organizational insanity of the African humans who were rolling all opposition. But these insane individuals still move among us today, and they are still the objects of curiosity, fear, and adulation.

Is this a crazy model? Yes, somewhat. But is it really anymore crazy than the model that there is a mutation which can encapsulate all that differentiates man from beast-man? I think not.

(Republished from Discover/GNXP by permission of author or representative)
 
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“There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare [children] to them, the same [became] mighty men which [were] of old, men of renown.”

- Genesis 6:4

The Pith: Pygmies and Khoisan have admixture from a distinct population at the level of ~2%. This population diverged from the other ~98% of their ancestry ~700,000 years before the present, and the hybridization occurred ~30-40,000 years before the present. Most other African groups have only traces of this element, with some West Africans lacking it.

I have read the paper in PNAS which I referred to below. There isn’t that much I can add at this point. A lot of the guts were pushed into the supplements, which aren’t on the web yet. I was correct that the Mbuti Pygmies of the eastern Congo likely have a special place in this possible admixture event. In particular, they seem to possess the diverged variants found in the western Pygmies, the Biaka, and the Khoisan populations of southern Africa. As assumed the pattern of admixture seems to be such that the two Pygmy groups and the Khoisan exhibit elevated signatures of archaic contributions, while other African groups manifest admixture in direct proportion to their known admixture to the aforementioned populations. For example, the Bantu group with the highest proportion of admixture are the Xhosa, who also have the most Khoisan ancestry of non-Khoisan populations. The West African Mandenka seem to have trivial admixture from this archaic group. What does this mean?


First, let’s stipulate that this is a model which infers the past from the variation we have on hand. In this way it is qualitatively a different method than that used to ascertain the Neandertal or Denisovan admixture events, which derived from comparisons of moderns with the concrete genome of these ancient lineages. The authors in the PNAS paper observe that the likelihood of ever replicating the non-African results within Africa is low because of the nature of fossil preservation. The likely region of admixture, central Africa, is simply not conducive to the preservation of fossils, let alone genetic material. Now, I have stated before that I am cautious of results from computational models because they regularly reported no admixture as well, further confirming “Out of Africa” with 100% replacement. The change here is that our expectations have been shifted by the possibility of admixture outside of Africa. By testing the power of their models on the Eurasian findings they firmed up their credibility in the absence of ancient DNA. These authors used 61 non-coding genomic regions to reach their conclusions. One presumes that these findings should become more compelling once researchers start performing full genome analyses. If not, then they may be spurious.

With that out of the way, let’s review the results and what they mean on the assumption that they’re valid. The PNAS paper supports a model where a subset of descendants of anatomically modern humans (AMH), and an unnamed archaic group, population X, hybridized relatively recently. Within the last ~40,000 years or so. It seems that this post-dates the “Out of Africa” migration. This should not be shocking, and hopefully will dispel the strange notion that Africa remained static after the emergence of AMH (which leads to some reconstructions of early Eurasians as looking like modern Africans!). It also hints at the possibility that contemporary Pygmies and Bushmen are not the ur-humans, the oldest of old, but rather novel morphs which derive from a recent hybridization event (just like non-Africans).

This brings us to why Pygmies and especially Bushmen were assumed to be ur-humans, the best exemplars of early AMH: they’re basal to other human populations, AMH fossils are found in eastern and southern Africa at a very early date, and they are the most genetically diverse. If this admixture event holds up my intuition tells me that both of these findings are in part derived from this component of the ancestry of these populations. The separation between population X and AMH occured ~700,000 years ago. If I recall my human evolution chronology correctly this is about two hundred thousand years greater than the divergence between AMH and the Neanderthal-Denisovan clade! Depending on the population genetics of the X group, they may significantly reshape a phylogenetic tree which does not incorporate the correct model of divergence and admixture (reticulation).

I assumed that the Mbuti would be special even before seeing the paper because physical anthropologists have long observed that there’s a greater phenotypic difference between them and their Bantu neighbors than the Biaka and their Bantu neighbors. Playing around with public data sets (HGDP) it’s also clear that the Mbuti are more distinctive than the Biaka from other Africans. Additionally, to my great surprise there is a “hunter-gatherer clade,” where the Pygmies and the Khoisan seem to form a cluster against other African populations. It seems implausible to me that these patterns are due purely to admixture from population X. But I think it must play a role. It may also explain the finding from some full genome analyses that West Africans are closer to non-Africans than they are to Pygmies or Khoisan. This may be a function of their lack of population X (and/or, possible back-migration from Eurasia).

At this point I feel a little strange referring to “population X.” It was nice that “X-woman” eventually become the Denisovans. What should we call these potential additions to the human family album? Greg Cochran suggested to me the term ‘Mangani’, by analogy with the use of ‘Hobbit’ for H. floresiensis. Don’t remember who the Mangani were? Here’s Wikipedia on the Mangani:

As described by Burroughs, Mangani are organized in tribal bands ruled by dominant males, or “kings,” which subsist by foraging for fruit, grubs, insects, and sometimes meat, in localized territories. Tribes are generally identified by the names of their kings. Burroughs portrays the Mangani (and indeed most jungle animals) as susceptible to occasional bouts of madness in which they will lash out violently and unpredictably at other living creatures in their vicinity. Tarzan is raised in the tribe of Kerchak, based in the coastal jungle of equatorial Africa, as shown in Tarzan of the Apes and Jungle Tales of Tarzan. As an adult he comes to lead this tribe; later, he becomes accepted in other tribes of Mangani, such as the tribe of Molak in The Beasts of Tarzan. Tarzan continued to associate occasionally with his original tribe until cast out in Tarzan and the Golden Lion, as the result of a Tarzan impersonator having murdered one of its members.

From what I recall in the films and television shows the Mangani are portrayed as rather more bestial, and ape-like, than the description above. It also made the story of Tarzan extremely implausible, more in the vein of Romulus and Remus or Mowgli. But Edgar Rice Burroughs original conception was clearly less fantastic, as the Mangani were intelligent, if profoundly different. If modern humans are the ‘third chimpanzee,’ the Mangani may have been another chimp tribe (H. floresiensis, Neandertals, and Denisovans would also be distinct tribes in this model).

At this point some of you might be alarmed. When evidence for Neandertal admixture surfaced in 2010 message boards had discussion threads with titles such as ‘White People Aren’t Human’. Whether you find this sort of joke amusing or not, it’s at least marginally acceptable to make light of scientific findings to poke fun at what is the dominant ethnic group in the developed world (e.g., see also ‘white people are mutants’). Substitute in black people, and the valence is entirely different. But these findings don’t actually imply this. Many African populations may have the highest quantum of AMH ancestry of all human groups. Rather, this new archaic element is found in Pygmies and Khoisan in particular. The ethnography is rather rich in documenting the dehumanization of these two populations at the hands of their Bantu neighbors. If you have tracked the conflict in the Democratic Republic of Congo you are also probably aware that the Pygmies in particular are targeted in the most grotesque fashion because they are perceived to be less than human. But don’t these results suggest that Pygmies are less than human?

I think on a deep level we may have to start putting this question into the “not even answerable” category. Recently I had an exchange with John Farrell in regards to how Christians, and in particular Catholics, are handling modifications to the “Out of Africa” model. I’m not expert on this obviously, but from what I can gather it seems that some Christian thinkers have taken succor in the romantic narrative of “mitochondrial Eve” and “Y chromosomal Adam” as scientific vindication of at least the general outlines of Genesis. For Roman Catholics, who otherwise can accept evolution without much qualification, the existence of these two individuals is necessary for ensoulment and the fall. Apparently some Catholics are discomfited by the opening toward polygenism implicit in the new model of admixture with archaics.

Since I don’t give much though to the religious implications of science, not being religious, I view the whole discussion with curiosity more than concern. But I think the Christian arguments about the implications of science still have something to teach secular people, because I believe we need to reconceptualize what it means to be human. The “Out of Africa” model, which is classical monogenesis on steroids, does not perturb our intuitions about ideal types and kinds. Rather, it reinforces a Platonic model of what it means to be human, as humans are all kith and kin, descendants in totality and universally from a small group of Africans who flourished ~100,000 years ago. This idea is so pervasive that it even pops up in the series finales of science fiction shows. I now believe that those of us without religious presuppositions should abandon more vigorously this model of humanity.* In a deep sense we already do, in that many of us accept without much controversy that we’re simply the product of material processes. There is nothing which makes us ineffably human. This is why many of us do not consider abortion the murder of a person. At some point the fetus becomes human in all the ways we understand to be human. The zygote’s putative descent from two individuals created in the image of God is not sufficient for us to grant it status as a person. We don’t accept the reality of this descent in the first place.

I don’t think we should be too terrified of this leap. Many of us have already abandoned a deep belief in the idea of ‘free will,’ religious and secular, and yet life goes on. For all practical purposes of decency all human populations present today are basically equivalent as humans. Whatever results we may uncover via science aren’t going to change that, because our intuitions about right or wrong don’t derive from our understanding of the latest science.


Tansey Coetzee

But let’s end on a fun note, because science is fun. To the left is an image of Miss South Africa 2007, Tansey Coetzee. Ms. Coetzee has an Indian mother, and a father who is Cape Coloured. So let’s assess her ancestry. Her mother is Indian, so she is half-Indian. But what about her father? The genetics seems to indicate that the Afrikaans speaking Coloured population has ancestry from Western Europe, India, the Khoisan, the Bantu, and from Southeast Asia. From the Khoisan there will be a dollop of archaic admixture from this new population X. From the Eurasian ancestors there will be Neandertal. The Southeast Asian ancestry of the Cape Colony generally derives from what is today Indonesia (then a Dutch colony). Therefore it is not impossible that Ms. Coetzee has some Melanesian ancestry, and therefore some Denisovan! Yes, the last is a stretch, but work with me. It seems then that Ms. Coetzee may have fractions of ancestry not only from diverse modern populations, but slivers from all the known “other humans!” Above I appealed to your intuition in simply discarding the model whereby humanity is contingent on pure descent from AMH. Individuals such as Ms. Coetzee, and Desmond Tutu, Nelson Mandela, and most of the readers of this weblog, are a refutation of the Platonic model of a human essence made concrete. I know I’m human despite my Neandertal blood. You know in your heart I’m right, so let us accept the finding of science with as much equanimity as we can muster. Our understanding of the details of the human past does not alter our humanity. Just because God is dead does not mean that everything is permissible.

* I generally hold to the position that artificial general intelligence, if it ever arises, should be given the same due consideration, rights, and respect, as organic intelligence. For all practical purposes, they should be treated as we would treat humans. So this isn’t a big leap for me personally.

Image credit: Jose Rosengurtt

(Republished from Discover/GNXP by permission of author or representative)
 
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Steve Hsu points me to a piece in The New Yorker on the science and personality of Svante Pääbo. The personality part includes references to Pääbo’s bisexuality, which to me seemed to be literally dropped into the prose to spice it up. Of course it was the science which I found interesting. There are many more bisexuals than there are heterodox scientists. And yet like many researchers of yore it seems that Pääbo is out to find the genes which make humanity distinctive as we understand it (if the reporting is accurate, which I don’t take as a given). There are some interesting tantalizing clues littered about; some genes implicated in autism seem to exhibit Neandertal vs. modern human differences (with the Neandertals carrying the autism-implicated variants).


But here’s a consideration: what if the premise that there are a set of traits which are disjoint between Neandertals and modern humans is false? What I’m saying here is that there are traits which are fixed and universal within a species, and totally differentiate species x from species y. Anatomically and behaviorally modern humans seem to be exceptionally strange creatures. As noted in The New Yorker this lineage was the one responsible for many of the megafaunal extinctions and the push into Oceania and the New World. And yet do we have to presume that whatever characteristics differentiated behaviorally modern humans from other human lineages were universal to all of the former and totally absent from the latter? It may be that the difference is not one of quality/kind, but of quantity/degree. In other words, a particularly novel personality type may have transitioned to critical mass amongst the neo-Africans ~50,000 years before the present, but that personality type may not have been universal, and may even have been present at far lower frequencies across the other branches of humankind.

If the above proposition is assumed, then the quest to find the “gene which made humanity” is going to be much harder. You can’t just compare a few Neandertals to humans, but would need many more Neandertal samples. That’s because there may not have been a gene which made humanity, but a subtle complex of numerous genetic and cultural changes which transitioned at a critical point. Do remember also that it may be the nature of statistical genetics that there are some loci where Neandertals and modern humans differ in totality, but these are the “genes which make us human” only if you presume that there are some genes which make all modern humans human and all Neandertals not quite human.

To be concrete about this idea, what if the archetype of the visionary/mystical leader with charisma is responsible for the distinctiveness of modern human groups? This is not a common individual, but not exceptionally rare. Most humans are not particular visionary, nor are they prone to mysticism. Perhaps the difference between Neandertals and behaviorally modern humans was less about large between group differences in individual level traits, and more about the fact than Neandertals simply lacked the leadership cadre which behaviorally modern humans possessed. In this scenario most modern humans are just like Neandertals, lacking vision, drive, and proximate insanity. Neandertals would not have had their Alexander the Greats, but perhaps they would not have had their Adolf Hitlers.

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John Hawks weighs in on the paper I pointed to yesterday. As someone who couldn’t make heads or tales of the stratigraphy I’m a little relieved that John took time out from his tour of Rome to comment. Not too surprisingly it seems that the relatively definitive seeming conclusion of the study authors, and especially the hyping in the press releases, should probably not be taken at face value.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Human Evolution, Neandertals 
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When the draft sequence of the Neandertal genome was analyzed it turned out that there was little difference across non-Africans in their proportion of admixture from this other human lineage. It was a rather strange finding as Neandertals seem to have flourished from Europe to the Altai, and from the ice sheets to the fringes of the Middle East. If Papuans had Neandertal admixture the logical conclusion was that that had to occur in the Middle East. Additionally, if Europeans didn’t have much more Neandertal admixture than Papuans, that means that after the initial absorption the modern humans simply swept the field as they pushed north and west.

But there’s a little problem here: the archeology indicates that Neandertals survived for nearly ten thousand years in Europe after the first arrival of moderns. So the necessary conclusion granting all the above is that after the initial hybridization some barrier prevented further leakage of Neandertal genes into Europeans (or, perhaps modern Europeans descend from recently arrived Middle Eastern farmers who lack the full Neandertal complement of Paleolithic Europeans?).

A new paper in PNAS overturns these paradoxes by re-dating the last Neandertals, allowing them to melt away rather quickly ~40,000 years B.P., just as modern humans were sweeping across Eurasia. Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus:

Advances in direct radiocarbon dating of Neanderthal and anatomically modern human (AMH) fossils and the development of archaeostratigraphic chronologies now allow refined regional models for Neanderthal–AMH coexistence. In addition, they allow us to explore the issue of late Neanderthal survival in regions of Western Eurasia located within early routes of AMH expansion such as the Caucasus. Here we report the direct radiocarbon (14C) dating of a late Neanderthal specimen from a Late Middle Paleolithic (LMP) layer in Mezmaiskaya Cave, northern Caucasus. Additionally, we provide a more accurate chronology for the timing of Neanderthal extinction in the region through a robust series of 16 ultrafiltered bone collagen radiocarbon dates from LMP layers and using Bayesian modeling to produce a boundary probability distribution function corresponding to the end of the LMP at Mezmaiskaya. The direct date of the fossil (39,700 ± 1,100 14C BP) is in good agreement with the probability distribution function, indicating at a high level of probability that Neanderthals did not survive at Mezmaiskaya Cave after 39 ka cal BP (“calendrical” age in kiloannum before present, based on IntCal09 calibration curve). This challenges previous claims for late Neanderthal survival in the northern Caucasus. We see striking and largely synchronous chronometric similarities between the Bayesian age modeling for the end of the LMP at Mezmaiskaya and chronometric data from Ortvale Klde for the end of the LMP in the southern Caucasus. Our results confirm the lack of reliably dated Neanderthal fossils younger than ∼40 ka cal BP in any other region of Western Eurasia, including the Caucasus.

Nick Wade gets some quotes from the principals in The New York Times. I found this part amusing though:

Richard Klein, a paleoanthropologist at Stanford University, said Dr. Higham’s re-dating was “compelling” and fit with his own view that “modern humans were technologically and intellectually far superior to the Neanderthals.” This, he said, “would have allowed them to spread very rapidly and to precipitate the extinction of the Neanderthals almost immediately on contact.”

Klein would think so, he edited the paper in PNAS!

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Anthropology, Human Evolution, Neandertals 
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Mr. James Winters at A Replicated Typo pointed me to a short hypothesis paper, Neanderthal-human Hybrids. This paper argues that selective mating of Neandertal males with females of human populations which had left Africa more recently, combined with Haldane’s rule, explains three facts:

- The lack of Neandertal Y chromosomal lineages in modern humans.

- The lack of Neandertal mtDNA lineages in modern humans.

- The probable existence of Neandertal autosomal ancestry in modern humans.

If you don’t know, Haldane’s rule basically suggests that there’s going to be some sort of breakdown in the heterogametic sex. In humans females are homogametic, XX, and males are heterogametic, XY. The breakdown need not be death (or spontaneous abortion). It could be sterility (e.g., some mutation or genetic incompatibility which results in the malfunctioning of the flagella of sperm would do it).

So you have a scenario where only Neandertal males are interbreeding with the intrusive groups from the south. The hybrids from these pairings would then lack Neandertal mtDNA, since mtDNA is passed only from mothers. But the male offspring would have Neandertal Y chromosomes. This is where Haldane’s rule kicks in: these males in their turn would not reproduce. Therefore only the female hybrids would pass on their genes. These females obviously don’t pass on a Y chromosome. And, they would pass on their non-Neandertal mother’s mtDNA.


Obviously this makes logical sense. How plausible do I judge it? That depends on the other options and the probabilities in the moving parts of the model above. My main issue with the idea of Haldane’s rule being operative in Neandertal-non-Neandertal pairings is this: the two lineages had not been separated for very long at all. The authors give ~250,000 years for the most recent common ancestor. Let’s just double that. That still isn’t that big of a divergence. A few years ago I read some stuff on hybridization in mammals. There’s some pretty straightforward reasons having to do with gestation why this is more of an issue in our lineage than birds, for example, where you have instances of viable crosses between species whose last common ancestor lived tens of millions of years in the past. But that doesn’t speak to the issue of Haldane’s rule necessarily. The problems with interfertility tend to crop up on the order of millions of years, not hundreds of thousands.

In any case, what about the alternatives? There could have been some sort of selective bias against mtDNA and Y chromosomal lineages. This can be straightforward biological. Imagine that Neandertal mtDNA is correlated with some diseases with reduce fitness. The authors allude to this sort of issue. But it might be social. Across Latin America there has been wholesale replacement of Amerindian Y chromosomal lineages among mixed-race populations. In fact you have replications across many societies of European Y chromosomal lineages + non-European mtDNA lineages being dominant, with variation in autosomes (e.g., in Mexico the autosome is balanced, in Argentina it is mostly European). There is also the issue that mtDNA and Y chromosomal lineages are subject to more vigorous stochastic dynamics because of smaller effective population sizes than autosomes. Autosomes are a combination of both parental contributions, but the uniparental lineages are passed from only one. Males are a total dead end in regards to the propagation of mtDNA lineages since they do not pass them on, while females naturally do not have a Y chromosome. The Neandertal mtDNA and Y lineages may simply have gone extinct, which is more probable if they were a small minority in the human population ~30,000 years before the present (the probability that a lineage with “fix” and replace all others is proportional to its frequency at time t = 0).

But really the main issue here for me really is the plausibility of hybrid incompatibility between Neandertals and non-Neandertals. This was a common idea a few years ago before the evidence for Neandertal-non-Neandertal admixture, and I’d started to get skeptical of it based on comparisons to other mammals. But now we have more thorough genetic data. To the left is a table from the supplement of Genetic history of an archaic hominin group from Denisova Cave in Siberia. It is showing the time since the last common ancestors between pairs of populations (F = French, the rest of the rows are the same as the columns). I wouldn’t take the dates that seriously. What I want to point out is that the last common ancestor between Neandertals and other human populations isn’t even a multiplicative factor greater than that between Africans and non-Africans. These particular estimates might be wrong in the details of their magnitude, but I think before we assent to the probability of hybrid incompatibilities we need to consider the high likelihood that Neandertals just weren’t nearly as different as we might think, or have thought.

The following video is for entertainment purposes only:

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Mitochondrial DNA and human evolution:

Mitochondrial DNA from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DMAs stem from one woman who is postulated to have lived ab7out 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that each area was colonised repeatedly

And so was published in the year 1987 the paper which established in the public’s mind the idea of mitochondrial Eve, which gave rise to a famous cover photo in Newsweek. This also led to the Children of Eve episode on the PBS documentary NOVA. Here is the summary:

NOVA examines a controversial theory that traces our ancestry to a small group of women living in Africa 300,000 years ago.

As Milford Wolpoff has complained it is probably accurate to characterize the documentary as not particularly “fair & balanced.” Mitochondrial Eve may have been controversial, and subsequently plagued by issues of molecular clock calibration as well as spurious interpretations of the cladograms, but the tide of history was on its side, and PBS was telling that story. And the story was not just the primary science, rather, one had to understand the controversy in light of the debates among paleontologists and between paleontologists and molecular biologists. A group of researchers, spearheaded by Chris Stringer argued for the recent origin of modern humans from Africa on the basis of fossils alone. They were challenged by an established school of multiregionalists who argued for deeper roots of modern human populations, which derived from local hominins which diversified after the the migration of H. erectus out of Africa. The argument of the multiregionalists was that selective sweeps across the full range of the human populations gave rise gradually to modern humanity as we know it, a compound of specific ancient local features and trans-population characters which unified us into a broader whole. Stringer and company presented a simpler model where anatomically modern human being arose ~200,000 years ago in Africa, and subsequently expanded to other parts of the world, by and large replacing the local hominin populations. In the multiregionalist telling Neandertals became human beings, while Out of Africa would imply that Neandertals were replaced by human beings.


ResearchBlogging.org Into this tendentious landscape of bones stepped the molecular biologists. The critical figure here is Allan Wilson, who in the 1970s argued forcefully from molecular clock evidence for a more recent separation of the human and ape lineage than paleontologists had favored. By the 1980s the paleontologists had generally conceded that Wilson et al. were correct. After this victory he put forward the mitochondrial Eve theory with his student Rebecca Cann. Here Wilson was getting involved with an argument about paleontology. From all the material I’ve read Wilson and Cann were confident that their techniques were superior to old fashioned analysis of fossils, a method which Wolpoff defended vociferously on NOVA. People who were not invested in recent human origins often did not know what to make of the debate. To give you a flavor of what was going on in the late 1980s, here’s Richard Leakey in Origins Reconsidered: In Search of What Makes Us Human:

……In the 1970s, I have been more reluctnant than most to accept Wilson and Sarich’s genetic evident in favor of a recent (five million years ago) origin of hominids, so I thought this would be a chance to redress the balance. In thecourse of my talk I mentioned the mitochondrial DNA evidence and indicated that “I was ready to be persuaded by it.” Surrounded as I was by molecular biologists and geneticists, I imagined it would be a wise think to do, and scientifically proper too.

I was therefore more than a little surprised when, in the bar after my talk, several participants, including the conference organizer, Stepehen O’Brien, cornered me and said, “You don’t have to swallow the Mitochondrial Eve line. We don’t.” Steve and his friends proceeded to tell me why they thought the Eve hypothesis was incorrect…Wilson may have miscalculated the rate of the mitochondrial clock, older mitochondria may have been lost by chance, promoted perhaps by occasional crashes in local pouplation size, natural selection may have favored some recent evolved mitochondrial variant, this eliminating the older lineages. Any of these possibilites might erroneously lave the impression of a recently emerged population….

…In February 1990, Milford and a half a dozen like-minded colleagues organized a session at the annual gathering of the American Association for the Advancement of Science, in New Orleans, the goal of which was to “nail this Mitochondrial Eve nonsense.” Speaker after speaker argued for evidence in support of regional continuity and against localized speciation; for alternative interpretations…It was a powerful presentation, and gathered a lot of press, with headlines like “Scientists Attack ‘Eve’ Theory of Human Evolution” and “Man Does not Owe Everything to Eve, Latest Finding Says.” Chris Stringer, who was speaking at a different session of the meeting, described the anti-Eve seminar as “high-powered salesmenship.” One of Milford’s assault team, David Frayer of the University of Kansas, summarized the deep reaction to Wilson’s work: “Fossils are the real evidence.”

In the 1990s Wolpoff came out with a book, Race and Human Evolution: A Fatal Attraction. It outlined a multiregionalist framework for the origin of modern humans, and also presented a wide ranging review of human paleoanthropology past to present, and, to my eyes made the case that the multiregionalists were on the “right side of history.” I was, and remain, a natural history nerd. Especially a natural history nerd of the human species. I devoured books on the topic in the 1980s and 1990s, and saw the slow shift away from multiregionalism toward an Out of Africa model as the orthodoxy, as transmitted by scientific journalists. As I did not have any horse in the race, it was not a matter of concern either way for me, but, I did observe that the disagreements were personal and sometimes politicized. Race and Human Evolution seems to have been written in part to debunk the idea that multiregionalism gave succor to racism. Rather, Wolpoff inverted the narrative, presenting Out of Africa models as genocidal and exterminationist, in contrast to his model of human populations gliding toward sapiency together through gene flow.

The flip side of course is that many people presented Out of Africa as anti-racist par excellence. Anatomically modern humans were portrayed as the latter day Julius Caesar’s of the hominin world. They came, they saw, and they conquered. The chasm between humans and non-humans may have been wide, but the more appealing aspect of the Out of Africa model is that we were the new kids on the block. All non-African humans derived from Africans, who were the reservoirs of our species’ genetic diversity. The dovetailing of implications of the model with the egalitarian ethos of the age was natural. Here is Pat Shipman in 2003, We Are All Africans:

I don’t expect that the subscribers of the Multiregional hypothesis will be waving a white flag of surrender, although they have lost the great majority of their supporters. At least one of the theory’s most ardent proponents, Wolpoff, is still steadfast in defense of the hypothesis he has so long espoused. While it remains possible that new findings will shift the balance in favor of the Multiregional viewpoint, the consilience of such evidence creates a powerful testament. It would take many new fossils and many new genetic studies to resculpt this intellectual landscape.

By and large the arguments which Shipman lays out were persuasive to someone like me who didn’t know much about bones & stones. Though even I knew of some instances of possible continuity, the mtDNA, Y chromosomal lineages, and autosomal results, did seem to roughly line up appropriately. In the battle between paleoanthropologists who saw continuity in the fossils and those who did not, it seemed reasonable to at the time to give the “tiebreaker” to the geneticists who were generating inferences consistent with Out of Africa.


Grendel

With all that said, it has to be stated that paleoanthropologists such as Chris Stringer did not hold necessarily to total replacement of non-Africans. Total replacement may have been the case, but quite often they did qualify that there may have been some admixture and assimilation with the pre-modern substrate. But the paucity of the genetic data pointing to interbreeding between distant lineages (as opposed to a very recent exclusive common ancestry), especially once the Neandertal mtDNA was shown to be an outgroup, seems to have pushed people to the model where modern humans were an entirely different beast which simply wouldn’t have deigned to to have intercourse with the creatures of yore. In The Dawn of Human Culture the paleoanthropologist Richard Klein lays out a scholarly and measured argument for what is close to a maximalist case for the unique and distinctive nature of modern neo-African humanity:

……the simplest and most economic explanation for the “dawn” is that it stemmed from a fortuitous mutation that promoted the fully modern human brain….an acknowledged genetic link between anatomy and behavior in yet earlier people persisted until the emergence of fully modern ones and that the postulated genetic change 50,000 years ago fostered the uniquely modern ability to adapt to a remarkable range of natural and social circumstances with little or no physiological change.

Arguably, the last key neural change promoted the modern capacity for rapidly spoken phonemic language, or for what anthropologists Duane Quiatt and Richard Milo have called “a fully vocal language, phonemicized, syntactical, and infintely open and productive.”

Wolpoff was on to something. Even if the original Out of Africa proponents did not mean to do so, there was a tendency to remove “higher faculties” from the suite of capabilities of the evolutionary “dead ends.” We were H. sapiens sapiens. If we deigned to allow Neandertals to be a branch of our own species, their subspecies was distinctive. They were less than we in the ways in which modern humans were exceptional, and universal.

This orthodoxy probably resulted in a positive feedback loop for the educated public, in which I include myself. The more the Out of Africa model of neo-African human exceptionalism settled into the received wisdom, the more animalized Neandertals and other human lineages became. Naturally a multiregionalist model of continuity became distasteful, because continuity implied a connection between modern humans and subhumans. The fact that the largest cranial capacities in the whole human lineage were sported by Neandertals became a counterintuitive fact, which just went to show that it was quality, not quantity.

When I was a freshman at university I took a biological anthropology course. The instructor threw out a question to the class. He noted that some paleoanthropologists observed a continuity between the skulls of Australian Aborigines and some Southeast Asian erectine populations. Australian Aborigines are a very robust people, and have been less affected by the trend toward gracility which has been the norm over the past 10,000 years for most human populations. In any case, the instructor asked for a show of hands whether such a possibility should even be discussed openly. The solid majority of the class rejected an open discussion. When asked by the instructor why, many of the students who rejected an examination of the thesis argued that such a possibility opened the path to de-humanization, oppression, and was politically too sensitive. Milford Wolpoff had obviously lost the propaganda war. The students did not consider the possibility of multiregionalism where all human populations exhibited continuity, rather, they assumed that continuity hypothesized for Australian Aborigines was specific to them, and so would associate that population with the less human branches of the hominin tree.

Science is a human cultural endeavour. It is about something real, something objective, but we do look through the glass somewhat darkly. The acceptance or rejection of models are contingent upon correspondence to reality and precision of prediction. But the rise and fall of models, and the rate of their rise and fall, may be subject to cultural dynamics. In The Price of Altruism Oren Harman shows how the cultures of Russia and Britain shaped how they viewed the social implications of evolutionary biology. Similarly, Newtonian mechanics and Darwinian evolution may have been retarded in their initial acceptance in France due to reasons of language and national chauvinism.

Not only do scientific theories have to swim through the waters of suspicion and incomprehension across societies, but they also have to overcome the inevitable confounding of their natural inferences with normative ones. Newtonian mechanics, relativity, and quantum mechanics, have all had many peculiar and surprising downstream social consequences. The line made between these physical theories and models and sociology, epistemology, and spirituality, would likely have surprised their originators (OK, perhaps not Isaac Newton). But the human imagination is fertile, and many cognitive anthropologists argue that the connections and analogies that we make, in addition to our promiscuous pattern recognition, gives rise the baroque and baffling complexity that is culture.

By the mid-2000s the paradigm of Out of Africa had crystallized to such a point that even the fossils purportedly betrayed the multiregionalists. In Bones, Stones and Molecules: “Out of Africa” and Human Origins the authors made the case that the fossil record, and its pattern of variation, complemented the molecular record. That is, Chris Stringer was right. Other more computationally intensive analyses of morphological variation reportedly tended to support an Out of Africa model.

And yet just as Out of Africa seemed to have cleared the field, pointers in the other direction were bubbling up out of genomics and genetics. In 2006 Bruce Lahn at the University of Chicago published Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Nevertheless several years later there seems to have been no wide support for this hypothesis. For eample, No evidence of a Neanderthal contribution to modern human diversity. But there were other papers nonetheless. Deep Haplotype Divergence and Long-Range Linkage Disequilibrium at Xp21.1 Provide Evidence That Humans Descend From a Structured Ancestral Population. Genomics refutes an exclusively African origin of humans. Granted, this was a minority perspective. For the first few years the Neandertal genome project did not seem to support any admixture either. I saw Svante Paabo speak in late 20008, and he was absolutely unequivocal. No sign of admixture. Period.

But the equilibrium of scientific orthodoxy is not eternally robust to a hard exogenous shock of falsification. Yes, some scientists remain obstinate in the face of overwhelming evidence. One could argue Milford Wolpoff could be numbered amongst these. Fred Hoyle certainly was. But the tide turns. In the fall of 2009 Svante Paabo seemed to be far less unequivocal about the issue of admixture. Then, in the spring of 2010:

A test of the New Mexico team’s proposals may come soon. Svante Pääbo and colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced early last year that they had finished sequencing a first draft of the Neanderthal genome, and they are expected to publish their work in the near future. Pääbo’s earlier studies on components of Neanderthal genomes largely ruled out interbreeding, but they were not based on more comprehensive analyses of the complete genome.

Linda Vigilant, an anthropologist at the Planck Institute, found Joyce’s talk a convincing answer to “subtle deviations” noticed in genetic variation in the Pacific region.

“This information is really helpful,” says Vigilant. “And it’s cool.”

By this point, in April of 2010, some graduate students who were not involved in the project itself had seen hard copy drafts of the Neandertal admixture paper. Word was spreading. I already knew of its likely probability, which resulted in me turning on Google Alerts (which got me in trouble for “breaking embargo” on an embargo which I was never privy to). The hammer-blows against the old tried & true orthodoxy in 2010 were ripening throughout the year, and many people were “in the know.” In the age of transparency it is interesting that science naturally has a culture of some secrecy. Who wants to be scooped? But how sustainable is this really over the long term?

To use a religious analogy which some may find offensive, this was an instance where the heretics were once the high priests of the faith. The media reports from last spring made it clear that most of the principals involved did not initially believe that admixture had occurred. Rather, they assumed that the results they were getting were anomalies. Science is influenced by culture, but ultimately nature remains the final arbiter. The truth is what it is, and honest men and women give it its due.

At this point you presumably know the score. Ancient DNA is a powerful judge and jury. It seems that the evidence for Neandertal admixture is already modifying the conventional Out of Africa narrative. But, it has to be admitted that Out of Africa is predominantly correct. The vast majority of our total genome content seems to be traceable to African populations within the last ~100,000 years. An older model of deep rooted lineages only periodically punctuated by selective sweeps which maintain species cohesiveness is not tenable. Phyletic gradualism seems implausible in light of the genetic evidence. Here is Wolpoff (and his wife, Rachel Caspari) in Race and Human Evolution:

We agree a punctuated evolutionary pattern best describes the evolutionary histories of many phyletic groups, including, we think, the earlier and much longer part of human prehistory when humans were only another African primate species. But we believe punctuated equilibrium does not reflect what happened to humans in the later part of human evolution as they became successful colonizers and when there was no macroevolutionary change. As we read the fossil record, there is no evidence of speciation events in the recent past; in fact, there is strong evidence against them. But the Eve interpretation promised to support a punctuated model for later human evolution that was denied by interpretations of the fossil evidence such as ours.

I’m not knowledgeable enough to know what would qualify as a “macroevolutionary change.” But the ‘Great Leap Forward’ seems a plausible candidate. Whatever the details, between 200 and 10 thousand years ago, there does seem to have been a series of rapid expansions of the human range and capacity for innovation. Sometime different was in the air. I do not know the nuance of Milford Wolpoff’s thinking. The most recent data do seem to refute the contention that all ancestry but the Out of African is trivial. But, they also seem to be broadly in line with the peculiarity, almost revolutionary character, of the changes in the human lineage over the past 200,000 years. Convergent patterns of morphological and genetic variation which seem to root back to an African base indicate that Chris Stringer and Allan Wilson had properly characterized a major first order dynamic in recent human prehistory. But now we move into the second and third orders. The rough paradigm is getting sculpted into something with more verisimilitude when judged against the diversity and peculiarity of nature.

Let’s jump to the paper. The main course. Genetic history of an archaic hominin group from Denisova Cave in Siberia:

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

John Hawks has covered a great deal of ground in his FAQ. In particular, he has a gestalt understanding of the fossil record so he can run “quick & dirty” checks on some of their assertions. He notes:

What the paper doesn’t point out is that there are Upper Paleolithic specimens that equal or exceed this tooth in size. For example, the measured length and breadth of an upper second molar from Oase, Romania, are larger than this specimen, and the third molar (in the crypt) of that specimen is yet larger. There is an Upper Paleolithic-associated molar from Turkey which is also exceedingly large.

I don’t take that as a sign of relationship between this specimen and early Upper Paleolithic people — even though these are some of the earliest. It is another sign of how non-diagnostic this tooth actually is. I would say that in the absence of genetic information, we’d be looking at these remains as likely early Upper Paleolithic people, and accentuating these similarities.

People interpret information in light of their background priors. Now that we know what we did not, it may behoove us to go back and double check we may once have dismissed. Consider this paper from 2006, Archaic admixture in the human genome:

One of the enduring questions in the evolution of our species surrounds the fate of ‘archaic’ forms of Homo. Did Neanderthals go extinct without interbreeding with modern humans 25–40 thousand years ago or are their genes present among modern-day Europeans? Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively. Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years.

5% is a nice round number. They could have lucked upon it, but the first author continued to plunge onward in 2009, generating models of archaic admixture. How fruitful would this be? Here is Sarah Tishkoff in December of 2009:

…Sarah Tishkoff, a geneticist at the University of Pennsylvania, agrees, adding that, after all, every population has a strong selective pressure for intelligence, the better to succeed in its respective environment. As far as consorting with Neanderthals, Tishkoff dismisses that notion as pure speculation: “I don’t know of any evidence for that.”

I suspect that Sarah Tishkoff’s opinion would have been common among most scholars of human evolution in late 2009 (though I suspect those who were Facebook friends with people in Svante Paabo’s lab perhaps not). To be fair to Tishkoff, she had no compunction about accepting Neandertal admixture six months later when presented with evidence. She even added that “…it is possible that interbreeding introduced traits into a few human populations.”

In regards to the paper, the top line is rather clear in the three figures in the article proper. I’ve reformatted them a bit below:

Top left: a phylogenetic tree which shows the total genome relationship of various human lineages. Extant modern humans represent one clade. The Denisovans and Neandertals another. In other words, the last common ancestral population of Denisovans and Neandertals is shallower in time than the last common ancestral population of neo-Africans and the Denisovans and Neandertals. All the Neandertals also are very closely related, at least when graded on this particular curve. The Denisovans are outgroups to them, just as the San are outgroups to other humans. The French are an outgroup to the Han and Papuans, though just barely. This sort of relationship is naturally why I cast a skeptical eye to arguments of the common ancestry of French and Han 20,000 years ago when we know that the Papuans settled their island 45,000 years ago.

Top right: a PCA where HGDP populations are projected onto the two largest components of variation which shake out of a data set of a chimpanzee, Denisovan, and Neandertal. In other words, the ones deciding the rules of the game here are chimps and the two archaic Eurasian populations. Humans are constrained onto the genetic variation space of non-/pre-humans. So the position of the humans tells you how they relate to the genetic variation of the Denisovans, Neandertals, and chimpanzees. The Eurasicans, Eurasians + Amerindians, form a relatively tight cluster, apart from Africans. If non-Africans have some Neandertal admixture, this is reasonable. But interestingly t he Melanesian groups stand apart as well. And, Papuans and Bougainville Islanders are also distinctive. The latter are shifted toward Eurasicans. Why? Probably because they have a minor, but significant, Austronesian ancestral component which the Papuans lack.

They estimate that 2.5% of the genes of Eurasicans and Oceanians is of Neandertal origin. And, a further 5% of the Melanesian genome is of Denisovan origin. So Melanesians are 92.5% neo-African. Eurasicans are 97.25% neo-African. At most.

Bottom: the last shows a stylized demographic model. Step 1, humans leave Africa. The neo-Africans interbreed with southwest Asian Neandertals. Step 2, the paleo-Eurasians push east, and some encounter the Denisovans, eventually reaching Sahul ~45,000 years ago.

Some people have asked me about the Denisovan in Polynesians and Australian Aborigines. Since Polynesians are ~20% Melanesian, they should have a fraction diluted appropriately. As for Australians, if they are only recently distinguished from the peoples of Papua because of rising sea levels I assume that they should carry the same fraction of Denisovan. Bougainville has always been isolated from Papua by water from what I know. A final question is in regards to Andaman Islanders and other isolated Asian peoples who seem to be hunter-gatherer relics such as the Ainu. Since the Pakistani HGDP populations share a large minor component of ancestry with the Andaman Islanders my assumption is that they should be somewhat deviated toward the Papuans. As the populations are not labeled I do not know if those groups are skewed toward the direction of the Papuans. In the supplements individual outcomes are given for the Han and French, and the Han seem somewhat shifted toward the Bougainville Islanders, though trivially. Additionally, some of the authors of this paper were involved in Reconstructing Indian History, and so I assume had access to Andaman Islander data. I would be curious if they ran some quick checks and decided to stick with the HGDP because there was unlikely to be anything there.

The main body of the paper is tightly and elegantly written. But there is so much more in the supplements. I have read through them at least once, but I can’t say I understand it very well. It is written with the tight economy of a mathematically minded individual, despite the fact that it runs to 90 pages. But much of it alludes to a “D-statistic” which actually goes back to the earlier Neandertal admixture paper, and its supplement. So let’s go back to that, and review the D-statistic at least cursorily. One might not gain a deep knowledge, but even a superficial knowledge of the technical arcana of these sorts of papers are often useful in my experience. To page 130:

To test whether Neandertals share more alleles with some present-day human populations than with others, we compared the Neandertal sequence that we generated to sequence from present-day human samples of diverse ancestry. Specifically, we discovered single nucleotide polymorphisms (SNPs) by comparing exactly two chromosomes from different individuals (H1 and H2). We then assessed whether a test individual (H3, e.g. Neandertal) tended to match either H1 or H2 more often at sites where H3 has the derived allele relative to chimpanzee. Under the null hypothesis that H3 belongs to an outgroup population, it should match H1 and H2 equally often. In contrast, if gene flow has occurred, H3 may match one more than the other.

Here’s a graphical illustration:

The ancestral state is A, which the chimpanzee (not shown as H4) presumably has. B represents the derived state. That means it has changed via mutation from the ancestral state at some point from the last common ancestor with the outgroup. To calculate the D-statistic you are looking at a case where H3 is B and H4 is naturally A. So you have two sets: BABA and ABBA. You are comparing the counts between these two combinations. If H3 is a clean outgroup to the H1H2 clade, D will be ~ 0, as BABA and ABBA counts will approximately be equal. In contrast, if there is gene flow to H1 or H2 from H3, D will deviate from ~0. The Z-score are the standard deviations away from ~0. The table below is from the current paper under consideration. I have highlighted and reformatted:

The D-statistics make sense of what you know verbally. There is some admixture from Neandertals to Eurisicans + Oceanians. Therefore when paired with each other as H1 and H2 they do not deviate as from 0 as much as they do when paired with Africans. There is a deviation away from equal ratios of ABBA and BABA because there is putative gene flow from from H3 to H1 or H2. Notice the Denisovans. Because they’re like Neandertals they produce some elevated deviation from D, though not as much. Interestingly the maximum Z-scores occur when comparing Denisovans, Melanesians, and Africans. Finally, Melanesians and Eurasicans also result in a deviation from 0 when paired with Denisovans in the H3 position.

A quick note from the supplements on ancient population structure. Dienekes does not believe that there was Neandertal admixture necessarily among Eurasicans and Oceanians. From what I can gather he believes that there was population structure within Africa, which is preserved in non-African populations. Rather than exogenous admixture between geographically separated lineages which had only recently met, what one is presumably arguing for here is that there were long term barriers between more closely placed populations in Africa. The authors do not find it parsimonious, though they can not reject it as totally without foundation. Below is a graphical representation of their two models:

So where does this leave us? Yesterday when I said something big was going to drop Ed Brayton expressed some frustration that paleoanthropologists tend to hype stories too much. The reality is everything doesn’t change. The Hobbits, the Darwinius fiasco, and the persistent controversy over Ida, can give anyone fits of human evolution fatigue. But there is a difference here. You don’t need to take their total word for it. At some point you will be able to go to the UCSC genome browser and poke around yourself. Or, you can pull down a 153 MB file with SNPs and indels.

This is a great time to be alive if you’re a hominin natural history nerd. You never know what surprise will greet you when you wake up in the morning. You never know how you’ll have to rearrange your conception of the world. Earlier in the post I mentioned that an instructor once asked a class where I was a student whether scientists should be allowed to talk about the erectine features of Aborigines, if they believed such features existed. You probably won’t be surprised that I said that such things shouldn’t be off limits if they seemed true. Obviously science has political implications. It is idealistic and philosophically consistent to say that it is value-free, but it is also naive. Rather, we need to think hard about how our values relate to the world around us. Or at least some of us need to think hard about that sort of thing.

We shouldn’t take for granted that we all have exactly the same moral intuitions. But on the margin some of our fears are I think overwrought. I know of an individual who admits frankly that they are a “blank slate” maximalist because they don’t know how they could sleep or live if many traits had some hereditary component. Similarly, I have met many conservative Christians and Muslims who admit that they would rape, murder and steal if they didn’t believe in God. In other words, if God doesn’t exist they would become psychopaths, because “why not.” This is ludicrous. God doesn’t exist, and they aren’t psychopaths. They may believe that they aren’t sodomizing their sister because the Lord God declared from On High believes that such behavior is forbidden, but I think that’s ridiculous on the face of it (on the margin there may be some effect of belief in God on behavior by the way, but that’s not what I’m getting at here obviously). Everything may be possible, but everything is not palatable. As for the possibility that humans may differ substantially from individual to individual and group to group, if you acknowledge this one day will you then as a matter of course raise in your arms in salute? If so, it is true that humans differ profoundly in matters of moral sense, because I could not comprehend such behavior.

So Papuans, and likely Aborigines, are likely ~7.5% non-neo-African. Does that matter? Do they bleed today where yesterday they did not? In deep matters of substance nothing is different from this moment than before. Let me quote John Hawks:

Our common ancestry as humans goes back to the Early and Middle Pleistocene. The (now multiple) Neandertal genomes and the Denisova genome share genes with some people and not others because of this common ancestry.

In addition, some living people carry even more genes from Neandertals because they have an appreciable fraction of Neandertal ancestry. That makes it nonsensical to talk about “Neandertals and the ancestors of modern humans”. Neandertals are among the ancestors of modern humans.

Just so with Denisova. It’s nonsensical to talk about a three-way split between Neandertals, Denisova and modern humans. We can talk about a population model with a clade separating an ancestral Neandertal-Denisova population from contemporary Africans.

I have to remind myself again and again when I talk to people about these issues that “modern human ancestors” is not a group that excludes these Pleistocene people.

Once we put ourselves into the mode where we are referring to a population model, it is important to recognize the limitations of those models. For example, we cannot presently exclude many kinds of gene flow among these Pleistocene populations. We can understand some limits to the level of gene flow — these populations were highly structured, it wasn’t Pleistocene panmixia. But it is premature to talk about isolation without recognizing the limits of our ability to test these population models.

The difficulty with terminology tells us something very important. A large-scale reorganization of the science of human origins is upon us. The terms we are used to using will, many of them, become obsolete. Some now-obscure terms will become very important.

What we know to be good and true is still good and true. It is a small soul who is so moved by matters of terminology, we should be cautious of allowing that to happen to ourselves. I think now to the fact that both the Romans and Muslims abhorred the idea of the king. The Romans overthrew their monarchy, established a republic, and replaced it with a despotism which was a monarchy in all but name. The Muslims had caliphs, vice-reagents of God, and sultans and emirs, who were vice-reagents of the caliphs. Despite the glory which is given over to their God the Muslim despotisms were things of men. Domination of the many by one is a matter of substance, not style. Human dignity should not be contingent on details of ancestry. Isn’t that obvious? I thought that was what the 20th century was to some extent all about.

Back to the science. I began with a long historical sketch, viewed through my own personal lens, because probabilities are always filtered through a glass of accreted priors. I was not as shocked by many at the idea of intogression and admixture because Greg Cochran, Henry Harpending, and John Hawks had already predisposed me to think about the plausibility of such phenomena. Additionally, I have always had an interest in conservation genetics, as well as modeling cultural evolution. Such lateral flows are not unknown in those domains. When I first discussed the Neandertal admixture results with Oren Harman last spring he reminded me that one should be cautious of such things; many splashy science stories often don’t pan out. And yet with all due respect to Oren, in this case we do need to observe that there has been a veritable mob of scholars pouring over these data. Additionally, this is something old, not something new.

These results will not remain isolated findings with only parochial relevance. I believe these two papers will probably shift the equilibrium orthodoxy in a new direction. Old models and genetic studies will be seen in a new light. Anomalies unconsidered will get a second look. In The New York Times Stanford geneticist Carlos Bustamante seemed to indicate to Carl Zimmer that the hunt was on. Perhaps the human genome is more of a mosaic than we thought?

Finally, one wonders how this was missed. 7.5% is not trivial. And yet a generation of mtDNA and NRY studies have seemingly missed this. I presume that the archaic admixture didn’t show up in STRUCTURE because it’s a stabilized part of the genetic background of Eurasicans and Oceanians. It reminds of us the limitations of interpretation. We know what we know contingent on what we already know. Since we know more, a different set of inferences may now be generated. Though with due humility. Not quite time yet for the hardening of a new orthodoxy.

Personal note: Merry Christmas! Obviously it is time for me to take a break. Best wishes, and let’s make 2011 more informative and data rich. Hopefully we won’t have to wait too long for Otzi’s genome.

Citation: Reich, David, Green, Richard E., Kircher, Martin, Krause, Johannes, Patterson, Nick, Durand, Eric Y., Viola, Bence, Briggs, Adrian W., Stenzel, Udo, Johnson, Philip L. F., Maricic, Tomislav, Good, Jeffrey M., Marques-Bonet, Tomas, Alkan, Can, Fu, Qiaomei, Mallick, Swapan, Li, Heng, Meyer, Matthias, Eichler, Evan E., Stoneking, Mark, Richards, Michael, Talamo, Sahra, Shunkov, Michael V., Derevianko, Anatoli P., Hublin, Jean-Jacques, Kelso, Janet, Slatkin, Montgomery, & Paabo, Svante (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia Nature : 10.1038/nature09710

(Republished from Discover/GNXP by permission of author or representative)
 
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8853_jpg_280x450_q85 I just purchased a copy of William Golding’s The Inheritors. Golding is famous for writing Lord of the Flies, a work of literature of such influence that it has made the transition into our everyday lexicon. But I just listened to a podcast of an interview with a biographer of the great author, and it seems that Golding and many of his admirers who are “close readers” judge The Inheritors as his finest novel.

The general outline of the plot is easy enough to find on Wikipedia, it is one of those stories about the transition from a “bushy” hominin tree of life to the dominance of H. sapiens sapiens. Neandertals are finally expiring as a species in the face of the advance of modern humans, who marginalize and extirpate all those who came before. But I get the impression that the execution of Golding’s attempt is very different from Clan of the Cave Bear. Not having read the book yet I do not know if William Golding’s depiction is up to snuff with the latest scholarship on the Neandertals (granted, I am not up to date on the latest scholarship on Neandertals!), though he did guess correctly in all likelihood as to their pigmentation. But, in light of the highly probable non-trivial Neandertal ancestry in over 80% of humans, I feel like revisiting Golding’s vision in the near future, as we carry within our genomes the shadows of both the inheritors and the dispossessed.

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• Category: Science • Tags: Culture, Human Evolution, Neandertals 
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John Hawks has a very long post up. This part caught my attention:

We don’t really know the answers, but now we have a chance to test hypotheses about ancient population size and expansion in Neandertals. My point at the moment is only this: If today Neandertal genes make up only one percent of the gene pool of the 5 billion people outside Africa, that’s the genetic equivalent of 50 million Neandertals.

As Hawks notes later, this paper comes pretty close to resolving whether Neandertals were of the same species as we moderns, at least using the biological species concept. There were fertile hybrids. That should not be too surprising, a few years ago when the Neandertal introgression story was big I looked into mammalian embryology, and our lineage had to be very special as mammals went for their to be inter-population sterility.

This is not just a science story. Dave Chamberlain observes:

Anyone else notice that the artists depictions of neanderthals have slowly changed from stupid brute monkey men to ruggedly handsome moderns with a protruding brow? Hmmm, I bet they get even more good looking now. Hawks promises all neanderthals all the time, I for one can’t get enough of it.

I think that this will change our perceptions, and “artists’ renderings” quite a bit. A few years ago when it seemed that Neandertals may have been highly depigmented I observed that it was a bit strange that in most depictions they tended to be rather dark and swarthy as Europeans go (most famously in Jean Auel’s work the H. sapiens sapiens were Aryan Übermensch while the Neandertals were small and dark). I think some of the same subconscious dynamic was at play as when Tom Coburn was outraged at the TV nudity of Schindler’s List. Coloured people naked on a National Geographic special is one thing, but white people should be decent! (and please, don’t accuse me of seeing racism where it isn’t. If you know me you know that I’m not super-obsessed with that sort of thing, but I think it’s pretty obvious that there’s a lot of implicit assumptions which go into being a white European, and how one views someone and how they should behave)

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• Category: Science • Tags: Evolution, Genetics, Genomics, Neandertals 
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Read Carl Zimmer’s post, Skull Caps and Genomes. The papers aren’t on the Science website yet. And of course, Google News. I think I’m just going to wait on the papers before I say much more….

Good time to be alive, no?

Update: John Hawks.

Update II: Science got the page up.

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neanderthal-615Mr. Carl Zimmer points me to a new article in Nature, Neanderthals may have interbred with humans. The details within the article are more tantalizing, it seems to me, than the headline would imply.

The topline is this, researchers presented the following at the recent meeting of the American Association of Physical Anthropologists:

* An analysis of 614 highly variant loci, microsatellites, in ~2,000 people from diverse populations imply some variants which seem to be derived from human lineages outside of the mainline which led to the anatomically modern humans who left Africa 50-100,000 years before the present to settle the world. I assume there were “long branches” on the phylogenies of some loci, indicating that some of the alleles were “separated” from others for long periods of time so that recombination wasn’t able to dissolve the differences between distinctive haplotypes (if we’re all descended from a small African populations which expanded demographically less than 100,000 years ago the common ancestor of the variants should have a shallow time depth).

* The data imply two admixture events, one 60,000 years ago in the eastern Mediterranean, the other 45,000 years ago in East Asia. I think of this as a floor to the number of events. The latter one seems particularly clear in Oceanic populations from the reporting.

* African populations do not have the variants for these two admixture events (there hasn’t been that much back migration to Africa aside from north of the Sahara and the Horn of Africa. I assume that’s because Africans are well adapted to their environment, and outsiders are not).

In light of the recent discovery of a Siberian hominin which lived ~30,000 years ago, and was not a H. sapiens sapiens or H. sapiens neanderthalis, as well as the confusing but intriguing Hobbits of Flores, I think we can conclude that the the evolutionary genetic past was much more complicated than we’d assumed 10 years ago. Remember three years ago when there was a spate of research on a few genes which were suggestive of introgression into the human genome from Neandertals? There are other hints here and there which pop up in the literature over the years, some in Asia. But the methods being imperfect, and interpretation being somewhat an art, a consensus of Out-of-Africa + total replacement has been assumed to be a null. So we look at isolated results with some skepticism (I think this is justified).

So is this going to be met with skepticism due to reliance on the orthodox model? This section of the article is intriguing:

A test of the New Mexico team’s proposals may come soon. Svante Pääbo and colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced early last year that they had finished sequencing a first draft of the Neanderthal genome, and they are expected to publish their work in the near future. Pääbo’s earlier studies on components of Neanderthal genomes largely ruled out interbreeding, but they were not based on more comprehensive analyses of the complete genome.

Linda Vigilant, an anthropologist at the Planck Institute, found Joyce’s talk a convincing answer to “subtle deviations” noticed in genetic variation in the Pacific region.

“This information is really helpful,” says Vigilant. “And it’s cool.”

rupertTrying to glean what results Paabo is going to come out with is like reading tea leaves, but it is notable that a colleague at Max Planck seems to be excited about the results of this study. I do not get the sense that any of these results would reject the model that the overwhelming signal of ancestry in non-African humans is African. There’s a reason that mtDNA, later analysis of classical markers, and finally modern genomics (as well as cladistic analysis of skeletal features) imply that there was an Out of Africa event, whereby anatomically modern humans entered into a period of massive demographic and range expansion from a small ancestral group. But that does not preclude the assimilation of other groups along the way, and there is circumstantial evidence of sex between the Others and modern humans (the time of separation between various hominin lineages is on the low side in relation to various other taxa which can still produce fertile hybrid young).

A final point is that if these results hold up, one might look to Africa itself for other hybridization events. It may be that ancient hominin genetic variation is preserved in modern Africans as H. sapiens sapiens entered its period of expansion within that continent. Those signals may be currently obscured because the archaics in Africa were genetically more similar than those outside of Africa, and the African genome hasn’t been as well characterized as that of other populations in relation to its great diversity (remember the finding of new SNPs in the recent paper on Bushmen).

Image credit: National Geographic, Wikimedia Commons

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Admixture, Evolution, Human Evolution, Neandertals 
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Neanderthals ‘had sex’ with modern man:

Professor Svante Paabo, director of genetics at the renowned Max Planck Institute for Evolutionary Anthropology in Leipzig, will shortly publish his analysis of the entire Neanderthal genome, using DNA retrieved from fossils. He aims to compare it with the genomes of modern humans and chimpanzees to work out the ancestry of all three species.

Paabo recently told a conference at the Cold Spring Harbor Laboratory near New York that he was now sure the two species had had sex – but a question remained about how “productive” it had been.

“What I’m really interested in is, did we have children back then and did those children contribute to our variation today?” he said. “I’m sure that they had sex, but did it give offspring that contributed to us? We will be able to answer quite rigorously with the new [Neanderthal genome] sequence.”

The way Paabo is couching it, what he has found then seems likely to be evidence that humans who had just expanded Out of Africa contributed to the genomes of Neandertals. In other words, modern human introgression into Neandertals. Of course if the gene flow was from modern human to Neandertals exclusively, then it would be an evolutionary dead end since that lineage went extinct.

H/T: Anthropology.net

(Republished from GNXP.com by permission of author or representative)
 
• Category: Science • Tags: Evolution, Neandertals 
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Razib Khan
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