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Hominin increase in cranial capacity, courtesy of Luke Jostins


A few years ago a statistical geneticist at Cambridge’s Sanger Institute, Luke Jostins, posted the chart above using data from fossils on cranial capacity of hominins (the human lineage). As you can see there was a gradual increase in cranial capacity until ~250,000 years before the present, and then a more rapid increase. I should also note that from what I know about the empirical data, mean human cranial capacity peaked around the Last Glacial Maximum. Our brains have been shrinking, even relative to our body sizes (we’re not as large as we were during the Ice Age). But that’s neither here nor there. In the comments Jostins observes:

The data above includes all known Homo skulls, but none of the results change if you exclude the 24 Neandertals. In fact, you see the same results if you exclude Sapiens but keep Neandertals; the trends are pan-Homo, and aren’t confined to a specific lineage….


In other words: the secular increase in cranial capacity for our lineage extends millions of years back into the past, and also shifts laterally to “side-branches” (with our specific terminal node, H. sapiens sapiens, as a reference). This is why I often contend as an aside that humanity was to some extent inevitable. By humanity I do not mean H. sapiens sapiens, the descendants of a subset of African hominins who flourished ~100,000 years before the present, but intelligent and cultural hominins who would inevitably construct a technological civilization. The parallel trends across the different distinct branches of the hominin family tree which Luke Jostins observed indicated to me that our lineage was not special, but simply first. That is, if African hominins were exterminated by aliens ~100,000 years before the present, at some point something akin to H. sapiens sapiens in creativity and rapidity of cultural production would eventually arise (in all likelihood later, but possibly earlier!).

This does not mean that I think humanity was inevitable upon earth. For most of the history of this planet life was unicellular. I do not find it implausible that life on earth may have reached its “sell by” date due to astronomical events before the emergence of complex organisms (in fact, from what I have heard the end of life is going to occur ~1 billion years into the future due to the persistent increase in the energy output of Sol, not ~4 billion years in the future when Sol turns into a red giant). But, once complex organisms arose it does seem that further complexity was inevitable. This was Richard Dawkins’ case in The Ancestor’s Tale based simply on the descriptive record. But did the emergence of complex organisms necessarily entail the evolution of a technological species? I don’t think so. It took 500 million years for that to occur (it does not seem that coal resources formed hundreds of millions of years ago were tapped before humans). Given enough time obviously a technological species would evolve (e.g., extend the time of evaluation to 1 trillion years), but note that the earth has only ~5 billion years. Homo arrived on the scene in the last 20% of that interval.

Here I am positing at a minimum two not excessively likely or inevitable events over a 5 billion year time span which would lead to a hyper-technological and cultural species:

- The emergence of multicellular life

- The emergence of a lineage with the propensities of Homo

One Homo evolved and expanded outside of Africa I suspect that something of the form of a technological civilization became inevitable n this planet. We see parallelism in our own short post-Pleistocene epoch. Multiple human societies shifted from hunter-gatherers to agriculturalists over the past 10,000 years. The experience of the New World civilizations in particular illustrates that human universal tendencies are real. Not only were “game changing” cultural forms such as agriculture and literacy invented independently during the Holocene, but they were not invented during earlier interglacials (at least in all likelihood).


Khufu, Necho, Augustus and Napoleon

Why not? Well, consider the cultural torpidity of Paleolithic toolkits, which might persist for hundreds of thousands of years! I suspect some of this due to biology. But even over the Holocene we do perceive that cultural change has proceeded at a more rapid clip as time has progressed (i.e., at a minimum cultural change has been accelerating, and it may be that the rate of acceleration itself is increasing!). Consider that the civilization of ancient Egypt spanned at least 2,000 years. Though there are clear differences, the continuity between Old Kingdom Egypt and the last dynasties before the Assyrian and Persian conquests is very obvious to us, and would be obvious to ancient Egyptians. In contrast, 2,000 years separates us from Augustan Rome. The continuities here are clear as well (e.g., the Roman alphabet), but the cultural change is also clear (if you wish to argue that the early modern and modern period are sui generis, the 1,500 year interval from Augustan Rome to the Neo-Classical Renaissance would still be a stark contrast when compared against an ancient Egyptian reference*, despite the latter’s aping of the forms of the former).

So far I have focused on the vertical dimension of time. But there is also the lateral dimension, of cross-fertilization across the branches of the hominin family tree. The admixture of a Neanderthal element into non-Africans has started to become widely accepted recently, thanks to the confluence of archaeology and genomics in the field of ancient DNA. Even if one rejects the viability of Neanderthal admixture, the solution to the conundrum of these results must still entail stepping away from a simple model of recent exclusive origin of humans from a small African population. There are also hints of admixture with other archaic lineages on the Pacific fringe, and within Africa.

Until recently it was common to posit that modern humans, our own lineage, had some special genius which allowed it to sweep the field and extinguish our cousins. The qualitative result of Luke Jostins’ plot was known; that other hominin lineages also exhibited encephalization. In fact, it was a curious fact that Neanderthals on average had larger cranial capacities than anatomically modern humans. But the reality remained that we replaced them, ergo, we must have a special genius. Until the lack of distinction between Neanderthals and modern humans on loci implicated in the necessary (if not sufficient) competency of language that trait was a prime candidate for what made “us” special. But now I put “us” in quotation marks. The data do point to an overwhelming descent from an African or near-African population for non-Africans over the past 100,000 years. But the “archaic admixture” is not trivial. What was they are us, and we have become what they might have been.

For over two centuries there has been a debate in the West between monogenesis and polygenesis. The former is the position that humankind derives from one single pair or population (the former a straightforward recapitulation of the standard Abrahamic model). The latter is the position that different races of humans derive from different proto-humans, or, for the Christian polygenists that only Europeans descent from Adam and Eve (the other races being “non-Adamic”). Echoes of this conflict persist down to the present era. Many of the earlier partisans of “Out of Africa” have claimed that the proponents of multiregionalism were latter-day polygenists (not without total justification in some cases).

But the conflict between monogenism and polygenism is not the appropriate frame for what is being unveiled by reality before our eyes. What we see in the creation of modern humanity is a monogenic base inflected with the flavors of polygenism. Modern humans descend, by and large, from an expansion of an African population over the past 200,000 years. But on the margins there are other strands and filaments of ancestry which tie disparate populations back to lineages which branched off far earlier from the main trunk. At a minimum hundreds of thousands, and perhaps an order of 1 million years, before our own age. Today genomics avails of us the statistical power to extract out these discordant signals from the fluid “Out of Africa” narrative, but I would not be surprised if in the near future we stumble upon more and more “long branches” of less noteworthy quantity. Admixture is likely to be an old and persistent story in the hominin lineage, with only the most recent substantial bouts of separation and hybridization being of notice and curiosity at this moment in time.

What does all this mean? And why have I juxtaposed deep time natural history across the tree of life with inferences of relatively recent paleoanthropology? Let’s start with two propositions:

- Technological civilization, an outward manifestation of radically complex sentience, is not inevitable, though it is probable given certain preconditions (I believe that the existence of Homo increased its probability to ~1.0 over a reasonable time period)

- Radically complex sentience is not the monopoly of a particular exclusive lineage which accrues its genius from a particular specific forebear

John Farrell has pointed out the possible issues that the Roman Catholic church may have with the new model of human origins. But the Catholic church is only but a reflection of more general human strain of thought. Descent-groups, whether real or fictive, loom large in the human imagination. The evolutionary rationale for this is not too hard to explain, but we co-opt the importance of kinship in many different domains. Like evolution, human cultural forms simply take what is already present, and retrofit and modify elements to taste.

So why are humans special? And why do humans have inalienable rights? Many of us may not agree with the proposition that we are the descendants of Adam and Eve, and therefore we were granted the divine grace of eternal souls. But a hint of this logic can be found in the assumptions of many thinkers who do not agree with the propositions of the Roman Catholic church. Recently I listened to Sherry Turkle arguing against a reliance on “robot companions” which are able to exhibit the verisimilitude of human emotions for those who may be lacking in companionship (e.g., the aged and infirm). Though Turkles’ arguments were not without foundation, some of her arguments were of the form that “they are not us, they are not real, we are real. And that matters.” This is certainly true now, but will it always be? Who is this “they” and this “we”? And what does “real” mean? Are emotions a mysterious human quality, which will remain outside of the grasp of those who do not descend from Adam, literal or metaphorical?

If there arises a point where non-human sentience is a reality, do they have the same rights as we? Though the difference is radical in terms of quantity to some extent I think we know the answer: they are human by the way they are, not by the way their ancestors were. The “taint” of admixture with diverse lineages across the present human tree of life has not resulted in an updating of our understanding of human rights. That is because the idea that we are all the children of Adam, or the descendants of mitochondrial Eve, is a post facto justification for our understanding of what the rights of humanity are, adn what humanity is. And what it is is a particular ecological niche, a way of being, not being who descend down in a line of biological relationship from a particular person or persons.

* The cultural fundamentals of Old Kingdom Egypt arguably persisted in a living fossil form in the temple at Philae down to the 6th century A.D.! Therefore, a 3,500 year lineage of literature continuity.

Image credits: all public domain images from Wikpedia

(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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Update: John Hawks’ lab is working in the same area, and he disagrees with the specific results presented here. Always reminds you to be careful about sexy results presented at conference! (someone should do a study!)

So claimed Peter Parham at a Royal Society meeting last week, Human evolution, migration and history revealed by genetics, immunity and infection. You can actually listen to the talk by pulling down the mp3 file. To get the part about human evolution and introgression, jump to 24 minutes in.

Here is the general sketch: It looks like ~50 percent of the HLA Class I alleles in Europeans derive from Neandertals, ~70-80 percent of HLA Class I alleles in East Asians derive from Denisovans, and that and ~90-95 percent of HLA Class I alleles in Papuans derive from Denisovans. If you recall, ~2.5% of the total genome content of non-Africans seems to be Neandertal, while ~5% of the total genome content of Papuans seems to be Denisovan. The total genome content proportions are rough estimates, there may be some wiggle room in there. But you can see that the HLA allele admixture estimates from these ancient Eurasian lineages is greater by an order of magnitude. Why?


Parham is at pains to point out that there is a major distinction in the nature of the genealogies of alleles which have generally been buffeted by neutral dynamics, and those which have been subject to selection. The HLA region is among the most polymorphic in the human genome, and that is due to the fact that balancing selection maintains diversity (likely a great deal of this through negative frequency dependence over the long term). Presumably this is the target of selection when one conceives of the Red Queen’s Hypothesis in terms of pathogen-host immune system coevolution.

In the presentation it is clear that something seemed off in some of the HLA haplotypes which these researchers had analyzed. They “looked” as if they were introgressed. There has been evidence of this before on other genes. But, with the draft sequences of ancient Neandertals and the Denisovan, scholars could check to see if inferences of admixture between archaic and neo-African lineages were borne out by matching them against the actual sequenced ancient DNA. In some cases they did. In others instances the inferences were wrong (or, the archaic introgression was from a lineage which hasn’t been sequenced yet). In this case Parham reports that his researchers found that the alleles found at high frequency in eastern Eurasia and Oceania seem to derive from the same lineage as that of the Denisovan. Intriguingly, he also adds that the Europeans are about ~50 percent admixed at the HLA Class I locus. If I heard Parham correctly, there are two major points in relation to human evolutionary history:

- East Asians have the Denisovan allele, when they don’t have Denisovan ancestry

- They don’t have the Neandertal alleles, when they do have Neandertal ancestry

- The Papuans are nearly fixed for the Denisovan allele, and lack the Neandertal one

This is why the term “introgression” is key. We’re not talking simple admixture. Rather, admixture followed by selection, whether negative selection which purges introduced alleles, or positive selection which increases the allele’s frequency. We already saw a recent possible case of introgression with a dystrophin allele. This is much more exciting, as the HLA alleles have clear functional relevance, and are known to be targets of natural selection. If adaptation occurs via introgression, this would be one of the key candidate regions a priori. Additionally, the deviation from expectation as inferred by admixture estimates is so great that you have to wonder if selection is responsible for the difference at such a functionally relevant locus. In the East Asian case if these results hold (and I hear Parhman correctly that East Asians carry the Denisovan variant) you see a case where admixture was at such a low level that it’s not detectable, but natural selection preserved a signature of the admixture by amplifying the frequency of an introgressed allele.

In the summation of his presentation Parhman makes a lot of good points about how useful the variation of the Neandertals and Denisovans probably was for the neo-Africans. First, if they went through a bottleneck they may have lacked a large complement of HLA alleles. Because of the need for diversity at this locus to combat pathogens admixture may have been like an injection of mutations which were already preselected for a high degree of utility. Secondarily, Eurasian hominins were probably well adapted to local Eurasian pathogens. The fast that East Asians have much more detectable Neandertal ancestry (~2.5%) than Denisovan (~0.0%), but the Denisovan HLA Class I allele is much more prominent in these populations, indicates that Neandertal and Deninsovan variants were adaptive for different pathogens endemic to their regions of Eurasia!

Finally, a special shout out to Greg Cochran and John Hawks. They’ve been talking to me about introgression as a concept relevant to human evolution since 2005, so a lot of these findings are pretty unsurprising.

(Republished from Discover/GNXP by permission of author or representative)
 
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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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Razib Khan
About Razib Khan

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