No scientists had to die for this paradigm shift!

By Razib Khan | May 7, 2010 1:17 am

In Science Ann Gibbons has a very long reported piece, Close Encounters of the Prehistoric Kind. It’s well worth reading, but behind a pay wall. If you don’t have access though, I want to spotlight one particular section:

The discovery of interbreeding in the nuclear genome surprised the team members. Neandertals did coexist with modern humans in Europe from 30,000 to 45,000 years ago, and perhaps in the Middle East as early as 80,000 years ago (see map, p. 681). But there was no sign of admixture in the complete Neandertal mitochondrial (mtDNA) genome or in earlier studies of other gene lineages…And many researchers had decided that there was no interbreeding that led to viable offspring. “We started with a very strong bias against mixture,” says co-author David Reich of Harvard Medical School in Boston. Indeed, when Pääbo first learned that the Neandertal DNA tended to be more similar to European DNA than to African DNA, he thought, “Ah, it’s probably just a statistical fluke.” When the link persisted, he thought it was a bias in the data. So the researchers used different methods in different labs to confirm the result. “I feel confident now because three different ways of analyzing the data all come to this conclusion of admixture,” says Pääbo.

The finding of interbreeding refutes the narrowest form of a long-standing model that predicts that all living humans can trace their ancestry back to a small African population that expanded and completely replaced archaic human species without any interbreeding. “It’s not a pure Out-of-Africa replacement model—2% interbreeding is not trivial,” says paleoanthropologist Chris Stringer of the Natural History Museum in London, one of the chief architects of a similar model. But it’s not wholesale mixing, either: “This isn’t like trading wives from cave to cave; the amount of admixture is tiny,” says molecular anthropologist Todd Disotell of New York University in New York City. “It’s replacement with leakage.”

The power of data to overwhelm human prejudice is sometimes very awesome. And the bias which Reich and Pääbo exhibited was not unfounded; Pääbo was involved in the sequencing of the Neandertal mtDNA, and found no evidence of admixture there. These data were strong, and I believe they should now shift our assessment of probabilities in relation to earlier papers which claimed some admixture between the population which derives from the Out-of-Africa expansion, and the Others.

In the second section it is notable that Chris Stringer has discarded replacement as not viable. He uses the term “not trivial,” which means that it’s a significant finding of note which one can’t simply ignore when generating inferences from a set of facts which one takes as axiomatic. Disotell’s attempt to minimize the finding is more a matter of rhetoric. He does not dismiss the admixture, he simply consigns it to the undefined category “tiny.” To some extent this reminds me of the neutralist vs. selectionist arguments of the 1970s, and more recently of the Out-of-Africa vs. Multi-regionalism disputes in human evolutionary origins. An argument over the meaning of words is a matter of law, an argument grounded in empirical data and quantitative estimates is an argument about science. No one holds to the extreme caricatures of any four of the models at this point; we’ve established that all these paradigms are unchaste, now we’re just haggling over price. We know that humans and the Others did the deed, we’re now mapping out the what, where, and how often.

But this is not the closing of the gate of itjihad. Dienekes presents an alternative model which may explain the data:

There is an alternative explanation. It involves the emergence of Homo sapiens and Homo neanderthalensis from a common ancestor and the subsequent admixture of Homo sapiens with populations that have branched out before this divergence. This would account for increased similarity between Eurasians and Neandertals, but without the problem of explaining how “Neandertal” ancestry is so similar in Europeans and East Asians.

What about Africans? Why do they stand further away from Neandertals? The answer is simple: low-level of admixture with archaic humans in Africa itself. It is fairly clear to me that the sapiens line whose earliest examples are in East/South Africa must have been an offshoot of an older African set of populations. We are lucky that Neandertals lived in a climate conducive to bone (or even DNA) preservation, while the African populations inhabiting the tropics left no traces of their existence.

In conclusion: I am not at all convinced that the authors have uncovered evidence of Neanderthal admixture in Eurasians; the alternative explanation is that modern humans and Neandertals were related, modern humans spread from East Africa/West Asia and as they entered deeper into Africa, they interacted with archaic human populations there.

In his magisterial post John Hawks has hinted at more wheels within wheels. From a Kate Wong story in Scientific American:

Intermixing does not surprise paleoanthropologists who have long argued on the basis of fossils that archaic humans, such as the Neandertals in Eurasia and Homo erectus in East Asia, mated with early moderns and can be counted among our ancestors—the so-called multiregional evolution theory of modern human origins. The detection of Neandertal DNA in present-day people thus comes as welcome news to these scientists. “It is important evidence for multiregional evolution,” comments Milford H. Wolpoff of the University of Michigan, the leading proponent of the theory.

The new finding shows that “gene flow across taxonomic boundaries happens,” observes geneticist Michael F. Hammer of the University of Arizona. Hammer is among the minority of geneticists who have espoused the idea of gene flow between archaic and modern populations. His own studies of the DNA of people living today have uncovered, for example, a stretch of DNA that seems to have come from encounters between moderns and H. erectus.

I assume Wolpoff is exultant. I do not personally think that this finding necessarily is going to result in a renaissance in Multi-regionalism, but Wolpoff has been the subject of a rising tide of skepticism and dismissal these past few decades. But rather than a more robust discussion between a revived Multi-regionaism and Out-of-Africa, I think these findings, and those that are likely to follow, will force us to move past simplistic typologies and accept that human evolutionary history works itself out through the principles of population genetics, and so can only roughly be modeled in words. The devil is in the parameters.

CATEGORIZED UNDER: Genetics, Genomics, Human Evolution

Comments (33)

  1. To their credit, the authors consider the scenario I am proposing as their “Scenario 4”, but dismiss it as less parsimonious, even though they say there is evidence for its main thesis, namely old African population structure, and their model has its own problem of explaining how a species that was distributed in Western Eurasia ended up contributing equal amounts of DNA to Europeans and Chinese.

    I don’t see why it would be less parsimonious, except perhaps that “we have Neanderthal in us” is more sexy as an explanation than the alternative.

  2. NewEnglandBob

    Fascinating alternate theories. It is like watching a baseball game of 2 out of town teams – one does not know who will win but one can enjoy watching the game and be interested in all the players. Current edge science is better than fiction.

  3. ponderingfool

    Really is that all that surprising? Or is this because of the bias we humans have towards ourselves? Classifying Neanderthals as a separate species to me seems somewhat arbitrary to begin with to fit into the notion that humans belong to a separate genus than chimps. We reclassify ourselves as chimps and the various humans we have found as subspecies/sub-subspecies of Pan homo and everything makes a lot more sense.

  4. Freddie Flintoff

    “For decades, scientists have agreed that human and chimpanzee DNA is 98.5 percent identical. A recent study suggests that number may need to be revised. Using a new, more sophisticated method to measure the similarities between human and chimp DNA, the two species may share only 95 percent genetic material.

    The result is surprising, said David Nelson, a geneticist at Baylor College of Medicine in Houston, “in that it’s more than twice as much difference as we thought” existed.”

    I thought that modern humans were said to be 99.9x% identical in DNA. How does this square with ‘that 1 to 4 percent of the genes carried by non-African people are traceable to the much-caricatured, beetle-browed cavemen’?

    Sorry, if I’m being a dimbulb….

  5. Longma

    It seems to me that Dienekes is closer to the truth…but it could be more simple…

    I think that we are seeing the result of interbreeding in the region of present-day Israel about 90 millennia ago (15-20 millennia before the Dispora). Sapiens and Neaderthalis briefly (a few thousand years) co-existed at that time and place. But then the climate changed and the region became uninhabitable to both species, driving Neandertals eastward back into Asia and driving Sapiens westward back into Africa. Then, 15-20 millinnia later, Sapiens crossed the straits of Bab-el-Mandeb and colonized the globe.

    That’s not my theory above.

    It could have been later that Sapien’s had contact with Neanderthals, the point is that they did at a time when the humans that would colonize Eurasia were still in the same general area in the Middle East or Central Asia and had not made any significant split.

    A few humans doing tribal raids on Neanderthals and stealing a few dozen women here and there (as hunter gathers still do today in the Amazon, Papua New Guinea, and herders did on the steppes even as late as Genghis Khan’s time) could easily shift a gene pool of a few 10’s of thousands, especially if they had something worth selecting for.

    It seems after humans entered Europe there was little to no admixture that late, so this had to be an earlier event.

  6. dave chamberlin

    It was Leo Slizard who said there are three stages of truth in science.

    1)It is not true
    2)It could be true but it doesn’t matter
    3)I knew it all along

    Anybody remember what they did to Bruce Lahn? This man has the distinction of getting run out of two countries for telling the truth before people were ready for it. He was a advocate for democracy in China, and then he got out of that place and came to freedom loving good ole USA. Here he became a brilliant scientist who was the first to provide evidence of the unwanted truth, that there were genes that are archaic but have not spread back to south of the Sahara.

    It appears we have just entered stage two in the ongoing saga of early human history. But do not forget why they went after Bruce Lahn. Because there wasn’t enough room for cold reality between racism and denialism. And guess what folks, there still isn’t. I wish I could share your idealism Razib that this is purely a matter for the scientists to parse and purify but it ain’t so. Galileo had it rough when he proposed a new order to the solar system, but now it gets personal. The racists are mean and ignorant, I hate them, but up to now there has been a steady drumbeat that we are all created equal, and we are not. Tred lightly my friends, racism is mean and ignorant, biodiversity isn’t racism, if we are different, no one is better than anyone else. If half of the country doesn’t even believe in evolution how in the hell are they going to comprehend this.

  7. Eric Johnson

    Hmmmmmm. I’m finding the uniformity across Eurasia of the sequences of interest to be suspect. Of course I do grasp that proto-Eurasian moderns, just beginning their Eurasian dispersal, could have breed with neanderthals in Israel or wherever, giving all Eurasian moderns equal neanderthal ancestry.

    But why didn’t moderns of Europe and SW Asia then breed with neanderthals again — many times, over the many millennia of contact? Therefore, why didn’t they end up much more neanderthal than E Asians or New Guineans did, since neanderthals aren’t attested outside Europe and SW Asia?

  8. dave chamberlin

    Eric johnson asks “but why didn’t moderns of Europe and SW Asia breed with neanderthals again?”

    I can think of two possible answers, kindly correct me if I’m wrong.

    1) They did, that is why there is a variability between 1 and 4%.

    2)There was a hybid zone between africans and neanderthals where all the successful matings took place.

  9. Eric Johnson

    Looks like everything I said was said better by Dienekes, and his commenters raised some interesting points.

  10. “Therefore, why didn’t they end up much more neanderthal than E Asians or New Guineans did, since neanderthals aren’t attested outside Europe and SW Asia?”

    Actually, the Neanderthals are attested in Central Asia and even parts of Siberia.

    This being said, I believe that the Neanderthal admixture took place primarily in Europe. I don’t believe that early modern humans made a beeline to Central Asia and then split in two, with one group going west to Europe and another going east to East Asia. That kind of itinerary makes sense only to armchair geographers.

    It’s more likely that early modern humans first spread through the Mediterranean environments of the Levant, Asia Minor, and southern Europe. They then stalled for awhile as they slowly adapted to the very different boreal and steppe-tundra environments to the north. The latter environments were most likely penetrated in southwestern France — the most southerly portion of the Eurasian tundra belt. From there, early modern humans could have rapidly spread eastward.

    In other words, the split between early Europeans and other Eurasians took place relatively late, c. 20,000 BP, and after the colonization of Europe. Early Europeans were ancestral not only to present-day Europeans but also to present-day East Asians.

  11. znz

    I think there’s a danger of “Do you have a little Neanderthal in you? Well, would you like one?” jokes proliferating.

  12. Damien RS

    “A few humans doing tribal raids on Neanderthals and stealing a few dozen women here and there”

    Given the lack of Neanderthal mtDNA in us, you might have the genders reversed.

  13. Milford Wolpoff

    Wolpoff is happy, because this was a real possibility that multiregional evolution could have been disproved, and it wasn’t. What has happened is that the species replacement theory has been disproved, and those scientists who did not accept the notion of significant evolutionary change WITHIN the human species can now entertain it. For the rest of us, its time to look at the details of populatioopn dynamics more carefully and ponder just where the anatomical evidence of these early modern Africans outside of Africa might be.

  14. gcochran

    “No scientists had to die for this paradigm shift! ”

    It’s not over yet.

  15. Dennis Ferguson

    “In other words, the split between early Europeans and other Eurasians took place relatively late, c. 20,000 BP, and after the colonization of Europe.”

    As I understand it the problem with this suggestion is that it conflicts with the current view, based on archaeological evidence, that New Guinea (and Australia, they were connected by a land bridge then) was populated by modern humans about 45,000 years ago, and that this original population was never replaced by more recent arrivals. That is, while the ancestors of the French genome donor (and maybe the Chinese donor, who knows?) probably lived in the same general area as Neanderthals until 30,000 years ago, the ancestors of the New Guinea donor are thought to have left that area at least 15,000 years earlier, a fact which is almost certainly why a New Guinea genome was included in the comparison. The fact that the New Guinea genome is as closely related to Neanderthals as the other Eurasians is probably why a lot of articles about this suggest the date when the interbreeding occurred is 45,000 to XX,000 years ago.

    Of course, this suggests that while modern humans and Neanderthals might have interbred in the middle east 50,000 or more years ago they didn’t continue to doing so after that time, even though they would have had ample opportunity to do so in Europe for another 20,000 years. Something about that doesn’t make sense.

  16. Sandgroper

    @Dennis, the paper addresses that point.

  17. blueshifter

    So when we used data derived from women to find out if sex with The Other happened, it turned out the data was false? I for one, I’m not surprised.

  18. Dennis,

    You’re right. I initially thought the Oceanic subject was from Melanesia (which would make it part Austronesian and, ultimately, part East Asian). But it’s a Papuan from the center of Papua/New Guinea.

    This would suggest that Neanderthal admixture happened in southwest Asia when modern humans first began to spread out of Africa. But, as you point out, why would admixture happen there but not in Europe, where the two populations co-existed for a much longer time? If there had been subsequent admixture in Europe, we would see more Neanderthal admixture in present-day Europeans, but we don’t.

    The only possibility I can imagine is that Neanderthal genes entered the modern human gene pool indirectly, via an intermediate population in the Middle East that already had Neanderthal admixture (because of prolonged contact) but was essentially modern human or close to modern human. There would have been no subsequent admixture in Europe because there was no intermediate population, and the behavioral distance between the two groups would have been just too great to facilitate admixture.

    Any other ideas?

  19. dave chamberlin

    Why is everyone talking about parsimony. I ate some of that stuff once, it tasted awful, then I was told you are not suposed to eat it, it’s a garnish. Well if you are not suposed to eat it then don’t put it on my plate. Everybody wants the most parsimony in their theories now, I don’t get it. I think we need some of these here DNA machines combined with shop vacs, then we spread out and suck every bit of dust out every limestone cave between here and Timbuktu. Then we’ll get some real parsimony, that’s what I think.

  20. Sandgroper

    Frosty – how about just lack of contact?

  21. Sandgroper

    Peter – what I mean is, we know that AMHs and Neandertals occupied the same cave in the Middle East, albeit at different times, so there’s at least prima facie evidence for possible contact.

    Two small populations coexisting in a space the size of Europe might translate into a small probability of sufficient chance encounters, even over a long time scale.

  22. Afterthought

    Intermediate hybrid zone in the Levant: yes.

    HSS not inseminating HSN females. Impossible.

    As to Freddie Flintoff, you are not a dimbulb, you are merely witnessing the mutilation of science by political correctness.

    The contemporary political scene needs to get used to genetic differences between humans as a scientific fact, not mere retrospectively, as when talking about the movement of ancient tribes, but also prospectively, as germ line genetic engineering comes on line.

    The most counter-productive thing the “left” could do would be to put their heads in the sand or attack science.

  23. dave chamberlin

    Well said afterthought

    Please note the distrust and suspicion given by liberals in general to Monsanto and genetically engineered foods. Even though it is a scientific breakthrough that enormously lowered the energy costs for farmers by creating no till farming with absolutely no negative side effects. The latest chapter was just well covered by Carl Zimmer here at Discover blogs. I have followed every article about Monsanto and it’s long list of round-up ready seeds for years and I have yet to read one scrap of news that is positive. I’m sure Monsanto as a profit motivated company has it’s faults, but the product itself has none, it has lowered farmings costs, increased productivity, saved topsoil erosion, and made our food considerably cheaper.

  24. Ben Goldman

    I think the possibility raised by the authors of the paper is that there might have been later intermixing between Neanderthals and Early Europeans, but the evidence is no longer apparent in the data for a number of reasons. For one, there is now some evidence that the original modern human European populations were wiped out [as I think was covered in this blog] or significantly reduced by subsequent agriculturalist immigrants. Also, the authors hypothesize that the signal they detected of hybridization may have resulted from “surfing” population genetic effect. If I understand correctly this happens when there is a small founder population (of modern humans) in which there is contact with a larger Neanderthal population. In this case any very rare events, such as hybridization, would be significantly expanded and preserved as the initial small population ballooned as it spread across Eurasia. Then again this could also be a consequence of Neanderthal’s later extremely low population density in Europe towards the end of the existence of their lineage. What I can’t get my head around is the negative finding for mitochondria. Haldane’s Rule would predict that the male XY hybrids would drop out, not women, in a sapiens X neanderthal cross. Unless of course the two are close enough that there are less post-zygotic barriers, which I guess is very possible, and I guess if the father was almost always a neanderthal.

  25. Ben Goldman

    Also I really don’t understand the political grousing above. A strict out of Africa stance was a perfectly reasonable stance given the data that up to now was available. In fact there are still plausible alternative explanations [i.e. ancient population structure] that explain the data. Even taking the study’s explanation at face value, Neanderthal’s only made a very tiny contribution to the modern human genome and most of the extant variation in humans is still African. I think it’s silly to fall back on bashing “the PC liberals who say everyone is equal.” Very nice of you to lump all the liberals together and beat that strawman. I consider myself very liberal, but I don’t think GMO crops are inherently evil. I do have issues with Monsanto suing farmers for the effrontery of having wind-pollinated crops, but I guess we could have some tedious political argument about that.

  26. dave chamberlin

    I am also very liberal, please note that blog postings are by consideration short and cannot delve into the complexity that these issues require. Monsanto has been rediculously heavy handed with individual farmers, no question about it. I just think it probable that liberals are more likely to distrust genetic engineering and make negative stereotypes about discussions of human biodiversity. There are all kinds in all groups.

  27. Doug1


    Good points.

    As for this:

    Of course, this suggests that while modern humans and Neanderthals might have interbred in the middle east 50,000 or more years ago they didn’t continue to doing so after that time, even though they would have had ample opportunity to do so in Europe for another 20,000 years. Something about that doesn’t make sense.

    Two possibilities occur to me to explain this lack of further increase in Neanderthal origin genes in Europeans who lived side by side with them for a longer period of time than the other racial genomes sampled in this study.

    1) The ancestors of people who became distinctly Europeans had already taken in all the Neanderthal genes that were helpful; the rest were harmful or neutral and there wasn’t enough interbreeding for neutral genes to remain fixed in the European genome and thus the additional rare mattings with Neanderthals which occurred didn’t add a higher percentage of Neanderthal genes which fixated (stuck around through subsequent human generations); or

    2) After the earlier introgression of Neanderthal genes somewhere around Israel, humans e.g. got enough of a brain boost through additional Neanderthal coding for post birth brain enlargement and maybe an enhanced visual cortex and memory such that humans were then on all accounts much smarter than Neanderthal and able to defeat and overawe them with ease, thus now almost completely effectively warding larger Neanderthal males off from mate snatching or raping of human females for example. And making them then really taboo for human males. Note this isn’t incompatible with the apparent fact that Neanderthals had less developed voice boxes and elaborate language ability and smaller foreheads. Human brains before any introgression of Neanderthal genes may well have been more complex with larger language areas and logical planning frontal cortex. Similarly all the useful and not also more harmful Neanderthal non brain genes for dealing with cold weather may also have already fixated during previously colder times in the Middle East when humans interbred a little with Neanderthals, before humans moved up into Europe as it started getting warmer.

  28. Paul Bishop

    ““A few humans doing tribal raids on Neanderthals and stealing a few dozen women here and there” Given the lack of Neanderthal mtDNA in us, you might have the genders reversed.”

    I see the scenario like this. A big nosed, heavy browed, Neanderthal female may be OK as a back-of-a-cave job but the pretty slim sapiens females newly out of Africa were more of a turn on to a Neanderthal male. Not that the Neanderthal missus would allow the new strumpet a place in her cave, so it was always a passing fling, then back to her own. And no attraction of sapiens males to butch Neanderthal women.

  29. susan

    @ Dave

    It was Leo Slizard who said there are three stages of truth in science.

    1)It is not true
    2)It could be true but it doesn’t matter
    3)I knew it all along

    I like the concept but it was actually Arthur Schopenhauer not Leo Szilard

    none the less the rest of your discussion is on target

  30. Paul Bishop

    @susan & dave

    “It was Leo Slizard who said…”

    Googling the web, I cannot find this precise quote attributed to anybody. Certainly not to Leo Szilard (not Slizard, a mutation which perhaps arises from conflation with Henry Tizard). The nearest I can come up with is indeed Arthur Schopenhauer:

    “All truth passes through three stages. First, it is ridiculed. Second, it is violently opposed. Third, it is accepted as being self-evident. “

  31. dave chamberlin

    I butchered Leo’s name but not his cool quote, he did say it. I don’t doubt he just paraphrased the more famous version from Schopenhauer.

  32. BMcDonnell

    Modern humans developing in the Middle East, and then mixing with another closely related hominid AND also mixing with more primitive humans are not mutually exclusive theories.

    Studies of modern human admixture, such as those showing the admixture of European decent males and Indigineous South American females would clearly give a modern example of exactly how this process happens.

    Both theories are likely correct. One theory doesn’t logically make the other impossible. The two theories actually bolster each other – showing how modern humans migrated.

    Other human variation is likely to show the same thing as groups migrating out of Africa into Asia following herd migrations were trapped into isolated pockets of temperate zones. When the ranges open back up and more modern humans met with thes isolated pockets the admixture of modern males with the isolated groups females should be the expect model of interaction.


Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


See More


RSS Razib’s Pinboard

Edifying books

Collapse bottom bar