The paradigm is dead, long live the paradigm!

By Razib Khan | December 23, 2010 3:24 am

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.orgInto 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 the 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

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  • J

    Merry Christmas Razib! I almost never comment, but I’m a big fan.

  • vg

    Well written post!
    2010 has been a good year indeed for palaeoanthropology.
    A Merry Christmas to you and your readers!

  • bioIgnoramus

    “… “modern human ancestors” is not a group that excludes these Pleistocene people” – aargh, the problem here is surely not a deep intellectual one, but a problem of Bad English. It comes – I suggest – from the disinclination (especially obvious in the US) to use prepositions and instead to press nouns into service as adjectives or quasi-adjectives. The ancestors of modern humans (note the “of”) includes ‘these Pleistocene people’. Ancestral modern humans (note the adjective) don’t include them. Easy peasy. To those who object to using prepositions because it “means more words” I answer that the Bad English I read, especially the preposition-deficient stuff, is almost all such wordy rubbish that adding a few prepositions would be more than cancelled by improving the English by shortening it.

    I’ve not noticed the same problem in scientific French. My German is now so poor that I can’t comment on whether it is afflicted likewise .

  • AG

    The comments I left on your blog before indicated that I have always believed multiregionalism, and skeptical of simple `out of Africa’ theory. Most mainland Chinese scientists also strongly believe multiregionalism since I can read Chinese blogs. Even during the peak time of `out of africa’, most of them still hold their belief and repeated found evidences supporting multiregionalism. Unfortunately, their findings are often ignored or ridiculed.

  • bioIgnoramus

    Oops, where’re my manners? Merry Christmas to you too. (And, may I say, what a fine essay to send us off with.)

  • Markk

    Wow – I can tell you were excited to write this; it’s breathless and chocked full of interesting stuff. You might want to edit it sometime, lots of spelling and grammar miscues – more than usual for you, but the breathlessness they imply is cool. I remember commenting several years ago on this blog that the stuff you were describing was blowing my mind and we were in an age of miracle and wonder. It seems like the new “microscope” of readily available genetic sequencing plus the computing power to take advantage is creating a tidal wave in a lot of areas. Paleontology, ecology, and many other things are being changed dramatically. I can see a sequencer and huge databases being in every extension office, every nature center, every museum that does research in 10 or 20 years.

    The statistical techniques used to look at these genomes to determine mixtures still seem to be evolving though. These studies all take pieces of genomes and look at parts. That is somewhat scary to me. Has there been work to show that this is robust? That is, what if a different chromosome showed a quite different admixture? Why couldn’t different areas of a genome have different sources and structures? These might be well answered questions but they kind of trouble me about this stuff.

    I do like your first order – second order language though. The out of Africa model is supported by all of this evidence and we are now seeing it modified with some mixture, but even 10% mix would mean 90% from the Out of Africa model. It does seem like people want to throw babies out with bathwater on this. Look at what you comment number 5 implies. We are really starting to get very testable models that work to describe at more complex levels, AND we have the tools now to get real evidence to blow them up or support them or tweak them. I am feeling very happy!

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  • omar

    Very nice essay..very helpful for non-specialists like us.
    And Merry Christmas, Happy New Year, etc. etc.

  • Pat Shuff

    Buddy can you s’paradigm, can you ever.
    Thanks for teasing out the subtlety and
    nuance for us uneducated retired laypeople.
    The cultural sensitivities were navigated
    particularly well, the inevitable
    ululating notwithstanding.

  • http://ted.kosmatka@yahoo.com T. Kosmatka

    Great post, Razib! Thanks!

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Most mainland Chinese scientists also strongly believe multiregionalism since I can read Chinese blogs. Even during the peak time of `out of africa’,

    you’re still 95% neo-african. the main issue from what i know is that many want to claim descent from peking man, which is not plausible. if there is more nuanced discussion in the chinese language media, sad that we don’t have access to it.

    mark, i spent most of yesterday reading through the supplements and then wanted to finish the post before i went to sleep. by 3 AM i did my edit, and collapsed ;-) but the moral is not to edit when you’re exhausted.

  • Fergus

    Another blow to Neandertal orthodoxy may be missed in the Denisova wave…Face not cold adapted

    The Neanderthal face is not cold adapted
    Todd C. Rae, Thomas Koppe, Chris B. Stringer Original Research Article
    Journal of Human Evolution

    http://dx.doi.org.libproxy.ucl.ac.uk/10.1016/j.jhevol.2010.10.003
    In Press, Corrected Proof, Available online 22 December 2010

    PS Razib..Thanks for many fine articles over the year

  • http://ted.kosmatka@yahoo.com T. Kosmatka

    Quothe Razib, “This is a great time to be alive if you’re a hominin natural history nerd.”

    So true.

  • Fergus

    Apologies
    wrong link given in last post

    corrrect version

    http://dx.doi.org/10.1016/j.jhevol.2010.10.003

  • http://www.consultingstatistics.org Basil

    Thanks for the very detailed blog. I feel much more informed about the “Eve” story.

  • http://www.consultingstatistics.org Basil

    How was your classification table calculated? I didn’t see a label for this graph, but it was described as “Top Left”.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    click the supplements and look for D statistic.

  • Colugo

    1. The very terms ‘archaic’ and ‘modern’ are misleading and prejudicial. Not simply in a politically correct way, but more importantly in an analytical way.

    2. The most parsimonious explanation is that all sapiens (neandertals, Kabwe, Denisovans, amhs etc.) are a single chronospecies with regional variants.

    3. Out of Africa was mostly right but multiregionalists still win. Because even though OaA was mainly correct on the details multiregional was right on the theory. Admixture and a single evolving variable species rather than allopatric speciation of small isolate.

    4. A lot of paleoanthro narratives and reconstructions are either too ludicrously minimalist – not too far from The Onion’s ‘skeleton people’ – or way too fancifully speculative. See Lewin’s Bones of Contention. Things haven’t changed that much since earlier misadventures like Ramapithecus, the too humanlike reconstructions of habilis, and the too apelike reconstructions of neandertals.

    5. Some racists want it both ways and simultaneously claim that neandertal admixture makes Europeans more evolutionarily advanced than Africans but Denisovan admixture makes Melanesians more evolutionarily primitive than Europeans. Stupid is as stupid does.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    3. Out of Africa was mostly right but multiregionalists still win. Because even though OaA was mainly correct on the details multiregional was right on the theory. Admixture and a single evolving variable species rather than allopatric speciation of small isolate.

    hm.

  • http://www.kinshipstudies.org German Dziebel

    “Out of Africa was mostly right but multiregionalists still win.”

    Science isn’t politics. It’s not about who is right or who wins. Multiregionalism and Out-of-Africa weren’t properly differentiated from each other in the first place. Out-of-Africa agreed with Multiregionalism that there was continuity in Africa. Multiregionalists always acknowledged that continental populations share a lot of biological and cultural features with each other. The two theories have always been pretty inadequate theoretically and now this primary confusion between the two is simply getting worse. Now we have the modern chin in Zhirendong (south China) at 100K and an erectine finger and molar at Denisova (south Siberia) at 30K. Now we have two bottlenecks out of Africa AND two archaic admixture events outside of Africa. Neither the bottlenecks nor the admixture events have counterparts in the fossil record. In addition, according to paleontologists, Neanderthals apparently replaced African AMH in Levant (Tabun) but then, according to genetics, they admixed mostly with Cambodians and not at all with Africans.

    Both theories lost. Nobody won.

  • dave chamberlin

    Merry Christmas, Happy New Year, and a thousand more archaic teeth and pinky bones with preserved DNA to you all.

  • Sandgroper

    #5 – “Most mainland Chinese scientists” (really? I would have said “some”) have taken a political/nationalist/racial position, which is why they are not taken seriously. My sense is that this is changing.

    In any case, instead of speaking on their behalf, you should give some references. You are not the only superior being in the blogosphere who can read Chinese.

  • http://www.isteve.blogspot.com Steve Sailer

    Cochran calls the emerging new paradigm: “Out of Africa, with Benefits.”

    By the way, Wolpoff’s book “Race and Human Evolution” has some excellent stuff on the class and ethnic side of the culture war between physical and cultural anthropologists. The physical anthropologists, such as Carleton Coon, tended to be WASP’s of “good blood, good bone” old rich families, with close connections to the Old Protestant Establishment, including in some cases the OSS, CIA, etc. For example, Howells, who died recently at about 100, was a direct descendant of novelist William Dean Howells, who was Mark Twain’s best friend. And there lots of other prominent Protestant upper crust figures in Howells’ family tree. It was not surprising that the physical anthropologists put a lot of emphasis on heredity.

    Wolpoff, who is Jewish and a physical anthropologist, argues that the cultural anthropologists who denounced the physical anthropologists tended to be from rising classes and/or Jewish.

  • Neuro-conservative

    Excellent post, Razib — easily the best science blog post of the year. Thank you.

  • http://bluetenlese.wordpress.com M. Möhling

    Merry Christmas and A Happy New Year from another lurker, too. I might find the time occasionally to run your posts through a spell checker, tell good from bad suggestions and do other little things. My English is funny sometimes, but it should do. I could post them somewhere else password protected, with the HTML source for copy & paste and a diff so you see the changes marked red.

  • http://entitledtoanopinion.wordpress.com TGGP

    Old post on kingless Romans & Muslims.

    I ceased believing in morality once I ceased believing in God. But trying to accommodate what I knew of science with the religion I had professed to hold resulted in an imagining of God as something like Azathoth.

  • http://www.riverellan.blogspot.com Tom Bri

    Thank you, Razib. Posts like this one explain why I read here almost daily. I have only a handful of sites I read daily; between a new job, family, and my own writing, there simply is no time.
    I have never interested myself in how this site is funded, but I hope to God you are getting paid and paid well for all of the work you put in here. I was amused when above you said “I can’t say I understand it very well.” Pretty often I have the same feeling reading here. I appreciate the effort you make to put all of this forth in a way those of us not educated in this field can follow, if we put in the mental effort to keep up.

    I do have a big problem with one side issue in the above post. You said: …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…

    Come on. I find it very hard to believe that you believe this. Regardless of the actual existence of God, our beliefs sharply affect our actions. Plunk a man with the religious beliefs of an ancient Roman, Norseman or Apache into modern North America, and he would likely be dead, shot by police, or in jail in short order. Romans believed fathers had the right to murder disobedient sons, for example. You seem to be arguing for a very broad and strong innate set of moral norms, in spite of the disclaimer in the first line of that paragraph. By current standards, most ancients were psychopaths, and this includes the early fathers of the faith I follow. Rape, murder and theft were all perfectly acceptable behaviors in many ancient (and modern) cultures, as long as a few rules, governing who was on the receiving end, were followed.

    By the way, am I the only one who googled ‘Melanesian’ to look at pictures of them, after reading this post? Silly, no way to simply look and see any particular ‘archaic’ trait. But this is just so cool. I have always regretted the extinction of Neanderthals and other ancient races, and here we find some of them never did go extinct. They Live!

  • Miley Cyrax

    @ Colugo

    “5. Some racists want it both ways and simultaneously claim that neandertal admixture makes Europeans more evolutionarily advanced than Africans but Denisovan admixture makes Melanesians more evolutionarily primitive than Europeans. Stupid is as stupid does.”

    Yes, because anyone who even entertains the possibility that genetic differences can manifest itself in behavioral differences must be a bonafide racist. Typical PC shrieking that helps nothing.

    Neanderthals and Denisovans group together genetically to the exclusion of humans, but it is possible that substantial decoupling of Neanderthals and Denisovans (with Neanderthals growing more “advanced” over time relative to Denisovans or Denisovans less “advanced” to the Neanderthals) could manifest itself in differences in their human descendants. There is no evidence to support this particular scenario, but it would be a parsimonious narrative to explain the disparities between the cultural achievements and cognitive abilities (as empirically demonstrated by a myriad of standardized tests) of modern human populations.

    It’s not unthinkable that Neanderthals were more “advanced” then contemporaneous early humans who were then smarter than Denisovans. Humans could have easily displaced a smarter population (Neanderthals)–smarter doesn’t always “win” evolutionarily.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Come on. I find it very hard to believe that you believe this. Regardless of the actual existence of God, our beliefs sharply affect our actions. Plunk a man with the religious beliefs of an ancient Roman, Norseman or Apache into modern North America, and he would likely be dead, shot by police, or in jail in short order. Romans believed fathers had the right to murder disobedient sons, for example. You seem to be arguing for a very broad and strong innate set of moral norms, in spite of the disclaimer in the first line of that paragraph. By current standards, most ancients were psychopaths, and this includes the early fathers of the faith I follow. Rape, murder and theft were all perfectly acceptable behaviors in many ancient (and modern) cultures, as long as a few rules, governing who was on the receiving end, were followed.

    my views are a bit more subtle than that paragraph you are responding to. in any case, i disagree with your assertions. i am not convinced that your understanding of roman mores is so superior to mine that i should weight your opinion highly (you may or may not be right). therefore, i do not. i have written extensively about the difficulty of mapping avowed beliefs to operational behaviors, so you must know about my concern of drawing lines as you just did. i do believe that we are more civilized than we once were, but i think the question of whether it is structural or ideology (e.g., economics vs. religion for example) is complex and not easily addressed.

    merry xmas!

  • http://www.riverellan.blogspot.com Tom Bri

    #29, Miley Cyrax, I don’t see much evidence that intelligence plays a great part in the relative advancement of any particular civilization. Are the Egyptians notably more intelligent than the Germans or Swedes?

    As soon as the Holocene hit, just about everywhere began to civilize, if the material prerequisites were there. We are still finding new, massively elaborate civilizations, for example, those recently discovered in the Amazon, that we had no knowledge of until very recently. We can’t know what arc of development the Melanesians would have taken had other, slightly more advanced cultures not intervened. Certainly they had agriculture, art, not inferior to my ancestors in northern Europe a mere thousand years earlier, who got a lot of their skills from more advanced neighbors.

  • http://www.riverellan.blogspot.com Tom Bri

    Razib, perhaps I was a bit harsher than I should have been. Actually, I figured that paragraph, tangential to the main post, was a throw-away, something you were pitching out to draw a reaction.

    Civilized behavior is progressing, becoming more universal. Christianity has always had a fine moral code, but damned difficult for someone brought up under a different code, living in a society that universally admired a different set of behaviors, to follow. When the barbarians of Europe were christianised, they remained barbarians, with a gloss of christian values painted thinly on top.

    It is structural and ideological. Christian ideology has gradually worked through the structure, reforming one small area then another, until it is now so ingrained in western societies that most people agree with Christian morality even if they consciously deny its supernatural claims. I can think of only a few modern liberal values that conflict with traditional Christian thought. Abortion, for example. Few of the others are anywhere central to Christian theology, however dear to conservative Christians.

    Sorry to drag this in, if it is too far away from the main point of the post.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Christian ideology has gradually worked through the structure, reforming one small area then another, until it is now so ingrained in western societies that most people agree with Christian morality even if they consciously deny its supernatural claims. I can think of only a few modern liberal values that conflict with traditional Christian thought.

    i don’t think christian ethical ideology is particularly distinctive. rather, i believe it is a specific case of a cluster of ethical-religious systems, most of whom have some root back in the ‘axial age.’ there is a school of thinking which contends that western (universal) liberalism is really just a descendant of christianity specifically. i do think that it is a descendant of christianity, but, i am not so sure that its characteristics are distinctive in a way that derives from the particularities of christianity. the sociologist-turned-religious apologist rodney stark does claim that basically all liberalism, science, etc., are all contingent upon christianity specifically of all religions. but, he admits that christianity is a necessary but not sufficient condition. this is natural because for most of its history christianity did not support liberal values at all (its spread into northern europe was concomitant with the rise of unitary monarchies), and only the northwestern christian tradition specifically has given rise to the positive attributes which stark claims for christianity. in other words, i am saying that in an alternate universe i can see a civilization with a different world religion at its heart giving rise to liberalism. the main difference i see is not between christianity and other religions, but islam and christianity and indian and east asian religions, insofar as islam and christianity historically established much tighter condominiums with their political orders and enforced a more thorough religious monopoly.

  • http://www.riverellan.blogspot.com Tom Bri

    You said: …i am not so sure that its characteristics are distinctive in a way that derives from the particularities of Christianity…

    Given. It is hard to speculate from an example of one. We have one religion and one civilization that developed together and became what we consider liberal. None of the others did so outside of its influence, so we are left with basically no data. Much of what we see in recent social evolution appears due to chance.

    Similar to ‘exo-biologists’ who speculate on life outside the Earth environment and history. It’s fun, but pretty futile without a few more data points.

    I am certainly not claiming that Christianity will always lead to our current social values. Simply that Christianity’s values have a handful of central tenets, which the more thoughtful and honest Christians will eventually return to, regardless of the parent society. They may succeed, sometimes, in dragging society along with them. Or not. Modern American values have gone a very long way toward imitating Christian values.

    I could go Marxist on you, and claim that the unitary monarchies were a necessary step in social evolution…but I’m not gonna.

  • Peter Ellis

    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.

    Y chromosomes don’t recombine: you couldn’t *make* an admixture of a Neandertal and neo-African Y chromosome if you tried. Either one haplotype ousts the other or both persist in the population.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    peter, i’m not a moron ;-) so yes, i was thinking of persistence of lineages with deep coalescence times.

  • Peter Ellis

    Apologies if I sounded rude, I was posting more for the benefit of readers. Overall I would be very surprised if there *aren’t* significant differences between X, Y, autosomal and mitochondrial phylogenies.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    could you say more? Ne is obviously lower for haploid uniparental lineages….

  • Peter Ellis

    For starters, it’s at least plausible that neo-Africans and Neandertals/Denisovans were not fully interfertile. In this case, generally the first thing to go is male fertility in the hybrid generations (Haldane’s Rule). If the male F1 offspring of Neandertals/African pairings were sterile, there’s no Y chromosome introgression. Autosomal and X loci can introgress via the female F1s.

    Cultural factors will have an impact too. Let’s hypothesise that in these early populations, children are deemed to belong to the mother’s tribe / social group. In that case, mitochondrial gene flow is restricted: Denisovan-derived mitochondria will stay within the Denisovan tribes and subsequently die out.

    It all looks to me quite like the developing story of speciation between house mouse subspecies (e.g. musculus/domesticus), and the hybrid origins of the lab mouse.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    the literature on mammalian hybridization makes haldane’s rule implausible at the evolutionary distance hypothesized a priori. but, it’s a possible explanation certainly.

  • miko

    @19: OoA with ~5% admixture means multiregionalism “wins”? I guess the USSR won the cold war because Cuba’s still communist.

    @29: You either need to look up “parsimonious” or learn something about circular reasoning. It’s not racist to “entertain” any idea, but you’re getting close if you spend that much effort contorting any piece of data into your racial preconceptions.

  • Colugo

    “OoA with ~5% admixture means multiregionalism “wins”?”

    It (mostly) loses the battle of regional continuity in the case of H. sapiens but wins the larger war over speciation and the debate of what a species is. Is speciation about the splitting off of small geographic isolates (Mayr) and updated by the punctuated equilbrium model (Gould & Eldredge), or is it a more complicated and messy affair involving gene flow between populations of a widely dispersed species highly variable over time and space?

    The reception of Wolpoff’s multiregional model suffered due to unwarranted conflation with Carleton Coon’s model.

    Now racemongers like the commenter @29 are embracing the notion of superior archiac genes in Europeans but inferior archaic genes in Melanesians. How predictable. They’re nothing if not adaptable; not long ago top scientific racists tended to be hardline Out Of Africanists who argued that race differences were recent and the result of strong selection rather than the artifact of mixture with archaics.

  • Colugo

    Stephen Jay Gould gave a gift on a silver platter to racists by insisting that racial equality is entirely historically contingent on Homo sapiens being very young, recently geographically divergent and having no admixture with other Homo populations. Well, genius, what say you if at least one of these is no longer the case? And then there was his characterization of multiregionalism as practically an updated version of polygenesis. Whatever else we think of Gould and his beliefs, I think we can agree that Gould didn’t do his antiracist cause a great favor.

    Poor Wolpoff.
    http://www.human-nature.com/nibbs/02/wolpoff.html

    Gould’s legacy continues.
    http://www.monthlyreview.org/0305york.htm

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    these results will have no effect on maximalist egalitarians or racial nationalists. people simply leverage parts of reality to support their own presuppositions. we are at a stage of inquiry that downstream inference is probably unwarranted. let’s see if others can replicate the results first. i do think that wolpoff’s critique of gould’s manner of argumentation and reasoning is powerful. i thought so even when i agreed more with gould than wolpoff on the details of recent human origins.

  • Miley Cyrax

    “Now racemongers like the commenter @29 are embracing the notion of superior archiac genes in Europeans but inferior archaic genes in Melanesians. How predictable. They’re nothing if not adaptable; not long ago top scientific racists tended to be hardline Out Of Africanists who argued that race differences were recent and the result of strong selection rather than the artifact of mixture with archaics.”

    Typical knee-jerk ad hominem attacks with side orders of indignation and appeal to historical racism. Colugo putting on a clinic here of how PC harpies operate. Not accepting PC egalitarian ideology a priori and being open to other possibilities makes one a card-carrying racist, it appears.

    My point is that those who point to the new findings with the smug satisfaction that these findings corroborate their own little egalitarian narrative are no better than the racists they love to look down upon, who point to the findings as supportive of their own narrative. I disagree slightly with Razib–egalitarians and racists (KKK-style, not the PC ideological conception of racists) will each take this opportunity to claim the findings as supportive of their faith, and thus each side will be all the more fervent.

  • gcochran

    miko it ought to be obvious, but admixture at that level has lots of potential to be interesting, in the sense of adding qualitatively different adaptive alleles. The difference between some admixture and none could, in principle, be important. But the picture isn’t real close to any version of multiregionalism promulgated in the 90s or earlier – none I’m familiar with, anyhow. It’s not lots of Fisher waves tying the populations together. But then it’s qualitatively different from pure OOA, also.
    Instead, it looks as if we have deep splits between populations with very low gene flow, followed by a massive expansion of one of those populations. As AMH expanded, they picked up significant amounts of genetic materials from the archaics – more than enough to pick up every noticeably adaptive allele. And there has certainly been time enough for adaptive alleles to increase in frequency.
    The pattern is more like that of an invasive species.

  • Henry Harpending

    Cyrax stick to your guns. In 1975, when Washburn called Bill Hamilton a racist, people noticed. No one except crazies notices any longer. The 1970s and 1980s are well behind us. Most of us in the trade have been called racist at one time or another: we simply nod and agree.

    What is distressing about Colugo’s posts is his concern with “superiority” and “inferiority”. In biology these mean one thing, fitness. By this metric most of us are inferior to Afghanis. But we all know that this ranking is transient and none of us, I presume, care much about it one way or another.

    I presume that Colugo is referring to IQ, wishing to deny world group differences in intellectual ability. Who cares? Likely most of us are, by this metric, “inferior” to Bobby Fisher or Stephen Hawking, among others. Does anyone care?

    Henry Harpending

  • http://psychohist.livejournal.com Warren Dew

    You wonder in your last paragraphs how this was missed, citing a generation of mitochondrial and Y chromosome data.

    Someone else mentioned this, but it bears repeating: the answer is that mitochondrial and Y chromosome DNA share a feature that they don’t share with any of the rest of the genome, which is that they are inherited asexually. For that reason, we should expect mitochondrial and Y chromosome lineages to be lost at a more rapid rate, and that means that we should expect the coalescence times to be relatively recent. You can’t get “persistence of lineages with deep coalescence times” because with any deep split, one side of the split will have been lost through chance alone.

    For that reason, I’ve been skeptical of the mitochondrially based reasoning for the recent African replacement model ever since it was proposed: the mitochondria had to be recently rooted somewhere, and the fact that it was Africa could have even been pure chance. The Y chromosome data rooting to Africa did provide evidence that a majority of our genes were from Africa, but the “replacement” part of the recent African replacement model was still virtually data free. It should always have been obvious that sexually transmitted autosomal data shouldn’t be expected to tell the same simple story that the mitochondrial and Y chromosome DNA did, though perhaps scientists can be excused for looking at the evidence they had and ignoring its limitations.

    I don’t think it’s accurate to say that autosomal data ever really supported recent African replacement. Green’s paper, which was probably the first relevant work in this respect – not counting a near simultaneous paper that was discounted due to apparent contamination with modern human DNA – did conclude that the modal probability was that humans had no neanderthal ancestry. However, Green’s data had a broad confidence interval, allowing for up to 20% neanderthal ancestry, and the mean probability was still for around 5% neanderthal ancestry, rather than none, and completely consistent with later findings.

    Other autosomal work, for example Michael Hammer’s work on coalescence times in the modern genome, also argued against the recent African replacement model. In fact, Hammer’s finding of a multimodal distribution of coalescence times with a secondary peak at 2 Mya, suggests that the primary nonafrican contributions from archaic humans is not from neanderthals, but from homo erectus, at least in east Asian populations. In one presentation, about 20% of the east Asian loci that he looked at were rooted around 2Mya rather than in the last 200kya.

    I think the excessive emphasis on the low neanderthal contribution to the exclusion of other archaic humans reflects a eurocentric prejudice, rather than enlightened thinking. Peking man was not a neanderthal, and Hammer’s data is completely consistent with Peking man being a modern human ancestor, contrary to what some other commenters imply. If AG has east Asian ancestry, then in all likelihood you are mistaken in saying that he’s “still 95% neo-african” – more likely he owes closer to only 75% of his ancestry to African ancestors within the last 200 kya or so.

    And Colugo is right – this has nothing to do with racism. For all we know, denisovans might have had even larger brains than neanderthals, for example.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    I don’t think it’s accurate to say that autosomal data ever really supported recent African replacement.

    i am aware of work which showed the admixture (i blogged about those papers as early as 2004), but it was clearly the minority view. your interpretation might have been that the results didn’t support that view, but not the majority of researchers. i expect you not to repeat your previous comment again.

  • http://psychohist.livejournal.com Warren Dew

    “previous comment”?

  • John Mitchell

    Having just finished Peter Heather’s “Empires and Barbarians: the Fall of Rome and the Birth of Europe,” I was struck by the analogous cultural lenses which have evolved surrounding an historical debate. He traces the paradigm shifts concerning the fall of Rome and the rise of the barbarian successor states: the older hypotheses were all variations on the invasion/volkerwanderung model where whole, insular “peoples” engaged in a kind of ethnic cleansing/ total population replacement. These models were largely overturned in the second half of the 20th century by the attenuated wave and limited elite replacement hypotheses, wherein at best only a tiny fraction of elite landowners where replaced ( for example, Romano-British villa owners were replaced in England by a similarly small militarized Germanic elite). For Heather, the pendulum had swung too far in the opposite direction, and largely for cultural-political reasons. His book builds a very convincing corrective model: the first millennium CE saw a constant flux of migration, invasion, cooperation, cultural admixtures, and so on, from the earliest interactions between Romans and The Germani on the Rhine frontier, through the collapse of the Western Empire and the foundation of Frankish, Gothic, and Vandalic successor states, to similar movements by Slavic speaking groups and the Viking diaspora in the final quarter of the millennium. Heather uses a core-periphery model to build another model of a “four gear” Europe. As individuals and groups interacted with the more developed gears closer tomthe core, they engaged in multiple strategies, some violent some not. None involved total genocide and wholesale replacement. Heather uses the 70% genetic Anglo-Saxon makeup of England today, for example, to postulate that the subsequent breeding advantage of an original 10% Germanic contribution is all that is necessary, not ethnic cleansing of all British Celts (he does not regard the process as non violent however). Is is possible that this historical model can help us understand prehistorical conditions as well? Perhaps favored hunting and foraging areas like estuarial territories and river valleys functioned as cores to peripheries of less advantageous lands. Complex mixtures of violent invasion, cooperation, trade, inter- mating, etc operated between hominin groups. Over long swathes of time whatever advantages existed in the African sapiens tool kit would lead to the submerging of Neandertal and Denisovan lineages to their apparent background role.

  • Henry Harpending

    Razib I think you are perhaps too abrupt with Warren Dew: I think his comments are right on the money. For example when the original CSW paper came out Kenichi Aoki of the University of Tokyo published a lovely simulation showing that after a colonizing cascade the root of a gene tree was as likely to be any of the daughters, oldest to newest, as any other. The implication was clear: the root of the mitochondrial tree in Africa could well mean nothing. You are correct that this did not become the ‘majority view’ but it was quite clear to those to whom it was clear.

    Rogers, Eswaran, and I published a paper a few years ago claiming that genomic patterns denied the exclusive African origin model. Again few paid attention although no one told us we were wrong. People like Hammer and Wall and Long have also pointed out the same thing.

    One interesting story here is the interaction between laboratory technologies and population genetics theory. For the last decade or two the focus of our interest has been lab stuff, while before that much of the action was in population genetics, like coalescence theory. Hence by citing the ‘majority of researchers’ you are obscuring some interesting history.

    And, BTW, Merry Christmas to you and everyone here.

    Henry

  • miko

    Cyrax, egalitarianism does not depend on any particular version of human history, or anything in particular about humans at all. It is about social institutions and equality under the law, it has nothing to do with assuming that people are identical or equivalent. Obviously, we are not all the same height, and just as obviously can vary in any other quantitative trait. I can never tell if people like you are merely stupid or willfully pretending that egalitarianism means something it doesn’t for ideological reasons.

    For most of the behavioral and cognitive traits that certain kinds of people fetishize, there is nothing approaching adequate evidence for causal gene variants between groups, and there often seem to be highly emotional motivations for or against particular kinds of biological explanations for historical specifics. For this reason, I’m agnostic on most of these and suspicious of the motives of people who whine that one interpretation or another is obvious but politically suppressed. My other annoyance is that very few of the people who seem obsessed with this seem to be involved or conversant with obtaining evidence, or even have a clear sense of what it would look like, and seem to actively enjoy imaging themselves victims of an ideological conspiracy, which is creepy and sad. Same goes with convoluted and baseless explanations for how some kinds of admixture must make you smart while other kinds make you stupid.

    And before you post a bunch of social science citations with “evidence” for group genetic differences driving cognitive traits (or–my favorite–correlations between SNPs and Likert scale responses in college students), consider what a behavioral geneticist might consider compelling evidence. I’ve said it before: just because human data is hard to get doesn’t mean we should use lower evidentiary standards.

  • gcochran

    Obviously, you can’t do anything with the mere fact that average brain sizes vary by a couple of standard deviations (from lowest to highest group ) – unless you know the causal gene variants. In much the same way, there was no point in trying to domesticate the horse before someone sequenced its genome. Unsound.

  • Miley Cyrax

    @ miko

    “I can never tell if people like you are merely stupid or willfully pretending that egalitarianism means something it doesn’t for ideological reasons.”

    Sometimes I can’t tell if people like you are merely stupid, or willfully pretending that terms can’t be borrowed from other contexts or have different meanings in different contexts. Or are didisdainful of Google:

    First result for “biological egalitariansim” actually happens to be our own gnxp: http://www.gnxp.com/blog/2009/10/biological-egalitarianism.php

    Ironically, we don’t have egalitarianism under the law (e.g. affirmative action, which is in violation of the equal protection clause but is exceptioned by the courts due to a “compelling state interest”), in part due to an unsubstantiated belief in biological egalitarianism.

    “enjoy imaging themselves victims of an ideological conspiracy, which is creepy and sad.”
    Do you mean sort of like how some blacks and latinos believe that “the white man” is constantly trying to keep them down? But I assume you mean some whites and Asians in respect to things like affirmative action, because they’re socially acceptable targets .

  • Mike Gordon

    We are all the same species in that we can and do interbreed and have fertile progeny.
    Findings of genes in modern humans similar to genes in Neanderthals or Denisovans
    tells us nothing about how we ought to treat each other societally, but they may be useful
    medically, same as all other genome data.

    Different gene frequencies do not justify disparate treatment but can serve as
    an excuse for it. That’s why racism is bad, irrespective of the science, to the extent that dominant groups use it to justify subjugation, and severe mistreatment of groups designated as the “other”. Unfortunately, some people seem to have a need for a group they can look down on. Such groups are social constructs, and sometimes (e.g. Eta in Japan) are physically indistinguishable from the dominant group.

  • Dzagre

    Stringer & Andrews concluded their pivotal 1988 Science paper with the sentence: “As has been proved to be the case in the study of hominid origins, paleoanthropologists who ignore the increasing wealth of genetic data on human populations relationships do so at their own peril.” Now one wonders if the same rules for them apply to DNA drawn from fossil people rather than placentas, none of which even came from Africa. In the same paper to account for morphological traits MRE theorists proposed to link fossil and recent Australasians, Stringer & Andrews referred to native Australians as “evolutionary reversals” and in a NYT editorial Robin McKie and Chris Stringer called MRE and “devisive theory,” equating it with racism. So, there was some justification for having fears of being labeled an opponent to the Eve theory. Racism was often leveled at MRE followers.
    The revolution in paleogenetics is being matched in Neandertal archaeology, where most of the old ideas about Neandertal cultural incompetence are being overturned. Now, new data even point to language origins extending well before the Neandertals. And there is a lot more coming in 2011.

  • jld

    @Mike Gordon
    severe mistreatment of groups designated as the “other”

    Is a common feature of any inter group competition, why should it be that it be seen as “much worse” when the groups are distinguished by ethnic criteria?

  • http://www.kinshipstudies.org German Dziebel

    @Warren Dew:

    “The Y chromosome data rooting to Africa did provide evidence that a majority of our genes were from Africa.”

    In fact it provided the opposite: evidence that the majority of African lineages (hg E) are derived from outside of Africa. We ended up with hg AB in Africa and CDEF outside of Africa at about 40-45K (all pre-YAP+).

    “Kenichi Aoki of the University of Tokyo published a lovely simulation showing that after a colonizing cascade the root of a gene tree was as likely to be any of the daughters, oldest to newest, as any other. The implication was clear: the root of the mitochondrial tree in Africa could well mean nothing. ”

    Very good. Now let’s look at the map of linguistic diversity. (And let’s ignore Greenberg and Ruhlen.) Interestingly, Melanesia, the inhabitatnts of which “admixed” with Denisovans, is one of the two regions with the highest levels of linguistic diversity. The other region is the New World.

  • http://psychohist.livejournal.com Warren Dew

    German, I’m not sure I understand what you’re saying. For Y chromosome coalescence to have happened outside of Africa, all Y chromosome lineages in Africa would have to be derived from outside Africa, not just a majority. Is that your contention? My understanding is that Africa was still the likely location of Y chromosome coalescence, but I confess to not having followed the Y chromosome literature very carefully.

  • http://www.kinshipstudies.org German Dziebel

    Warren,

    Ever since the publication by Hammer et al. (the same Hammer as you mentioned in conjunction with a 2 MYA coalescence in East Asia) of “Out of Africa and Back again” (mbe.oxfordjournals.org/cgi/reprint/15/4/427.pdf), there’s been a recurrent argument that the majority of African Y chromosomes (the huge pan-African E clade characterized by YAP+) are in fact derived from Asia. This would mean that immediately before the founding migration of the would-be E lineages to Sub-Saharan Africa (roughly at 40-45K YBP) there were two big clusters of Y-DNA diversity in the world – the African one, or the AB cluster, and the extra-African one – most likely East Asian, which encompassed CF and pre-DE lineages.

  • http://washparkprophet.blogspot.com ohwilleke

    “yet a generation of mtDNA and NRY studies have seemingly missed this.”

    It isn’t hard to come up with multiple models with fairly weak assumptions that eliminate mtDNA and NRY traces while preserving autosomal DNA in low frequencies, and the models that achieve that result for Neanderthal admixture work just as well for the Denisovians.

  • miko

    @cyrax: so because some people don’t know what egalitarianism means, you are free to misuse it as well? just because homeopaths call the water they sell “alternative medicine” doesn’t mean thinking people have to include it in their conception of “medicine” or refer to it as such. but, i took your advice and used the google and discovered that “biological egalitarianism” is a term used almost solely by its detractors to caricature something or other…i got bored pretty fast. i am unaware of anyone who has ever advanced an argument for an egalitarian society based on the claim that humans lack genetic–or any other kind of–diversity. if so, they sound pretty fringe and probably not in a position to provoke such self-righteous outrage. as for social policies, you must be the first person to notice that in the service of political goals sometimes people stray from ideological purity. thank goodness, because then the states-rights-lovers on the supreme court couldn’t have installed gw, right?

    words lose meaning in the mouths of ideologues, but the discourse here is normally somewhat elevated above such nonsense. your rant was so typical of paranoid noisemakers that i found it difficult to tell if it was genuine, and your baseless assertion about the cognitive effects of archaic genetic admixture (and calling it “parsimonious”) was such a crystalline example of ideological dumbing down of three or four branches of the life sciences at once, i felt it warranted comment.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    you can reread gould’s old essay about human equality being a contingent fact of history. i don’t know what he was really getting at at this point after rereading it

    http://www.scribd.com/doc/18185121/Human-Equality-Is-a-Contingent-Fact-of-History

  • miko

    “Human equality is a contingent fact of history. Equality is not given a priori; it is neither an ethical principle (though equal treatment may be) nor a statement about norms of social action.”

    Ha! You know I won’t defend the master confuser…I have no idea what he could mean by “equality” if not an ethical principle or the same thing as equal treatment.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    if i read gould correct it seems he’s trying to buttress ought through is, but, he isn’t going to explicitly do it because he is aware that science can change. on a related note, cannibalism, genocide, etc., happened between very closely related groups genetically until the rise of agriculture. also he seems to have elaborated on this issue in his huge last mega-book, when out of africa had really cleared the field (he also caricatures multiregionalism).

    in any case, as paul krugman noted in the USA sj gould was the evolutionary biologist par excellence in the public eye. so his confused and convoluted musings held great weight, and from what i can tell his readers did connect the dots that recent human ancestry refuted human equality in some ethical sense.

    ‘biological egalitarianism’ is probably used by detractors precisely because it is in some sense a default position held in polite society. the converse of the mainstream position in the west between 1850 and sometime in the early-mid-20th century.

  • miko

    “default position held in polite society”

    Maybe, but I feel like most civil rights liberals explicitly see equality as a rule of law issue or equal protection entitlement and are understandably suspicious of biological bases for anything political. That said, when a prominent biologist like Gould emits handy sound bites they are happy to selectively include biology. Dennet–raving liberal that he is–is good on the general misinformed-ness created among non-scientist intellectuals by Gould.

  • http://jgg-online.blogspot.com/ Stiofan

    Razib:

    There are threads on Neanderthal and Denisovan SNPs at 23andme.com. Comparing my self to the 5 SNPs 23andme recognizes from the Denisovans I get the following results:

    My results at the 4 v.2 tested SNPs:

    rs17324735 (C or T) CT chr 9 results AFR 0/46 CEU 4/44 ASN 0/48
    rs10971319 (A or G) AG chr 9 results AFR 0/46 CEU 4/44 ASN 0/48
    rs1148274 (G or T) TT chr 10 results AFR 0/46 CEU 8/40 ASN 0/48
    rs2241970 (A or G) AG chr 10 results AFR 46/0 CEU 38/10 ASN 39/9

    The last seems so wide spread as to not be a reliable marker for Denisovan ancestry and to indicate a marker from before the split.

    rs17226291 is recognized as a SNP but says “Not Tested” in my results

    Hopefully the Denisovan SNPs, the Neaqnderthal SNPs, and the archaic Asian(?) SNPs Hammer found, can be placed on a chip so we can compare to them.

    Thanks for your article and blog.

  • http://psychohist.livejournal.com Warren Dew

    German, thanks for the reference. It seems to me Hammer’s Y chromosome paper does still confirm coalescence in Africa around 200 kya, similar to mitochondrial coalescence data. I do agree that the bidirectional gene flow that he found did suggest that idea of an earlier unidirectional replacement expansion out of Africa might be suspect. The ~70% replacement of Y chromosomes in Africa from an Asian root in a much shorter period of time does look like it could eventually have resulted in a complete replacement that would have masked more complex underlying population genetics, suggesting the same might apply to the 200 kya coalescences, but it’s not clear to me that that implication ought to have been obvious to everyone.

    Miko, the modern civil rights liberals in my social circles seem to see equality of results, not equality of opportunity, as the goal; unequal results due to unequal diligence or unequal talent seems anathema to them. That’s what I would mean by “egalitarianism”, though its actual philosophical roots seem to trace only to Rawls.

  • Pingback: Beware of British newspapers: fossils edition | Gene Expression | Discover Magazine()

  • http://www.humanoriginsolved.com/book.html Alvah Hicks

    Thank you Razib and your Bloggers for another year of fine insights. Looking forward to 2011!

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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 http://www.razib.com

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