Out-of-Africa as Ghost Science
PNAS doi: 10.1073/pnas.1212380109
The Great Human Expansion
Brenna M. Henn, Luca L. Cavalli-Sforza, and Marcus W. Feldman
Genetic and paleoanthropological evidence is in accord that today’s human population is the result of a great demic (demographic and geographic) expansion that began approximately 45,000 to 60,000 y ago in Africa and rapidly resulted in human occupation of almost all of the Earth’s habitable regions. Genomic data from contemporary humans suggest that this expansion was accompanied by a continuous loss of genetic diversity, a result of what is called the “serial founder effect.” In addition to genomic data, the serial founder effect model is now supported by the genetics of human parasites, morphology, and linguistics. This particular population history gave rise to the two defining features of genetic variation in humans: genomes from the substructured populations of Africa retain an exceptional number of unique variants, and there is a dramatic reduction in genetic diversity within populations living outside of Africa. These two patterns are relevant for medical genetic studies mapping genotypes to phenotypes and for inferring the power of natural selection in human history. It should be appreciated that the initial expansion and subsequent serial founder effect were determined by demographic and sociocultural factors associated with hunter-gatherer populations. How do we reconcile this major demic expansion with the population stability that followed for thousands years until the inventions of agriculture? We review advances in understanding the genetic diversity within Africa and the great human expansion out of Africa and offer hypotheses that can help to establish a more synthetic view of modern human evolution.
It is instructive to observe how the maitres (some retired) of a once-dominant and seemingly bulletproof scientific paradigm go about denying that a fundamental shift has occurred, doing an intellectual CPR on what is clearly dead and replacing the once moving limbs with awkward and embarrassing props. Yes, this is how I read the upcoming paper by Henn, Cavalli-Sforza and Feldman (2012). The lapses of fact, structure and logic in this paper are sometimes so egregious that I was even tempted to begin calling the journal that published it “Proceedings of the National Academy of Pseudoscience” but I thought this would be too presumptuous, sweeping and unfair. Especially so since the authors, just like me, are of Stanford extraction: Brenna Henn was part of my cohort and Cavalli-Sforza and Feldman are highly respectable scholars. But had I called PNAS “Proceedings of the National Academy of Pseudoscience,” I wouldn’t be too far from the truth as there is a growing discontent with the way the social sciences (and, specifically, linguistics) are manhandled in high-profile “science” journals (see, Martin Lewis and Asya Pereltsvaig’s polemical series here and in other posts on GeoCurrents).
So, I decided to call Henn et al.’s (2012) writing an example of “ghost science,” not pseudoscience. Their paper is a hodgepodge of divergent authorial styles, declarative statements and mechanical pullouts from other publications and is often completely insensitive to the living and breathing complexity of the interdisciplinary evidence underlying current human origins research. Let’s look at some examples:
“Genetic data indicate that, approximately 45 to 60 kya, a very rapid population expansion occurred outside of Africa, and spread in all directions across the Eurasian continents, eventually populating the entire world.”
In reality, molecular clock is ambiguous regarding the timing of the major demographic events in human history, with at least three methods generating very different time estimates.
“We dub this event the Great Expansion.”
It is very easy to dub something. It is much more difficult to prove that what you dubbed actually happened. Over the years since geneticists have championed an out-of-Africa model they forgot that describing a theory does not mean proving it. In the absence of a consensus between archaeology, paleobiology, social anthropology, linguistics and genetics on the central tenets of out-of-Africa thinking, it’s a bit premature to play naming games.
“The precise location of the exit from Africa, and the relative timing of the southern coastal migration vs. the expansion into northern Eurasia, are still under intense debate.”
We do not have any evidence – genetic or otherwise – for a southern coastal migration. One example is the peopling of the Andaman islands. It has recently been shown that Andaman islands were peopled not in the course of an early coastal migration but, much later, during LGM when the islands were conjoined with the mainland. Hence, it is impossible to assess the “relative timing” between this phantom migration and any other one. The “precise location” of exit from Africa is not the only thing that’s under intense debate – at least three different locations within Africa (South Africa, East Africa and Northwest Africa) have been proposed as a geographic source of human diversity in and outside of Africa. The authors advocate for South Africa as the source of modern humans ignoring the studies that built the case for other source areas within Africa.
“The defining genetic feature of populations historically residing outside of Africa is the tremendous reduction in genetic diversity compared with populations residing in sub-Saharan Africa.” But also “It is unclear what precipitated the tremendous population growth associated with this second occupation of the Near East and subsequent dispersal.”
The authors fly blind through a gaping logical contradiction in their argument postulating at the same time “tremendous population growth” and “tremendous reduction in genetic diversity,” while noting that “effective population sizes will generally be less than census population sizes, especially under extinction and recolonization.” By how much should effective size be smaller than census size in the same population for both growth and diversity reduction in this population to be “tremendous”?
“The loss of genetic variation during the Great Expansion is assumed to have resulted from the way the world was settled by hunter-gatherer groups that, after colonizing a new habitat and expanding there, shed small groups that founded new colonies nearby. This genetic sampling process led to the successive reduction of variation in the newly founded colonies, with the reduction being proportional to the number of founders.”
This passage borders on a parody on scientific reasoning. First of all, how is one supposed to reconcile “tremendous population growth” with “small groups” of colonists? Second, why is an “assumption” introduced after the main argument that “genetic data indicate that, approximately 45 to 60 kya, a very rapid population expansion occurred outside of Africa” had been made and even a name for this “event” coined? Henn et al. (2012) do not marshal any evidence that every time a forager population sheds an offshoot, there is a genetic bottleneck and interbreeding between between the source and the daughter population is completely severed. In reality, it has become commonplace in the studies of forager genetics and demography to talk about the cycles of fission and fusion. Instead of using contemporary hunter-gatherer groups as examples of how genetic diversity, social structure and demography may have interacted in the Pleistocene, Henn et al. (2012) turn the purported pattern of difference between Africans and non-Africans into a single standard for how forager populations must have behaved throughout the Pleistocene. But where exactly is the empirical evidence that this kind of demographic and genetic process is dominant in forager populations?
“The pattern of average heterozygosities of today’s populations suggest that, during the Great Expansion, there was a continuous decrease of genetic diversity with geographic distance from the place of origin in Africa (this takes account of the likely path of migration over land). The linear correlation between loss of genetic diversity and geographic distance from the origin of expansion in Africa is close to 90%.”
Henn et al. (2012) are clearly stacking the deck for themselves here. There’s no linear correlation between loss of genetic diversity and geographic distance from the origin of expansion in Africa. Two most geographically separated populations (assuming land routes of migration and not the direct distance between Africa and South America across the Atlantic), namely South American Indians and Sub-Saharan Africans are most divergent from each other genetically. Sub-Saharan Africans have the largest effective population size, while South American Indians the smallest. This is what observation over today’s populations can tell us. By observing current populations, we can’t say whether the pattern of diversity involves loss or gain. Human populations have grown and intermixed tremendously since the Pleistocene and diversity gain was just as much part of this demographic process as diversity loss. There is nothing in the data that compels one to interpret the observed pattern as evidence of diversity loss from Africa to America. Henn et al. (2012) tacitly weave their biased interpretation into the evidence and present it as a necessary conclusion to naturally derived from the data.
They continue to illustrate their out-of-Africa Great Expansion with the following map:
This map is a bizarre concoction of possible ancient population events cobbled together against the background of modern geography. (Stanford geographer, Martin Lewis, who launched a scathing critique of the treatment of the Indo-European homeland question by a team of computational biologists, may find here another confirmation that the practitioners of methods derived from what are ostensibly “hard sciences” are universally geography-challenged.) For some reason, Beringia is depicted as a strait, which it is now, not as an ice-covered landmass, which it was 15K years ago. Australia and Papua New Guinea are not conjoined into Sahul, while island Southeast Asia and Indonesia are not united into Sunda, which they were 45K years ago. Thick arrows are supposed to represent ancient population bottlenecks, and apparently the features of modern geography (islands and straits) provided a better rationale for the Henn et al.’s (2012) serial founder effect model than ancient geography, so they went ahead and swapped the former for the latter. In addition, the massive colonization of the New World from 1492 on is strangely missing from this comprehensive map of the “Great Expansion.” By placing the recent colonization of the Americas outside of history (why not simply use a medieval T-in-O map?), Henn et al. (2012) conveniently doctored the fact that the New World now, arguably, represents the area of highest genetic diversity but for a reason different from the reason postulated by Out-of-Africa proponents as being a universal “password” for unlocking the mysteries of human population history. The New World post-1492 is most diverse genetically not because humans were there the longest but because they have migrated there recently en masse and aggregated thenceforth into a melting pot of populations.
“If the source population for the expansion suffered a severe bottleneck that reduced its genetic diversity, we should see a poorer linear fit to the decline of heterozygosity with distance from Africa, or erroneously assign a population with higher genetic diversity as the source population. It is this third assumption we believe deserves additional consideration.”
This passage comes out of the blue. Ideally, it would belong in the opening paragraph as it actually introduces a population genetic and demographic model that is very different from the serial founder effect model advocated for throughout the paper. The model that the authors presented at the beginning of the paper as the only possible interpretation of modern human population history suddenly loses its singularity. One gets an impression that a stranger just dropped this sentence into a copy under preparation without the authors’ knowledge. The rest of the paper does nothing to follow up on this thought. But this is precisely what the out-of-America model predicts: American Indian populations have low diversity compared to Old World populations not because they are a recent offshoot of a Siberian population but because they went through a prolonged bottleneck, or, better to say, remained in a state of depressed population numbers, high inbreeding and low density for as long as modern humans existed as a separate species, thus retaining (and not re-enacting, as the serial founder effect model wants it) the Mid-to-Late Pleistocene human adaptive condition.
“On the contrary, analysis of several genomes indicated 1% to 7% differential archaic admixture among populations outside of Africa. Importantly for the serial founder effect theory, a limited amount of archaic admixture does not destroy our power to detect a serial founder migration of the kind modeled for humans.”
Henn et al. (2012) again sweep under the carpet the fact that the evolution of genetic techniques in recent years has brought up not just evidence for archaic admixture but also evidence that admixture between different, originally isolated modern human populations has been part and parcel of modern human genetic history in the Old World. South Asia was an arena of intense intermixing between Ancient South Indians (ASI) and Ancient North Indians (ANI). Modern European diversity is the product of admixture between Paleolithic foragers, on the one hand, and the successive waves of Neolithic agropastoralists, on the other. The formation of modern Japanese involved the blending of the original Jomon component and the intrusive Yayoi component. (Odontological studies supply evidence that the existing dental diversity in Southeast Asia resulted from the intermixing of aboriginal Australo-Melanesian populations with Sinodont, or northern Mongoloid populations that expanded southward in the Holocene.) It was argued that high genetic diversity in East Africa indicates not so much great antiquity as cycles of isolation and intermixing across a large geographic area. South African Khoisan contain an East African component likely derived from pastoralist migrations. There is a long string of publications documenting across multiple hominin subspecies, time periods and geographic areas the failure of the serial founding effect model to explain the patterns of modern human genetic diversity accretion. Henn et al. (2012) decided not to mention them and thus create an impression that less than 10% of modern human genetic variation is attributable to admixture.
“Studies of patterns of autosomal DNA polymorphisms in present-day African hunter-gatherers show that they maintain exceptionally high genetic diversity, and several of these groups (e.g., KhoeSan, Hadza, Sandawe, Forest Pygmies) were the first to diverge from the ancestors that went on to become the larger agricultural groups in Africa and all populations outside Africa. In particular, the speakers of southern Khoisan or “click” languages (sometimes referred to as bushmen) show the greatest nucleotide diversity and the lowest association between pairs of nucleotides (i.e., linkage disequilibrium) along the same chromosome.”
That’s the first time the authors introduce linguistic data, which instantly poses problems for their serial founder effect out of South Africa model. First of all, they seemingly can’t agree on how to spell “Khoisan”/”KhoeSan” and choose a strange lower-case spelling of “bushmen.” Second, they attribute click speaking capabilities to southern Khoisan forgetting that Hadza and Sandawe have these sounds, too. Most importantly, they support the overall Khoisan linguistic grouping, but Hadza is the most divergent language within Khoisan and Hadza shows the lowest nucleotide diversity and strongest linkage disequilibrium among Khoisan groups. Southern Khoisans are a later offshoot from the Khoisan family, linguistically speaking, while exhibiting what Henn et al. (2012) consider to be the signs of greatest genetic antiquity.
After showing their lack of understanding of linguistic labels and groupings, Henn et al. (2012) went on to completely abuse the linguistic classifications and the distribution of typological features worldwide.
“There is a remarkable similarity between the linguistic tree and the genetic tree, confirming Darwin’s speculation that, if we knew the biological tree of humans, we could predict that of their languages.”
Henn et al. (2012) do not seem to know that there is no such thing as the “linguistic tree” to match the “genetic tree.” There are hundreds of language families spoken across the globe with no demonstrable genetic links between them.
“Ruhlen has extended greatly the linguistic tree that goes back to a single origin, and connects all 15 language families for which validity is fairly widely accepted.”
What??? Ruhlen’s proto-World ideas, just like his and Greenberg’s reduction of worldwide linguistic diversity to just 15 families, have been rejected by virtually every single linguist. The linguistic community does not consider these efforts to be serious science. Henn et al. (2012) are trying to smuggle into a peer consensus a few biologists and geneticists (including Cavalli-Sforza and Feldman themselves) who rally behind Ruhlen and Greenberg but their opinions on language do not really matter as long as professional linguists are overwhelmingly on the other side of the barricade.
“A recent analysis of phonemic diversity in 504 worldwide languages shows that this diversity exhibits the same serial founder effect discussed earlier for genetic variation, namely a loss of phonemic diversity proportional to distance from Africa. Moreover, within Africa, the greatest diversity is in the southern central region. Although the regression of phonemic diversity on distance from Africa is not as strong as seen with DNA polymorphisms, this finding nevertheless suggests that the genetic and linguistic expansion from Africa could have been part of the same process.”
Again, Henn et al. (2012) failed to mention that Quentin Atkinson’s results (“Phonemic diversity supports a serial founder effect model of language expansion from Africa,” Science 332 (6027): 346-349) were tested and rejected by an international group of linguists. Some scholars even decried his approach as incompetent.
In both cases (the genealogical classification of languages and the patterns of phonemic diversity) the “independent evidence” that Henn et al. (2012) bring up in support of their out-of-African model evaporates at the first touch by a professional.
“As all modern human populations maintain the ability to acquire and speak complex language, it is clear that, before the Great Expansion, language must have been fully developed in the ancestral population.”
The logic is strong here: if Khoisan populations diverged from the rest of modern humans some 150,000 years ago but they are fully behaviorally modern now, then modern human language and behavior must have been in place by as early as 200,000 years ago. But when Henn et al. (2012) get the logic right, they run into an empirical problem: there are no signs of modern human behavior in the African archaeological record until 70-50,000 years ago and none of the anatomically modern human skulls in Africa are associated with modern technologies. If modern humans were equipped with language and the whole symbolic capacity writ large as early as 200,000 years ago, why did it take them 150,000 years to exit Africa and replace all the archaic hominins everywhere (including Africa) and, finally, why did they not bring African megafauna to extinction as they presumably did once they colonized Australia and America? Henn et al. (2012) go against the theory of the other eminent Stanfordite, Richard Klein, who used exactly this very empirical considerations to postulate that human symbolic behavior must be only some 50,000 years old.
“In summary, we have suggested that, during the Great Expansion, birth rate may have been more culturally regulated than the death rate, which is more constrained by biological phenomena. Additionally, these two rates may have opposite patterns of stability. As populations disperse into new, abundant environments, the birth rate may increase initially and then eventually stabilize if resources are limited by density.”
This summary concludes an interesting and important section on the demographic parameters found in modern forager populations and their implication for the out-of-Africa model. It is unclear, however, 1) why this section comes in the very end, instead as part of a set-up for the serial founder effect model; 2) what exactly in this overview of forager demographies supports the serial founder effect model; 3) why there is no discussion of social regulations around mating which play a central role in the vast majority of modern human populations and which affect genetic diversity in the direction away from the panmictic model assumed by out-of-Africa theorists. Finally, it is questionable that human populations expanding out-of-Africa faced new, abundant environments. What they must have faced was the fierce competition for resources from Neandertals who even replaced an anatomically modern human population in the Levant. The question of how interactions with other hominins in and outside of Africa affected modern human demography and epidemiology is something Henn et al. (2012) altogether omitted.