Population structure within Africa

By Razib Khan | March 16, 2011 12:50 am

John Hawks, reviews Henn et al., and notes:

By the time we find “modern” humans in West Asia, the African population had long since diversified into regional populations. This is not news; the mtDNA evidence has suggested for several years that southern Africa and the remainder of sub-Saharan Africa were already regionally differentiated before 120,000 years ago. There have also been hints of this diversification from whole-genome evidence (including the supplement of the Neandertal genome paper last year). Here we have a clear indication that the regionality extends to every African hunter-gatherer population.

For more than a generation we’ve stated the conventional wisdom that Africa has more genetic diversity than the rest of the world. And yet far too often we’ve left it at that. With the bigger data set of Henn et al. you can get a sense that there’s a fair amount of structured variation within Africa which is very interesting. It is not one amorphous undifferentiated Dark Continent. Sarah Tishkoff’s recent work has been very informative in this domain, but I’m looking for what we might find out of whole genome sequencing in particular.

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  • http://www.buildinghistory.org/distantpast/ Jean

    John Hawks asks where the Aterian Culture can be found. I suspect that it may be found in the percentage of our modern DNA currently claimed to be inherited from Neanderthals. See Not Neanderthal but North African?

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

    Let’s compare two statements by Hawks: 1) “Some of the diversity that once existed among these populations has now been spread within them instead. The populations got genetically closer over time,” 2) “No historical linguist has ever successfully demonstrated a system of sound changes or detailed correspondences among these [click-G.D.] languages, the genetic relations are just the opposite that would be expected if speakers of these click languages had shared a common origin. ” Statement 1 suggests that genetics in Africa captures the history of population admixture, not the history of population divergence. Statement 2 attributes to click-speaking populations a high degree of genetic divergence and criticizes some linguists for trying to subsume these populations under the (macro-)Khoisan phylum/family. Not only Statement 1 is in direct contradiction with statement 2, but both of them give away the confusion that reigns in the minds such as John Hawks’s. Common origin isn’t the opposite from divergence, but the necessary pre-condition thereof, no matter how great the divergence is. Contrary to geneticists’ naive assumption that genes are all about ancient kinship, while languages are all about elite dominance, the genetics of Sub-Saharan Africa, with the exception of Hadza, captures the history of admixture and not divergence, hence high levels of allele diversity is no indication of age.

    Suppl Mat clearly states: “Bantu-speaking populations, which have recently absorbed migrants during the Bantu expansion, have the highest haplotype heterozygosity at 100Kb windows; the hunter-gatherer Sandawe and ≠Khomani San groups have elevated haplotype heterozygosity, possibly in part due to recent gene flow from agriculturalist into these populations. The Hadza have the lowest heterozygosity within Africa.” And from the paper itself: “On the basis of an ob- served fROHHadza of 8%, the most likely estimate of effective population size (Ne) of the Hadza was 2,590. Single population estimates of Ne vary widely (19, 31), but among a global sample of HGDP populations only Native Americans and the Kalash have an Ne <3,000."

    As for linguistics, some linguists indeed believe that all Khoisan languages share a common origin. Others, dispute it on the basis of lacking sound correspondences. But both camps consider it most likely that clicks are shared across Khoisan language not because of convergent innovation. It means that, even if Hadza and San languages are not related, the areas in East and South Africa that are now occupied by click-speaking languages were once part of a continuous language area conducive to both gene flow and language borrowing. This would simply add validity to the genetic evidence for extensive admixture across Africa and would make the African origin for modern humans an untestable hypothesis. If Hadza is indeed the earliest branch in the Khoisan language tree, then this linguistic fact would still be consistent with genetic data, but in this case it would point decisively to a non-African origin for modern humans. Genetics is between a rock and a hard place now.

    Most likely, Hadza is one of the earliest African populations, and it still preserves the low intragroup/high intergroup diversity factor otherwise so well attested for other foraging (with some exceptions) populations outside of Africa (especially in the Americas), while South Khoisan and Bantu acquired high diversity through millennia of gene flow. Hence, the famous cline of increasing intragroup diversity that leads into Africa describes a progressive build-up of diversity through successive waves of gene flow, and not a migration out of Africa.

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

    “John Hawks asks where the Aterian Culture can be found. I suspect that it may be found in the percentage of our modern DNA currently claimed to be inherited from Neanderthals. ”

    Then how come some of the important signatures of “archaic admixture” in modern humans (see http://blogs.discovermagazine.com/gnxp/2011/02/friday-fluff-%E2%80%93-february-4th-2011/) are found at high frequencies in the Americas? North Africa is even further away from the New World than West Asia…

  • http://www.buildinghistory.org/distantpast/ Jean

    The idea here is that people of the Aterian Culture moved from North Africa to the Levant c. 100,000 years ago and then spread along the southern route to Australasia. See M.A. Schillaci, Human cranial diversity and evidence for an ancient lineage of modern humans, Journal of Human Evolution, vol. 54, no. 6 (June 2008), pp. 814-26.

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

    “The idea here is that people of the Aterian Culture moved from North Africa to the Levant c. 100,000 years ago and then spread along the southern route to Australasia.”

    Still pretty far from America. But the paper you cited, I remember, was an interesting read.

  • http://www.buildinghistory.org/distantpast/ Jean

    Neaderthals didn’t enter the New World either. :)

    It has been postulated on the basis of computer models that there were two events in human history of mixing with a more archaic hominid lineage which left a record in modern human DNA, one about 60,000 years ago in the eastern Mediterranean and, more recently, about 45,000 years ago in eastern Asia. (See Neanderthals may have interbred with humans

    Most people have jumped to the conclusion that said archaic hominid was Neanderthal. All I’m saying is that it looks as though there is a more plausible alternative.

  • http://johnhawks.net/weblog John Hawks

    The population model that demonstrates mixture does entail that one of the populations is genetically identical to the Neandertal draft genome. If the Aterians were Neandertals, that would of course do it, but that still leaves the problem of explaining the near-total disappearance of Aterian ancestry in North Africa.

    Confusion typically reigns in my mind, but thankfully doesn’t rein it in very often.

  • http://washparkprophet.blogspot.com ohwilleke

    Off topic, but the new Gene Expression blog logo is really ugly.

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

    The press release you quoted says: “Using projected rates of genetic mutation and data from the fossil record, the researchers suggest that the interbreeding happened about 60,000 years ago in the eastern Mediterranean and, more recently, about 45,000 years ago in eastern Asia.” The first date was inspired by Tabun Neanderthals, the second one by the Denisova sequence from South Siberia that showed similarities with modern Melanesians. It’s really a hodgepodge of arbitrary data points welded into a “theory.” BTW, the “coastal route” theory that earlier you connected to Aterian was originally invented to explain the absence of signs of Neaderthal-human interbreeding. Now that the fact of this interbreeding is seriously entertained, there’s no need (or archaeological evidence) for a southern route theory.

    “Neaderthals didn’t enter the New World either…Most people have jumped to the conclusion that said archaic hominid was Neanderthal. All I’m saying is that it looks as though there is a more plausible alternative.”

    So, while the genetic data is pointing to American Indians as the best contemporary proxy for that “other” human population, you are pointing to northern Africans? :)

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

    “Confusion typically reigns in my mind, but thankfully doesn’t rein it in very often.”

    Nice footwork there, John.

  • Jean

    @ German Dziebel

    I finally managed to track down the post to which you tried to give a link. It turns out to be a comment by you making the unsupported claim that American Indians are archaic. As far as I am aware, no paper has shown that they are more like Neanderthals or any other archaic hominid than East Asians are.

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

    Jean,

    I don’t know which post you tracked down. Here’s a list of genetic systems in which American Indians popped as having purported “archaic lineages” (including B006 in X chromosome and blood group O attested in neanderthals) at highest frequencies, higher than in East Asians. The references follow. Sorry for the broken link. I don’t know why it didn’t work.
    1. X chromosome B006 (the oldest dys 44 lineage, highest frequencies in the New World, lowest frequencies in Africa, worldwide distribution, Neanderthals have it, Yotova et al. 2011).
    2. Clade B of Pediculus humanus (2 MM years old, highest frequencies in the Americas, worldwide distribution, lowest frequencies in Africa; archaic introgression suggested by Reed et al. 2004).
    3. Blood group O (universal donor blood group, worldwide distribution, highest frequencies in the New World, attested in 2 Neanderthals by Lalueza-Fox).
    4. MCPH1 haplogroup D (1 MM years old, highest frequencies in the New World, worldwide distribution, lowest frequencies in Africa, archaic introgression suggested in Evans 2006).
    5. mtDNA insert in the nuclear genome (the most divergent human mtDNA sequence, clustered with the Mungo man sequence, highest frequencies in the New World, lowest frequencies in Africa, worldwide distribution; Zischler et al. 1995).
    6. mtDNA restriction site morph 1 (modal type, highest frequencies in the New World, worldwide distribution, lowest frequencies in Africa; Johnson et al. 1983).

    To this we can add shovel-shaped incisors, an important dental marker found at high frequencies in Neanderthals and Amerindians (East Asians also have it but at lower frequencies than Amerindians) and at low frequencies in Sub-Saharan Africa. Neanderthal shoveling is of slightly different shape but it’s still recognizably the same.

  • Jean

    “The population model that demonstrates mixture does entail that one of the populations is genetically identical to the Neandertal draft genome.”

    Not the model to which I refer, by Jeffrey Long and Sarah Joyce, which was presented at the annual meeting of the American Association of Physical Anthropologists in Albuquerque, New Mexico, on 17 April, before publication of the Neandertal draft genome.

    “that still leaves the problem of explaining the near-total disappearance of Aterian ancestry in North Africa.”

    No it doesn’t. If we are talking about the supposed “Neanderthal” DNA carried by Europeans and Asians, then that should be present in North Africa, the population of which is mainly derived from Europe and the Near East. But that doesn’t tell us anything. The Aterians are extinct. If the model shows mixture with Modern Man in two places only – the Eastern Med and East Asia, then obviously there was no mixing in North Africa which left traces in the modern human genome specifically there.

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

    Jean,

    It’s also possible that Y-DNA hg P can be added to this list, although we don’t know of Neanderthals had it. It’s geographic range (R in Europe, low frequencies in Sub-Saharan Africa, e.g., R1b in Fulani, Q at highest frequencies in America, rare in Siberia, but also found in West Asia, India and northern Europe) is reminiscent of the footprints left by X chromosome B006 lineage and also by blood group O (both attested in Neanderthals). Note that, although P is part of the MNOPS clade, the NO subset thereof is widely spread in Asia and among the Uralics but is not found in the Americas, whereas hg Q is found at high frequencies in Siberia in Kets and Selkups, a pattern suggestive of a pre-NO distribution. This situation is similar to the distribution of blood groups O and B. B is very high in Siberia and the rest of Asia, all the way into Polynesia, but is barely found in the New World. It’s possible therefore that Q is a relic lineage similar to X chromosome B006. Its downstream position in the current Y-DNA phylogeny may be misleading. The other Amerindian Y-DNA hg C is way upstream in the phylogeny and also has a pre-NO distribution in Asia. I wouldn’t be surprised if one looked at the Y-DNA phylogeny from this broader point of view hgs P and F would swap places.

  • Lars Smith

    German,

    Why would the Hadza be an “earlier” population than e.g. the Sandawe?

  • onur

    Why would the Hadza be an “earlier” population than e.g. the Sandawe?

    German’s theory of Hadza being the earliest extant Sub-Saharan population based on their current low genetic diversity/heterozygosity and high linkage disequilibrium is implausible. As Razib points out in his post “Where in the world did anatomically modern humans come from?”, their current low genetic diversity/heterozygosity and high linkage disequilibrium is almost certainly the result of the recent bottleneck they have been going through. The current Hadza population is under 1000, while Sandawe and San each have tens of thousands of individuals. So it isn’t clear how early a population Hadza are.

    BTW, according to genetics, Hadza have significant Bantu admixture, so they aren’t as genetically isolated as German seems to imply.

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

    @Lars Smith:

    “Why would the Hadza be an “earlier” population than e.g. the Sandawe?”

    Hadza would be less admixed than Sandawe, hence preserving more of the original population structure (low effective population size, low intra- high-interpopulation variability, high homozygosity) widely attested among non-African foragers. Apparently, they stayed away from the waves of gene flow that crosscut Sub-Saharan Africa.

    @onur

    “their current low genetic diversity/heterozygosity and high linkage disequilibrium is almost certainly the result of the recent bottleneck they have been going through.”

    IMO, it’s not a recent bottleneck but a survival from the original low diversity condition, widely attested outside of Africa.

    “The current Hadza population is under 1000″

    This is typical for, say, New World tribes that have long been considered examples of an original human population structure. Comp.: “Indeed, among the current human populations, South American aboriginals can be considered a reference for microsatellite variation in an ancient
    African ancestor because their population size is low and might be compared with that estimated for an African ancestor, from one to a few thousand gametes (Rogers and Harpending 1992; Rogers 1995; Rogers and Jorde 1995; Zhivotovsky et al. 2000), and they have maintained their style of life probably since they arrived in this area.” (Zhivotovsky, 2001, “Estimating Divergence Time with the Use of Microsatellite Genetic Distances: Impacts of Population Growth and Gene Flow”).

    “according to genetics, Hadza have significant Bantu admixture.”

    At least judging by the results of this study, which is a genetic study, this admixture is negligible compared to the admixture among South African Khoisan. Admixture would’ve driven Hadza diversity values up. You can’t have a recent bottleneck AND recent gene flow and still arrive at the lowest diversity values in Africa, like you can’t have the cake and eat it too.

    “So it isn’t clear how early a population Hadza are.”

    If genetically Hadza can be thought of as the best example of Pleistocene population structure in Africa (it’s certainly possible judging, again, by extra-African tribal demography), then it jibes well with those linguists who believe Hadza are related to other Khoisan languages as the primary branch of the (Macro-Khoisan) language family. This in turn would reinforce the idea that South Khoisans are derived from an ancient East African Hadzoid population and acquired their high diversity values from admixture with each other and with agriculturalists.

    The overall picture, therefore, is that the proverbial phenomenal genetic diversity in Sub-Saharan Africa comes from several waves of population admixture between agriculturalsits, pastoralists and ancient foragers and is, therefore, of recent origin. The original stage of dispersal of demes that colonized Africa in the Pleistocene, which produced high interpopulation diversity, was replaced by a stage of population aggregation that drove Fst down and increased interpopulation diversity. Pleistocene Africa was more like Melanesia and the New World, rather than the other way around.

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

    As far as the so-called “Neanderthal admixture” is concerned, I would suggest flipping it around, so that the archaic non-African component in modern humans comes from our common descent from a non-African hominid (e.g., Neanderthals), which has largely been replaced/diluted by waves of internal (between modern human populations [!], thanks to Jean for the tip) gene flow that aggregated modern human (and especially African) populations into a “melting pot” as they progressively colonized Europe, Asia and Africa. The survivals of the original archaic lineages are mostly found on the margins of the current human geographic range, namely in the New World and the Sahul. Those areas served as refugia that kept Amerindians and Australasians out of the gene flow that linked the other regions.

  • onur

    At least judging by the results of this study, which is a genetic study, this admixture is negligible compared to the admixture among South African Khoisan. Admixture would’ve driven Hadza diversity values up. You can’t have a recent bottleneck AND recent gene flow and still arrive at the lowest diversity values in Africa, like you can’t have the cake and eat it too.

    This study doesn’t show that Hadza have negligible Bantu admixture compared to Khoisan, and the significant Bantu admixture in Hadza may be from anytime since the Bantu expansion to the Hadza territory so doesn’t have to be recent and doesn’t contradict the current low genetic diversity/heterozygosity and high linkage disequilibrium in Hadza, which is almost certainly entirely to do with the recent population bottleneck in Hadza.

    IMO, it’s not a recent bottleneck but a survival from the original low diversity condition, widely attested outside of Africa.

    You are of course free to believe what you wish, but you should at least try to be realistic.

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

    Onur,

    Look at the unique bright yellow bar for Hadza in Tishkoff’s “The Genetic Structure and History of Africans and African Americans” and compare it to a much more homogeneous and overlapping East, South and West African populations. This couldn’t have been caused by a bottleneck in Hadza that postdated Bantu admixture. The Bantu admixture created that very sea of homogeneity around Hadza that Hadza doesn’t have. BTW, Sandawe is part of that homogeneous and overlapping melting pot in that ADMIXTURE plot.

    “You are of course free to believe what you wish, but you should at least try to be realistic.”

    If you don’t like to face facts, don’t call reality for help.

  • onur

    Look at the unique bright yellow bar for Hadza in Tishkoff’s “The Genetic Structure and History of Africans and African Americans” and compare it to a much more homogeneous and overlapping East, South and West African populations. This couldn’t have been caused by a bottleneck in Hadza that postdated Bantu admixture. The Bantu admixture created that very sea of homogeneity around Hadza that Hadza doesn’t have. BTW, Sandawe is part of that homogeneous and overlapping melting pot in that ADMIXTURE plot.

    ADMIXTURE doesn’t tell anything about bottleneck times and ADMIXTURE components don’t come with ages, a population can be very recent and form its own component, so your example is wrong. Also the ADMIXTURE plot you mention doesn’t tell anything about the Bantu expansion, at least not in any clear way.

  • onur

    Also the ADMIXTURE plot you mention doesn’t tell anything about the Bantu expansion

    and Bantu admixture

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

    “ADMIXTURE doesn’t tell anything about bottleneck times and ADMIXTURE components don’t come with ages, a population can be very recent and form its own component, so your example is wrong. Also the same ADMIXTURE plot doesn’t tell anything about the Bantu expansion, at least not in any clear way.”

    This borders on absurdity. Or on agnosticism. I’m not sure. You have PCAs and ADMIXTURE telling the same story, but you’re still on the fence about everything that contradicts your expectations. Arms in the air, rest my case, science is over because prince onur is not happy with anything.

  • onur

    This borders on absurdity. Or on agnosticism. I’m not sure. You have PCAs and ADMIXTURE telling the same story, but you’re still on the fence about everything that contradicts your expectations. Arms in the air, rest my case, science is over because prince onur is not happy with anything.

    German, ask anyone knowledgeable about population genetics what ADMIXTURE and PCA plots tell and do not tell and they will all agree with me and disagree with you. And BTW, my name is Onur, not onur.

  • onur

    but you’re still on the fence about everything that contradicts your expectations

    It is you who is on the fence about that, not me.

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

    “ask anyone knowledgeable about population genetics what ADMIXTURE and PCA plots tell and do not tell and they will all agree with me and disagree with you.”

    So, according to onur 16, they tells us that Hadza went through a recent bottleneck. But according to onur 21, they can’t tell us anything about “bottleneck times.” And according to onur 24, he is not onur but “Onur.” What kind of “knowledgeable” people should we bring into the discussion?

  • onur

    German, the plot in question in my comment #16 is a linkage disequilibrium plot, and, as you know, bottlenecks increase linkage disequilibrium. I infer that the bottleneck in Hadza is post-Bantu expansion to the Hadza territory and recent based on: their current extremely low genetic diversity/heterozygosity and high linkage disequilibrium for their region + their extremely small (<1000) current population size + the significant Bantu admixture in them that was shown in previous genetic studies + recent history of remnant hunter-gatherers in Africa and elsewhere.

  • onur

    Together with the above factors (and not by itself), the fact that the Hadza component (yellow) in Hadza is unique to them (it isn’t found in any other population) and dominates them in the Tishkoff et al. study strongly indicate that there is a very strong recent population bottleneck in Hadza.

  • onur

    What kind of “knowledgeable” people should we bring into the discussion?

    Ask Razib for example.

  • onur

    You can also ask Dienekes, David and Zack or a professional in the field of population genetics.

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

    Onur, is Sarah Tishkoff and her team knowledgeable enough for you? If so, then let’s hear what they have to say:

    From Tishkoff et al. 2009, 1041: “The Hadza, with a census size of ~1000, were genetically distinct on a global level with STRUCTURE, PCA, and TESS (Figs. 2 to 5), consistent with linguistic data indicating that the Hadza language is divergent from or unrelated to other Khoesan languages (42, 51, 52). The Hadza, who have maintained a traditional hunter-gatherer lifestyle, show low levels of asymmetric gene flow from neighboring populations, whereas the Sandawe, with a census size of >30,000 (39), show evidence of bidirectional gene flow with neighboring populations, from whom they may have adopted mixed farming technologies (Figs. 3 to 5 and fig. S15). Although the Hadza and Sandawe show evidence of common ancestry (Fig. 1 and figs. S7, S8, S14, S18, and S21), we observe no evidence of recent gene flow between them despite their geographic proximity, consistent with mtDNA and Y chromosome studies indicating divergence >15,000 years ago (19).”

    Note that Hadza stand out not only in African but in global PCA as well (Tishkoff’s Fig. 2), which strongly suggests a split far predating the Bantu expansion.

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

    “the significant Bantu admixture in them that was shown in previous genetic studies”

    Of course, they have some Bantu (likely Sukuma) admixture. In Tishkoff 2009 you can see thin threads of other colors running through the yellow bar in a few Ks. This is nothing compared to admixture levels in, say, Sandawe. So, in the case of Hadza, we’re probably dealing with ancient divergence and recent admixture. Not recent bottleneck and ancient admixture. We don’t have any evidence for a recent bottleneck in Hadza, but we do know that they’ve been interacting with the Sukuma in the last decades. Admixture increases diversity; without some Bantu admixture Hadza would show even stronger LD and even lower diversity. This means that, insofar as we have data to ascertain the nature of a recent demographic process that affected Hadza, it can only be admixture and not a bottleneck, and admixture drives diversity up and LD down. Knight et al. (2003) “African Y Chromosome and mtDNA Divergence Provides Insight into the History of Click Languages” noted low mtDNA diversity in Hadza and attributed it to their low effective population size. Low effective population size is not a necessary consequence of a recent bottleneck but, rather, of long-term isolation and drift. And, consequently, as Knight et al. note, “All Ju|’hoansi mtDNA haplotypes diverge from all those of the Hadzabe at the root of the human mtDNA phylogenetic tree,” which again indicates great antiquity for Hadza.

  • onur

    German, you cannot explain the significant Bantu admixture in Hadza with only recent admixture; admixture with Bantus must have begun not very long after the Bantu expansion to the Hadza territory. And that admixture must surely have been bidirectional (in fact, that admixture must have been more in the Hadza -> Bantu direction as the admixing Bantus were the expanding and assimilationist group while Hadza were the conservative and indigenous group). The fact that we see no Hadza component (yellow) in any other population (including Sukuma) in the Tishkoff et al. study supports the view that the Hadza-Bantu admixture is relatively ancient rather than recent and the Hadza component is actually the result of a post-admixture population bottleneck in Hadza.

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

    “you cannot explain the significant Bantu admixture in Hadza with only recent admixture.”

    And where’s the evidence for this “significant” admixture, onur? Fig. 1 in Henn et al. and Fig. 3 is Tishkoff et al. show that this admixture is insignificant as compared to admixture in Sandawe and South Khoisan and it’s not bidirectional. Strong gene outflow from Hadza was detected by Tishkoff et al. for Biaka Pygmies, which suggests that Hadza’s interaction with non-Hadza may have been been more significant prior to the main wave of Bantu expansion. It’s of course possible that Hadza have gone through serial founder effects throughout its history, exactly like the Native American groups mentioned by Henn et al., so that its old territory and numbers shrank as Bantu approached.

    In Henn’s K=4 we see the Hadza component underlying most Sub-Saharan Africans, especially Maasai and Sandawe, which suggests that Maasai, Sandawe and Hadza (among others) share a common ancestral component that survived mostly in Hadza and Maasai. This again supports the antiquity of Hadza: it’s a remnant of an early East African population. And it has very little in common with, say, Kenyan Bantu (on that graph).

    “admixture must have been more in the Hadza -> Bantu direction as the admixing Bantus were the expanding and assimilationist group while Hadza were the conservative and indigenous group)”

    I don’t know where you get the inspiration to write this nonsense. The only good evidence for admixture between Bantu (Sukuma) and Hadza was provided by Knight et al. 2003 for Y-DNA, and this admixture involved Sukuma males. This is typical for Y-DNA: all the instances of hg R in Amerindians, for instance, comes from European males.

    “the view that the Hadza-Bantu admixture is relatively ancient rather than recent and the Hadza component is actually the result of a post-admixture population bottleneck in Hadza.”

    This should settle the debate: “The distribution of admixture varies between the hunter-gatherer populations according to the cluster analysis in Figure 1. At k=8 about a third of the Hadza and
    !Khomani Bushmen are inferred to share ancestry with Bantu, Maasai or Europeans,
    whereas the remainder of the individuals show little detectable recent admixture (Fig. 1).
    The variation in admixture between individuals within these populations indicates that
    the gene flow may have occurred ONLY DURING THE PAST FEW GENERATIONS, and random
    mating within the population has not had time to equilibrate admixed allele frequencies.
    In contrast, the Sandawe and Biaka populations show less intra-population variation in
    the extent of Bantu admixture, suggesting gene flow into these populations occurred over
    longer periods of time.” (Henn et al. Suppl Mat, p. 3).

  • onur

    And where’s the evidence for this “significant” admixture, onur? Fig. 1 in Henn et al. and Fig. 3 is Tishkoff et al. show that this admixture is insignificant as compared to admixture in Sandawe and South Khoisan and it’s not bidirectional.

    The significance of Bantu admixture in Hadza compared to that in Sandawe is open to debate. But Hadza do have significant Bantu admixture according to Knight et al. (2003) and Tishkoff et al. (2007).

    Tishkoff et al. (2007) explicitly state that the admixture between Hadza and Bantu was bidirectional, with Hadza contributing genes to nearby Bantu and other non-Hadza mainly via females while nearby Bantu and other non-Hadza contributing genes to Hadza mainly via males.

    Strong gene outflow from Hadza was detected by Tishkoff et al. for Biaka Pygmies, which suggests that Hadza’s interaction with non-Hadza may have been been more significant prior to the main wave of Bantu expansion. It’s of course possible that Hadza have gone through serial founder effects throughout its history, exactly like the Native American groups mentioned by Henn et al., so that its old territory and numbers shrank as Bantu approached.

    In addition to that, Tishkoff et al. (2007) state that that bottleneck in Hadza was likely recent:

    “In both these scenarios, the mtDNA L0d lineages would have existed in the populations ancestral to all 3 groups and were lost subsequently in the Hadza. The latter lineage loss is quite likely given the estimated time depth of L0d common ancestry between the Sandawe and SAK (>58 kya) and the likelihood of a recent bottleneck in the Hadza population (Blurton Jones et al. 1992). Additionally, the observation in a Turkana population from northern Kenya of an L0d lineage that is phylogenetically close to the Tanzanian L0d lineages (fig. 5b) suggests that at one time the L0d haplogroup may have been more widespread across eastern Africa (Watson et al. 1997).”

    In Henn’s K=4 we see the Hadza component underlying most Sub-Saharan Africans, especially Maasai and Sandawe, which suggests that Maasai, Sandawe and Hadza (among others) share a common ancestral component that survived mostly in Hadza and Maasai. This again supports the antiquity of Hadza: it’s a remnant of an early East African population. And it has very little in common with, say, Kenyan Bantu (on that graph).

    The meaning of that component is very much open to debate and the label “Hadza” is misleading.

    I don’t know where you get the inspiration to write this nonsense. The only good evidence for admixture between Bantu (Sukuma) and Hadza was provided by Knight et al. 2003 for Y-DNA, and this admixture involved Sukuma males. This is typical for Y-DNA: all the instances of hg R in Amerindians, for instance, comes from European males.

    As I wrote above, the bidirectional gene flow between Hadza and Bantu was sex-biased. As Tishkoff et al. (2007) state:

    “Phylogeographic analyses of mtDNA and Y chromosome lineages indicate recent gene flow between both the Hadza and Sandawe and their neighboring populations. For example, we observe mtDNA L0a lineages shared by the Sandawe and Burunge (fig. 5a), and we observe several L3 lineages shared by the Hadza and Sukuma (fig. 5d). We also observe L4g lineages shared by the Hadza and Datog and other L4g lineages shared by the Sandawe, Turu, and Burunge (fig. 5d). Given the relatively high haplotype frequencies of the L4g haplogroup in the Hadza and Sandawe, it is possible that these lineages originated in the Hadza and Sandawe populations and then were introduced via females into the neighboring agriculturalist and pastoralist populations. By contrast, the Y chromosome data suggest gene flow from the neighboring groups into the Hadza/Sandawe (e.g., E3a-M2). For example, the Hadza and Sandawe populations appear to have absorbed Y chromosome E3a lineages associated with Bantu speakers, and yet have contributed little in terms of the B2b lineages to their neighbors (fig. 7). These data suggest the possibility of a biased migration pattern, with higher female migration from hunter-gatherer groups into neighboring agriculturalist/pastoralist populations and higher male migration from agriculturalists/pastoralist populations into the hunter-gatherer populations. This pattern is consistent with other studies of hunter-gatherer populations in central Africa (Destro-Bisol, Donati, et al. 2004).”

    This should settle the debate: “The distribution of admixture varies between the hunter-gatherer populations according to the cluster analysis in Figure 1. At k=8 about a third of the Hadza and !Khomani Bushmen are inferred to share ancestry with Bantu, Maasai or Europeans, whereas the remainder of the individuals show little detectable recent admixture (Fig. 1). The variation in admixture between individuals within these populations indicates that the gene flow may have occurred ONLY DURING THE PAST FEW GENERATIONS, and random mating within the population has not had time to equilibrate admixed allele frequencies. In contrast, the Sandawe and Biaka populations show less intra-population variation in the extent of Bantu admixture, suggesting gene flow into these populations occurred over longer periods of time.” (Henn et al. Suppl Mat, p. 3).

    Those ADMIXTURE components don’t say anything explicit about relatively ancient admixture events.

  • onur

    BTW, according to the figure 2B of Henn et al., African populations with the lowest linkage disequilibrium values are the hunter-gatherers (as they should have, because they are the most ancient coherent African populations) and among them only Hadza disobey this rule with their unusually high LD for not only African hunter-gatherers but also Sub-Saharan Africans as a whole. From previous genetic studies it is clear that Hadza are a very ancient population like all other African hunter-gatherer populations, so recent population bottleneck is the most plausible explanation for their extremely high (for their region) LD.

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

    “Tishkoff et al. (2007) explicitly state that the admixture between Hadza and Bantu was bidirectional, with Hadza contributing genes to nearby Bantu and other non-Hadza mainly via females while nearby Bantu and other non-Hadza contributing genes to Hadza mainly via males.”

    Finally, onur (you should change your signature to Onur, BTW, if lower-case bothers you), you’re offering some sourced analyses. Sex-biased admixture makes sense. This is more precise than “bidrectional admixture.” And thanks for pulling up data for mtDNA admixture. I couldn’t find exact mentions. Per Henn and Tishkoff, though, this admixture is recent and shallow, as compared to admixture between Sandawe and Pygmies, on the one hand, and Bantu, on the other. It’s also noteworthy that Hadza and Sandawe share very little admixture despite geographic proximity – and both Henn and Tishkoff emphasize this – which again suggests long-term isolation for Hadza, prior to the recent gene flow between them and Bantu.

    “Those ADMIXTURE components don’t say anything explicit about relatively ancient admixture events.”

    Those components rather clearly show the separation of Hadza from a common East African pool, its long-term isolation and recent Bantu admixture.

    “Additionally, the observation in a Turkana population from northern Kenya of an L0d lineage that is phylogenetically close to the Tanzanian L0d lineages (fig. 5b) suggests that at one time the L0d haplogroup may have been more widespread across eastern Africa (Watson et al. 1997).”

    A good factoid. This squares well with the yellow component in Fig 1 of Henn et al. most strongly represented in K=4 in Maasai (Nilo-Saharans just like Turkana) and Hadza. But Henn et al. report L0a2 in Hadza, which means better sampling can help identify L0 lineages in Hadza.

    “African populations with the lowest linkage disequilibrium values are the hunter-gatherers (as they should have, because they are the most ancient coherent African populations) and among them only Hadza disobey this rule with their unusually high LD for not only African hunter-gatherers but also Sub-Saharan Africans as a whole. From previous genetic studies it is clear that Hadza are a very ancient population like all other African hunter-gatherer populations, so recent population bottleneck is the most plausible explanation for their extremely high (for their region) LD.”

    If a recent bottleneck is responsible for low heterozygosity/high LD in Hadza (and Hadza, per Henn, have “the lowest heterozygosity within Africa” (Suppl Mat, p. 3)), then these metrics are very unstable and large heterozygosity can’t be used as an indication of population antiquity. As Razib pointed out, agricultural Fang/Bulala and foraging San in Henn’s Fig. 2b are very close to each other, although the former are agricultural newcomers and the latter are indigenous foragers. And as John Hawks noted in the post addressed here by Razib, “Some of the diversity that once existed among these populations has now been spread within them instead. The populations got genetically closer over time.” This means that what drives LD down in South Africa is not great age but high levels of admixture between formerly divergent populations. This is consistent with South Africa being a repository of several migrations from East and West Africa, and not a source of African and world diversity. Hadza is being pulled into this African “melting pot” only recently.

    Henn et al. wisely caveat the recent bottleneck in Hadza with a qualifier “possibly.” gene inflow and bottlenecking, if both of them were recent and simultaneous, would cancel each other out. “Recent severe bottleneck” in Hadza most likely equals the compounded effects of long-term genetic drift. Hadza who “stayed behind” in East Africa, like all “normal” foragers, have maintained low population numbers and experienced genetic drift for a long time, whereas East African Nilotes developed pastoralism and expanded in size and South African Khoisan expanded into a new territory and consequently also expanded in size and then absorbed the earliest waves of East African pastoralists and Bantu agriculturalists. This interpretation will be consistent with the upstream position of the Hadza language in Macro-Khoisan language classifications and with them having unique cultural features such as musical structures that seem to be slow-changing (see http://soundingthedepths.blogspot.com/2011/02/chapter-five-hunter-gatherers.html). Hadza music is especially interesting, as it’s different from Bantu, Pygmies and South African Khoisans but similar to music styles found in abundance outside of Africa. Otherwise, again, allele diversity and LD metrics become too volatile to indicate anything of deep historical value: Hadza went through a “recent severe bottleneck,” South African Khoisans went through “recent dramatic population growth,” etc.

  • onur

    By bidirectional admixture, I mean admixture in which admixed individuals do not stay in just one of the admixing populations but are dispersed between both of the admixing populations, irrespective of whether the admixture is sex-biased or not. In unidirectional admixture, in contrast, admixed individuals stay in just one of the admixing populations. The admixtures of Muslim Turks and Arabs with their subject non-Muslim populations in history are examples to unidirectional admixture; in both of these cases admixed individuals almost totally stayed in the Muslim side. We do not see such a pattern in the admixture of Hadza with nearby Bantu and other nearby non-Hadza populations, as in their case the admixed individuals were dispersed between the admixing populations, even if not in equal proportions.

    As to the main subject of our discussion, I think the real issue (I think we have got too much stuck on the Hadza issue, which is only a collateral issue) is the contrast between the diversity and LD levels of Sub-Saharans and the rest of the world. IMO, it cannot just be explained with homogenization via intensive admixture in Sub-Saharan Africa, as similar homogenizations via intensive admixture happened in most of the the world. There is nothing to suggest that the homogenization in Sub-Saharan Africa was particularly intense compared to the rest of the world.

    As for your Out-of-America hypothesis, even if the Americas were colonized, say, 50,000-60,000 years ago, there were modern humans in the Old World much before there was any human being in the New World. The artificial anatomically modern-behaviorally modern dichotomy is laughable. Languages didn’t suddenly appear 50,000-60,000 years ago, there were already languages, however primitive, even before the modern human-Neanderthal human separation (BTW, I don’t mean an absolute separation), and likely much before.

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

    “(I think we have got too much stuck on the Hadza issue, which is only a collateral issue)”

    An important case study.

    “it cannot just be explained with homogenization via intensive admixture in Sub-Saharan Africa, as similar homogenizations via intensive admixture happened in most of the the world. There is nothing to suggest that the homogenization in Sub-Saharan Africa was particularly intense compared to the rest of the world.”

    I think the pattern of high intragroup genetic diversity (especially in South Africa and by some metrics among pastoralists and agriculturalists) and low intergroup genetic/low linguistic diversity is suggestive of intense hybridization and homogenization in Africa. Europe and West Asia show a similar pattern. In America, parts of Asia and Australasia the pattern is the opposite. It’s suggestive of population divergence without much hybridization. Hadza fits with the pattern common in the New World, parts of Asia and Australasia but is an odd ball in Africa. Mid-Pleistocene hominids outside of Africa such as Neanderthals seem have maintained the low intragroup diversity profile similar to the one attested in modern humans in the New World. Coupled with the apparent retention of some “archaic,” including clearly Neanderthaloid, lineages in Amerindians (see my comment 12 above) and Melanesians (precisely the two areas where Fst, LD and linguistic diversity are high) this suggests that humans may have evolved outside of Africa and recolonized it much more recently than the fossil chronologies seem to indicate.

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

    “As for your Out-of-America hypothesis, even if the Americas were colonized, say, 50,000-60,000 years ago, there were modern humans in the Old World much before there was any human being in the New World. The artificial anatomically modern-behaviorally modern dichotomy is laughable. Languages didn’t suddenly appear 50,000-60,000 years ago, there were already languages, however primitive, even before the modern human-Neanderthal human separation (BTW, I don’t mean an absolute separation), and likely much before.”

    Humans are behaviorally unique. This is the only important phenomenon that “intelligent” human origins research should answer. Yes, humans are also anatomically “modern” but we can’t build a theory on the basis of the so-called AMH skulls in Africa when all we have is chronology. Unless we get ancient DNA samples from Omo, etc., I don’t even know what to make of them. Many of them used to be dated to Late Stone Age, then they re-dated them to build a case for out of Africa. Human origins research has so far put the cart before the horse: you can’t pose intelligent questions and deliver intelligent answers on the basis of such a patchy and ever-changing record as fossils and tools. All our human uniqueness is in our minds, not in lithics, and in what we pass down to next generations, not in what we leave behind in a garbage pit. Cross-cultural data from linguistics and ethnology (my kinship studies, for example) should be part and parcel of human origins research, not a poor relative of bones and stones.

    Not only that humans are behaviorally unique. We are also genetically very close to each other. Hence, it’s likely that we evolved relatively recently in a unique ecological niche, with no hominids around to interfere with our speciation and survival. (How could we speciate in Africa or in Europe, continents that were so well settled by archaics?) But we also must have descended from a hominid population, hence it’s likely that we went through a “severe bottleneck” (the traces of that ancient bottleneck are still visible in foraging populations outside of Africa and in Africa apparently among Hadza). The only place in the world that meets all these conditions is the New World: no hominids, connected to Asia via a geographic bottleneck, Neanderthals and Homo erectus would provide an ancestor population. Woolly mammoths provide an analogue in the mammalian world: originated from an Asian antecedent, crossed the Bering Strait, speciated in isolation, migrated back, replaced their original brethren in East Asia.

    And yes, the “language gene” must have been successful in a Eurasian hominid lineage (and in Amerindians and Melanesians as direct survivals thereof), not in the African one. It’s possible, though, that it was already present in the African ancestor of both African erectus and Asian erectus (or at least in the African ancestor of Neanderthals and African archaics), but didn’t make it very far in Africa.

  • onur

    As to the main subject of our discussion, I think the real issue (I think we have got too much stuck on the Hadza issue, which is only a collateral issue) is the contrast between the diversity and LD levels of Sub-Saharans and the rest of the world. IMO, it cannot just be explained with homogenization via intensive admixture in Sub-Saharan Africa, as similar homogenizations via intensive admixture happened in most of the the world. There is nothing to suggest that the homogenization in Sub-Saharan Africa was particularly intense compared to the rest of the world.

    German, when I wrote the above lines I had in mind Sub-Saharan Africa, North Africa, Europe, West Asia, South Asia, East Asia and Southeast Asia, in other words, regions of the world long inhabited by crowded modern human populations. Of all these regions, Sub-Saharan Africa is unique with its extremely high genetic diversity/heterozygosity and extremely low linkage disequilibrium (Hadza are an exception, but their extremely low population size and relative isolation easily explains their difference from other Sub-Saharan populations) despite the fact that all these regions have had high population densities and intensive internal migrations for quite a long time. This uniqueness of Sub-Saharan Africa compared to the other regions I mention strengthen the view that Sub-Saharan Africa is the region inhabited by modern humans the earliest.

    Many of them used to be dated to Late Stone Age, then they re-dated them to build a case for out of Africa.

    This very much sounds like a conspiracy theory.

    Note: I am intentionally refraining from responding to your every argument and diversifying the discussion, as this thread will very soon be closed to comments.

  • onur

    This uniqueness of Sub-Saharan Africa compared to the other regions I mention strengthen

    This uniqueness of Sub-Saharan Africa compared to the other regions I mention strengthens

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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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