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 Gene Expression Blog / AfricaTeasers

300px-Hamito-Semitic_languagesIf you follow Y genealogy you know that the distribution of R1ba2 exhibits a peculiar pattern. R1b is the most common haplgroup in Western Eurasia, and shares a deep common ancestry with R1a. It seems to have risen to high frequencies in Europe only during the Bronze Age, though has been found in earlier periods. But within Africa R1b is found in very high concentrations around Lake Chad. This particular R1b lineage seems to have diverged from other Eurasian branches in the latter portion of the Pleistocene, so one possible consideration is that this was an instance of Eurasian backflow during the Ice Age.

One reason I have been somewhat skeptical of this model is that the Sahara desert was much more extensive and arid during much of the Pleistocene than today. And during this period humans had less cultural technology to endure the rigors of the deep desert. Or, if they did, their population densities were likely much lower, which probably served as an impediment to gene flow.

A new paper in The American Journal of Human Genetics sheds light on what might have been going on here. Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations. The major findings are straightforward. First, much greater sampling of populations, and a better depth/density of marker coverage, allowed the researchers to detect low levels, on the order of ~1%, Eurasian admixture in some Central African groups. This admixture seems to date to the Holocene, ~5,000 to ~7,000 years before the present (they used LD based methods on the autosome). Interestingly, the R1b lineage common in Central Africa also seems to coalesce during this time. Finally, the admixture seems to be closest to Sardinians among extant populations.

The Sardinian affinity of much of African Eurasian admixture may seem peculiar, but it makes more sense when one considers that Sardianians are probably the best modern proxies for the earliest Neolithic farmers from the Eastern Mediterranean. Modern Middle Eastern populations are very different from those which flourished in the prehistory between the rise of agriculture and complex civilizations because of admixture within Middle Eastern groups. The initial push into Africa by the agriculturalists dates to a period before we have a good understanding of the ethnographic balance.

Very high frequencies of R1b in modern Central Africa groups may indicate drift. But another possibility is that the migration was male-mediated. This seems to have been the case in much of Eurasia, so it would not be surprising in this context. The status of these males was such that despite their diminishing genetic impact on overall ancestry, their Y chromosomes, and possibly their language, with varied forms of Afro-Asiatic, persisting down to the present.

Finally, here’s the last paragraph of the discussion:

Our study has shown that human genetic diversity in Africa is still incompletely understood and that ancient admixture adds to its complexity. This work highlights the importance of exploring underrepresented populations, such as those from Chad, in genetic studies to improve our understanding of the demographic processes that shaped genetic variation in Africa and globally.

• Category: Science • Tags: Africa, Genetics 

The figure in Ewen Callaway’s piece in Nature, Evidence mounts for interbreeding bonanza in ancient human species, does a good job at relaying what we know about admixture between different human lineages informed by ancient DNA. But is that all there is? Before ancient DNA in large quantities came online there were attempts to infer admixture based on the available data (mtDNA, modern populations) and model building and simulations. There were two natural conclusions.

First, admixture happened. Second, it did not. Here’s a paper from 2004, Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe, in PLOS BIOLOGY. And from 2006, Possible Ancestral Structure in Human Populations, in PLOS GENETICS (the first paper has 100 more citations, ~250 vs. ~150, as was in the more mainstream journal). The relatively tentative title of the second paper as opposed to the bold aspect of the first publication does I think reflect the strength of the two positions across academia as a whole at the time (I grant that many population geneticists in particular were skeptical at “Out of Africa” with-total-replacement triumphalism, which was evident in Richard Dawkins’ The Ancestor’s Tale, published at about that time).

Screenshot from 2016-02-18 09-16-07 Ancient DNA has changed things. But it has not changed everything, because ancient DNA has been retrieved predominantly from northern Eurasia, for various reasons. I was careful to state above that Callway’s piece was informed by ancient DNA, because I think it omits the likelihood of archaic admixture within Africa. A group associated with Jeff Wall and Michael Hammer have been arguing for gene flow between highly diverged lineages within Africa for many years (and archaic admixture more generally going back to the mid-2000s), and yesterday they came out with two papers in Genome Research.

First, Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies:

Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.

And, Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection:

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba farmers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

I have to say that sometimes I think that selection scans in population genomics are a bit little neuroscience. Neuroscience tells us that stuff happens in the brain. Selection scans tell us that adaptation targets a bunch of functional regions of the genome. Though I’m sure you would feel different in “your gene” shows up on the laundry list.

In any case, two points that I want to emphasize. Haplotypes which seem introgressed from an archaic lineage are underrepresented in genic regions. The same sort of purifying selection you see in archaic admixture in Eurasians (and now in the Altai Neanderthal) seem to be at work here. Second, the divergence between western Pygmies and African farmer populations is nearly double the time of the “Out of Africa” event. And, the results from this group seem consistent that admixture continued to occur after it had ceased to occur in Eurasians because the archaics outside of Africa had been absorbed by then (at least to our knowledge, I would not be surprised if there was later in some groups detectable at very low levels). This reinforces the idea that we need to update and complexify our idea of how modern humans came to be.

• Category: Science • Tags: Africa, Genomics 

In many ways the image of Africa in the minds of Westerners has become a trope. The “Dark Continent,” eternal, and primal. Like many tropes the realized existence of this Africa is only within the imagination. The real Africa is far different. For there is no real Africa, there Africa s. This truth is on my mind this week as two papers of great importance in understanding African genetic history finally saw the light of day. First, Dr. Joseph Pickrell et al. posted their preprint, The genetic prehistory of southern Africa, to arXiv. Second, out of the Tishkoff lab came Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers. Let me step aside here and observe a secondary, but non-trivial, detail. The former is an open access preprint. The second is a complete paper published in a relatively high impact journal, Cell, for which the paper itself does not seem typical or appropriate. This is fair enough, most people do not read journals front to back in this day. But unlike Dr. Joseph Pickrell’s paper the paper in Cell is paywalled, and from what I can tell you can not obtain the supporting information without getting beyond the gate! So if you need that paper, email me and I will send it onward (I would just post it on a server, but I’ve gotten nasty emails from the legal departments of publishers, so I am wary of doing that).

From where I stand these two papers have different strengths. The genetic prehistory of southern Africa has a wide and expansive sampling of individuals and to some extent populations, and, utilizes very clever statistical genetic techniques on SNP data (i.e., hundreds of thousands of variants among the ~3 billion base pairs). Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers, as the title suggests, is a very deep and relatively complete read of the whole genomes of ~15 hunter-gatherers, from three populations, Western Pygmies, and two non-Bantu populations from Tanzania, the Hadza and Sandawe (there are other whole genome analyses already of groups to which they can compare these). Personally, I would have preferred genomic analyses of the Eastern Pygmies, who seem more genetically distinctive in relation to the Bantu, but there were likely logistic constraints.

Probably the most interesting finding of the Pickrell et al. paper is that the Hadza and Bushmen seem to share deep common ancestry. More precisely, the Hadza can be modeled as a combination of East Africans and Bushmen, with a 3:1 ratio. Please note: can be modeled as. This does not mean that that is the real history, but, this stylized result probably gives us some insight into the more complex picture. The Hadza and Bushmen are both hunter-gatherers who have clicks in their language. That should shape prior expectations. Additionally, in various genetic analyses they cluster with the Pygmies of Central Africa as a distinct clade from the agriculturalists of Africa. There are other suggestive results in the Pickrell et al. paper. For example, there is evidence of back-migration from Eurasia into the Sandawe. This is not surprising to me, as I’ve explored this issue with coarser techniques (thanks to Brenna Henn & company for releasing these genotypes). Additionally, there are suggestive results in this paper that the Khoikhoi, a pastoralist Khoisan group, have some genetic influence from East Africans (detected in part via old Eurasian affinities). There have been arguments that pastoralism came to the Khoikhoi not through the Bantu, but via earlier peoples, so this is clearly something that needs to be followed up. Overall, this paper seems to have made more precise and sharpened vague outlines which were already established. Tenuous connections between the Hadza and the Bushmen have been confirmed. Very deep separation between the distinct Bushmen groups is reinforced. And finally, the big chasm between a few groups of hunter-gatherer, and other Africans, is illustrated again.

As a final product the Cell paper is rather polished in comparison. The media has emphasized the evidence of archaic admixture into hunter-gather lineages. This is not that surprising of a finding, other groups have reported the same. If anything, I suspect that there is some underestimate here, because it seems to me that the statistical methods have a hard going at this age range, and without ancient genomes at that (i.e., the decay of linkage disequilibrium). Dienekes has commented extensively on this, offering up his own theories. I don’t have any grand model to propose. Rather, I would suggest that even a “leaky” “Out of Africa” model somewhat misleads the public, by again relegating Africa into a sort of inert black-box. There is deep ancient structure within Africa (e.g., Pickrell et al. confirm that San lineages have been diverged on the order of tens of thousands of years!). Though the dates are not totally clear, it seems possible that the most diverged African groups (e.g., Bushmen) separated from the lineage that led to other populations only moderately more recently than non-African archaics! (e.g., Neanderthals) This may not be multi-regionalism, but it does suggest a very deep history and structure for humanity, as opposed to the “old” model that modern humans as such were the product of a single discrete speciation event ~50,000 years ago. There may be no “behold man!” moment.

There’s a large section on adaptation within the Cell paper. I’ll quote their conclusion, because I have no interest in recapitulating genomic alphabet soup:

We find evidence of selective constraint near genes, and these patterns are replicated in each hunter-gatherer population. We also observe signatures of local adaptation in Pygmy, Hadza,and Sandawe populations, including high locus-specific branch lengths for genes involved in taste/olfactory perception, pituitary
development, reproduction, and immune function. These genetic differences reflect differences in local diets, pathogen pressures, and environments. Thus, Pygmies, Hadza, and Sandawe have continued to adapt to local conditions while sustaining their own unique cultures of hunting and gathering.

Surprised that “ancient” hunter-gatherers continue to evolve? I hope not. At this point, let me take a step back. You may wonder: what does this post have to do with Atlantis and the Azores? (or, for that matter Shaka Zulu!) Reading this sort of paper is very interesting to me obviously. The relic hunter-gatherers of Africa can tell us a great deal about our human past. But at some point we need to remember that these are relics. A few years ago I ran into someone who told me that an anthropologist friend explained that the Bantu expansion had been debunked. This sort of thing is why I think cultural anthropology is quite often such a joke discipline. They should stick to their picketing the econ department, and leave the description of the human conditon as it is to those with a genuine interest. Not only are the Bantu languages a dialect continuum, but the genetic evidence seems rather clear that you can find relative unity across the vast swath of Central, Eastern, and Southern Africa. Though Africans have a great deal of genetic variation, the distance between the various Bantu groups is not that great (e.g., using Fst).

And, the genetic distance between Bantus and Khoisan is such that we can conclude that the Bantu expansion into South Africa, for example, was one of demographics, not cultural diffusion. The Xhosa, who are the outer edge of the expansion, and even had integrated clicks into their language, are only minority Khoisan in ancestry. How did this occur? One model might be one of demic diffusion, the sort promoted by L. L. Cavalli-Sforza, and still favored some researchers. In this model you have raw demographic expansion pushing a population outward, diluting their original genetic signal over time on the wave of advance. This is a “thermodynamic” model, not requiring concerted or coordinated state action, as family and clan groups are constantly expanding on the frontier. I do not believe this is how it played out. The Bantu expansion was very thorough. I think Shaka Zulu and his cruel military formations tell us a lot more than small villages of female farmers. No, I’m not suggesting a continent wide confederacy. Rather, the genetic signal from the region of the East-Central Africa lakes is so strong as far south as the Natal that I have difficulty understanding how there could not have been aggressive actions taken against the smaller and less organized hunter-gatherers. Imagine, if you will, the Bantu expansion being driven by men racing forward in Zulu-like military units, clearing territory of hunter-gatherers, killing and starving them out (and taking the occasional girl as a concubine). A Mfecane writ large! What stopped them in the end in Southwest Africa was ecology: the agricultural toolkit of the Bantu was not suitable for the arid or Mediterranean climates of this region. Until then the Bantu knife cut through the hunter-gatherers like butter, wiping them from the surface of the earth.

With this as a backdrop the hunter-gatherers, and their genomes, are then like mountaintops flooded by farmers. Like the idea that the Azores are the last fragments of Atlantis, so the Pygmies, Hadza, and Khoisan, are the least of the vast domains of pre-Bantu peoples who once inhabited the southern half of the continent. They show deep genealogical relationships, but they are simply a shadow of what once was, and what has disappeared from the face of the earth. The eternal “Dark Continent” was in fact roiled by a demographic revolution of gargantuan proportions within the last 3,000 years. We may debate whether the farmers or hunter-gatherers are the ancestors of modern Europeans, but we know the answer for Africans. The hunter-gatherers lost. In the time of ancient Egypt Africa to the far South was a very different place, the Bantus did not start moving in large numbers until the collapse of the New Kingdom. When the pyramids were young there was a different world across the vast savannas and plains of East and South Africa, and world we’ll never show, and only see through the pinholes provided by the last hunters of the continent.

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

In the post yesterday I reported what was generally known about the Horn of Africa, that its populations seem to lie between those of Sub-Saharan African and Eurasia genetically. This is totally reasonable as a function of geography, but there are also suggestions that this is not simply a function of isolation by distance (i.e., populations at position 0.5 on the interval 0.0 to 1.0 would presumably exhibit equal affinities in both directions due to gene flow). For example, you observe the almost total lack of “Bantu” genetic influence on the Semitic and Cushitic populations of the Horn of Africa, and the lack of Eurasian influence in groups to the south and west of the Horn except to some extent the Masai.

Tacking horizontally in terms of discipline, over the past few generations there has been a veritable cottage industry making the case for the recent origin of many ethno-linguistic populations through a process of cultural self-creation. Clearly there are many cases of this, some of them studied in depth by anthropologists (e.g., the shift from Dinka to Nuer identity). But there has been an unfortunate tendency to over-generalize in this direction. In some ways this is peculiar insofar as these models presuppose the infinite plasticity of culture without observing the sharp and strong norms which those very same phenomenon can enforce. The genetic isolation of non-Muslims in the Middle East after the rise of Islam seems rather well validated by the evidence from genomics. The norms of both Muslims and non-Muslims strongly biased them toward endogamy, and nature of Islamic hegemony and domination was such that Muslims were the ones who were likely to have cosmopolitan affinities with the “Islamic international.” In contrast, non-Muslim minorities began a long process of involution after the Islamic Arab conquests, only disrupted in the past century by emigration and to a lesser extent emancipation.

So back to the Horn of Africa. The vast majority of the people of the Horn of Africa speak an Afro-Asiatic language. Arabic and Hebrew are the most famous members of this group, but it is a very broad classification, ranging from the dialects of the Berbers in the Maghreb all the way to ancient Akkaddian. There are two large subfamilies of particular note and interest here: Semitic and Cushitic. The map above shows the distribution within the Horn of Africa. One can “quick & dirty” summarize the pattern here by observing that Semitic languages in Ethiopia tend to be concentrated in the north-central Christian highlands, while Cushitic is found everywhere else. Additionally, there is the confluence between religion and ethnicity, as there are Cushitic Muslims (Somalis, Afar, etc.) and Cushitic Christians (many Oromo, etc.). From what I can gather many Cushitic social and political elites have had a tendency toward assimilating into an Amhara Semitic identity (Haile Selassie’s mother was a Muslim Oromo). We could therefore generate a possible model where Semitic langauges arrived late to Ethiopia and spread through elite emulation, so the difference between Semitic and Cushitic peoples should be marginal in the genomic dimension (such as the marginal differences between Hausa and Yoruba in Nigeria). Or, we could posit that the Semitic element is distinctive from a pre-existent Cushitic substratum.

To make a long story short by running more ADMIXTURE with a Horn of Africa centered data set I have discerned that one can actually differentiate Cushitic and Semitic elements in the Horn and tentatively identify them with different ancestral components. First, the technical details….

I began with the data set I started with in the runs I posted yesterday. Strange outliers in the Masai were removed. These are a few sets of individuals who “fix” for minority ancestral components. This is a tell that there’s structure within the Masai being picked up, but more like distantly related individuals, not ethnic level differences. After running this I noticed that a lot of the same then popped up in the non-Jewish Yemeni and Saudi samples. To some extent this is like “whack-a-mole.” If you remove one problem others simply pop out of the woodwork. So I removed all the non-Jewish Yemenis and Saudis. The number of markers remained the same, 210,000 SNPs.

There were still a few issues with outliers, especially with the Bantu Kenya, and to a lesser extent the Levantine samples. But at this point I decided to go with it, since these are marginal to the story of the Horn of Africa in any case. I stated yesterday that in general Horn of Africa populations don’t present their own clusters, but are a composite of others, mostly East African and Arabian. After I removed some of the spurious Masai components and ran ADMIXTURE up to K = 10 I did finally get a Horn of Africa cluster, “HoAc”. Additionally, I also found that you can see systematic differences between Cushitic Oromo and Somalis, and the Semitic Ahmara, Ethopian Jews, and Tigray.

Below are bar plots of K = 7 and K = 9. The lower K’s aren’t too different from what I posted yesterday, while K = 8 and K = 10 has too many minor components. I’ve posted only fine-grained and Horn of Africa focused plots, instead of the more general summary plots which show average ancestral quanta. Also, below these I’ve posted two dimensional representations of genetic distances between inferred ancestral groups for K = 7 and K = 9. I’ve removed several components though, in the case of one because it was clearly a spurious “extended family” cluster, and in some cases to better visualize relationships.

To cut to the chase, it looks like all Horn of Africa populations share a HoAc base, which one might term “Cushitic,” though that is not totally accurate. On top of that base you see differences based on language family. The Semitic speaking groups have an ancestral component which is identical to the one fixed in Yemeni Jews, while the Cushitic speaking ones tend to lack this. But observe that the Semitic speaking populations generally have the component found in the Cushitic speaking groups, and especially the Somalis in which it often fixes. This is why I put the sequence of language-population expansions so that the Semitic is overlain upon a Cushitic base. Additionally, there does seem to be admixture from Nilotic groups into Ethiopian, but not Somali, populations. This is most consistent and evident in the Oromo, and where an isolation by distance model seems plausible, as the Oromo are geographically the most likely to have interacted with Nilo-Saharan populations and the Somali the least.

Finally, please keep in mind that if the Somalis are 100% cluster X, that does not mean that the Somalis are derived from some real homogeneous ancestral cluster X. These ADMIXTURE components are very interesting in helping to flesh out relationships horizontally across populations today, but we should be cautious about what they can tell us about relationships vertically in terms of how populations emerged over time. A thoroughly admixed group can break out into its own distinctive cluster if it exhibits a level of internal homogeneity and the ancestral “reference” populations themselves no longer exist. This seems to be what has occurred in South Asia, where certain groups shake out as “100% South Asian,” but themselves on the deeper genomic level seem to be stabilized admixtures of ancient fusions between two ancestral groups which were very diverged. A South Asian analogy to the Horn of Africa might lead us to infer that Somalis are the equivalent of these populations, where they lack admixture with more recent arrivals to the region after the initial admixture event between “Ancestral East Africans” (AEA) the Arabians of yore. This may simply be a function of geography and historical contingency, as the position of Somalis is more “sheltered” because of the quasi-peninsular nature of their region of the Horn. Additionally, Somalia is relatively dry and unsuitable for agriculture, making it perhaps less ecologically friendly than the highlands of Ethiopia to Semitic populations bringing a new agricultural toolkit.

There’s plenty more you can say, but I’ll hold off, and add a word of caution: it is very possible that I was looking for these specific clusters and arrived at them via confirmation bias. As I’ve noted before, if you tune ADMIXTURE’s parameters in the proper fashion you can “arrive” at the answers you want. How to protect against this? If I keep performing ad hoc runs and going by intuition, lots of repetition often helps. You naturally arrive at a sense of the underlying distribution of possibilities, can guard against anchoring upon an outlier result, because you know that it is atypical (this is though on reason that ground-breaking results are ignored, as they don’t fit the paradigm, so there’s a flip-side to this bias). I also run cross-validation now and then to find the optimal number of K’s, but that really slows down the program, so I this is a matter of trade offs for me. I’m rather sure that the differences between Ethiopian and Somali groups are robust, because the same pattern of relationships (e.g., the Amhara tendency to resemble the Tigray more than the Somali) reoccurs over and over. But I’m not so confident about the inference I’ve drawn here about the Afro-Asiatic language families and the partitioning of the Cushitic and Semitic groups.

You can find some more files here.

Image credit: Wikipedia

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

I recall years ago reading Spencer Wells discuss how important it was to sample “indigenous people”* before they were swallowed up by the cresting panmixia. Of course panmixia has to be conditioned on the fact that the vast majority of Han Chinese are stilling reproducing with other Han Chinese, and so forth. But it seems plausible to argue that the great agricultural Diasporas are only today swallowing up the residual of marginalized groups outside of the farming frontier. These populations which expanded from agricultural hearths over the Holocene may only be a shadow of the genetic variation which was once extant after the last Ice Age, as the thinly populated landscape was fractionated into endogamous networks as a matter of necessity rather than preference.

First, let’s recall that over the long term “effective population size” is defined by the harmonic mean. Concretely, a population of 1 billion can be far more genetically homogeneous than a population of 1,000, if, those 1 billion only recently expanded from far smaller populations. Imagine a toy example of two populations, A & B. They both begin in generation 1 with a population size of 1,000. In generation 3 both experience a population drop, A to 750, and B to 85. Now, assume that A bounces back to 1000 and maintains that population for the next 20+ generations. In contrast, B begins to double in population size each generation. Here’s a log-transformed chart illustrating the different population sizes:

In generation 25 population B is at a census size of 350 million. What’s the long term effective population of these two groups?

- Population A = 987

- Population B = 979

As you see a population bottleneck can have long term consequences in terms of effective population size. Think about it in terms of evolutionary genetics. Any given population begin with a certain amount of standing genetic variation, but if they crash in size then a lot of that variation is lost through the sampling process of random genetic drift. A small population can be a good representation of the variation of a larger population, but as a practical matter usually there is some information lost in the sampling, with more information lost the smaller the N. If the population rebounds then migration and mutation can eventually replenish the lost variation, but that can take a great deal of time. Even after ~10,000 years as a minimum the populations of the New World seem to exhibit evidence of a population bottleneck.

Coming back to the real world, these are the sorts of dynamics which make me interested in events such as the Bantu expansion. If the model outlined in First Farmers is correct then the past 10,000 years have witnessed a massive reordering and diminution of genetic variation around the world, as small core populations of agriculturalists radiated and replaced hunter-gathers. This makes Spencer Wells’ argument more persuasive, insofar as the remaining twigs of non-agriculturalists may be reservoirs for the shadow of variation past.

As an amateur prehistorian then my interest in populations such as the Mbuti, Bushmen, and Andaman Islanders has been piqued. Yesterday I ran a set of populations in ADMIXTURE with ~170,000 markers. At K = 11, unsupervised, they partitioned relatively cleanly (and the cross-validation error crept back up at K = 12).

As you can see most of the populations are dominated by their own unique element here (the Druze and Mandenka are different shades of green). Here are the pairwise genetic distance values:

San Mbuti Han W African Druze Hadza N European Masai Papuan Maya Sandawe
San 0.00 0.17 0.35 0.17 0.30 0.25 0.32 0.22 0.44 0.41 0.16
Mbuti 0.17 0.00 0.31 0.12 0.27 0.22 0.29 0.18 0.40 0.37 0.12
Han 0.35 0.31 0.00 0.24 0.16 0.34 0.17 0.25 0.23 0.15 0.21
W African 0.17 0.12 0.24 0.00 0.20 0.18 0.22 0.12 0.33 0.30 0.08
Druze 0.30 0.27 0.16 0.20 0.00 0.29 0.09 0.19 0.25 0.19 0.16
Hadza 0.25 0.22 0.34 0.18 0.29 0.00 0.31 0.21 0.44 0.41 0.16
N European 0.32 0.29 0.17 0.22 0.09 0.31 0.00 0.21 0.26 0.20 0.18
Masai 0.22 0.18 0.25 0.12 0.19 0.21 0.21 0.00 0.33 0.30 0.12
Papuan 0.44 0.40 0.23 0.33 0.25 0.44 0.26 0.33 0.00 0.30 0.29
Maya 0.41 0.37 0.15 0.30 0.19 0.41 0.20 0.30 0.30 0.00 0.26
Sandawe 0.16 0.12 0.21 0.08 0.16 0.16 0.18 0.12 0.29 0.26 0.00

My main interest right now is the Sandawe. Who are they? What are their relationships? The Hadza seem a genetic isolate of some sort. The Khoisan and Pygmy seem to be part of a broad hunter-gatherer substrate which was overlain by the Bantu expansion. The Sandawe presumably speak a language related to that of the Khoisan, and most of the stuff in the academic literature is linguistic. But they also are genetically distant from the Hadza, and there is some dispute as to their linguistic affinities. I am currently reading The ecological basis for subsistence change among the Sandawe of Tanzania (free on Google Books, so I pulled it to my Kindle). For now, plots and charts using the genetic distance values above. The two dimensional charts are representations of the genetic distances….

* The quotes because the term “indigenous” seems to be politically loaded and fraught. There’s a fair amount of evidence that many indigenous people replaced other indigenous people, relatively recently in time. The exceptions may be amongst groups who were first settlers on islands, like the Maori, relatively late in history.

(Republished from Discover/GNXP by permission of author or representative)
• Category: History, Science • Tags: Africa 

Image Credit: Mark Dingemanse

I recall years ago someone on the blog of Jonathan Edelstein, a soc.history.what-if alum as well, mentioning offhand that archaeologists had “debunked” the idea of the Bantu demographic expansion. Because, unfortunately, much of archaeology consists of ideologically contingent fashion it was certainly plausible to me that archaeologists had “debunked” the expansion of the Bantu peoples. But how to explain the clear linguistic uniformity of the Bantu dialects, from Xhosa of South Africa, up through Angola and Kenya, to Cameroon? One extreme model could be a sort of rapid cultural diffusion, perhaps mediated by a trivial demographic impact. The spread of English exhibits this hybrid dynamic. In some areas (e.g., Australia) there was a substantial, even dominant, English demographic migration coincident with the rise of Anglo culture. In other areas, such as Jamaica, by and large the crystallization of an Anglophone culture arose atop a different demographic substrate, which synthesized with the Anglo institutions (e.g., English language and Protestant religion). The United States could arguably be held up as a in-between case, with an English founding core population, around which there was an accretion of a non-Anglo-Saxon stream of immigrants who serial adopted the Anglo culture, more or less. Sometimes this co-option of Anglo-Saxon norms may surprise. “Black English” (i.e., Ebonics) actually seems to be a genetic descendant of lower class northern English dialects. Other distinctive components of black American (e.g., “jumping the broom“) culture can also plausibly be derived back to the British Isles.

So cultural change is in the “its complicated” segment of dynamics. We have to go on a case-by-case basis. For the Bantu expansion though we have a good answer now thanks to genetics: this cultural change almost certainly was accompanied by a massive demographic migration. Thanks to Brenna Henn and company you can even run some analyses on your desktop to confirm the reality of this model. I pulled down the 55,000 SNPs from various African populations, merged with Palestinians, Tuscans, and Maya as outgroups, and pruned down to ~40,000 after removing those which were missing in more than 1% of the cases. The Hadza are also gone, as they’re such a small isolated group who always hogged up K’s all by themselves. I ran a bunch of different ADMIXTURES, from K = 2 to 12. You can see all 12 here, but let’s just focus on the 12th.

Below is a bar plot, somewhat sorted by ADMIXTURE elements. I’ve reedited some of the labels for clarity, adding regions. I’m sure some of you are ignorant of where the Brong people (Ghana) are from as I was before I looked them up. Also, please be careful about ADMIXTURE. There is a “Fulani” ancestral component below, but I’m 90% sure that’s just an artifact of recent Fulani demograhics + their unique genetic admixture.

K4, the dark green component, seems associated with Bantus and Bantu neighbors all across Africa. The lack of correspondence to geography is clearly suggestive of demographic leapfrogging. The existence of non-Bantu peoples in the wake of their migration (e.g., the Nilotic peoples in northeast Africa, the Pygmies, and the Sandawe) could be indicative of either ecological constraints on the Bantu toolkit (so the migrants simply moved around the uncongenial zones), or a later intrusion (this is often hypothesized to be what occurred to bring the Masai to Tanzania). There are no Horn of Africa samples here, but I have some 23andMe files, and I can tell you that it seems as Dienekes observed, the Sub-Saharan component among the people of Ethiopia and Somali seems singularly lacking the Bantu element. Why? My own suspicion is that this region had its own agricultural (or pastoralist) way of life which rendered them demographically robust in the face of the Bantu, who simply turned south once they reached a zone of serious cultural resistance.

But there’s more. Of course there are Fst, genetic distances, between these “ancestral” populations. You can find these, along with the frequencies, in an Excel file I uploaded. But let’s look at how the populations related to each other on an MDS plot, which visualizes the pairwise distances on a two dimensional plane. I’ve added labels this time. They should be pretty clear in terms of which K’s they correspond to.


For what it’s worth, the Sandawe are presumed to be the aboriginal people of Tanzania, at least in relation to the dominant Bantu around them.

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

The-Tenth-Parallel On the face of it Eliza Griswold’s The Tenth Parallel: Dispatches from the Fault Line Between Christianity and Islam is a book whose content is summed up accurately by the title. The author recounts her experiences in various African and Asian lands which straddle the tenth parallel north of the equator: Nigeria, Sudan, Somalia, Indonesia, Malaysia, and the Philippines. It is a story told through personal narrative, the author’s, and the numerous people who are themselves embedded in larger forces welling up from below and descending from above. One can accurately describe The Tenth Parallel as a travelogue. But it is also a time machine, as Griswold surveys worlds which are a clear simulacrum of those which we know only through works of history; empires of faith, the lands of God’s platoons. As such, The Tenth Parallel is also a narrative which describes an alien world of ideas, outside of our conventional categories and classes. Many of the preconceptions and expectations which we bring to the table are “not even wrong” in the lands Griswold traverses, and what has been learned must sometimes be unlearned. This is not Newtonian Mechanics, where a cold and objective eye surveys the terrain and reports back positions and trajectories across space and time. An awareness of the author’s viewpoint is critical, while the viewpoint of her sources are plain. Finally, your own presuppositions and experiences as a reader shape the ultimate “take home” message which Eliza Griswold stitches together across her disparate sojourns.

eliza-newAs for the author, she is informs you about the details of her background repeatedly. Judging a book by its “cover” you see a young white Christian woman tasked to report on the turmoil in the lands of black and brown folk, many of whom are not Christian themselves, and many of whom are ardently Christian. But Griswold’s vantage point is more nuanced, she is the daughter of Frank Griswold, a prominent cleric in the Episcopal Church of America, who was a participant in the consecration of Gene Robinson, the first openly gay bishop in the Anglican Communion. This event has come close to rending asunder the Anglican Communion, of which the second largest district is covered by the Church of Nigeria (though arguably Nigeria has more practicing Anglicans than Britain, the largest district). In many ways in terms of core values I suspect that Muslims and Christians in Nigeria share more with each other than they do with Eliza Griswold. Her meetings with Franklin Graham, son of Billy Graham, always seem fraught with tension because it is as if Eliza Griswold’s very being serves as a witness for the liberal mainline Protestant tradition in the face of the muscular and unsubtle evangelical Protestant Christianity she observes all around her. The author’s own subjective viewpoint as a liberal Christian (at a minimum culturally, she published no precise statement of faith) interweaves with the story she tells much more subtly in most contexts than it does when she engages with Graham and his coterie. It is as if they bring with them an awareness of American culture wars and to some extent force Griswold to play her part. The author’s peculiar perspective is always there and should never be forgotten. It does not take much reading between the lines to infer that Eliza Griswold is not sympathetic to the methods of Western evangelical Protestants who believe it is their Great Commission to bring the whole world to their own faith. This is not a conclusion which is “wrong” or “right” in a conventional sense, but derived from a set of values, which the reader may or may not share.

1040The bigger canvas on which The Tenth Parallel is painted is is the idea of the 10/40 Window. This is the broad swath of the World Island between the tenth and fortieth parallels north latitude. These are the lands of Islam, Hinduism, Buddhism, and traditional Chinese religion. The vast majority of the world’s non-Christians reside in this zone, and in the past generation Western evangelicals have focused their efforts on spreading their message from Morocco to China. All of the specific conflicts explored in The Tenth Parallel can be viewed through a 10/40 lens, though Griswold is obviously surveying the world of Islam more specifically.

The author emphasizes that the conflict between Islam and Christianity in these lands is often an old one, and she illustrates this point by retelling the story of the first age of global muscular evangelical Christianity, that of the late 19th and early 20th centuries. But even that is simply a later episode of a millennial story. Globalization is often conceived of in terms of economic factors of production moving across borders, but in the pre-modern world it was more often ideas which spanned political units of organization. The expense of moving goods and services across civilizational boundaries meant that such international commerce was restricted to high-value luxuries. But ideas could flow easily because they were theoretically weightless for each marginal unit of meme.

Prior to the rise of Islam there was a Buddhist Age in Asia. From the south of India, to Transoxiana, to Japan, Buddhists traveled via the Silk Road. The monk Kumārajīva, who was instrumental in translating many Buddhist texts into Chinese, was reputedly the son of an Indian Brahmin and a Tocharian princess, a native of the Silk Road city of Kucha. In the 7th century the young Anglo-Saxon Christian Church was headed by an Archbishop of Canterbury, Theodore of Tarsus, who was born in Anatolia, lived under Persian rule, and finally fled the Islamic conquests. The Christians of South India have a long history of communion and connection with Middle Eastern Christianity, first the Persian Church, and later the Syrian Orthodox Church. The current phase of religious globalization is far less of a departure from the norm than the current age of mass migration, economic specialization, and the movement of commodities and manufactured goods.

In fact the ultimate roots of the story in The Tenth Parallel go back to the Axial Age, over 2,000 years ago, with the emergence of what we used to term “higher religions,” forms of supernatural belief which are embedded in institutions, have philosophical scaffolding, and are formalized and flexible enough to move across tribal boundaries in a coherent manner so as to maintain their integrity of identity. That is, religious ideas don’t simply transfer across groups, religious systems do. In our more sensitive age these are referred to as world religions, or organized religion. Christianity, Islam and Buddhism are exemplars. In the past Judaism, Hinduism and Zoroastrianism all had variants which transcended tribal boundaries, though these are traditions which have more or less re-tribalized themselves of late. These tribe-transcending religious systems have served to smooth the paths of travelers who could appeal to the solidarity of belief and practice across differences of ethnicity or geographical origin. The lives of Ibn Battuta and Xuanzang both attest to this. Without the charity and hospitality of co-religionists they would never have been able to complete their treks. But what brings us together can also divide, and the boundaries between world religions are often fraught with misunderstanding and incommensurability of religious foundations. Quantitative historian Peter Turchin terms the regions where world religions meet “meta-ethnic frontiers.”

Clash_of_Civilizations_mapMeta-ethnic frontiers are a touchy subject today. “Right thinking people” tend to dismiss the importance of the concept, it being too associated with Samuel P. Huntington’s The Clash of Civilizations. They reject the idea of the clash of civilizations, and assume that the book which gave rise to the term aligns with their preconceptions of the central argument. Most of the criticisms of Samuel Huntington’s work, imperfect and yet thought provoking, are of a kind where I strongly suspect that the critic hasn’t read the original, but rather is engaging nth hand expositions of the thesis. Many of the enthusiastic exponents of the clash thesis also have clearly not read Huntington’s work, which warns against neoconservative enthusiasms and suggests the necessity of a practical modus vivendi in a multipolar world riven with fissures of values. Macrohistory is generally slotted into one’s ideological preference, in large part because the principals in the discussion aren’t genuinely interested in academic issues but are looking for rhetorical devices. Academics can themselves get caught up in the game. Consider, Historian challenges assumptions about religious conflicts:

Associate professor of history Brian Catlos has spent years researching how Christians, Muslims, and Jews interact.

“Where my research and data leads, though not intentionally, is to debunk the notion of a conflict of civilizations–a conflict between groups of people who identify themselves as Christians, Jews, or Muslims and who articulate their struggle as a result of ideology and national identity,” said Catlos. “Rather what’s really behind history and contemporary human affairs is the interest of relatively small groups who often interact without regard to ideologies, national, or religious boundaries.”

Catlos observed that engaging in this type of historical research is his way of testing common assertions that there is a fundamental and irresolvable conflict between Christian and Muslim, or Jewish and Muslim, cultures. He points out that throughout history, there has been a widespread phenomenon of elites interacting with whoever will serve them best.

Such grand “common assertions” are propounded by people who are stupid. The stupidity can at the root be due to ideological preference (i.e., they know that reality varies with their ideology, but they ignore reality), ignorance, or simple lack of cognitive ability which would allow for the ability to construct models with greater subtly and nuance. It’s just as ridiculous as the inverted narratives which presuppose that religious conflicts are simply aberrations against a long history of interfaith amity. The “interfaith” movement as we understand it today is to a great extent a product of a historical moment. In particular, its roots lay in the ecumenical strand within liberal Protestantism, which eventually expanded to Christianity more generally, and finally to all world religions.

map-konfBrian Catlos’ book, The Victors and the Vanquished: Christians and Muslims of Catalonia and Aragon, 1050-1300, does refute a simple narrative of religious conflict, but, I do not believe it refutes a complex narrative of religious conflict. It is plainly wrong to assert that in every case a Muslim sides with a Muslim, and a Christian sides with a Christian. Reality is not carved out of such stark simplicities, else all scholarly endeavors would have transformed themselves into physics. There are exceptions even in cases where meta-ethnic solidarity was in clear evidence. In 1683 the Habsburg monarchy managed to obtain the support of many of the German princes who owed notional fealty to them and the crown of Poland in their battle against the Ottomans. Much of the rest of Christian European sentiment was on the side of the Hapsburgs, a fact which is notable because of the relatively recency of the Thirty Years War between Catholics and Protestants in Germany. This set of conflicts had polarized elite opinion on the continent and in the British Isles. But by the 1680s the tide had turned and Europe wearied of internecine divides in the face of the Ottoman attack. The unanimity was such that France was vilified in some circles because of its tacit alliance with the Ottomans, despite the fact that the French relationship with the Ottomans stretched back centuries. This was to a very large extent a religious war in the minds of many despite the fact that it could also be interpreted in a more conventional framework of how geopolitical conflicts emerge out of structural parameters.

But there were Christians who traveled with the advancing Ottomans to batter themselves against the walls of Christendom. When it came to the Eastern Orthodox, who had long been Ottoman subjects, and had little necessary affinity for Western Christianity, this may seem somewhat unsurprising. But there were Protestants who fought for the Ottomans. Protestants such as Thököly Imre fomented the conflict, and supported the Ottomans, against their fellow Christians. But the historical context of this alliance makes it entirely comprehensible why these Protestants had little fellow feeling for their Roman Catholic brethren. For decades the Austrian Habsburgs had persecuted Protestants and slowly re-Catholicized their domains by means soft and hard (on the soft side, inducements so that prominent Protestant families would return to the Roman fold, on the hard side a choice between expulsion or conversion in the towns). A grand Christian front against Islam was all well and good in the abstract, but for Hungarian Protestants their proximate existence as a people was dependent on a Muslim shield against their aspirant overlords, who they knew would have reimposed Catholicism upon them. The present day religious map of Hungary reflects these historical accidents. Culturally about ~25% of Hungarians are of Protestant origin, and they are concentrated in the eastern regions of the Magyar lands which were not re-Catholicized because they were under Ottoman hegemony. In contrast, what was Royal Hungary, became overwhelmingly Catholic thanks to the success of the Hapsburgs and their confederates in grinding down the Protestant majority to triviality.

scatterWhat is important is not to deny systematic biases and long term trends when you average out the seemingly random set of alliances which emerge between peoples and individuals based on immediate contingencies. It could be that in most cases alliances between polities don’t line up neatly on civilizational or confessional lines, but, over centuries non-trivial systematic biases matter. They matter insofar as the Reconquesta succeeded despite the infighting between Christian potentates. The rivalries were put aside at the battle of Las Navas de Tolosa. Over most of Iberia’s history in these centuries because of geographical proximity it may have been that most of the conflict was between Muslims and Muslims, Christians and Christians. But when evaluating on a civilizational scale if these lower level conflicts “average out,” then the systematic biases which track meta-ethnic identities can be highly significant. In the course of a few years it is ridiculous to speak in civilizational terms, but in the course of centuries it is precisely the boundaries of civilizations which wax and wane.

These intergenerational ebbs and flows of affinity, ideology and identity, are at the heart of Eliza Griswold’s narrative. In the early 20th century black Africa was operationally a “pagan” continent. Muslims and Christians were thin on the ground, generally restricted to narrow elites. The vast populace still adhered to their traditional tribal religions. As an example, Senegal, which is ~90% Muslim today, was probably only minority Muslim in 1900. Though it has arguably been part of the Dar-ul-Islam for a thousand years the peoples to the south of the Senegal river were only lightly touched by Islamic civilization. In the 20th century modernization, the rise of mass culture and communication, has produced a much deeper Islamicization in African societies where organized religion had previously been a feature of narrow urban elites. But as Eliza Griswold notes the Muslims were not the only ones at the march in Africa. European Christians saw in the “Dark Continent” a treasure trove of souls to be won, so that today Africa is split between Muslims and Christians, with Sub-Saharan Africa being majority Christian. Only in enclaves in coastal West African nations does traditional religion manifest in the public sphere, organizing itself as Vodun. Elsewhere the God of Abraham reigns supreme.

Religion_distribution_Africa_cropAfrica’s adherence to world religions has resulted in the believers aligning themselves with international concerns. Griswold points to this when observing that the religiously split city of Kaduna has Christian neighborhoods with the names Haifa, Jerusalem, and Television, while the Muslim neighborhoods are Baghdad and Afghanistan. What has Kaduna to do with Jerusalem? In concrete terms not much, but symbolically a great deal, and for humans symbolism has concrete consequences. The story Griswold tells throughout The Tenth Parallel is the integration of local concerns and tensions with global dynamics. In Nigeria Islam is closely connected to the Hausa and Fulani identities, while many of the southern ethnic groups are staunchly Christian (though many of the Yoruba have converted to Islam as well). Islam has a long history in Nigeria’s north, and clearly the southerners associate it with the past depredations of Muslim states. In Islamic law it is not legal for Muslims to enslave Muslims (though there are a fair number of “work arounds”), so the fact that West African Muslims were on the border of the Dar-ul-Islam meant that they had a ready export to the rest of the Muslim world in the form of black slaves. Long before Europeans were purchasing Africans “sold down the river,” African Muslims were selling slaves across the Sahara. With the rise to dominance of Christianity in southern Nigeria there was now an organized rival to Islam as meta-ethnic identity. A meta-ethnic frontier had come into being in central Nigeria.

In the Philippines, Malaysia Indonesia and Sudan, Griswold observes repeatedly the intricate dance between ethnicity, history, and religion. In both Indonesia and Malaysia non-Muslim ethnic minorities adhere to Christianity as a way to preserve their distinctive identity and particular history in the face of the assimilative power of the dominant Islamic culture of maritime Southeast Asia. Though outside the purview of The Tenth Parallel the same dynamic is operative in non-Muslim mainland Southeast Asia. Karens in Burma, Montongards in Vietnam, and Hmong in northern Thailand, view adherence to the Buddhism of the ethnic majority of these nations as a step toward assimilation and loss of ethnic identity. Though Christianity is just as alien in nature to the shamanic spiritual traditions of these peoples as Buddhism, it serves as a distinctive ethnic marker in regions where affiliation to the two religions tracks ethnicity perfectly. And, it also allies the Christian minorities with a powerful civilizational international.

In eastern Indonesia the Christian Ambonese, converted during the period of Dutch rule before Islam had swept so far east, were often partisans of the colonial regime against the efforts of the predominantly Muslim independenc movement. The case of the Ambonese points to a general resentment of the majority culture in many regions impacted by European colonialism. It seems plausible that without European involvement many of the “hill tribes” of eastern India and Southeast Asia would eventually have been assimilated into the ethno-religious mainstream, as many of their predecessors had been. In the process though they would have lost their identity, the cost of social harmony being conformity and homogenization. Whether the perpetuation of ethno-cultural distinctiveness through the alignment of particular groups with different meta-ethnic world religious identities is good or bad is strongly conditioned upon your own specific viewpoint. But in The Tenth Parallel Eliza Griswold shows that from Africa to Southeast Asia the general dynamic is similar. The cleavages shake out in a familiar form, despite the local origins of the conflicts.

800px-Taj_Mahal,_Agra,_IndiaOf course despite the subtitle there’s more to religious conflict than that between religions. There is also the conflict within religions. Eliza Griswold’s clear discomfort with the image which evangelical Protestants were projecting to the Muslim world of Christianity is an instance of that. But so is the strife which emerges within and across the sects of Islam. The standard model posits the rise of a Fundamentalist Islam at war with local Sufi traditions. There is a great deal to this story, as far as it goes. But there is a precision and clarity with Fundamentalist Islam, which is really often world normative Islam shifted toward a Saudi Salafi tinge, which does not exist with “moderate Islam” or “Sufi Islam.” By its very nature locally inflected Islam is diverse, and can’t be bracketed under a catchall term on any substantive grounds except to point to its negation of Salafi or reformist Islam. The rise of internationalist Salafi Islams is another case of cultural globalization, and its roots go back centuries. Several hundred years ago many regions of the Islamic world, confronting European powers on the rise, or declining Islamic orders such as that of the Ottomans, entered into a period of reform which gave birth to fundamentalisms of various flavors. The Deobandi movement in India, the Wahhabis of Arabia, and the Fulani jihad may all be considered instantiations of a broader international pattern. Pushing against this were a diverse array of local Islams, many of which lacked the coherency of the reformists who claimed to be bringing Islam back to its first principles. The success of the local Islams varied. In Arabia the Wahhabis allied with the House of Saud and eventually rode the latter’s victories to religious supremacy in most of the peninsula. The Wahhabi ascendancy has been marked by a physical destruction of monuments to rival Islamic traditions, as well as the despised position of Shia within the kingdom. In South Asia the fundamentalist reformists have not swept all before them, as the numerical preponderance of other traditions attests to, though arguably in in Pakistan they have influence out of proportion to their numbers. In Indonesia and Malaysia the fundamentalists are a small minority among the Muslim majority, which varies in its adherence to world normative Islam in any case.

And yet how much should we make of this division within Islam, or those within Christianity? In both Malaysia and Indonesia the governments encourage conversion to Islam by the remaining groups not aligned with a world religion. Despite her conflicts with fundamentalists in her own religion Eliza Griswold did in the end agree to pray with Franklin Graham. There are wheels within wheels. Focusing on one specific wheel, one layer of the dynamic, does not deny that that wheel and dynamic may be nested within others, and that others may be nested within it. The frictions and conflicts on the tenth parallel play out on multiple hierarchical levels. Individuals have their own interests, as do ethnic groups, and finally meta-ethnic groups. Modern Westerners tend to have a methodological individualistic bias, and so reduce group actions to an aggregate of the material incentives and preferences of groups of individuals. This is far too pat and simple. But how to define interests and a meta-ethnic group, a religion, can be easily problematized. As I noted above it is highly likely that the Nigerians killing each other over ethno-religious differences share much more in values and outlook with each other than they do with Westerners. But human conflict often hinges on symbolic markers and issues. One can muse in the vein of “War, what is it good for?”, but at the end of the day war is. Similarly, as an atheist I do not believe that there is a God in fact, but the fact of the beliefs of others that God is is highly consequential. It is less important what the real Islam or Christianity is, than what Islam or Christianity is for the people at any specific place and time. By and large in a world characterized by economic growth driven by non-zero sum interactions violent physical conflict produces absolute losers on all sides. But the heuristics and biases research tells us that quite often people care less about the height of the hill than their own peak position atop it. What Eliza Griswold documents in The Tenth Parallel is of great interest precisely because it puts the spotlight on the individual psychology of people who are caught up in eternal macrohistorical dynamics, processes which we’ve only begun to see as destructive for the aims of greater human wealth and health in the last few centuries.

Addendum: I believe that anyone who finds The Tenth Parallel of interest would benefit from reading some of Philip Jenkins and Peter Turchin‘s works.

Image Credit: Wikimedia, Antonin Kratochvil

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

Today I listened to a Planet Money podcast about Angola’s oil economy, which is an extreme manifestation of the typical dysfunctions which occur due to the presence of black gold. But it got me to thinking about a book I read recently, Africa: Altered States, Ordinary Miracles. Though the author is a journalist and not a scholar there is a good balance between historical and economic framing and the expected travelogue. Most of the chapters can be read a la carte, and are geographically or topically constrained. For instance, one of the last chapters is about the arrival of Chinese to Africa. Some estimates suggest that at any given time there are 5 million Chinese workers on the continent!

For me the most interesting chapter was on Angola. I would be interested in what a scholar of the history of this nation would say about the historical sketch presented. Like many Portuguese possessions Angola has a mixed-race population, mesticos. They are predominantly European in culture and outlook, and according to the author they generally played the role of middlemen minority in this region between Europeans and native Africans. For most of the colonial period the mesticos engaged in arbitrage activity involving human capital. They were slavers. The 20th century brought unexpected, and unwanted changes, for the mesticos. The Salazar dictatorship encouraged a mass migration of white Portuguese, particularly of working or lower classes, to Angola in an effort to relieve population pressures. The mesticos then found their indispensable role as middlemen irrelevant, and in fact the new immigrants received preference in a host of jobs which had traditionally been in the purview of the mesticos. While in other colonial possessions mixed-race minorities tended to identify with the mother country, the mesticos did not, because the mother country was destroying their niche within Angola.

From what I can tell the mesticos are only a few percent of the population. Angola, like most African nations, is ethnically diverse. According to the author of Africa: Altered States, Ordinary Miracles most of the nationalist movements were taking an Africanist position, and de facto aligned with particular ethnic groups. The mesticos lacked the numbers to be of importance within these ethnic coalitions. Additionally, they could not align themselves with the colonialist position because 20th century Portuguese colonialism was qualitatively different from what had come before and was leading to their dispossession.

There was one political grouping, which had a presence in Portugal, which was open to them. And that was the Communist party. The Communist party spoke in terms of class, and not nationalism or ethnic loyalties, and so mesticos were accepted within its apparatus. An argument therefore emerges that Angola’s Marxist-Leninist political movement was in fact a vehicle for the empowerment of a mercantile middleman minority! Though the bete noire of the Marxists, Jonas Savimbi, wore many ideological hats, his movement to a first approximation a reassertion of the indigenous African groups of the interior in opposition to the coastal mesticos and the arriviste Portuguese. By the 1990s Communism was spent as an international force, and the Popular Movement for the Liberation of Angola rapidly transformed into an officially socialist party, but its commitment to socialism is notional. Rather, Angola operates in a fashion similar to most one-party petro-states.

Note: The current President of Angola is not a mestico, but the child of immigrants from Sao Tome and Principe.

(Republished from by permission of author or representative)
• Category: Science • Tags: Africa 

Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a Multilocus Resequencing Data Set:

The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter-gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter-gatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic events–size changes, population splits, and gene flow–ultimately giving rise to contemporary Pygmy (Western and Eastern) groups and neighboring agricultural populations. We studied the branching history of Pygmy hunter-gatherers and agricultural populations from Africa and estimated separation times and gene flow between these populations. We resequenced 24 independent noncoding regions across the genome, corresponding to a total of ~33 kb per individual, in 236 samples from seven Pygmy and five agricultural populations dispersed over the African continent. We used simulation-based inference to identify the historical model best fitting our data . The model identified included the early divergence of the ancestors of Pygmy hunter-gatherers and farming populations ~60,000 years ago, followed by a split of the Pygmies’ ancestors into the Western and Eastern Pygmy groups ~20,000 years ago. Our findings increase knowledge of the history of the peopling of the African continent in a region lacking archaeological data. An appreciation of the demographic and adaptive history of African populations with different modes of subsistence should improve our
understanding of the influence of human lifestyles on genome diversity.

Most people know the standard Out of Africa model. ~50-10,000 years before the present modern humans left the African continent, therefore extant human populations today are descendants of this migration event. The main argument on the margins is only about the possibility of" href="">introgression of genetic variants from other non-African lineages into the human gene pool as a supplementary assimilation to the dominant dynamic of replacement. But the story in Africa did not end with that. It is famously well known that Africans have the most genetic diversity of human populations, arguably more than all other populations combined (from mtDNA, Y lineages and more recent autosomal studies). There is population structure, Africa did not remain in stasis after the ancestors of non-Africans left ~75,000 years ago. This paper addresses some of the deeper questions about African structure.

pygmyfig5.pngThe hypotheses being tested by the researchers in this paper are outlined in Figure 5. To the left you can see the 4 models. “AGR” = Agricultural, “WPYG” = Western Pygmies and “EPYG” = Eastern Pygmies. The usage of a cultural term like “Agricultural” is due to the fact that the Pygmies are distinctive in their language, as they speak the dominant dialects of their region, but their lifestyle, which is dissimilar from that of their neighbors. The Pygmies still engage hunter-gathering, while other populations do not. Additionally they are characterized by the physical peculiarity of relatively short stature, ergo the name “Pygmy.”
Pygmies have been of intense scholarly interest, most famously the work of Colin Turnbull, but also by the geneticist L. L. Cavalli-Sforza in his book African Pygmies. While the cultural details of the Pygmies were of interest to anthropologists, the short stature naturally would pique the curiosity of geneticists. Additionally the Pygmy groups could not be understood except in light of a relatively recent event, the Bantu Expansion. As I noted above Africa has not been in stasis. Genetically adaptations to malaria are relatively recent, and almost certainly due to ecological changes wrought by the rise of agriculture as the dominant mode of life across much of the continent. The spread of the Bantu seems to fall into L. L. Cavalli-Sforza’s classic demic diffusion, whereby a population which adopts farming begins to rapidly increase in population up to the Malthusian limit, and then advance as a demographic wave which carries their cultural toolkit forward at a rapid clip. From Cameroun these peoples swept east across the savanna, then south along the littoral of the Indian ocean until they reached the margins of the Cape of Good Hope, where a Mediterranean climatic regime renders the Bantu agricultural techniques relatively inefficient. Another group pushed south through central Africa and the Congo basin down into what is today Angola. All the while these peoples admixed with the local populations, as evidenced by the obvious Khoisan phenotypes among the Xhosa people (e.g., Nelson Mandela) who were along the leading edge of the demographic advance. But they retained their language, whose relatively recent diversification is indicated by the similarities of the Bantu languages from the margins of West Africa all the way into modern South Africa (I have read that most Bantu languages are intelligible, though obviously can not attest to this personally).
Culturally the Pygmies were swept up in the Bantu Expansion, as they speak Bantu languages. This is not exceptional for indigenous peoples, the Vedda of Sri Lanka speak Sinhalese. The similarites and interdependencies between the agriculturalists and Pygmies in a given region have of course given rise to models which suggest that the Pygmies are not autochthonous at all, but rather instances of convergent evolution across the forest zone of Central Africa which were shaped by local adaptation to the hunter-gatherer lifestyle. The recurrent physical motif of Pygmy and Pygmoid peoples across Island Southeast Asia without any suggestion of a phylogenetic closeness between these groups opens up this as a plausible option. The geographic separation between the West Africa and East African Pygmies is not trivial, on the order of 1,000 miles or 1/3 the distance across of the United States. And the terrain across the interval is fragmented by forests and river systems. In fact the Congo river serves as the north-south division line between Bonobos and the Common Chimpanzee, suggesting the power of geography in driving speciation.
pygmystructure.pngThe data reported here do not support the position that the Pygmies evolved recently from agricultural populations. Here is a reedit of Figure 1 from the paper (so it can fit on the screen easily). You see the agricultural populations the researchers used, as well as the two Pygmy groups, and where they are located. The second set of figures shows how the results are displayed using Structure. Assuming a number of populations defined by K you see where individuals within these populations sort out. Admixed individuals exhibit the admixture in their genotypes, while those who are not do not. At K = 2 you see immediately that there is a difference between Pygmies and non-Pygmies. Additionally the researchers observe that the two Pygmy populations which are sometimes termed “Pygmoid” because of their comparative acculturation to Bantu populations among whom they live show the greatest evidence of admixture and gene flow. Then at K = 3 the two Pygmy groups separate out. In other words, the agriculturalists are the outgroup to the Pygmies, and Pygmies are a phylogenetically supported group, though one with two branches. This does not prove that Pygmy stature is necessarily a common derived feature inherited from the ancestral population, for that you would need to look closely at the genetic architecture of the trait in question and the phylogeny of the haplotypes on the implicated loci. In any case the second set of Structure results are filtered for individuals with less than 20% admixture, and so the between group differences are even starker. It seems likely then that whatever the origin of the Pygmy phenotype, they are the descendants of the pre-Bantu substrate which was extant across Central Africa before the great expansion, and these pre-Bantu populations had a common ancestry.
Now the relationship the populations in question is established, the temporal dynamics are next up. Using a standard molecular evolutionary method, Tajimas D, they infer that the agricultural populations have been through a demographic expansion recently. Going back to the Bantu Expansion this gels well with what we know from non-genetic disciplines. Farming populations expand fast up to the Malthusian limit. But what about the Pygmies? If the model of Pygmies as non-farmers is true, combined with their long residence in their localities, one would assume less evidence of a recent expansion. The carrying capacity for a hunter-gatherer lifestyle is lower, the rapid expansion of farmers is due to their switch to that lifestyle, or their emigration to “virgin land.” Neither of these would hold for hunter-gatherers who are indigenous of long standing. Though classical tests implied constant population size, putting more assumptions into the model (ones which are likely or supported, such as gene flow between populations and so forth) gives a more nuanced result:

A bottleneck beginning 2,500-25,000 years ago with an 80% decrease in population size, followed by a recovery starting 125 years later with a size increase of between 100% and 400% (Figure 4), fitted the WPYG data significantly better than the constant-sized population model (P = 0.04, see Materials and Methods). For the EPYG group, a bottleneck starting 250-2,500 years ago with a 90 to 95% decrease in population size (Figure 4) fitted the observed genetic diversity significantly better than the constant-sized population model

I wouldn’t get too caught up in the specific numbers here, but the evidence of a population bottleneck is suggestive in light of what we know from history and anthropology when farmers and hunter-gatherers come into contact: the latter are often decimated by disease and warfare due to the appearance on the scene of the former. The genetic data opens up the a more detailed historical narrative which would be impossible otherwise because there are no extant records from this period in this region, and archaeological evidence is difficult to extract due to the unfavorable ecology for preservation. The bounce-back of the Pygmy population could be because after the initial shock of contact with the relatively rapacious agricultural societies the hunter-gatherers retreated to the regions where their lifestyle was still at a comparative advantage and eventually established a symbiotic mondus vivendi whereby both groups might benefit. But that’s just a story, more numbers. Using a combination of the molecular genetic data, demographic assumptions and simulations they come up with some time frames for separation of the populations:

…finding that the ancestors of AGR and PYG populations diverged ca. 60 Kya is consistent with our recent single-locus estimation based on the mtDNA diversity of African farmers and Western Pygmies…Most of the large waves of population expansion and migration, both within and out of Africa, have been dated at ca. 50-80 Kya, based on several genetic markers…It has been suggested that these early population movements within and out of Africa may have been triggered by rapid environmental changes. During this period, sub-Saharan Africa witnessed a major episode of climatic change: a sharp oscillation towards a drier climate, with annual rainfall decreasing by up to 50%…In this context, our estimated date of the initial divergence between the ancestors of present-day farmers and Pygmies implies that this period was characterized not only by major human movements, but also by early episodes of population differentiation within the African continent.
Our evidence for a separation of the ancestors of Western and Eastern Pygmy groups ca. 20 Kya is also consistent with a previous mtDNA study, dating the time of separation of these two Pygmy groups to at least 18 Kya…These estimates coincide with another period of major climatic change, the Last Glacial Maximum, which led to a massive retreat of tropical forests in Central Africa…Our genetic results thus support the anthropological hypothesis that the ancestors of present-day forest specialists — Western and Eastern Pygmies — began to diverge at the same time as the rainforest retreated into refugia, ~20 Kya…Finally, our estimates of gene flow between each group of Pygmies and agricultural populations yielded contrasting values, with levels of gene flow between WPYG and AGR populations three to seven times higher than those between EPYG and AGR populations…

These data suggest the intriguing possibility that concurrently with the Out of Africa event the seeds for the structure in modern African populations was already being laid. No doubt there were many populations between the ancestors of the Bantus and the Pygmies whom they enveloped, but as I suggest above it may be that the Pygmy groups we see are trivial remnants of the extant populations which were pushed aside by the agriculturalists as they expanded. The Western and Eastern Pygmies may have had the good luck to be in close proximity to ecological domains where their lifestyle was at a comparative advantage and so were able to maintain some sort of demographic and population genetic integrity in the face of the agricultural onslaught. Ergo, the genetic discontinuity might be an outcome of these details of history, as the groups which span the gap between the proto-Bantu and the Pygmies left very few descendants.
I wonder therefore the need to appeal to refugia ~20,000 years ago, as opposed to the Western and Eastern Pygmy simply being the western and eastern edges of a continuous population of which they are the last fragments. I do know that there are data which suggest that the speciation of some African monkeys is a function of the fragmentation of the rainforest during the Last Glacial Maximum, but most monkeys are by nature forest animals, while humans are not. Therefore I am skeptical of the thesis that ecological fragmentation is the reason behind the genetic differences between the two Pygmy groups dating to ~20,000 before the present. Much more likely that the Pygmy populations retreated to regions where hunter-gathering was still viable, and their genetic distance is simply an echo of population structure since erased by the Bantu demographic expansion. On the other hand, if subsequent data showed that the Pygmy phenotype is of very ancient pedigree, then perhaps the concept of perpetually forest resident populations might seem more plausible.
Hopefully there will be some examination of the other pre-Bantu populations of Southern Africa in the near future, the Hadza and Khoisan.
Citation: Patin E, Laval G, Barreiro LB, Salas A, Semino O, et al. (2009) Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a
Multilocus Resequencing Data Set. PLoS Genet 5(4): e1000448. doi:10.1371/journal.pgen.1000448

(Republished from Discover/GNXP by permission of author or representative)
• Category: History, Science • Tags: Africa, Evolution, Genetics, Human Evolution, Pygmies 
Razib Khan
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