Tag: Africa

Azores to Atlantis: Africa through the shadows

By Razib Khan | July 27, 2012 9:55 pm

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 Africas. 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).

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MORE ABOUT: Africa, Genetics, Genomics

Flavors of Afro-Asiatic

By Razib Khan | June 10, 2011 4:48 pm

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….

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CATEGORIZED UNDER: Anthroplogy, Genomics

The islands of genetic uniqueness in the swell

By Razib Khan | April 8, 2011 1:44 pm

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:

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CATEGORIZED UNDER: History
MORE ABOUT: Africa, History

The Bantu völkerwanderung

By Razib Khan | March 31, 2011 3:34 pm


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.

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CATEGORIZED UNDER: Genetics, Genomics

In the lands of the living God

By Razib Khan | September 6, 2010 2:44 am

The-Tenth-ParallelOn 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.

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CATEGORIZED UNDER: Anthroplogy, History, Religion

The ancient origins of African pygmies

By Razib Khan | April 9, 2009 8:00 pm

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 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.

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CATEGORIZED UNDER: Evolution, Genetics
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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!
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