African and Near East Update

* South Sudan less than two weeks from becoming a new nation. There is still unfinished business and conflict, however. Nuba, which is geographically in North Sudan, but ethnically and politically more like South Sudan has seen continuing violent conflict within the last month and sees itself as stranded on the wrong side of the border. Ethiopian peacekeepers have moved into an oil rich contested border region that has seen recent clashes (also on the wrong side of the proposed border). Darfur (essentially all of Western rump Sudan) remains a powder-keg of disaffected people, if not the full fledged genocide in progress that it was - but independence won't necessarily help because the oppressed populations there are a minority. South Sudan also faces the challenges involved in having a tremendously uneducated people with an economy left in tatters by decades of war.

* Morocco has passed a new constitution that in theory turns the nearly absolute monarchy into a constitutional monarchy a bit like that of the British monarch in the period between that when the monarch was absolute and the one when the monarch was purely symbolic. The military and foreign affairs remain royal perogatives, but the elected legislature has a greater say in domestic affairs and the courts are supposed to be more independent. The Moroccan king is fairly popular at the moment, so in the short term it may not matter much.

* In Yemen, the beginning of the end of the dictatorship seems near as the ruling dictator is in exile, but violent unrest in the divided country continues as a new regime takes shape.

* The civil war in Libya, in which the Western powers have united against the outgoing regime is not at a stalemate, but the outgoing regime is seeing its power slip away slowly and domestic politics in the U.S. aren't strongly mobilized in favor of our halfway involvement.

* Sudan's reform protesters have been among the least successful of the Arab spring who were facing mere dictators rather than monarchs. They regime has not hestitated to kill many hundreds of protestors and to apprehend every able bodied man and boy in some villages. Refugees have poured into Turkey and Lebanon. In some cases, refugees first fled Iraq and now must flee again. Reform proposals have been half-hearted and not won popular support.

* Dissent was crushed in Saudi Arabia and in Bahrain (with Saudi support). There is discontent in these places, but it is only the usual boil, not of Arab spring proportions.

* Egypt seems to be struggling to consolidate the revolution. The old regime is gone, but the successor is not entirely clear. There were riots when police were acquitted for actions taken during the uprising.

* In Palestine, even elections for posts such as medical society board of directors have partisan contestants.  The Israeli imposed embargo of Gaza also increasingly appears to be counterproductive overkill as a relatively educated and healthy population is denied the means to import basic building supplies for civilian projects which must instead be smuggled into the area.  Greek forces headed off a high profile publicity boat mission there by human rights activists, but situation remains, as ever, unstable.

 * Vile suicide bombings continue in Afghanistan.  Iraq has been comparatively quite lately as the U.S. prepares its departure from the region.  Related to Afghanistan, militant leaks in the Pakistani security complex have been released and an apparently military linked hit killed a reporter who revealed those leaks.

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South Sudan Holds Independence Vote

A vote is being held today to create a new country of South Sudan, a predominantly Christian/animist part of the the predominantly Arab Muslim nation of Sudan, that has endured a long insurgency that has killed two million people. About four million people are expected to vote and the outcome is almost certain to be a vote for independence, assuming the orderly voting allows the quorum for the election to be secured. I share the view of almost everyone in the West that this is a positive development compared to what came before it.

The new nation would be oil rich, but short of the educated people needed to give a nation real hope. I've read that 80% of its people are illiterate and that only 2% complete elementary school. I have little doubt that among women, the percentages are even lower. The new people share a larger "macro-culture" but are divided by local languages and tribal affiliations. All of the usual horrors of sub-Saharan Africa are present there enhanced by the additional burden of a long period of war. Mostly locals hope that a sovereign government's military and security resources may better protect them than the Sudanese government has in the past.

The ethnic divide between Muslims predominantly in the North, and Christian/animists predominantly in the South, is found across Africa at roughly the same latitude. This shouldn't be construed to mean that the Christians are the good guys and the Muslims are the bad guys, however. Uganda, adjacent to the new landlocked country and its principal connection to the outside world, for example, if famous for its virulent Christianity based anti-gay fervor and Christian based violent political movements. Rwanda and Burundi which are part of the same larger Christian/animist layer of sub-Saharan Africa are famous mostly for their repeated waves of genocidal slaughter in Hutu-Tutsi clashes. Over in Nigeria, religious compatriots still burn witches.

The area seeking independence does not include Darfur in West Central Sudan where genocidal killings have taken place with the approval of the government, although not always with its direct involvement. Indeed, to some extent, the removal of Darfur allies with South Sudan's independence from the political scene may undermine Darfur politically, although it may also provide a place of refuge for those fleeing the Darfur region.

Together with the persecution of Coptic Christians in Egypt by violent Muslim extremists, and the wholesale exile of a large share of the Iraqi Christian population in the Iraq War and subsequent political and religious violence, it also marks of trend in which there are fewer Christian presences and those that remain are threatened, in predominantly Muslim nations.

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Out of Eastern Africa

Where did modern humans originate?

We can be very comfortable in saying that all non-Africans had their origins in an African population whose closest living relatives are now centered in East Africa, more or less in the region from Ethiopia through the Rift Valley, where mtDNA haplogroup L3 from which all Eurasian specific mtDNA types (which are inherited matrilineally) arise.

There are several other mtDNA L haplogroups. All of the significant mtDNA haplogroup L subhalogroups, except L2 and L3 are found mostly in hunter-gatherer populations of Bushmen (aka the Khoisan) and Pygmies, and there are linguistic remnants in Bantu language populations of East Africa (whom we know adopted the Bantu languages no earlier than the last few hundred to couple thousand years) as well as genetic indicators of people with genetic connection to Bushmen and Pygmies, that suggest that populations of Bushmen once extended all the way to East Africa, although the Bushmen and Pygmies now live in Southern Africa and the West African tropics respectively.

We also know from matrilineal and patrlineal DNA evidence that mtDNA and Y-DNA haplogroups associated with Bushmen and Pygmies are the most and second most basal branches of the uniparental DNA family tree respectively. These relict African hunter-gatherer populations are the modal populations in Y-DNA haplogroups A and B which are the most basal Y-DNA haplogroups.

All Eurasians Y-DNA haplogroups, and Y-DNA haplogroup E which is predominantly African today, are branches of Y-DNA macro-haplogroup B.

The predominant Y-DNA haplogroup in Africa is E1b1 and a new study has refined our understanding of the branching family tree of that patrilineally inherited trait. Its bottom line is that new discoveries regarding how branches of the E1b1 family tree previously believed to be independent are related to each other "strongly supports the hypothesis that haplogroup E1b1 originated in eastern Africa." Eastern Africa is the geographic location that provides the most plausibe source for the roots of the Y-DNA genetic tree given the current dispersal patterns of the branches when arranged properly.

The inference, supported by the admittedly shaky evidence of the mutation rate estimated ages of the lineages in question, is that modern humans radiated out from East Africa not only to Eurasia, but also to West Africa and Southern Africa at roughly the same times, give or take thirty thousand years or so, with the highest order lineages within mtDNA haplogroup L possibly arising in subpopulations within East Africa prior to their dispersal or not long afterwards.

This is hardly surprising, because it lines up rather neatly with the fact that the oldest hominin fossils in the world, but modern human and archaic pre-modern human are found in Eastern Africa.

Now, E1b1 is not the bottom of the Y-DNA tree. Indeed, it is quite a few mutations removed even from the basal splitoff of Y-DNA haplogroup E from Y-DNA haplogroup DE. More basal examples of the Y-DNA E lineage, and even of the pre-Y-DNA E lineage called haplogroup DE are found in West Africa, and if modern humans originated in West Africa there is good reason to think that the evidence of that fact might not survive, because places that are periodically hot and wet create poor conditions for preserving bones and artifacts, and places that are constantly inhabited over long periods of time with all sorts of climate change can get muddled. Similarly, if the Khoisans originated in West Africa and migrated early on from there to Eastern Africa before ending up in Southern Africa there is really no way that we could distinguish that scenario from an Eastern African origin scenario with existing data.

But, while the evidence that we have is not definitive enough to say with great confidence that "Eden" was in Eastern Africa, rather than Western Africa, for example, it is definitive enough to say with considerable confidence that the vast majority of Africans living today probably have significant Eastern African ancestry. The paper notes that:

Haplogroup E1b1 now contains two basal branches, E-V38 (E1b1a) and E-M215 (E1b1b), with V38/V100 joining the two previously separated lineages E-M2 (former E1b1a) and E-M329 (former E1b1c). Each of these two lineages has a peculiar geographic distribution. E-M2 is the most common haplogroup in sub-Saharan Africa, with frequency peaks in western (about 80%) and central Africa (about 60%). The same haplogroup is also present in North Africa, although at a lower frequency (usually below 10%) [9]–[11]. Haplogroup E-M329, on the other hand, was observed almost exclusively in eastern Africa [10], [12 and R.S. unpublished data], where E-M2 is virtually absent.

Patriline E-M2 seems to correspond fairly closely to to matriline L2, while patriline E-M329 seems to correspond closely, but not quite so closely, to matriline L3, and these two patrilines which have a common origin, and these two matrilines (with L3 being mostly closely related to L2 among the African mtDNA haplogroups) include most Africans alive today. It is natural to assume that the corresponding patrilines and matrilines expanded together as parts of a single population, although there are certainly plenty of historical examples of patriline and matriline source populations becoming dissimilar due to conquest or caste or some other factor of that kind.

If the two Y-DNA lineages and mtDNA lineages do indeed correspond to each other and were parts of the same populations, then the common Easterns African origin of the E1b1 lineages must also have been the place of origin of the mtDNA L2 and L3 lineages.

Thus, we have a pre-history scenario where all Eurasian and the lion's share of Africans arose from founding populations in East Africa that were in existence much later the time of Y-DNA Adam and mitochondrial Eve, and fairly close in time to each other on the order of several tens of thousands of years, still a broad range of time, but a much narrower one. And, this time during which each of the founder populations who descendants went on to become almost all modern humans were each present in Eastern Africa in a time period much more recent (by something on the order of a factor of two or three) than the date that marks the common ancestors of all modern humans.

On the other hand, since the splits that separate the predominantly non-African Y-DNA haplogroups CF and D from the predominantly African Y-DNA haplogroup E take place many mutations before predominantly African Y-DNA haplogroup E-V38, one can say with some confidence that there was population structure that separated the Eurasian founding population from the predominant founder population of Africans alive today many thousands of years before the predominant founder population of Africans alive today emerged from Eastern Africa to eventually become predominant across the continent. (Note that I have intentionally not provided any clarity on where precisely the Eurasian founder population lived at the time that it became genetically distinct, which could be in Africa, in the Near East, in South Asia, or perhaps even other places.)

If one assumes that the non-African to African split happened sometime close to the Out of Africa founder population's migration (probably at least 75,000 years ago, as we can't be sure that the first Out of Africa founding population in the Levant and the founding population of the people that migrated along the Southern Coastal route of Asia was the same one, although that would be plausible), then that means that most non-Africans in West Africa have genetic roots in Eastern Africa quite a bit more recent than then (most Southern Africans, although certainly not all, have some genetic roots in the Bantu population near the Cameroon-Nigeria border and trace their roots to Eastern Africa only via that source Bantu population). The best estimates of the dates when the pygmy population starts to split, perhaps due to disruption from new migrating populations, is around 20,000 years ago. My gut instinct is to associate the E1b1 expansion out of Eastern Africa with the Sahel and Ethiopian Highlands Neolithic (which was more or less independent of the Near Eastern Neolithic and may even have started a little sooner), or perhaps a few thousand years before then, but I can't definitively support that conclusion and there are other plausible scenarios.

The potential to cross-calibrate mtDNA mutation rate date estimates, and Y-DNA mutation rate date estimates, to the extent that correspondences can be made, also offers the potential for making both kinds of dating more accurate.

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Stopping AIDS in Africa

Some very serious problems have pretty cheap solutions. This one jumped out at me today:

[HIV/AIDS] has an extremely high prevalence among heterosexual women in Sub-Saharan Africa; 40% of pregnant women in Botswana and 25% in South Africa are infected with the disease. . . .

[A new study by] Jeremy Magruder . . . at the University of California at Berkeley . . . shows that African women have become infected with HIV through doing what we all do; shopping for a mate. . . . Women and men in Africa experience a brief period in their lives while searching for the right marriage partner in which they are in a series of monogamous relationships with high turnover. This searching behavior generates a constant pool of individuals in short-term relationships. Rates of HIV transmission . . . from a person who has become recently infected is as much as 10 times higher. So, introduce one recently infected person into this pool of people who are searching for a mate and the whole pool are at risk of being infected. . . . the introduction of one person per hundred into a searching pool will lead to an HIV prevalence similar to that in Kenya or Tanzania. The introduction of just three infected people per hundred into the searching pool will lead to South Africa's epidemic prevalence rates. . . .

The economic model suggests that if only 50% of the participants in the marital searching pool use condoms for the first three months of their relationships, the prevalence rates would drop to those comparable to the West.

This is huge, although I suspect that it overstates the case somewhat because the mathematical model probably assumes greater homogeneity in relationship turnover rates than is present in reality, and it is safe to guess that a subgroup that is more likely to use condoms is also a subgroup that has a somewhat lower velocity of transmission. Still, the key observation, which is that herd immunity effects associated with condom use by a large share of the relatively small subgroup of people who are in the first three months of a sexual relationship, can dramatically reduce the proportion of people who get AIDS, is surely correct and is an attainable goal to achieve with targeted public relations and condom distribution campaigns.

The other practice that I've seen elsewhere noted as protective is male circumcision which reduced transmission risk by about 61% in a rigorous 2005 study. Nota bene: The benefits of circumcision for men who have sex with men is not so clear.

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