mtDNA and ethnic differentiation in East Africa

From the paper:

The pattern observed in East Africa (with the exception of the Khoisan-related Hadza and Sandawe populations), which combines a high level of within-population diversity with strong genetic structure among populations, suggests the occurrence of periodical episodes of admixture in these populations, separated by periods of isolation and genetic drift. Indeed, the observation of high levels of diversity within populations could be due to long-term large effective population sizes maintained in East Africa. In this case, however, little genetic structure between populations should be expected, since there would be little opportunity for genetic drift to act. Alternatively, gene flow can produce high within population diversity, and in the present case, it could also account for the extensive sharing of haplotypes and haplogroups observed between the Nyangatom and the Daasanach, as well as with other populations.

This seems like a very clever observation: substantial gene flow and a large effective population size would be inconsistent with population structure, as the different populations would be homogenized and drift would not be able to differentiate them. Long-term lack of gene flow, on the other hand, would not explain the sharing of haplotypes between populations, as each population would develop its own distinctive genetic signatures over time. Thus, the simplest explanation for the observed pattern is that gene flow has indeed occurred (accounting for the sharing of haplotypes), but that it was not continuous (accounting for the fact that populations are, after all, substantially differentiated).

From the paper:

The intermediate linkage disequilibrium (LD) found in East Africa (Tishkoff et al., 1996) in contrast with Europe (high LD) and Sub-Saharan Africa (low LD, Tishkoff & Kidd, 2004; Conrad et al., 2006), could be due to such admixture events, more frequently occurring in this region compared to other Sub-Saharan populations. Substantial levels of gene flow among Nilo-Saharan, Afro-Asiatic and Niger-Congo populations from Tanzania have already been inferred by Tishkoff et al. (2007a) and our results suggest that these gene flows could have occurred in a larger region extending up to Southern Ethiopia.

Indeed, in the absence of recent admixture, the East African populations would exhibit similar levels of LD with Sub-Saharan Africans., or even lower, as the indigenous East Africans are arguably older than those of the interior of the continent. The fact that they exhibit higher LD (intermediate between Europe and Sub-Saharan Africa) can be explained by admixture, i.e., the fact that they have inherited long stretches of DNA from the parental populations in each admixture event, and that time since that event has not been sufficiently long to cause the decay of these chunks into smaller pieces.

And, from the conclusions of the paper:

The high diversity in East Africa was interpreted as a sign of an ancient origin. However, our results might indicate that this high diversity could also come from a particular history of recent migrations and admixture promoted by the pastoralist societies that dominate in the region.

Note, that an East African origin of mankind is still the best hypothesis on palaeoanthropological and simply geographical grounds. However, the high genetic diversity found in East Africa does not necessarily reflect the antiquity of that population, but rather its history of repeated admixture by peoples of different origins.

There are two alternative hypotheses for why East Africans accumulated so much genetic diversity:

1. They are the oldest population, and have been accumulating genetic diversity for the longest period of time
2. They are substantially admixed with very divergent components (e.g., Semites, Nilo-Saharans, Cushitic speakers, and so on)

A not-so-bad example would be to compare them with other known population sources in the world, e.g., Anatolia, from where multiple waves of humans entered Europe in Paleolithic and Neolithic times. Many would agree that such movements took place, but it would be incorrect to see the population of Anatolia as a little-altered descendant of its earliest inhabitants, as the current genetic diversity observed there is -at least in part- the result of the settlement of the region by peoples from the Balkans, Central Asia, Levant, and even Western Europe.

Ann Hum Genet. 2009 Aug 25. [Epub ahead of print]

Genetic Evidence for Complexity in Ethnic Differentiation and History in East Africa.

Poloni ES, Naciri Y, Bucho R, Niba R, Kervaire B, Excoffier L, Langaney A, Sanchez-Mazas A.

Summary

The Afro-Asiatic and Nilo-Saharan language families come into contact in Western Ethiopia. Ethnic diversity is particularly high in the South, where the Nilo-Saharan Nyangatom and the Afro-Asiatic Daasanach dwell. Despite their linguistic differentiation, both populations rely on a similar agripastoralist mode of subsistence. Analysis of mitochondrial DNA extracted from Nyangatom and Daasanach archival sera revealed high levels of diversity, with most sequences belonging to the L haplogroups, the basal branches of the mitochondrial phylogeny. However, in sharp contrast with other Ethiopian populations, only 5% of the Nyangatom and Daasanach sequences belong to haplogroups M and N. The Nyangatom and Daasanach were found to be significantly differentiated, while each of them displays close affinities with some Tanzanian populations. The strong genetic structure found over East Africa was neither associated with geography nor with language, a result confirmed by the analysis of 6711 HVS-I sequences of 136 populations mainly from Africa. Processes of migration, language shift and group absorption are documented by linguists and ethnographers for the Nyangatom and Daasanach, thus pointing to the probably transient and plastic nature of these ethnic groups. These processes, associated with periods of isolation, could explain the high diversity and strong genetic structure found in East Africa.

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