mtDNA variation in East Africa (Boattini et al. 2013)

mtDNA variation in East Africa (Boattini et al. 2013)

From the paper:

Language diversity in EA fits well with its complicated genetic history. In Fleming words, ‘‘Ethiopia by itself has more languages than all of Europe, even counting all the so-called dialects of the Romance family’’ (Fleming, 2006). All African linguistic phyla are found in EA: Afro-Asiatic (AA), Nilo-Saharan, Niger-Congo and Khoisan (however, the genealogical unit of Khoisan is no longer generally accepted). Among them, AA is the most differentiated, being represented by three (Omotic, Cushitic, Semitic) of its six major clades (the others being Chadic, Berber and Egyptian). Omotic and Cushitic are considered the deepest clades of AA, and both are found almost exclusively in the Horn of Africa, along with the linguistic relict Ongota that is traditionally assigned to the Cushitic family but whose classification is still widely debated (Fleming, 2006). These observations are in agreement with a North-Eastern African origin of the AA languages, most probably in pre-Neolithic times (Ehret, 1979, 1995; Kitchen et al., 2009).

and:

This study confirms the central role of EA and the Horn of Africa in the genetic and linguistic history of a wide area spanning from Central and Northern Africa to the Levant. Our results confirm high mtDNA diversity and strong genetic structuring in EA. We were indeed able to identify three population clusters (A, B1, B2) that are related both to geography and linguistics, and signaling different population events in the history of the region. The Horn of Africa (cluster A), in accordance with its role as a major gateway between sub-Saharan Africa and the Levant, shows widespread contacts with populations from CA (AA-Chadic speakers), the Arabian peninsula and the Nile Valley. Southwards, Kenya, and Tanzania (clusters B1 and B2), despite being both heavily involved in Bantu and Nilo-Saharan pastoralist expansions, reveal traces of a more ancient genetic stratum associated with Cushitic-speaking groups (cluster B2). Conversely, Berber- and Semitic-speaking populations of NA and the Levant show only marginal traces of admixture with sub-Saharan groups, as well as a different mtDNA genetic background, making the hypothesis of a Levantine origin of AA unlikely. In conclusion, EA genetic structure configures itself as a complicated palimpsest in which more ancient strata (AA-Cushiticspeaking groups) are largely overridden by recent different migration events. Further explorations of AA-Cushitic- speaking populations – both in terms of sampled groups and typed genetic markers – will be of great importance for the reconstruction of the genetic history of EA and AA-speakers. 

The African origin of Afroasiatic would agree with its linguistic separateness from Eurasian languages, and the fact that a single branch of the family (Semitic) is likely to have originated in Asia, and fairly recently at that.

Related:

• Disentangling the histories of mtDNA haplogroups M1 and U6
• Ethiopian origins (Pagani et al. 2012)
• mtDNA and ethnic differentiation in East Africa

Am J Phys Anthropol DOI: 10.1002/ajpa.22212

mtDNA variation in East Africa unravels the history of afro-asiatic groups

Alessio Boattini et al.

East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long-term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro-Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno-linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations—explored using spatial Principal Component Analysis and Model-based clustering—turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA-speaking populations, and shows shared ancestry with Semitic-speaking groups from Yemen and Egypt and AA-Chadic-speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene-flow (Bantu, Nilo-Saharan pastoralists), one of them is associated with a more ancient AA-Cushitic stratum. Most North-African and Levantine populations (AA-Berber, AA-Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata.

Link

Disentangling the histories of mtDNA haplogroups M1 and U6

Disentangling the histories of mtDNA haplogroups M1 and U6

mtDNA haplogroups M1 and U6 are often mentioned in terms of Eurasian back-migration in Africa. The former is the only clade of the Asian haplogroup M which occurs in Africa at all; the latter is the only clade of the West Eurasian haplogroup U that does the same. These haplogroups also tend to co-exist in North and East Africa, although they are largely absent in sub-Saharan Africa. Different ideas have been offered for their occurrence, including a "Paleolithic" spread or a more recent one associated with the spread of Afroasiatic languages.

The new paper offers useful new data on this debate. The most important conclusion is that despite their oft-mentioned association, these two haplogroups appear to have distinct histories. One argument for this is their separate geographic distribution:

M1 (on panel A) is much more common in Northeast Africa and the Near East (including the Caucasus), whereas U6 (panel B) is more confined in Africa, and has its stronger peak in NW Africa, being rare in NE Africa.

An interesting aside, is that all the mysterious M1 from the Caucasus belongs to subclade M1a, while the smaller M1b clade tends to co-occur with M1a in other parts of Africa and the Near East. This indicates a founder effect for the origin of Caucasian M1a, but leaves open the issue of the immediate origins of M1. Hopefully it will become possible to place this haplogroup within the broader M phylogeny in the future.

The Bayesian skyline plots also contrast M1 and U6 in terms of their demographic histories:

The authors argue that these histories are inconsistent with either a very early dispersal history with the Dabban industry, as well as a more recent spread with Afroasiatic. From the paper:

The transition from the Middle Palaeolithic to Upper Palaeolithic in North Africa is characterised by the appearance of the “Dabban”, an industry that is restricted to Cyrenaica in northeast Libya and represented at the caves of Hagfet ed Dabba and Haua Fteah [19]. Whilst a techno-typological shift occurred within the Dabban ~33 KYA [19], starker changes in the archaeological record occurred throughout North Africa and Southwest Asia ~23-20 KYA, represented by the widespread appearance of backed bladelet technologies. The appearance of these backed bladelet industries more or less coincides with the timing of the Last Glacial Maximum (LGM) (~23-18 KYA), including: ~21 KYA in Upper Egypt [20]; ~20 KYA at Haua Fteah with the Oranian [21]; the Iberomaurusian expansion in the Jebel Gharbi ~20 KYA [22]; and the first Iberomaurusian at Tamar Hat in Algeria ~20 KYA [23]. The earliest Iberomaurusian sites in Morocco appear to be only slightly younger ~18 KYA [24].

A disassociation of these haplogroups from the UP in North Africa might be consistent with my idea that the UP was in part a cultural revolution that spread not only with people, but often with ideas across a species that already had the "biological machinery" for behavioral modernity and was already established in both Africa and the Near East.

As for the connection to Afroasiatic, the authors detect a linguistic correlation with M1a, which, however, appears too old to have been involved directly in the spread of this language family:

Concerning haplogroup M1 individually, a significant correlation with languages was observed. Furthermore, within M1, it appears that the correlation is mostly due to M1a. However, given the small sample size of M1b, any potential signal correlating with language might not be detectable. Interestingly, M1a has a likely East African origin, but its coalescent age of ~21 KYA still largely predates that of the proto-AA. Maybe a sub-clade of M1a would still give a similar correlation, but there are not sufficient samples to allow splitting M1a into its various sub-clades, and to test for a correlation. Although we found a correlation, limited sample sizes do not allow drawing unambiguous connection between genes and languages. Furthermore, it is also possible that this putative sub-clade of M1 does not testify for the expansion of AA speaking people, but was already present among the people who inhabited the area before the spread of the AA languages.

Personally, I am in favor of an East African origin of Afroasiatic, as this makes sense of various lines of evidence, one of which is the African shift of the "Southwest_Asian" component that is modal in Semitic populations. I envision that M1 was geographically circumscribed in a NE African population after its much earlier arrival from Asia and piggy-backed onto the expansion of Afroasiatic speakers, thus explaining the observed correlation. A good analogy would be with the expansion of, say, haplogroup H in the Americas which piggybacked on the European colonization, even though the coalescence age of H predates the arrival of Europeans in the New World by many millennia.

BMC Evolutionary Biology 2012, 12:234 doi:10.1186/1471-2148-12-234


Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa

Erwan Pennarun et al.

Abstract (provisional)
Background
A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories.

Results
We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups' phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000-22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture.

Conclusions
Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.

Link

Ethiopian origins (Pagani et al. 2012)

Ethiopian origins (Pagani et al. 2012)

The study attempts to answer four questions:

Our current study is motivated by four questions. First, where do the Ethiopians stand in the African genetic landscape? Second, what is the extent of recent gene flow from outside Africa into Ethiopia, when did it occur, and is there evidence of selection effects? Third, do genomic data support a route for out-of-Africa migration of modern humans across the mouth of the Red Sea? Fourth, assuming temporal stability of current populations, what are the estimated ages of Ethiopian populations relative to other African groups?

Link to press release. Link the supplemental data.

The authors reiterate that modern humans left Africa 50-70kya, a hypothesis that seems to me pretty much dead in the light of recent archaeological evidence.

The lack of antiquity in the Ethiopian population, even in only the African component thereof argues against that population being ancestral to modern humans. Note that if the Out-of-East Africa hypothesis is correct, then skulls like Omo I represent ancestral modern humans and they are followed much later by modern humans anywhere else. So, while anatomical modernity may have emerged in East Africa --or maybe not; let's not forget that we have early modern skulls from the region in part because of the excellent preservation conditions and excess of scholarly interest-- there is no evidence that they spread from there.

I have little doubt that my own theory about substantial back-migration of Eurasians into Africa will eventually win the day. Of course, I am not referring to the recent (in the last 3,000 years) admixture with West Eurasians that the Ethiopian population has undergone, but rather to the more ancient migration that was probably associated with Y-haplogroup DE-YAP.

The fact that the African component of diverse African populations is more closely related to West than to East Eurasians is one piece of evidence among many for that scenario. Hopefully, it can be tested soon using whole genome data which may have enough density to detect much older admixture events.

UPDATE I: Since the dates in the paper are based on ROLLOFF, a piece of software that is not publicly available more than a year after its announcement, and which contradicts other software released by the same authors, I will take the Queen of Sheba stories circulated in the media with a huge grain of salt.

The American Journal of Human Genetics, 21 June 2012 doi:10.1016/j.ajhg.2012.05.015

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

Luca Pagani et al.

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified “African” and “non-African” haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.

Link

mtDNA and ethnic differentiation in East Africa

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.

Link