"In Africa" project

"In Africa" project

The new 5-year "In Africa" project headed by Marta Mirazon Lahr has a wonderful website filled with information. From the Aims section:


"The project hopes to achieve five main goals:

1. to increase significantly the number of human and other mammalian fossils in East Africa dating to the last 250,000 years;
2. to map changes in human morphology, behaviour and occupation in different basins of East Africa in the period before and after the main modern human dispersals across and out of Africa;
3. to map the character and timing of the Middle to Later Stone Age transition in the Central Rift Valley;
4. to integrate the human prehistoric record with local palaeoenvironmental data to explore the role climate change and its expression in the African tropics may have played in our recent evolutionary history;
5. to increase the scientific and public awareness of how important it is to understand what happened in Africa in order to understand why Homo sapiens and its diversity evolved."

An example of the information that can be found in this site is this list of Middle Pleistocene Sub-Saharan African fossils (pdf). Please note that some of the given dates (such as that of Broken Hill/Kabwe) are controversial. The e-library is also full of a large number of  papers and is a very useful resource.

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

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

Samaritan mtDNA and Y chromosomes

Samaritan mtDNA and Y chromosomes

Hum Mutat. 2004 Sep;24(3):248-60.

Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-Chromosome and mitochondrial DNA sequence Variation.
P. Shen et al.

The Samaritan community, which numbered more than a million in late Roman times and only 146 in 1917, numbers today about 640 people representing four large families. They are culturally different from both Jewish and non-Jewish populations in the Middle East and their origin remains a question of great interest. Genetic differences between the Samaritans and neighboring Jewish and non-Jewish populations are corroborated in the present study of 7,280 bp of nonrecombining Y-chromosome and 5,622 bp of coding and hypervariable segment I (HVS-I) mitochondrial DNA (mtDNA) sequences. Comparative sequence analysis was carried out on 12 Samaritan Y-chromosome, and mtDNA samples from nine male and seven female Samaritans separated by at least two generations. In addition, 18-20 male individuals were analyzed, each representing Ethiopian, Ashkenazi, Iraqi, Libyan, Moroccan, and Yemenite Jews, as well as Druze and Palestinians, all currently living in Israel. The four Samaritan families clustered to four distinct Y-chromosome haplogroups according to their patrilineal identity. Of the 16 Samaritan mtDNA samples, 14 carry either of two mitochondrial haplotypes that are rare or absent among other worldwide ethnic groups. Principal component analysis suggests a common ancestry of Samaritan and Jewish patrilineages. Most of the former may be traced back to a common ancestor in the paternally-inherited Jewish high priesthood (Cohanim) at the time of the Assyrian conquest of the kingdom of Israel.
Link