Haplotype AF-24: An Ancient African Gene

An important haplotype in Africa is Af-24. AF-24 is delineated by a DdeI site at 10394 and AluI site of np 10397. This haplotype is a branch of the African subhaplogroup LOd. The TMRCA for LOd is 106kya (Gonder et al, 2006). This makes haplotype AF-24 much older than L3a.

The basal L3 motif is characterized by the Ddel site np 10394 and Alul site np 10397. The DdeI site np 10394 and AluI site np 10397 in haplotype AF24 (DQ112852) are at the base of the M macrohaplogroup.

The mtDNA LOd is mainly found in West Africa and among the Khoisan of South Africa and Tanzania.

Since the TMRCA of LOd dates to 106kya Anatomically modern humans (amh) had plenty of time to take this haplogroup to Senegal. In West Africa the presence of amh date to the Upper Palaeolithic (Giresse,2008).

Anatomically modern humans arrived in Senegal during the Sangoan period. Sangoan artifacts spread from East Africa to West Africa between 100-80kya. In Senegal Sangoan material has been found near Cap Manuel, Gambia(Giresse, 2008).

In conclusion, the earliest evidence of human activity in West Africa is typified by the Sangoan industry (Phillipson,2005). The amh associated with the Sangoan culture may have deposited Hg LOd and haplotype AF-24 in Senegal thousands of years before the exit of amh from Africa.

References:

Giresse,P. (2008). Tropical and sub-Tropical West Africa—marine and Continental changes during the late Quaternary. Volume 10. Elsevier Science.

Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA: Whole mtDNA Genome Sequence Analysis of Ancient African Lineages. Mol Biol Evol. 2006, Dec 28.

Phillipson, D.W.(2005). African Archaeology. Cambrige.

The Expansion of haplogroup LOd from East to West Africa

LOd is the oldest haplogroup (1-4). This haplogroup is primarily carried by the Khoisan people (1-2,4). It is also found among Niger-Congo speakers in East Africa (4) and we find LOa in West Africa (3). In this paper we will examine and discuss the demic diffusion of LOd across the African continent into West Africa. This is important because we discuss an early expansion of carriers of LOd from East Africa to West Africa before the exit of homo sapien sapiens from Africa.

Results

The majority of carriers of Haplogroup LOd live in East (and South Africa) and speak Khoisan . Haplogroup LOd probably originated in east Africa (5).

Haplogroup LOd is the most ancient genome. The LOd transitions include 14381,4232,6815,8113A, 8152,8251, 12121, 15466, 15930, 15941, 16243.

Haplogroup LOd is found at the root of human mtDNA. Gonder et al maintains that LOd is “the most basal branch of the gene tree”(5). The TMRCA for LOd is 106kya.

Haplogroup LOd predicts a significant period of time for anatomically modern humans (amh) living in Africa to spread across the continent. The existence of the LOd haplotype AF-24 among Senegalese supports this view. AF-24 is an ancient haplotype associated with LOd .

The TMRCA of LOd dates to 106kya. As a result, anatomically modern humans (amh) had plenty of time to spread this haplogroup to Senegal. In West Africa the presence of amh date to the Upper Palaeolithic (6). The archaeological evidence makes it clear that amh had ample opportunity to spread LOd to West Africa during this early period of demic diffusion.

The earliest evidence of human activity in West Africa is typified by the Sangoan industry (7). The amh associated with the Sangoan culture may have deposited Hg LOd in Senegal thousands of years before the exit of amh from Africa.
Anatomically modern humans arrived in Senegal during the Sangoan period. Sangoan artifacts spread from East Africa to West Africa between 100-80kya. In Senegal Sangoan material has been found near Cap Manuel (6), Gambia River in Senegal (8-9); and Cap Vert (7). The distribution of the Sangoan culture supports the demic diffusion of LOd into the Senegambia over 100kya.

Conclusion

The first amh to reach Senegal belonged to the Sangoan culture which spread from East Africa to West Africa probably between 100-80kya . Gonder et al claimed that LOd is exclusive to the southern African Khoisan (SAK) population (5). The presence of the ancient AF-24 haplotype among the Senegalese (10), that is absent in other parts of Africa, suggest a long-term LOd population in the Senegambia that preserved this rare haplotype—that originated early in the history of amh.

References:

1. Soares, Pedro; Luca Ermini, Noel Thomson, Maru Mormina, Teresa Rito, Arne Röhl, Antonio Salas, Stephen Oppenheimer, Vincent Macaulay and Martin B. Richards (04 Jun 2009). "Supplemental Data Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". The American Society of Human Genetics 84 (6): 82–93. PMID 19500773 doi:10.1016/j.ajhg.2009.05.001. http://www.cell.com/AJHG/abstract/S0002-9297(09)00163-3. Retrieved 2009-08-13.

2. van Oven, Mannis; Manfred Kayser (13 Oct 2008). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation 30 (2): E386-E394. PMID 18853457 doi:10.1002/humu.20921. http://www3.interscience.wiley.com/journal/121449735/abstract?CRETRY=1&SRETRY=0. Retrieved 2009-05-20.

3. Rosa, A. et al. 2004 July. "MtDNA Profile of West Africa Guineans: Towards a Better Understanding of the Senegambia Region", "Annals of Human Genetics", 68(Pt 4): 344

4. Sarah A. Tishkoff et al. 2007, History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution 2007 24(10):2180-2195

5. Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA.(2006).: Whole mtDNA Genome Sequence Analysis of Ancient African Lineages. Mol Biol Evol., Dec 28.

6. Giresse,P. (2008). Tropical and sub-Tropical West Africa—marine and Continental changes during the late Quaternary. Volume 10. Elsevier Science.

7. Phillipson, D.W.(2005). African Archaeology. Cambrige.

8. Davies,O. (1967). West Africa before the Europeans. London.

9. Wai-Ogusu,A.(1973). Was there a Sangoan industry in West Africa, West African Jour of Arcaheo,3:191-96.

10. Chen YS, Olckers A, Schurr TG, Kogelnik AM, Huroponen K, Wallace DC. (2000). mtDNA variation in the South African Kung and Khwe—and Their genetic relationships to other African populations. Am J Hum Genet, 66(4): 1362-1383.

The Hadza are related to the South African Khoisan

In The Myth of East African Bushman, Morris presents evidence that the Bushmen were not present in East Africa. He based this on osteological and linguistic data and the relationship between the Hadza and Sandawe.

Morris makes it clear that the material he published denying the presence of Khoisan in East Africa is “arguable at best and must be rejected at worst” (Morris,p.87). This means that there is evidence supporting the presence and/or absence of the Khoisan in East Africa. As a result, his paper needs confirmation of his hypothesis since there is an alternative view.

The genetic, linguistic and osteological data does not support his hypothesis. It suggest that the Hadza are Khoisan and that they probably originally lived in East Africa and later migrated to South Africa.

We can reject Morris’ discussion of the osteological evidence in relation to the Hadza, because the only Hadza osteological crania for comparisons was destroyed during the WWII bombing of Berlin. As a result, you can not use this paper to claim that the Hadza are not Khoisan based on osteological evidence.

In the studies cited by Morris the researchers compared contemporary Sandawe and Khoisan crania with ancient East African skeletal remains. This does not prove anything because microevolutionary processes such as genetic drift and natural selection have probably affected skull morphology and may account for variations in ancient and contemporary crania.

I. Ribat claims that there are two extremes in African craniometrics: the khoisan and the west Africans. Craniofacial features, in relation to the skull can be shaped, in evolutionary terms by lower heritability and high biomechanical load. This is reflected in the morphological heterogeneity within the same population. Carlson and Gerven observed this phenomenon in their study of Nubian craniometrics.


Carlson and Gerven explained that the differences in Nubian skeletal remains was not the result of populaton changes resulting from invasion. They argued that the skeletal remains represented the same population.

They argued that instead of the changes in crania reflecting biological diffusion, the changes in facial features resulted from changes in diet that resulted in less masticatory stress associated with changes in subsistence patterns from the Mesolithic to Neolithic.

Given this reality, a relationship probably did exist between the ancient East Africans and Khoisan as indicated by typological features, while detail study of the crania might show difference between contemporary and ancient East African Khoisan as a result of changes in diet that led to variation in the size and position of the muscles of mastication which inturn led to reduction in the robustness of the craniofacial complex. This would explain why the use of multivariate techniques show variability between modern and ancient crania and skulls.

In relation to linguistic evidence, Morris noted that “the linguistic [relationship] is compelling” (p.87) and they are not rejected (p.89). As a result we cannot deny that a linguistic relationship exist between the speakers of Khoisan languages.

Morris claims that little if any genetic connect the Hadza and the other Khoisan people in South Africa. Morris ask us to ignore the presence of biological connections between the Hadza and SAK, because Ethiopians share with the SAK mtDNA and y-chromosome. As a result some differences between the SAK ,and the Hadza and Sandaw may be explained by interactions with neighboring East African populations.

But we can not ignore the phylogenetic evidence. And if molecular evidence exist for a relationship we must recognize it for what it is: a family relationship.


The South African Khoisan (SAK) have a distinct morphology that link them to the Hadza. In Tishkoff et al results have considerable relevancy in understanding the morophology of the Hadza. Morris mentions the research of Knight et al (2003) which was based on a small sample. The Tishkoff et al sample is much larger and can tell us considerably more about the Hadza.


In your post you discuss the Sandawe. We can not discuss the Hadza based on Sandawe , we must look at them based on their own characteristics. The Hadza surrounded by non-Khoisan speakers has remarkably sustained their genetic and cultural distinctiveness.

Tishkoff et al in The genetic structure and History of Aficans and African Americans (2009) noted that Hadza cluster near the SAK whose mtDNA, y-chromosome and autosomal chromosome indicates the most diverged genetic lineages in phylogenetic trees constructed from RST genetjc distance. These researchers found that the STRUCTURE and PCA indicate that the Hadza cluster near the SAK. They also pointed out that the Hadza and Sandawe show evidence of common ancestry but there is no evidence of recent gene flow; and that Khosian related art work is found in the area where these people reside.


Tishkoff et al in Y-chromosome evidence of a pastoral Migration through Tanzania
to South Africa(2008) noted that the Hadza have a high frequentcy of L3 and L2 (haplogroup common to west Africans). It was also made clear that the Hadza , Sandawe and SAK share the Eb1f-M293 haplotype.

Overall, Tishkoff et al in the Genetic History of African Click Speaking Populations (2007) found that the mtDNA of the Hadza cluster closely with the SAK, not other Tanzanians. This along with the high frequency of y-chromosome B2b which is shared with the SAK indicates a common ancestor.

There is some evidence of interactions between other Tanzanians and the Hadza. Tishkoff et al, suggest that the L4 lineages originated among the Hadza, and was introduced to neighboring groups via Hadza females.

Among the Khoisan there is a high frequentcy of LOd, but none has been found among the Hadza. Tishkoff et al (2007) believes that the loss of LOd may be the result of genetic drift.

In conclusion the biological and linguistic evidence suggest that the Hadza are a Khoisan population. The Morris (2003) paper does nothing to disconfirm my findings.
This fact is supported by the research of Tishkoff et al that indicate that the SAK originally lived in East Africa and that they later migrated into South Arfrica.

It was also revealed that the muscles of mastication probably led to reduction in the robustness of the craniofacial complex as Khoisan populations changed their diet. This would explain why the use of multivariate techniques show variability between modern and ancient Khoisan crania and skulls, while the typological features are consistent with a Khoisan origin.

The research shows that the effect of history have influenced the relationship between the Hadza and SAK, but the genetic evidence indicates a close relationship between the Hadza and SAK as indicated by y-chromosome Eb1f-M293, and B2b.

The absence of hg N among the Sandawe and SAK is probably the result of genetic drift. The fact that the Hadza mtDNA does not cluster with other Tanzanians is an indication that haplogroup N may be native to the Hadza.

It is interesting to note that mtDNA LO is primarily found among Khoisan and West Africans. Shows that at some point in prehistory the Khoisan had migrated into West Africa. As I point out in my paper that it was Khoisan from West Africa who migrated into North Africa and thence Iberia.

Given these reasons, I believe that the Khoisan took hg N to Eurasia. I do not believe the Khosian replaced any homo sapien sapien population. The Khoisan was the first anatomically modern human population to settle western Eurasia .


References:

History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation
Mol. Biol. Evol. 2007 24: 2180-2195.


Genetic Structure in African Populations: Implications for Human Demographic History Cold Spring Harb Symp Quant Biol (2010) 0(2010): sqb.2009.74.053v1-sqb.2009.74.053

The Genetic Structure and History of Africans and African Americans Science (2009) 324(5930): 1035-1044

Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa Proc. Natl. Acad. Sci. USA (2008) 105(31): 10693-10698

Carlson,D. and Van Gerven,D.P(1979). Diffussion, biological determinism and bioculdtural adaptation in the Nubian corridor,American Anthropologist, 81, 561-580.)

Morris, AG.(2003).The Myth of the East African 'Bushmen' The South African Archaeological Bulletin Vol. 58 ( 178): 85-90

The African Variety

The spread of early man does nothing to deny the fact that the Australians reflect the first migrants from Africa. They reflect this population because they have traits common to early homosapien sapiens, e.g., Australoid brows are sloping and with prominent ridges so we can assume that this population is associated with the OOA event 60kya.

In addition, Australians have curly, wavy or straight hair and abundant body hair. Although these traits are common to the Australians—some researchers interpret them as Caucasoid—when clearly that were present among the Australians millenia before they engaged European explorers and settlers of Australia.

This indicates that straight hair was a characteristic of early Africans. A trait maintained by East Indians and other African populations today.

Laubenfels argues that the Australians are remnants of the original African migration to the region 60kya . This view is supported by David Bulbeck who found that the Australian craniometrics are different from the Mongoloid (Polynesian), and Melanoid crania metrics .


The Australian aborigines and Melanesians show cranonical variates and represent two distinct Black populations. Laubenfiels explained that Negroids/Melanoids such as the Tasmanians are characterized by wooly black hair and sparse body hair . Australoids or Australians on the otherhand have curly, wavy or straight hair and abundant body hair. Other differences between these Black populations include Negroid / Melanoid brows being vertical and without eyebrow ridges, whereas Australoid brows are sloping and with prominent ridges


This research indicates that whereas Australian aborigine crania agree with the archaic population of Asia and first group of Africans to exit Africa, they fail to correspond to the Sahulland crania which are distinctly of Southwest Pacific or Melanoid affinity . This suggests that by the rise of Sahulland there were two distinct Black populations in Asia one Austroloid and the other Melanoid .

The OOA population found in Qafzeh cave, Israel and the 80,000-100,000 year old human in China were isolated homo sapien sapien population because 70,000 years ago during the Lower Pleniglacial most of northern Europe and Canada were covered by thick ice sheets. It was this glacial period which made it possible for the Australians to walk to Australia because of the evaporation of oceans during this dry period. Moreover the dominant homo population was Neanderthal.

Your major problem is that researchers assign specific physical traits to Africans , Europeans and Mongoloids—which are common to African populations generally. This has led some researchers to reflect on the light skin of the Khoisan, and straight hair of the Australians and then take this evidence to indicate some association with Caucasoids—when in reality diverse African populations possessed these characteristics.

We must accept the fact that the physical traits of Africans have always varied and the appearance of so-called “white features” among blacks has nothing to do with admixture with Europeans.

Uthman dan Fodio Institute

Much of my research is conducted at the Uthman dan Fodio Institute in Chicago Illinois.


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