Wednesday, July 9, 2014

Early Spread of Haplogroup L3(M,N) supported by Stephan Schiffels and Richard Durbin (2014) Inferring human population size and separation history from multiple genome sequences


In several papers I have discussed the possibility that L3(M,N,) probably spread across Africa prior to the proposed out of Africa (OoA) event 60-50kya.  A recent paper:  Stephan Schiffels and Richard Durbin. (2014). Inferring human population size and separation history from multiple genome sequences. bioRxiv posted online May 21, 201 , presents convincing evidence that supports the demic diffusion of L3(M,N) prior to the proposed OoA event. Schiffels and Durbin noted that : “ We find strong evidence that the Yoruban/Non-African separation took place over a long time period of about 100,000 years, starting long before the known spatial dispersal into Eurasia around 50kya. Because we model directly an arbitrary history over time of relative cross coalescence rate between populations, we can see more clearly a progressive separation than earlier analyses based on a single separation time with some subsequent migration [7, 17, 33, 41]. However Yoruba does not represent all of Africa. Wenow see that the Maasai separation from the out-of-Africa populations occurred within the last 100,000 years. The older part of the separation from Yoruba may therefore be a consequence of ancient population structure within Africa, though the direct picture of relationships between African populations is complicated by extensive more recent exchange that we see between all three of Yoruba, Maasai and Luhya within the last 100,000 years. This scenario still does not rule out a possible contribution from an intermediate modern human population that dispersed out of Africa into the Middle-East or the Arabian peninsula but continued extensive genetic exchange with its African ancestors until about 50kya [17, 42,43].”

    The authors conclude that : “Our results are scaled to real times using a mutation rate of 1.25×10-8 per nucleotide per generation, as proposed recently [16] and supported by several direct mutation studies [14-16]. Using a value of 2.5×10-8 as was common previously [44, 45] would halve the times. This would bring the midpoint of the out-of-Africa separation to an uncomfortably recent 30-40kya, but more concerningly it would bring the separation of Native American ancestors (MXL) from East-Asian populations to 5-10kya, inconsistent with the paleontological record [25, 26]. We suggest that the establishment and spread of the Native American populations may provide a good time point for calibrating population genetic demographic models. We note that the extended period of divergence between African and non-African ancestors that we observe reconciles the timing of the most recent common ancestor of African and Non-African mtDNA around 70kya [1, 18] with the lower autosomal nuclear mutation rate used here, which in simple split models would suggest a separation around 90-130kya [7, 17, 33,41, 46]. Given that we observe extensive cross-coalescence at nuclear loci around 60-80kya, sharing a common ancestor during that time for mtDNA, which acts as a single locus with reduced effective population size, is entirely likely.”

      The  separation of Native American ancestors (MXL) from East-Asian populations to 5-10kya, indicated by the findings of Schiffels and Durbin is not  inconsistent with the paleontological record, because the crainiometrics suggest a divergence between the first Americans who were analogous to a Australian or African populations, while the contemporary native Americans are mongoloid. As a result, the archaeological evidence supports the recent date for the separation of the East Asian and Native American populations.

       In C. Winters (2011). The Demic Diffussion of the M-Haplogroup from East Africa to the Senegambia. BioResearch Bulletin ,4:51-54( Retrieved 7/9/2014 at , Winters argues that populations associated with the Sangoan culture expanded L3(M,N) across Africa prior to 60kya.

 In addition to haplogroups M1, M* and N in Sub-Saharan Africa we also find among the Senegambians hapotype AF24 (DQ112852) , which is delineated by a DdeI site at 10394 and AluI site of np 10397. The AF-24 haplotype is a branch of the African subhaplogroup L3 (Chen, 2000). This is the same delineation of haplogroup M*. It is clear from the molecular evidence that the M1, M and N haplogroups are found not only in Northeast Africa, but across Africa from East to West (Winters, 2007). Haplogroup LOd is found at the root of human mtDNA. Gonder et al (2006) maintains that LOd is “the most basal branch of the gene tree”. The TMRCA for LOd is 106kya. This makes haplotype AF-24 much older than L3a and probably explains why this haplotype is found among the Khwe/Khoisan (Chen et al,2000). 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 (Giresse,2008).

        The archaeological evidence makes it clear that amh had ample opportunity to spread LOd and L3(M,N) which has an affinity to AF-24 (Chen,2000), to West Africa during this early period of demic diffusion of amh in Africa. 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. This is because it was not until 65kya that the TMRCA of non-African L3(M,N) exited Africa (Kivisild et al, 2006). 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 (Giresse, 2008), Gambia River in Senegal (Davies,1967; Wai-Ogussu,1973); and Cap Vert (Phillipson,2005).

       Gonder et al (8) claimed that LOd is exclusive to the southern African Khoisan (SAK) population. The presence of the ancient AF-24 haplotype among the Senegalese, that is absent in other parts of Africa, suggest a long-term population in the Senegambia that preserved this rare haplotype—that originated early in the history of amh.
       Moreover, the existence of the L3a-M motif in the Senegambia characterized by the DdeI site np 10394 and AluI site np 10397 in haplotype AF24 (DQ112852) make a ‘back migration’ of haplogroup M to Africa highly unlikely, since this haplotype is associated with LOd . The first amh to reach Senegal carrying haplogroup M probably belonged to the Sangoan culture which spread from East Africa to West Africa probably between 100-80kya.

  In conclusion,  the TMRCA of mtDNA L3(M,N) and their derivatives probably appear around 94.3kya.  Most researchers agree that ,it was not until 60kya that the TMRCA of non-African L3(M,N) exited Africa. This was 30,000 years after the rise of L3 and LOd and predicts a significant period of time for anatomically modern humans (amh) living in Africa to spread L3(M) haplogroups across the continent. This would explain the findings of Schiffels and Durban(2014) of the co-existence of the ancestors of African and non-African populations.  The existence of the basal L3a(M) motif and the LOd haplotype AF-24 among Senegalese supports this view.

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