Dr. Oppenheimer (2012b) implies that L3(M,N) originated in Asia. This is false. We know that L3 originated long before the OoA event. He does not present any evidence falsifying my conclusion. His entire argument is that M1 is ‘rare’ in Asia.
Haplotypes with HVSI transitions defining 16129-16223-16249-16278-16311-16362; and 16129-16223-16234-16249-16211-16362 have been found in Thailand and among the Han Chinese (Fucharoen et al., 2001; Yao et al., 2002) and these were originally thought to be members of Haplogroup M1. However, on the basis of currently available FGS sequences, carriers of these markers have been found to be in the D4a branch of Haplogroup D, the most widespread branch of M 1 in East Asia (Fucharoen et al., 2001; Yao et al., 2002). The transitions 16129, 16189, 16249 and 16311 are known to be recurrent in various branches of Haplogroup M, especially M1 and D4.
Dr. Oppenheimer (2012b)claims that there are a string of mistakes and misquotes in my response to his article which are not substantiated by the literature. For example, Dr. Oppenheimer claims that LOd is not the TMRC for AMH. This is false. I claim that LOd is older than L3, this is not contradicted by Soares.
Atkinson et al (2009) makes it clear that L3 is the youngest African haplogroup and LO is the oldest. As a result, when Dr. Oppenheimer claims that LOd is not the TMRC of AMH, he is false. LO is the oldest haplogroup, since LOd is dated to 106kya and one of the LO clades it. Atkinson et al (2009) observed that “Haplogroups L0 and L1 (figure 2b,c, respectively) show slow constant growth over the last 100–200 kyr (TMRCAs: L0, 124–172 kyr ago; L1, 87–139 kyr ago; L0 and L1 combined, 156–213 kyr ago; 95% HPDs)”. This makes it clear that haplogroup LO is the oldest mtDNA haplogroup in Africa.
Dr. Oppenheimer also claims that haplotype AF-24 is “ poorly resolved”. This is false, Chen et al make it clear that” The samples included complete haplotypes of 62 Senegalese (AF01–AF24, AF26–AF36, AF45–AF59, AF64–AF65, and AF70–AF79)”. As a result, how can he make the claim AF-24 is poorly resolved when Chen et al (2002) make it clear that he used “complete haplotypes of 62 Senegalese” samples that include AF-24.
Chen et al makes it clear that AF-24 could be of either Asian or African origin”Similarly, L3a was found to have a close affinity to haplotype AF24, a mtDNA that has the DdeI np-10394 and AluI np-10397 site gains characteristic of Asian macrohaplogroup M (figs.(figs.22 andand3).3). Therefore, it is possible that subhaplogroup L3a was the progenitor of Asian mtDNAs belonging to M. Although the age of subhaplogroup L3a is somewhat less than our estimate for the age of Asian haplogroup M (Torroni et al. 1994b; Chen et al. 1995), the differences could be due to the limited number of L3a mtDNAs in our African sample. Alternatively, AF24 may have been introduced from Asia into Africa more recently.” The fact that Atkinson et al (2009) makes it clear that AF-24 is a haplotype of LO, make it unlikely that AF-24 originated in Asia, since it was already in existence prior to the OoA event.
Finally, Oppenheimer claims that you can not infer population movements relating to the expansion of the ancient tool kits. This is a false statement since the demic expansion of LO(d) and L3 from East Africa to West Africa is cross referenced with specific founding lineage which is assumed to have originated in the East. This assumption is just as valid as Oppenheimer’s view relating to the Tonga event’s impact on the OoA.
In summary, it is obvious that Dr. Oppenheimer has little knowledge of the expansion of haplogroups in Africa. I am surprised the he didn’t know that the GenBank Accession number for Haplotype AF-24 is DQ112852, this suggest that he is not keeping up with the literature. Moreover, the earliest examples of L3(N) come from Iberia, not East Asia. Since this area was first occupied by Neanderthals until the expansion of the Aurignacian culture which had to have crossed the Straits of Gibraltar from Africa (Winters,2012). No where in Dr. Oppenhiemer’s response dose he present textual evidence supporting his conclusions. He only provides his opinions—not evidence.
Atkinson Q D, Gray R D, Drummond A J. 2009. Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa. http://rspb.royalsocietypublishing.org/content/276/1655/367.full
Chen Y-S., Olckers A., Schurr T.G., Kogelnik A.M., Huoponen K., Wallace D.C. 2000 mtDNA variation in the South African Kung and Khwe - and their genetic relationships to other African populations. Am. J. Hum. Genet., 66, 1362-1383
Fucharoen, G., S. Fucharoen and S. Horai, 2001. Mitochondrial DNA polymorphism in Thailand. J.Hum. Genet., 46: 115-125.
Gonder M.K., Mortensen H.M., Reed F.A., de Sousa A., Tishkoff S.A. 2007 Whole mtDNA genome sequence analysis of ancient African lineages. Mol. Biol. Evol., 24, 757-768. (doi: 10.1093/molbev/msl209).
Oppenheimer S. 2012 Out-of-Africa, the peopling of continents and islands: tracing uniparental gene trees across the map. Phil. Trans. R. Soc. Lond. B, 367, 770-784. (doi: 10.1098/rstb.2011.0306
Oppenheimer, S. 2012b .Response to Winters (2012) 'Haplogroup L3 (M,N) probably spread across Africa before the Out of Africa event'. http://rstb.royalsocietypublishing.org/content/367/1590/770.full/reply#royptb_el_319
Soares P., Ermini L., Thomson, N., Mormina M., Rito T., Rohl A., Salas A., Oppenheimer S., Macaulay V., Richards M.B. 2009 Correcting for purifying selection: an improved human mitochondrial molecular clock. Am. J. Hum. Genet., 84, 740-759. (doi:10.1016/j.ajhg.2009.05.001)
Winters C. The Gibraltar Out of Africa Exit for Anatomically Modern Humans . WebmedCentral BIOLOGY 2011;2(10):WMC002319. http://www.webmedcentral.com/article_view/2319
Yao, Y.G., Q.P. Kong, H.J. Bandelt, T. Kivisild and Y.P.Zhang, 2002. Phylogeographic differentiation of mitochondrial DNA in Han chinese. Am. J. Hum.Genet., 70: 635-651.