Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans
Recent advances in the understanding of the maternal and paternal heritage of southand southwest Asian populations have highlighted their role in the colonization of Eurasia byanatomically modern humans. Further understanding requires a deeper insight into the topology ofthe branches of the Indian mtDNA phylogenetic tree, which should be contextualized within thephylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzedmtDNA control and coding region variation in 796 Indian (including both tribal and castepopulations from different parts of India) and 436 Iranian mtDNAs.
The results were integratedand analyzed together with published data from South, Southeast Asia and West Eurasia.Results: Four new Indian-specific haplogroup M sub-clades were defined. These, in combinationwith two previously described haplogroups, encompass approximately one third of the haplogroupM mtDNAs in India. Their phylogeography and spread among different linguistic phyla and socialstrata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealedpatterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed theidentification of different assemblies of shared mtDNA sub-clades.
Conclusions: Since the initial peopling of South and West Asia by anatomically modern humans,when this region may well have provided the initial settlers who colonized much of the rest ofEurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared betweenIndian and Iranian populations and exhibit coalescence ages corresponding to around the earlyUpper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. Incontrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent
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The quest for finding the origin of haplogroup M and a plausible scenario for the peopling of Eurasia.
Based on the high frequency and diversity of haplogroupM in India and elsewhere in Asia, some authors have suggested (versus ) that M may have arisen in SouthwestAsia [16,17,31]. Finding M1 or a lineage ancestral to M1 in India, could help to explain the presence of M1 inAfrica as a result of a back migration from India. Yet, to date this has not been achieved , this study). Therefore, one cannot rule out the still most parsimonious scenario that haplogroup M arose in East Africa .Furthermore, the lack of L3 lineages other than M and N(indeed, L3M and L3N) in India is more consistent withthe African launch of haplogroup M. On the other hand,one also observes that: i) M1 is the only variant of haplo-group M found in Africa; ii) M1 has a fairly restricted phy-logeography in Africa, barely penetrating into sub-Saharan populations, being found predominantly inassociation with the Afro-Asiatic linguistic phylum – afinding that appears to be inconsistent with the distribu-tion of sub-clades of haplogroups L3 and L2 that havesimilar time depths. That, plus the presence of M1 without accompanying L lineages in the Caucasus  and [ourunpublished data], leaves the question about the origin of haplogroup M still open.
The paper gives the age of M2 at about 70k, with 21k either way. Reading through it there seems to be more of a case for M appearing in the Arabian area, the same for the later M1 and U. Call me mad but I think the absence of M in general could be down to the Toba eruption, which must have had some serious impact in South Asia as it put down ash 2m thick all over India.