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The mitochondrial macrohaplogroup M is a descendant of the macrohaplogroup L3, a really old East African haplogroup thought to have originated around 104,000 years ago. Sun et al., explained that within haplogroup M, lie many smaller haplogroups of which the M2 lineage is thought to be the oldest mitochondrial lineage in India. You can check out this preliminary assessment in this Molecular Biology and Evolution paper, “The Dazzling Array of Basal Branches in the mtDNA Macrohaplogroup M from India as Inferred from Complete Genomes.” Ever since the Sun et al. paper, people have wondered why M2 is way more prevalent in southern India. One of the leading hypothesis is that M2 may represent the phylogenetic signature of early settlers. And by early we’re talking 50,000 years old.

To investigate the impact of Middle/Early Upper Paleolithic settlers on the genetic diversity of current populations in India, a dozen or so Indian academics sequenced 72 mitochondrial genomes from 16 different populations in India. Their results are published in this provisional BMC Evolutionary Biology paper, The earliest settlers’ antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage

Except for the Sonowal Kachari, the M2 lineage is completely absent from tribes in northeast India. Whereas in southern India, the Kuruba show a high frequency of M2 signatures at 39%. Furthermore, M2 signatures are found in high frequencies of Dravidian and in Korku, an Austro-Asiatic tribe.

Upon sequencing the mitochondrial genomes of 72 people, the authors identified a deep split between two sister clades, M2a and M2b. M2a differs from M2b in a transitional mutation at positions 7961 and 12,810. Subclades within M2a, which I won’t get into, differ from subclades in M2b — one that shows late branching patterns.

Coalescent estimates were determined, and the authors figured that the founder age for the m2 mtDNA lineage is 50,000 years old, plus or mine a couple thousand. M2a and M2b are believed to have diverged around 21,600 years ago.

The authors next investigated the effects of population decline due to the glaciation. They were able to determine a rapid population growth from 7,000 years ago to 3,000 years ago — with a 500 year decline between 1,000 years ago and 1,500 years ago — which I think could be in part because of the first wave of black plague that swept thru Asia, Europe and Africa.

Because of the persistence of the M2 lineage and its alignment to the L3 macrohaplogroup, the authors believe that the Dravidian people and the Korku represent modern variants of earliest settlers of India. That’s because these people do not exhibit such a high frequency of Eurasian specific mtDNA haplogroups, as other Indian population. Furthermore, there are not any significant M2 signatures in Tibetan nor Burmese people, suggesting that these populations have remain relatively isolated both genetically and linguistically.

    Kumar, S., Padmanabham, P.b., Ravuri, R.R., Uttaravalli, K., Koneru, P., Mukherjee, P.A., Das, B., Kotal, M., Xaviour, D., Saheb, S.Y., Rao, V.r. (2008). The earliest settlers’ antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage. BMC Evolutionary Biology, 8(1), 230. DOI: 10.1186/1471-2148-8-230