When did Homo sapiens enter and settle in India? What was their subsequent population history? Can we identify the descendants of the first settlers in contemporary Indian populations or has subsequent migrations removed any genetic evidence of the pioneers? Anthropology.net has a post on research which adds to our understanding of these questions.
Mitochondrial DNA (MtDNA) has been used quite extensively to trace the genetic ancestry of populations. MtDNA has some advantages in such studies. MtDNA is passed down independently of the nuclear genes. It is not subject to the recombination that results in different parts of the chromosomes being swapped around over generations. MtDNA in contrast is inherited as one unit. Different genes on the mitochondrion therefore have experienced the same history. Such chunks of DNA passed down as single units are called haplotypes. Also MtDNA is passed down only via the female line and so you would be tracing your maternal ancestry. This makes tracing your ancestry using MtDNA less complicated than using nuclear genes.
Now populations isolated from other populations will be evolve over time a unique set of variations on their MtDNA which will define a particular MtDNA haplogroup. If you compare the MtDNA of one population with another you should be able to tell from the differences they have accumulated and our understanding of the mutation rate of sections of MtDNA, how long ago they shared an ancestral mitochondrion. These are the types of studies that this recent research has done on MtDNA on several tribal populations of India. Tribals were chosen because cultural, ethnographic and linguistic studies indicate their ancestors may be early settlers of India and they appear to show the least amount of mixing with later immigrants. So they offer the best chance of preserving genetic signals of the earliest settlers.
This research has shown that several of the sampled tribes for example the Korku and the Kuruba contain a high frequency of the M2 haplogroup, which using the tracing back of genes method I mentioned has been found to have originated around 50,000 years ago. The M2 itself belongs to a larger family of MtDNA lineages within the M macrohaplogroup, which is thought to be a descendant of the African L macrohaplogroup. This indicates that populations migrating out of Africa around 50-60,000 years ago entered India, became isolated from other Asian populations and evolved a unique M haplogroup out of which M2 is the oldest lineage. Figure below shows the distribution of the M2 haplogroup in the sampled tribes.
Source: The earliest settlers’ antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage
So the picture seems to be that there is a 50,000 year old genetic continuity of the female line preserved in some tribal populations, making them likely descendants of the first Homo sapien settlers in India. Notice the near complete absence of M2 from northeast tribes. Did the immigrating population not settle the northeast? Maybe a species adapted to a woodland-savanna ecology may have initially found it difficult to occupy a mountainous thickly forested terrain. Or were there original settlers in the northeast also but who were later removed or assimilated by more recent immigrants?
And what about human presence in India before 50,000 years. There is plenty of evidence of that too. But that human belonged to an earlier species Homo erectus, which also migrated from Africa. The tool record of erectus in India goes back to 1.2 million years ago. Did the immigrating Homo sapien populations encounter resident Homo erectus populations. Could they have interbred or had erectus already gone extinct. Unfortunately we don't have any fossils of erectus to tell us any details of its presence in India. But can genes tell us anything more? The mitochondrial trail goes back only 50,000 years, but could there be other genes in Indian populations of even more ancient ancestry?