Out of Africa and into India?

A recent study (February 2006) published in The American Journal of Human Genetics suggests that the origins of Indians are largely indigenous, dating back to the Palaeolithic period. According to the study, the genetic influence of the Indo-European-speakers who established the caste system was small.
Their conclusion is that while some lineages did move in from the outside, many of the major ones are likely to have arisen within India. Specifically, five major haplogroups (C5-M356, F*-M89, H-M69, L1-M76 and R2-M124) were likely to have originated within the subcontinent. The origins of one common haplogroup (R1a1-M17) could not be determined.
(- Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists, S. Sengupta, et al.)

Modern humans can be traced back to a group of people who lived in Africa around 100,000 years ago. We know this by analyzing genetic markers in the Y-chromosome and mtDNA (mitochondrial DNA) structure of contemporary populations and projecting them back in time. People with similar sets of genetic markers are grouped into haplogroups and links are established between the members of a haplogroup and the marker's first appearance in the group's most recent common ancestor (MRCA).
Determining the origination of a genetic lineage and its subsequent spread is a science fraught with uncertainty. In its simplest form current high frequency and high diversity may mark the origin of a lineage. But there are other ways by which these can arise – high frequency by genetic drift, and high diversity by admixture. And of course there is the fact that people move. There is high frequency and high diversity of genetic markers in Australia. Yet there is no origination in Australia theory.
The time is generally calculated by imputing mutation rates. There are a variety of different techniques, so molecular dates tend to be less certain than archaeological ones.
Notwithstanding the dangers, there is growing genetic evidence that the subcontinent of India has been a major corridor for the migration of people between Africa and the rest of the world.

Studies of maternally inherited mitochondrial DNA are revealing the excursion choices of our earliest ancestors. In their Perspective, Forster and Matsumura discuss two new studies of the mitochondrial DNA of the indigenous peoples of Malaysia and the Andaman islands (Macaulay et al., Thangaraj et al.). These studies suggest that the earliest humans took a southern route along the coastline of the Indian Ocean before fanning out over the rest of the world. - Forster P and Matsumura S. 2005. Did early humans go north or south? Science 308:965-966. Science Online