The earliest civilisation in the region was a highly urbanised and developed culture settled in the fertile Indus Valley in about c. 5000 BC. The Indus valley civilisation is thought to have been a maritime and trading culture, with strong links to Mesopotamia (modern day Iraq).
It is assumed that this culture was swamped by the Aryan invasions, believed to have originated from Central Asia, from about 2000 BC, which was also thought to have brought Vedic Hinduism to the northern sub-continent. This was at the expense of the indigenous people who were pushed further and further into remote and isolated central areas, or absorbed into the social order at the lowest level of the caste system.
The people of the sub-continent evolved into what is seen as two groups, the northern Aryan and the southern Dravidian, albeit a melting pot of races. Elements of indigenous culture were fused into the dominant Vedic culture to form the deep roots of Indian civilisation.
In the south, it is thought that incursions started somewhat later, originating from Arab traders in the Middle East seeking to extend their networks of trading settlements to dominate the spice trade routes from Asia. These contacts go back to the middle of the 2nd or 3rd centuries BC.
Although agriculture in India starts later than in China and the Near East, there is some evidence of independent origin of some crops, including native pulses, and perhaps the indica form of rice. However, Indus Valley civilisation was firmly based on crops imported from the Near East, including wheat and barley.
Imported or local origins?
This rather patchy version of history is now being systematically (and politically) challenged at a number of levels; nevertheless one reality does seem to remain. In prehistoric times, it is very difficult to distinguish between what was of local origin and what was not. The subcontinent has the capacity to absorb external influences into its social and cultural fabric, which it then turns around and claims to be indigenous. This makes the task of distinguishing between indigenous and imported, well nigh impossible. It is also nothing short of astonishing that so much seems to have happened with little recorded evidence - a feature of Indian history that has been widely commented upon by observers throughout recorded history.
Disentangling fact from hypothesis is additionally difficult because of the lack of a culture of recorded history, and leaves early Indian history, especially, a matter for speculative theories.