Namrata Kalsi: back migration of South East Asian ancestors to South Asia during LGM. #SMBE2018
— Charleston Chiang (@CharlestonCWKC) July 11, 2018
At the Society for Molecular Biology and Evolution conference in Japan there is a presentation which reports evidence for gene flow from Pleistocene Southeast Asians into South Asia. I have long suggested this was possible for several reasons.
During the Last Glacial Maximum ~20,000 years ago Southeast Asia would have been a relatively protected and well-watered region in comparison to South Asia. My understanding is that moist savanna has higher population densities of hunter-gatherers than dry scrubland. Southeast Asia would have had a great deal of the former, and almost none of the latter (the LGM was drier, and the rainforest zone in Southeast Asia would have been smaller, and Sundaland was probably mostly savanna). The Thar desert zone would have been much more expansive, pushing south and east. The summer monsoons were far weaker.
All this indicates Southeast Asia would have had larger populations than South Asia during this period. And large populations tend to impact smaller populations genetically.
Additionally, looking closely at haplogroup M, which is highly diverse in South Asia, some of them look to be intrusive and related to branches in Southeast Asia. Though I do believe some of the M branches in South Asia are very old and probably native, others may have been brought by Southeast Asian people related to the Hoabinhian culture (which was mostly absorbed by rice farmers from the north during the Holocene).
During the Pleistocene Southeast Asia and Southern Asia were probably part of the same biogeographic zone, just as they are today. The ancestors and relatives of the Negrito peoples of Southeast Asia probably displayed a continuity from South Asia down toward Oceania. The preponderant gene flow at some points from the east to the was probably just a function of population size and climate.
Today the genetic differences on the border between South and Southeast Asia are striking. Though Pathans and Punjabis are quite different, they are far closer genetically than Bengalis and Burmese (notably, linguistically the chasm is also far greater). I think that has partly to do with agricultural and sedentarism. The mountainous zones in northeast India and western Burma are far harder for farmers to traverse than small groups of hunter-gatherers.