Mitochondrial DNA haplogroup R:
From most remote from Africa to closest to Africa:
P: Across Wallace's Line to Sahul. Minor in the Philippines. Forms seven branches. Four branches, P5, P6, P7 and P9, are Australian, especially in the northwest near where the haplogroup presumably entered the continent. A fifth branch consists of P3a from Australia and P3b from New Guinea. Then we have and P4a in New Guinea/Melanesia with P4b in Australia. The final branch contains three subclades, P1 in New Guinea and Melanesia, with a minor presence in Australia, P8 in the Philippines, and P2'10, with P2 in New Guinea and P10 in the Philippines. We can therefore be confident that people moved from Australia to the Philippines via New Guinea at some stage. (5) (10) (12)
R12'21: R12 Australia, R21 Malay Negritos. Which direction? Possibly intermediate members of the haplogroup have been obliterated by the expansion of the next three haplogroups. (10) (11)
R14: Lesser Sunda Islands, New Guinea, Nicobar Islands. The last a relatively recent addition.
R22: Indonesia, esp. Lesser Sunda Islands. Malaysia. The root is in the Lombok/Alor region. (8) (10)
R23: Bali, Sumba. Straddles Wallace's Line. (8)
R11'B6/B4'5/R24: Haplogroup R24, is Philippines. Members of the other two haplogroups are extremely widespread in East Asia. The three haplogroups are united by a single control region mutation. Such mutations are considered unreliable indicators of phylogeny and so this single haplogroup could perhaps be considered three separate haplogroups. R11 is recorded in Yunnan and Hainan but not in Laos; B6 is centred on South China, recorded in Laos but not in Hainan. Further south both B4 and B5 are found in Hainan, Vietnam and Laos, and diverse in the three places. B4a reached Eastern Polynesia while a member of B4b (B2) reached America. (3) (4) (6) (7) (8) (10) (11)
R9: Includes F within R9c. Present, and diverse, in both Hainan and Laos. R9b in Aboriginal Malays, South China. R9c further afield as well, to Palawan, Taiwan and Lesser Sunda Islands. F widespread through Southeast Asia, East Asia, Philippines. And even isolated groups in Central Asia and Arunachal Pradesh. Perhaps spread from within Malaysia. (3) (4) (6) (7) (8) (10) (11)
R7: Frequent in Munda-speakers. Centred on NE India, reaching south into Andhra Pradesh. Not present in the most westerly tribal, the Bhil, but present in the other two. (1) (2)
R8: Perhaps originated in Orissa. Present in all regions within the Godavari River catchment: Andhra Pradesh, Orissa, Maharashtra. Also especially in South India and Sri Lanka. Not present in the Sahariya, the northernmost of the Madhya Pradesh tribals, but present in the other two. Perhaps associated with Austro-Asiatic and Munda-speaking people. Munda is usually considered an Austo-Asiatic language, so perhaps the haplogroup is from the eastern margin of its geographic range. (1) (2) (6) (9)
R6: Kashmir and SE coast. Uttar Pradesh (in effect the Ganges Valley). Present in all three Madhya Pradesh tribals. 1.5-3% over India. Also in Pakistan. (1) (2)
R30: Not recorded in the Madhya Pradesh tribals but is widespread in India, esp. NW and Central. Uttar Pradesh, Punjab, Rajasthan, Gujarat, Maharashtra. Said to be associated with IE-speaking people but that is probably more a product of it being basically a northwest Indian haplogroup. (1)
R5: Right across Central India except SE coast. Perhaps spread via the Son/Narmada River system. Especially common along the SW coast and in Sri Lanka. Said to be more frequent in castes than in tribals. Present only in the most westerly of the Madhya Pradesh tribals, the Bhil. (1) (2)
R31: Of the Madhya Pradesh tribals recorded only in the Bhil, the most westerly. Present in Rajasthan, Southern India and Sri Lanka. (1) (2)
U: West Eurasia, India. Not recorded in the most westerly of the Madhya Pradesh tribals (the Bhil), although U2 and U7 are the most frequent R haplogroups in India and recorded in the other two tribals. Other U haplogroups are present only at low frequencies in India. (2) (6) (7)
R2'JT: West Asia. Low presence in India. Of the Madhya Pradesh tribals R2 is recorded only in the Sahariya, the most northerly of them. R2 claimed as centred north of Afghanistan. Present in Punjab, and the southwest of the Indian peninsula. (1) (2) (6) (7)
R1: West Asia, Turkmenistan, Kurds, India.
R0: Almost certainly originated in SW Eurasia, Arabia. Includes H and V. Became widespread in West Eurasia and North Africa. Low presence in India. (2)
R3: West Eurasia. Probably Jordan?
So we can now discern the geographic distribution of the basal R haplogroups and the pattern of their distribution through India:
R7 formed from basal R somewhere in Northeast India round that entry point and, after a period of 8 mutations, moved south through eastern India. R8 coalesced from basal R in Orissa, and carried on, after 5 mutations, as far south as Sri Lanka and up the Godavari River. Basal R also moved into the Ganges valley. R6 spread along the southeast coast and moved upstream from where R7 and R8 had coalesced. As did basal R.
R30 coalesced further upstream along the Ganges. From the upper Ganges basal R spread both south and northwest. R31 may have coalesced in Rajasthan, between the Ganges and the Indus, with R5 a little further south. Both these last haplogroups (R5, R31) moved south along along the west side of India, through southern India to Sri Lanka. In the northwest basal R emerged into SW Asia, where U, R2'JT, R1, R0 and R3 coalesced.
So R's spread in India is coastal and along the major river systems, and rapid. Such a spread could only have been possible if it was through an unexploited habitat. That is a convincing argument against an original coastal OoA M and N expansion.
So did R coalesce in South Asia?
R11'B too has all the characteristics of a haplogroup that entered a new region and expanded rapidly. The haplogroup expanded all round the South China Sea from the Philippines in the east (R24) to South/Southeast China in the west (R11'B6). In between we have B4'5 which looks to have split into a western haplogroup (B5 in Sumatra/Malaya) and an eastern haplogroup (B4 in Taiwan/Philippines/Lesser Sunda Islands). But there is a great deal of overlap and both B4 and B5 are present, and diverse, in both Hainan and Laos. B4, especially, later expanded greatly, spreading in an arc around the Pacific from America to Polynesia.
Haplogroup F, especially F1, also eventually expanded greatly. But the basal haplogroups within R9 may have coalesced as far south as the Malay peninsula. But again both R9 and F are present and diverse in both Hainan and Laos.
We also know that members of P were, or rapidly became, excellent island navigators. P's ancestor R must have crossed Wallace's Line. And P itself crossed back, unless you're going to claim the Philippines as being part of Wallacea.
Four basal branches of P are Australian, found especially in the northwest just across the water from Timor: P5, P6, P7 and P9. Two more show that after 3 or 4 mutations P reached New Guinea. P3 and P4 each have basal clades in both New Guinea and Australia. The final P haplogroup is most interesting. It shows that members of P moved north and spread along the margin of the open Pacific between New Guinea and the Philippines almost as soon as P had coalesced.
So we're left with this string of R haplogroups between the Malay peninsula and Australia/New Guinea that appear not to be involved with R's original expansion much at all (R12'21, R14, R22 and R23). They look very much to be haplogroups that remained behind in Southern Wallacea when R expanded.