There are too many conflicting studies about the origins of Haplogroup R1A[1,2]. I'll use this opportunity to propose one more theory of Aryans and Dravidians.
Three distinct cultural migrations:
Hinduism has three distinct cultural influences.
1. Tribal nature worship
2. Dravidian* Shiva-Shakti (Symbols male-female reproductive organs)
3. Indo-Aryan Vaidik culture (Indra, Agni, Vayu, Mitra and so on)
Based on these and Haplogroup H, L and R1A studies I would propose there were three major migrations to Indians.
1. Africa-> Middle East -> India (Tribals)
2. Africa-> Middle East -> Central Asia -> India (Dravidians)
3. Africa-> Middle East -> Central Asia -> Kurgan -> India (Indo-Aryans)
Indra and other gods of Indo-Aryans have too much similarities with other European pagan gods. Indra worshipping Indo-Aryans must have developed their religion before entering India.
The initial Vaidik works ridicule the natives of India as penis worshippers. So worship of Shiva and Shakti must be prevalent at that time(Not necessarily in those names). Now the question is
how Shiva and Shakti attained the highest status in Vaidik religion.
I think inclusion of Indian local deities into broader Vaidik religion may not be the work of Indo-Aryans. The priestly class of Dravidians creating a caste system along with priestly class
of Indo-Aryans might have included their deities to the large Indo-Aryan pantheon. Along the process they also created Brahma and Vishnu to complete a meaningful trinity with Shiva(Creator, preserver and destroyer).
The following would be the most likely candidates for Dravidian priestly class who became Brahmins later. Historically, these groups were identified with Shiva and Devi(Shakti) worship.
1. Saraswat Brahmins
2. Kashmiri Pundits (possibly a branch of Saraswat Brahmins)
3. Aradhyas (Telugu Brahmins)
4. Iyers (Tamil Brahmins)
5. Shivalli Brahmins(Tulu Brahmins)
6. Namboothiris(Malayalee Brahmins, a branch of Tulu Brahmins)
Though Havyaka Brahmins(a Kannada Brahmin caste) follow Shankara, I don't consider them
as Dravidian Brahmins since they differ a lot in many respects. But, Shivalli Brahmins eventhough mostly Maadhvas(Vaishnavites) are indeed Dravidian Brahmins since Shankara founder of Advaitism, was a Shaivite Namboothiri(but sought to merge Shaivism with other Vaidik worships), who inturn were actually a branch of Tulu Brahmins.
Iyers' Shaivism has nothing to do with Shankara. Most probably Advaitism brought other Indo-Aryan gods to a strong Shaiva region of Tamilnadu creating a Shaivite and Vaishnavite
divisions among Iyers.
However, now Hindus believe in all the gods. In all probability this was achieved by Dravidian priestly class and not by Indo-Aryans. Also, both these priestly classes together responsible for the creation and propagation of caste system.
*People inhabiting India before the arrival of Indo-Aryans. No relation with linguistic identities.
1. A discussion about origin of R1A at Genealogy-DNA mailing list.
2. A Genographic report about an Indian staffer at IBM. Interestingly, the official line of Genographic project was that R1A was originated in Europe around 10000 years ago. However, this report from the same project says something different.