Aryan invasion and imposition of caste system:
This model is built upon a naive premise that a community native to one place is totally incapable of messing up its own society. Probably, the inexplicably vulgar and blatantly biased nature of caste sytem might have driven the mainstream Indian anthropologists and historians to accept that theory in the past. However, presently instead of a single Aryan invasion, multiple migration model is gaining ground.
Other models and their relevence:
At present, three models try to explain the colonization of India and the development of caste system.
1. Aryan invasion model: The oldest. The light skinned Aryans migrated from Central Asia or South-Eastern Europe to present day Pakistan. Created the caste system and imposed themselves upon the dark skinned natives.
2. Aryan multiple migration: Gradual migrations of many Aryan tribes to India. I'm not sure what's their model for the caste system.
3. Vedic continuity theory: Pure propagandist and sometimes ridiculously unscientific. This envisages Indus valley civilization as a proto-Vedic civilization. The caste system was created as a division of labour.
Of course, none of these models bring any kind of solace to the victims of the system(Brahmins to Dalits). The interesting point is the creation of caste system is some kind of a puzzle that everybody wants to crack. But it's not some 19th century racist and narcissist Europeans who first tried to give the answer.
How Varnas were created?
The question was first asked some 2500-3000 years ago by the natives themselves. Poor things! They didn't have modern linguistic studies; there was no archeology; most importantly there were no written records. Unfortunately, they were in no position to check whether their ancestors invaded or migrated. Also, they would be totally unaware that there was a civilization where people when not taking bath would go for trading.
Of course, the first clue was the name itself. Varna, the colour. Sage Bhrigu opines that caste differences were related to skin colour differences. However, sage Bharadwaja rejects it saying that if that's the case all castes are mixed castes. This conversation was described in Mahabharata, which was supposedly composed around 500 BCE. What are the things that could be inferred from here?
1. The caste divisions were no longer 'division of labour', as division of labour would identify a person with a particular Varna based on his work and neither Bhrigu nor Bharadwaja needed to ponder over the question.
2. The castes had become endogamous units and were exclusively determined by birth.
3. Neither of the sages knew that they were the descendents of the invaders.
4. For their obvious sense none of the castes exclusively into the professions dictated by their caste position. Therefore, the 'labour' was not even discussed.
5. Both Bhrigu and Bharadwaja were light skinned.
Just as today even then the question of caste identity became a very puzzling issue and needed to be addressed and justified. And this reasoning and justification ofthe caste system is what led to its eventual "purity-pollution" degradation.
Not so scientific theories:
Krishna said he created Varnas according to character(guna) and Karma. Anyway, our gods' scientific temperament is always a suspect. What can we infer from his words?
1. Krishna himself was dark and that's the reason he didn't even mention about colour differences(Though I wonder what red(Kshatriya) and yellow(Vaishya) colours would mean).
2. Eventhough he was supposed to be god, he was unaware that his ancestors came from outside and imposed the caste system to keep their racial purity.
3. He being a god, infact knew whatever happened some thousand years back(or might be million in those days' system) but since both he and Arjuna being dark skinned, it would be a disgrace to say the truth. If this is the case, Krishna comes across as a god with a very low self-esteem and weak personality(a perfectly expected characters in our gods, no surprises here). Again since the question was asked by Arjuna because of the hereditary nature of the caste, he just cooked up a story.
4. Neither Krishna nor Arjuna were as sharp as Bhrigu and Bharadwaja to observe that people of a caste could take up the occupations of other castes.
Anyway, the damage had been done. Now the answer has been given for the origins of caste system. Only thing left was to enhance the "character" and keep the Karma safe. Here comes Manu with his laws.
The problem with racial construction of caste system is that it won't account for purity and pollution rules which determines not only the sexual relationship but all aspects of life.
Now, only Brahmins and Shudras:
As I have discussed above, the caste identity became hereditary around 2500-3000 years ago. By this time the Vedic religion was spread mostly North and West of India. Its introduction in East and South India was a much later phenomenon. Till 1000-1500 years ago East and South India were having an ideal casteless society where the feudal lords force landless men to work in their fields for next to nothing and force poor/weak family women into prostitution and to their entertainment without any religious justification and holy mythology to go with those practices.
Brahmins, who moved from North-West of India to East and South, were used to take Kshatriyas and Vaishyas granted in that part of India. The rest were of course Shudras but by this time because of purity-pollution rules there was a new community called Asprishyas or untouchables. Neither colour and nor division of labour was the defining of an identity in East and South. Also no priest even considered himself a Brahmin. Though they might have worshipped goddesses or phallus like Brahmins, there could have been hardly any traces of Vedas. Brahmins, who were hardly missionaries, had no option but to divide everyone into either Shudra or Asprishya positions but with varying degrees of purity as it could have been difficult to even move out of the house without those compromises. Of course, as Buddhist, Jain and Shaivite rulers made way to pro-Vedic rulers, the caste rules were implemented in the society, probably around 1000-1500 years ago.
What was in the beginning anyway?
I would say, the migration and invasion would have affected a small part of North-West of India(or Pakistan or Southern Afghanistan). Well, none of Vedic scripts seem to have any memory of migration from outside. Within few centuries the migrating or invading, the past might have been forgotten. However, since being a small community, Indo-Aryans might have developed marital relationship with other communities. The priests of Indo-Aryans might have marital relationships with priests of Dravidian and Semitic communities. As time passed, may be around 500-600 years after invasion/migration the individual classes became self-sustained in marital relationships because of bigger close family numbers and marriages became increasingly within the community. Probably, for the last 2000-2500 years there is hardly any mixing of blood between various castes. I would say, Brahmins might be least mixed especially the ones who moved South and they represent the original genetic make up of North-West of India from 3500BP to 2500BP.
Brahmins have Y-Haplogroup H, L, R2, J2b2 around 50-60% and these form 80-90% of other caste South Indian population. However, I don't think there were lot of intermixing (especially male lines) between these two groups. I would propose that those Haplogroups in fact throwback to North-West Indian genetic make up during a period when caste identities were just occupation markers and not represented the purity of birth. I would predict, South Indian Brahmins would make a close cluster with North-West Indian or Pakistani populations with rare to non-existent R1b, E and I Haplogroups(as these are mostly historical).