Endogamous social stratification preexisted the Varna system. Admixture analyses supporting a West Eurasian origin of the Brahmin may be biased due to the high frequencies of R1a1-M17 shared between these populations, as
the rest of their Y-chromosomal variation shows little similarity.
Moreover,
the recent discovery of new markers within R1a1-M17 has allowed Eastern European Y-lineages to be differentiated from those in Central/South Asia,
locating the oldest expansion times with this lineage in Indus Valley populations, suggesting an earlier, possibly autochthonous origin of this HG in South Asia.
The highest STR variances for HG R1a1-M17 observed in SC and DLF, along with the lack of population-specific clusters in the R1a1- M17 network and the failure of BATWING to generate a definitive modal tree for this HG,
all argue against the introduction of these paternal haplotypes through a single wave of Brahmin (i.e. Indo-Aryan) migration into the region.
Previous studies of Indian populations have grouped and analyzed the genetic data in the light of the Hindu Varna system even though its origin and antiquity are still an ongoing topic of debate. One of the theories that has acquired wide support relates the establishment of the caste system to Indo-Aryan expansions from Western Eurasia into India around 3 Kya.
An alternative view would see an earlier Indo-Aryan expansion with an introduction of cereal farming into Pakistan/North India around 8–7 kya. Genetic evidence reported by other studies that support these theories are mainly based on
the high frequency of HG R1a1-M17 in Brahmin castes and their closer genetic affinity with West Eurasian populations compared to other Indian non-Brahmin castes and tribes.