Gv. Ramana et al., Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India, EUR J HUM G, 9(9), 2001, pp. 695-700
From observations of lack of haplotype sharing based on Y-chromosome specif
ic short tandem repeat (STR) loci, previous reports suggested negligible ge
ne flow among different geographic populations of India. Using Single Nucle
otide Polymorphism (SNP) sites in combination with STIRS, we observed evide
nce of haplotype sharing across caste-tribe boundaries in South India. We e
xamined 27 SNPs in the non-recombining region of the Y chromosome to invest
igate gene flow in 204 individuals belonging to three caste groups (Vizag B
rahmins, Peruru Brahmins, Kammas), three tribes (Bagata, Poroja, Valmiki) a
nd an additional group (the Siddis) of African ancestry. Principal componen
t and AMOVA analyses show that the between group component of variation is
non-significant (P >0.05), while that among populations within the caste an
d tribal groups is significant (P <0.001). In particular, the Valmikis and
Siddis are close to the caste groups. Of a total of 11 distinct SNP-haploty
pes observed, the two tribal groups (Bagata and Poroja) lack the haplotypes
H4, H4A, H5A and H16, which are seen in the caste groups. In contrast, all
three tribal groups exhibit the Southeast Asian haplotype H11 that is abse
nt in the caste populations. The presence of haplotypes H4, H5, H14, and H1
6 in the Siddis indicate that they have assimilated considerable non-Africa
n admixture. The evidence of haplotype sharing between castes and tribes is
also found when the H14 lineage was further subdivided by five STR loci. W
e conclude that even though these SNP-based Y-haplotypes are able to distin
guish the populations, gene flow in these South Indian populations is not a
s negligible as that inferred from other studies based on Y-specific short
tandem repeat markers.