Maharashtra Caste Haplogroup distribution

Maharashtra Caste Haplogroup distribution.

H1 is major component here ~ 33%, compared to ~ 30% in Karnataka, probably ~ 28 % in Andhra/Telangana

Population	Position*	Language	Social Status		F*(M89)	H(M69)	J(xJ2)	J2(M172)	L(M11)	O2a(M95)	O3(M122)	P*(M45)	R*(M207)	R1a1(M17)	R2(M124)	Reference
Maratha	East	Indo-European	Caste	53	0	0.39	0	0.15	0.06	0	0	0	0	0.19	0.06	Trivedi et al. 2008
Dhangar	East	Indo-European	Caste	33	0	0.38	0	0.06	0.06	0	0	0	0	0.31	0.18	Trivedi et al. 2008
Pawara	East	Indo-European	Tribe	16	0	0.75	0	0.06	0.06	0	0	0	0	0.06	0.06	Trivedi et al. 2008
Katkari	East	Indo-European	Tribe	19	0	0.63	0	0.05	0.05	0	0	0.05	0.05	0.16	0	Trivedi et al. 2008
Madia-Gond	East	Dravidian	Tribe	14	0	0.57	0	0	0.29	0	0[	0.07	0	0	0.07	Trivedi et al. 2008
Maratha	East	Indo-European	Caste	20	0.05	0.35	0	0.15	0.15	0	0	0	0	0.10	0.20	Sengupta et al. 2006
Naba-Baudh	East	Indo-European	Religious group	14	0	0.43	0	0.14	0.07	0	0	0	0	0.21	0	Sengupta et al. 2006
Korku	East	Austroasiatic	Tribe	59	0.07	0.08	0	0	0	0.81	0.02	0.02	0	0.00	0	Kumar et al. 2007
Desasth Brahmin	West	Indo-European	Caste	35	0.05	0.13	0	0.18	0.11	0	0	0	0	0.37	0.16	Trivedi et al. 2008
Chitpavana Brahmin	West	Indo-European	Caste	39	0	0.23	0	0.17	0.13	0	0	0	0	0.27	0.20	Trivedi et al. 2008
Konkan Brahmins	West	Indo-European	Caste	23	0	0.08	0	0.16	0.04	0	0	0	0	0.48	0.20	Sengupta et al. 2006
Mahadeo-Koli	West	Indo-European	Tribe	50	0.24	0.18	0.04	0.14	0.02	0	0	0	0	0.26	0.12	Present Study
Thakur	West	Indo-European	Tribe	48	0.13	0.08	0	0.27	0.06	0	0	0	0	0.29	0.04	Present Study

Karnataka Haplogroup

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Karnataka Castes

Vokkaliga - L, H1, F, R2, G, H2, R1, J2b, D, O, C
Lingayath - H1, L, R1, R2, J2, G, Q, C
Kurumba - H1, L, F
Brahmin - R1, H1, L, Q, J2a

from http://dienekes.blogspot.com/2013/07/y-chromosomes-in-lingayat-and-vokkaliga.html

Our results revealed that the majority of the Lingayat and Vokkaliga paternal gene pools are composed of four Y-chromosomal haplogroups (H, L, F* and R2) that are frequent in the Indian subcontinent. The high level of L1-M76 chromosomes in the Vokkaligas suggests an agricultural expansion in the region, while the predominance of R1a1a1b2-Z93 and J2a-M410 lineages in the Lingayat indicates gene flow from neighboring south Indian populations and West Asia, respectively. Lingayat (0.9981) also exhibits a relatively high haplotype diversity compared to Vokkaliga (0.9901), supporting the historical record that the Lingayat originated from multiple source populations. In addition, we detected ancient lineages such as F*-M213, H*-M69 and C*-M216 that may be indicative of genetic signatures of the earliest settlers who reached India after their migration out of Africa.

In our dataset, haplogroup R-M207 lineages were the most abundant in the Lingayat population (35.64%), while the Vokkaliga males (32.35%) were predominantly characterized by the L-M20 mutation. Within haplogroup R, the R1a1a1b2-Z93 subclade is detected at a higher frequency in the Lingayat paternal gene pool (19.8%) compared to the Vokkaligas (7.84%), while sub-haplogroup R2a-M124 is observed at relatively equivalent proportions in both populations (15.84% and 13.73%, respectively). Haplogroup L-M20, on the other hand, is largely represented by sub-haplogroup L1-M76, with the exception of four Vokkaliga males that belong to the paralogous L3*-M357 branch.

The second most frequent major clade observed in the two studied groups is haplogroup H-M69, an Indian-specific lineage that is particularly frequent among Dravidian-speaking groups (Sahoo et al., 2006). Therefore, it is not surprising that this haplogroup is comparably distributed in both the Lingayat (24.75%) and Vokkaliga (23.53%) populations, with the majority of the males in each collection exhibiting the H1a-M82 mutation (18.81% and 12.75%, respectively). It is interesting to note, however, that H2-Apt chromosomes, which are reported at low frequencies in Indo-European (9.52%) and Dravidian (5.0%) tribes (Sengupta et al., 2006), are restricted to the Vokkaliga population (7.84%).

The frequency of the paraphyletic haplogroup F*-M213 in the Vokkaliga paternal gene pool (13.73%) is comparable to levels reported for the Dravidian populations (13.89%) by Sengupta et al. (2006), although the proportion of F* chromosomes is lower in the Lingayat (4.95%). A reversal of this distribution pattern is observed for haplogroup J, with the Lingayat population (11.88%) exhibiting a much higher frequency of M304 derived lineages relative to Vokkaligas (3.92%). Within the J-M304 clade, the majority of males in both groups are represented by the J2b2*-M241 branch (3.96% and 2.94% in Lingayat and Vokkaliga, respectively), whereas the J2a*-M410 paragroup is observed exclusively in the Lingayat population (3.96%). The J2a3-M68 sublineage, however, is present, albeit at low frequencies (< 2%), in both south Indian collections.

Other informative haplogroups shared between the two Dravidian populations include C-M216 and G-M201. With the exceptions of an undifferentiated C*-M216 chromosome in Vokkaliga and one G1*-M285 derived individual in Lingayat, the C5a-P92 (2.97% and 1.96% in Lingayat and Vokkaliga, respectively) and G2a*-P15 (0.99% and 0.98% in Lingayat and Vokkaliga, respectively) sub-clades are similarly represented in both populations.

Of all the haplogroups analyzed, H-M69 lineages in the Vokkaliga population yield the oldest dates using both the evolutionary (26.97 ± 5.3 kya) and genealogical (10.42 ± 2.1 kya) mutation rates, while slightly younger ages are estimated for the Lingayat collection (22.03 ± 4.2 kya and 8.51 ± 1.6 kya, respectively). The Vokkaligas also exhibit older coalescence times for haplogroup L-M20 (15.52 ± 4.6 kya and 6.00 ± 1.8 kya, respectively) relative to the Lingayat population (11.14 ± 3.1 kya and 4.30 ± 1.2 kya, respectively). These findings are consistent with higher microsatellite variances as well as greater genetic differentiation within the haplogroups H and L in the Vokkaliga collection, which harbors additional sub-clades, namely H2*-Apt and L3*-M357, respectively. The evolutionary time estimates for haplogroups F*-M213 and R2a-M124, in contrast, are considerably older in the Lingayat population (24.64 ± 6.4 kya and 22.34 ± 3.5 kya, respectively) than in the Vokkaligas (11.91 ± 4.3 kya and 14.92 ± 3.6 kya, respectively).

Another haplogroup that is associated with the spread of agriculture from the Fertile Crescent and Anatolia regions is J2-M172 (Cinnioğlu et al., 2004 and Semino et al., 2004). According to Sahoo et al. (2006), only J2 lineages, originating from West Asia rather than Central Asia, represent an external contribution to the Indian paternal gene pool. In particular, subclade J2a-M410 is believed to have entered through the northwestern corridor and subsequently diffused to the south and east (Sahoo et al., 2006 and Thangaraj et al., 2010). This haplogroup is present exclusively in the Lingayat (6.93%), except for one individual from Vokkaliga, suggesting gene flow from West Asia (Sahoo et al., 2006 and Thangaraj et al., 2010). Interestingly, four J2b2-M241 Lingayat males displayed a null allele at DYS458 and failed to produce the AMGY PCR amplicon while their X homolog (AMGX) amplified successfully. Comparison of Y-STR haplotypes of the affected males from the present study with those from the literature (Cadenas et al., 2006), demonstrated a high level of allele sharing, implying shared paternal lineages or a recent common ancestry for these groups of individuals.

This study extends the results of Pamjav et al. 2012 which found only Z93 within R1a1 in mainland Indian populations. The authors estimate 12.8ky as the age of R-Z93 in the Lingayat, but since this uses the evolutionary mutation rate it should actually be divided by a factor of 3.6 which translates into ~1,500BC. So, it seems quite likely that R-Z93 moved from Central->South Asia during the Bronze Age, both on account of its age and the fact that it is a subset of Central Asian diversity. Haplogroup R2 with a nominal age of ~22ky in the Lingayat seems more like a Neolithic lineage.

The percent of H+L+J2b is > 50% for Vokkaliga caste and for Lingayat caste similar to Kamma caste

Telugu haplogoups

Haplogroup information on Telugu People gathered from scientific journal

Y Haplo	Castes
R1a	Brahmin, Kamma, Kapu, Komati, Chenchu
R1* R1a*	Brahmin, Kamma, Lambadi
R2	Kapu, Velama, Kamma, Komati, Reddy
H1	Kamma, Brahmin, Reddy, Telaga, Kapu, Balija, Yadav
H2	Raju, Brahmin
J2b	Balija, Komati, Brahmin, Pichakuntla, Nadikuruvar, Chenchu, Valmiki, Kamma
L	Kamma, Brahmin, Komati, Raju, Reddy, Chenchu, Yerukula
T	Raju, Mala, Yerukula
F	Brahmin, Raju, Mala, Kapu, Koya, Komati, Kamma
G	Brahmin, Kamma
Q	Kamma, Brahmin
O2	Kamma, Telaga, Brahmin
O3	Kapu, Raju
C	Brahmin, Lambadi, Chenchu, Kamma
D	Reddy, Brahmin, Kapu, Komati

High O2* among tribal populations of East and South East India

Porja population is mainly distributed near the hill slopes of Munchingputtu, Anantagiri, and Peddabayalu regions of Visakhapatnam, Andhra Pradesh (AP), India. They migrated from Odisha to the present habitat about 300 years back. Savara population can be seen in Lakaiguda, Mettiguda, Chintalaguda, and Manduguda regions of Srikakulam, AP, India. Savara language is included in the Kol Munda group of Austro-Asiatic language family.

 Y chromosome haplogroup O-M175 is present in 84.79% of the studied population and is significantly important, as it is the most ubiquitous Y lineage in mainland India, China, Malaysia, Indonesia, and Vietnam (Southeast Asian populations)

Haplogroup O

Haplogroup O identified by M175 (5-bp deletion) was found with highest frequency of 84.79%. It possibly originated in East Asia (Karafet et al. 2008) and then migrated to South Asia Pacific. Paternal signature of haplogroup O can be traced at moderate or low frequencies in some parts of Central Asia and Oceania (Cai et al. 2011; Karafet et al. 2001; Underhill et al. 2001 and Deng et al. 2004). Haplogroup O is further divided into three sub-clades which are defined by the presence of O1-MSY 2.2, O2-P31, and O3-M122. Although the most frequent sub-clade observed in the present study was O2a*, it occurs with a frequency of 42.86% in Porja and 41.94% in Savara. O2a lineages are found in Southeast Asian populations of Malaysia, Vietnam, Indonesia, and Southern China (Sengupta et al. 2006).

Haplogroup R

Haplogroup R is characterized by M207 and is further segregated into two sub-clades R1, which is identified by M173 A>C allele, and R2, identified by M124 C>T allele. This haplogroup R1-M173 is estimated to have arisen during the Last Glacial Maximum (LGM) and is likely to be found in Southwestern Asia (Zhao et al. 2009), which is believed to have arisen 27,000 years ago in Asia. In the present study, haplogroup R2 lineage is present in 3.23% and 3.69% of Porja and Savara population respectively.

Haplogroup H

Haplogroup H is identified by M69 T>C allele. It is further divided into two sub-clades H1 which is identified by M52 A>C allele and H2 which is identified by APT G>A allele. Because of the high frequency of the H haplogroup in Indian tribal groups, it is often regarded as the original Indian haplogroup belonging to be the ancient settlers. We found the presence of H1* and H1a* in the present studied samples in low frequencies, about 4.61% and 3.69% respectively. Haplogroup H has also been reported from Central Asia, Western Asia, and Europe (Wells et al. 2001; Regueiro et al. 2006). 

Figure 3 presents the MDS plot based on Y (SNPs) haplogroup frequencies showing that Birja (AA), Juang (AA), Santhal (AA), and Ho (AA) tribes are more closely related to the present studied population groups, viz., Porja and Savara, showing closer genetic affinity between them. Among the two language groups, Austro-Asiatic and Dravidian, all the AA populations show critically closer genetic affinities with Porja and Savara. Yerukula and Chenchu as well as Naikpodgond form different clusters in the multi-dimensional scaling (MDS) (Fig. 1), which is probably due to the absence of O2a haplogroups (Table 1) which is specific to AA linguistic groups.

Comparision of Brahmin, Bhumihar, Rajput and Kayastha

Genetic profile based upon 15 microsatellites of four caste

Genetic profile based upon 15 microsatellites of four caste groups of the eastern Indian state, Bihar

R Asma and V.K Kashyap, 

September 2003

Annals of Human Biology 30(5):570-8

DOI:10.1080/0301446032000112670

Since microsatellite markers are more informative than classical serological and other protein markers, in the current study, 15 microsatellite markers present in the Combined DNA Index System (CODIS), validated for the population of India, were chosen to estimate the impact of the deep-seated man-made caste system on the gene flow among four socio-culturally predominant caste groups(Brahmin, Bhumihar, Rajput and Kayasth) of Bihar. The chosen social groups share a common geographical area, socio-cultural practices and language that could result in high gene flow among them, due to the intrinsic drive to reproduce. An attempt has been made to understand the existing affinity due to inter-caste geneflow and relative diversity due to the high degree of endogamy practiced at the caste level. This is perhaps the first genetic study based upon 15 short tandem repeat(STR) loci to understand the impact of the caste system on human gene pool.

Subjects and methods

The populations In Bihar, the majority of people practices Hinduism and follows the caste system, hierarchically organized into upper, middle and lower strata. Social orders selected for the present study occupy the upper strata and are the major and dominant castes of the state having Caucasian features. Predominantly, they speak the Bhojpuri or Maithli dialect that belongs to the Indo-European linguistic family—the major contributor to the development of Indian culture and society (Meenakshi 1995).The mainstay of their food habit is identical, consisting of wheat and rice. Their regional deities are also similar and they celebrate the same festivals. Brahmin occupy the top slot in the Hindu society, having 186 sub-castes distributed in as many as 12 states and union territories, with historical accounts of extensive migration, mostly from the upper Gangetic region to the other parts of the country. There is a striking range of diversities in terms of morphology and genetic traits, though they strictly observe endogamy at the community level (>90%)(Singh 1998). Bhumihar (the third largest category of Brahmins) was attempted to be declassified by the Brahmins during the late 19th century, owing to their occupation as agriculturists, and was placed below Brahmin. Perhaps, because of the use of surnames such as Mishra, Tiwari, Chaudhary, Singh, Thakur, etc., by Bhumihar, which are common among Brahmin as well as in Rajput, their status in the Hindu caste system is a matter of controversy. Rajput constituted the most heterogeneous community of traditional warriors, rulers, landlords, peasants and even workers, and was more numerous in Uttar Pradesh, followed by Punjab and Bihar. Major clans of the Rajput are spread over 110 districts in the country. 

 Pairwise genetic distance (DA) between the populations clearly demonstrates that Bhumihar is closer to Brahmin (0.0298)than Rajput (0.035) or Kayasth (0.0653). Again, Rajput is closer to Bhumihar(0.032) than Brahmin (0.035) and Kayasth (0.0683), i.e. the position of Bhumihar lies somewhere between Brahmins and Rajput, while Kayasth comes after Rajput

the Brahmin has relatively high rii value(1.52 x 10 power -4) but has the lowest value of average heterozygosity (0.739), and lies below the regression line, indicating that Brahmin practices high endogamy and has lesser gene flow than the rest of the three groups, i.e. the Brahmin community is still under extreme reproductive isolation from the rest of the advanced caste groups of the state. 

Like Brahmin, Bhumihar is also below the regression line but has a high average heterozygosity value (0.757) and low rii value(0.26 x10 power -4), demonstrating reasonable amount of gene flow.

Rajput has low average heterozygosity (0.742) like Brahmin but also has low rii values (0.23 x10-4), situated below the regression line that portrays them as an endogamous community. Kayasth has a high value of rii (0.37 x10-4) com-pared with Bhumihar and Rajput. Level of average heterozygosity (0.782) is also highest and the community is above the regression line depicting very high gene flow, which may be on account of their traditional occupation as accountants in the past. Kayasth had a very close interaction with poor villagers who were not able to paytheir tax. Since there was a system of bonded labour in the state and Kayasth is among the dominant group, they may have reproductively exploited the low caste groups.