Uttarkhand

 we have grouped populations according to their classical social status—Brahmins, Kshatriya, Vaishya (Goswami and Shah) and Shudra (Arya and Tamta). Interestingly, the maternal structure of this region was in congruent with the classical social system, where distance from Brahmins to other groups was following a social ladder type structure . However, the male line of descent did not reveal any kind of such local structure. Notably, the distance from Brahmins to Vaishya was significantly higher than Brahmins to Shudra (t-test P<0.001). Moreover, Arya (Shudra) was closest to Brahmins and Kshatriya than to any other non-Brahmin and Kshatriya populations. The affinity of Arya towards Brahmins and Kshatriya is due to the analogous high frequency of haplogroups R1a1a-M17 and R2a-M124. 

A similar observation was reported elsewhere, however, the most parsimonious reason given for such discrepancy is highly unlikely in our case giving out the closer paternal ancestry of Shudra (Arya) with the Brahmin and Kshatriya 

from https://www.nature.com/articles/jhg2015121

 our data showed significant (unpaired t-test P<0.0001) higher proportion of West Eurasian-specific lineages among traditionally higher caste (Brahmin and Kshatriya) populations for maternal lineages, although it was non-significant for the paternal ancestry (unpaired t-test P=0.5468).

Four Y chromosome haplogroups were the major predictors of the principal component analysis structure. East Eurasian-specific haplogroups (for example, O2a1-M95 and O3a2c1-M134) were responsible for their affinity with East/Southeast Asia, whereas haplogroups R1a1a-M17 and R2a-M124 were playing antagonistic roles. The substantial presence of Y chromosomal haplogroup Q-P36.2 also links them with the Central Asian populations. In turn, the West Eurasian-specific lineages show substantial elevation than observed in the state of Uttar Pradesh.

Principal component analysis (PCA) plots constructed on the basis of mtDNA (upper panel) and Y chromosome (lower panel) haplogroup frequencies. Data from neighboring regions are compiled from published sources (given in Materials and methods section). 

The genetic distance of each population and population groups based on mtDNA (a) and Y chromosome (b) data. As Brahmins were attaining outlier position, all the distances were shown with respect to the Brahmins.

Figure 2. The NJ Tree Illustrating Genomic Affinities Among Five Tribal Populations of Uttarakhand Based on Eight Human-specific Alu Insertion Polymorphisms

In the present study, from the NJ tree, the genetic affinity of five tribal populations of Uttarakhand were found in two clusters of populations—in one cluster, Buxa, Jaunsari, Tharu and Bhotia were found and in another, alone Raji was found. Further, from the MDS plot between Buxa, Jaunsari, Tharu and Bhotia, Buxa–Jaunsari and Tharu–Bhotia were found to have a close genetic affinity and again Raji was found distinct from other populations. The present genetic study results were correlated with the earlier study of cultural diversity and it was emphasised that except Raji’s, the rest of four scheduled tribe bear a long history of cultural contact. Certain sections of Bhotia and Buxa have imbibed many cultural traits of upper caste Hindus. Instances of similar influence are reported from upper social categories of Jaunsaries (Mann & Mann, 1999). Another study has mentioned that physical appearance of Rajis exhibit mixed physical traits of Aryans, Dravidians and Mongoloids. They are of whitish complexion, of average height, have straight and scanty hair of slight brownish colour, intermediate headed type with medium nose, round to long face and small eyes with grey pigments (Rastogi, 2015). This explains the present study’s findings from the NJ tree and also from the MDS plot that Raji’s genetic profile was distinct from other studied populations in Uttarakhand. Except Raji, the genomic affinities by the MDS plot correlate well with their geographic affiliation, Tharu and Bhotia confined to the Kumaun region and Buxa and Jaunsari confined to the Garhwal region of Uttarakhand.

The result of the present study showed that Raji and Buxa scheduled tribal (ST) communities were the ancestral populations among five studied populations. However, our findings were correlating with Ministry of Tribal Affairs Statistical Report 2013, which stated, across India out of 75 Particularly Vulnerable Tribal Groups (PVTG’s), Raji and Buxa ST communities were one among them due to their socioeconomic backwardness and living still in primitive conditions. A few decades back, a researcher opined, ‘Ragi’s are one of the very few tribal communities still inhabiting the caves and rock shelters’ (Bora, 1988). Regarding origin, the Rajis were descendants of prehistoric Kiratas, who were comparatively early settlers of this region than the Nagas and Khasas (Rastogi, 2015). Kiratas were the first to arrive India, in course of time, they were uprooted and their few descendants remained in Kumaun and Nepal (Atkinson, 1973). Presently, Raji’s are found both in India and Nepal, the frequency of Raji population was found more in Nepal than in India (Bisht & Bankoti, 2004). Raji population was included in Tibeto-Burman linguistic family but originally Raji language was a paleo-linguistic relic of Munda dialect, which can be classified under the Austro-Asiatic linguistic family.

Andhra caste relation tree

 

Neighbor-joining network of genetic distances among caste communities estimated from 40 Alu polymorphisms. Distances between upper castes (U; Brahmin, Vysya, Kshatriya), middle castes (M; Yadava, Kapu), and lower castes (L; Mala, Madiga, Relli) are significantly correlated with social rank.

Our analysis of 40 autosomal markers indicates clearly that the upper castes have a higher affinity to Europeans than to Asians. The high affinity of caste Y chromosomes with those of Europeans suggests that the majority of immigrating West Eurasians may have been males. As might be expected if West Eurasian males appropriated the highest positions in the caste system, the upper caste group exhibits a lower genetic distance to Europeans than the middle or lower castes. This is underscored by the observation that the Kshatriya (an upper caste), whose members served as warriors, are closer to Europeans than any other caste (data not shown). Furthermore, the 32-bp deletion polymorphism in CC chemokine receptor 5, whose frequency peaks in populations of Eastern Europe, is found only in two Brahmin males (M. Bamshad and S.K. Ahuja, unpubl.). The stratification of Y-chromosome distances with Europeans could also be caused by male-specific gene flow among caste populations of different rank. However, we and others have demonstrated that there is little sharing of Y-chromosome haplotypes among castes of different rank

from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311057/

Jat Haplogroup

 Ancestral geographic origins of 9 Y-chromosome haplogroups of the Jats.

Haplogroup	India	Pakistan	Total	Percent	Marker	Age (kya)	Geographic origins
E	3	0	3	1.0%	M96	~30–40	Northeast Africa, part of second migration out of Africa, initially settled in Middle East
G	11	0	11	3.6%	M201	~10–23	Eastern edge of the Middle East, close to Himalayan foothills, Indus Valley
H	10	1	11	3.6%	M69	~30	South central Asia, known as the “Indian Marker”
I	3	0	3	1.0%	M170	~25	Europe, Near East, Central Asia, known as the “European haplogroup”
J	28	1	29	9.6%	M304	~15	Fertile Crescent (Mesopotamia, the land in and around the Tigris and Euphrates rivers)
L	110	1	111	36.8%	M11	~25–30	Pamir Knot region (Hindu Kush, Tian Shan, Himalayas) in Tajikistan, Indus Valley
Q	47	0	47	15.6%	M242	~15–20	Siberia (North Asia), descendants first arrivals in North America
R	81	5	86	28.5%	M207	~4–27	Central Asia (Caspian Sea to border of western China), Kazakhstan, Uzbekistan, Turkmenistan
T	1	0	1	0.3%	M184	~25	Low frequencies Europe, the Middle East, North Africa, and East Africa
Totals	294	8	302	100.0%

Migration diagram for major Haplogroups

 The migration diagram for major Haplogroup and Castes shown below

As shown in the diagram many castes are recent formed during Medieval period from multiple ancient Sources. Gangetic Brahmins in UP look include recent mix from multiple sources post Buddhist era especially Uttarkhand and Bhumihars and parts of UP. Whereas Southern and Eastern Brahmins are more from the earlier era. The Middle castes that are Farmer/Ruler category are also very highly mixed. The Kshatriyas are from multiple waves of input some of whom harbor the Eneolithic Steppe. There was also an North african migration in very ancient times which brought in new crops and technologies, even today we see some Haplo T and very small E present in parts of India.

 

The oldest migrations are 

  H1 from 35000BC, 

J2a from 8000BC, 

O2 from 6000BC, 

J2b from 4000BC, 

L1 from 2000BC and 

R1a/R2 from 1500BC.

The migrations at the Neolithic time probably looked like this,

From Reich lab figures for latest dates of caste formation and their admix

Migrations using True Ancestry

 

Heavy Roopkund samples and Tuscan influence which is present through some ancient migrations through Brahui/Balouch and West Asia

Late Medieval shows some Huns, Tuscan, North African and Ghaznavid influence

Iron age shows heavy Swat valley like, Buddhist Saidu Sharif mixed, some Xiongnu and Saka mixed origins

Early Medieval and Late IA shows some of the Tuscan samples, Rugii, Roman, Sarmatian, Hun samples which are all mixed Steppe

Cooper Age and Early Bronze age shows major influence from North East Asia, Eneolithic Steppe, Italian and Armenian Copper age Altai Afansievo, some Yamnaya and Oetzi culture 

Bronze age shows major influence from Iran Shahr-e-Sokhte, Tepe Hissar, BMAC and Syrian Ebla, Alalakh, Amorite samples, and Canaannite, Ashkelon, Hittite and Greek Island and Central Asian Karasuk samples

The timeline around 3000BC shows highest input from the LC_EBA timeframe of Oetzi, Parkhai 2, Greek LN, Shahr-e-SokhteBA2 etc... which determines most part of the autosomal content.