Category Archives: Papers

Genetic Affinities of the Central Indian Tribal Populations

Posted by on March 1, 2012 2 comments

Genetic Affinities of the Central Indian Tribal Populations by Gunjan Sharma, Rakesh Tamang, Ruchira Chaudhary, Vipin Kumar Singh, Anish M. Shah, Sharath Anugula, Deepa Selvi Rani, Alla G. Reddy, Muthukrishnan Eaaswarkhanth, Gyaneshwer Chaubey, Lalji Singh, Kumarasamy Thangaraj:

Background
The central Indian state Madhya Pradesh is often called as ‘heart of India’ and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers.

Methodology/Principal Findings
Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results.

Conclusions/Significance
Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints.

Did they seriously use only 48 AIMs (ancestrally informative markers) for their autosomal analysis?

UPDATE: Here is their autosomal analysis using STRUCTURE on 48 AIMs.

Can't say I am impressed. It is very noisy. They have the African component varying from 6.2% to 13.2% in populations that should have none. They also have Bhil at 10.8% East Asian (I got 0%), Sahariya at 15.8% (me at 12%), and Gond at 9.2% (I got 7%).

In short, using 48 AIMs instead of 118,000 SNPs leads to really noisy results.

Related Reading:

Battling and building amongst the Bhils
Tribal Arts and Crafts of Madhya Pradesh (Living Traditions of India)
Developmental State and the Dalit Question in Madhya Pradesh: Congress Response
Valley of the Golden Mummies

Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia

Posted by on December 8, 2011 21 comments

Metspalu et al have a new paper in American Journal of Human Genetics about South Asian genetics. Here's the abstract:

South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes.

I'll have some comments later today.

Related Reading:

Frommer's Southeast Asia (Frommer's Complete Guides)
Human Mitochondrial DNA and the Evolution of Homo sapiens (Nucleic Acids and Molecular Biology)
The Evolution and History of Human Populations in South Asia: Inter-disciplinary Studies in Archaeology, Biological Anthropology, Linguistics and ... Paleobiology and Paleoanthropology)
Lonely Planet Southeast Asia: On a Shoestring (Shoestring Travel Guide)
The Ultimate Guide to Teaching English in Thailand (Teaching English in Southeast Asia)

ANI/ASI Admixture Dating

Posted by on September 1, 2011 36 comments

Via Razib, here's an interesting abstract from the International Congress of Human Genetics by David Reich's group:

Estimating a date of mixture of ancestral South Asian populations.

Linguistic and genetic studies have shown that most Indian groups have ancestry from two genetically divergent populations, Ancestral North Indians (ANI) and Ancestral South Indians (ASI). However, the date of mixture still remains unknown. We analyze genome-wide data from about 60 South Asian groups using a newly developed method that utilizes information related to admixture linkage disequilibrium to estimate mixture dates. Our analyses suggest that major ANI-ASI mixture occurred in the ancestors of both northern and southern Indians 1,200-3,500 years ago, overlapping the time when Indo-European languages first began to be spoken in the subcontinent. These results suggest that this formative period of Indian history was accompanied by mixtures between two highly diverged populations, although our results do not rule other, older ANI-ASI admixture events. A cultural shift subsequently led to widespread endogamy, which decreased the rate of additional population mixtures.

I would be very interested in reading that paper. Also, I wonder how many new samples did they genotype beyond the ones in Reich et al' Reconstructing Indian Population History and if I could get my hands on the new data.

I have a feeling that ANI (Ancestral North Indian) captures a bunch of different migrations and conquests etc, so I am not sure if it can be equated to Indo-European language movement.

I wonder if I can use HAPMIX or StepPCO to get similar admixture dating.

Related Reading:

Ani's Raw Food Essentials: Recipes and Techniques for Mastering the Art of Live Food
Over the Anvil We Stretch
Blind Date with a Vampire
Así que pasen cinco años. Leyenda del Tiempo (Spanish Edition)
DOUBLE TEAMED ON A BLIND DATE (A MMF Ménage erotica story) (Blind Date Sex Encounters)