Ethnic populations of India as seen from an evolutionary perspective

It is now widely accepted that (i) modern humans,Homo sapiens sapiens, evolved in Africa, (ii) migrated out of Africa and replaced archaic humans in other parts of the world, and (iii) one of the first waves of out-of-Africa migration came into India. India, therefore, served as a major corridor for dispersal of modern humans. By studying variation at DNA level in contemporary human populations of India, we have provided evidence that mitochondrial DNA haplotypes based on RFLPs are strikingly similar across ethnic groups of India, consistent with the hypothesis that a small number of females entered India during the initial process of the peopling of India. We have also provided evidence that there may have been dispersal of humans from India to southeast Asia. In conjunction with haplotype data, nucleotide sequence data of a hypervariable segment (HVS-1) of the mitochondrial genome indicate that the ancestors of the present austro-asiatic tribal populations may have been the most ancient inhabitants of India. Based on Y-chromosomal RFLP and STRP data, we have also been able to trace footprints of human movements from west and central Asia into India

Indian caste origins: genomic insights and future outlook

This article does not have an abstract

Southward Ho!

This article does not have an abstract

Dissecting the genetics of cardiomyopathy in India: a tale of ten steps

This article does not have an abstract

An improved procedure of mapping a quantitative trait locus via the EM algorithm using posterior probabilities

Mapping a locus controlling a quantitative genetic trait (e.g. blood pressure) to a specific genomic region is of considerable contemporary interest. Data on the quantitative trait under consideration and several codominant genetic markers with known genomic locations are collected from members of families and statistically analysed to estimate the recombination fraction, θ, between the putative quantitative trait locus and a genetic marker. One of the major complications in estimating θ for a quantitative trait in humans is the lack of haplotype information on members of families. We have devised a computationally simple two-stage method of estimation of θ in the absence of haplotypic information using the expectation-maximization (EM) algorithm. In the first stage, parameters of the quantitative trait locus (QTL) are estimated on the basis of data of a sample of unrelated individuals and a Bayes's rule is used to classify each parent into a QTL genotypic class. In the second stage, we have proposed an EM algorithm for obtaining the maximum-likelihood estimate of θ based on data of informative families (which are identified upon inferring parental QTL genotypes performed in the first stage). The purpose of this paper is to investigate whether, instead of using genotypically 'classified' data of parents, the use of posterior probabilities of QT genotypes of parents at the second stage yields better estimators. We show, using simulated data, that the proposed procedure using posterior probabilities is statistically more efficient than our earlier classification procedure, although it is computationally heavier

A comparison of two popular statistical methods for estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences

We have compared two statistical methods of estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences, which have been proposed by Templeton (1993) and Bandeltet al. (1995). Monte-Carlo simulations were used for generating DNA sequence data. Different evolutionary scenarios were simulated and the estimation procedures were evaluated. We have found that for both methods (i) the estimates are insensitive to demographic parameters and (ii) the standard deviations of the estimates are too high for these methods to be reliably used in practice

Genetic load in an isolated tribal population of south India

The Kota of Nilgiri Hills, Tamilnadu, are an isolated tribal population and occupy the lowest stratum in the local social hierarchy. They have developed an economic symbiotic relationship with other tribes of the Nilgiri Hills (e.g., Toda, Kurumba, Badaga), but have almost no social relationship with other communities, such as the Hindu and Muslim, communities, etc. The total population of the Kota is about 1200. Consanguineous marriages are highly favoured in this group. This paper presents data on prenatal, infant and adolescent mortality in relation to the degree of inbreeding. No perceptible difference has been found in mortality figures between consanguineous and non-consanguineous marriages. This may be due to the long history of inbreeding among the Kota. No case of visible congenital malformation has been noticed. The estimates of genetic load as revealed by inbreeding data indicate that genetic load in the Kota is low (perhaps about 1 lethal equivalent per gamete); it is also low in comparison with that in other Indian populations

Fast Detection of Community Structures using Graph Traversal in Social Networks

Finding community structures in social networks is considered to be a challenging task as many of the proposed algorithms are computationally expensive and does not scale well for large graphs. Most of the community detection algorithms proposed till date are unsuitable for applications that would require detection of communities in real-time, especially for massive networks. The Louvain method, which uses modularity maximization to detect clusters, is usually considered to be one of the fastest community detection algorithms even without any provable bound on its running time. We propose a novel graph traversal-based community detection framework, which not only runs faster than the Louvain method but also generates clusters of better quality for most of the benchmark datasets. We show that our algorithms run in O(|V | + |E|) time to create an initial cover before using modularity maximization to get the final cover. Keywords - community detection; Influenced Neighbor Score; brokers; community nodes; communitiesComment: 29 pages, 9 tables, and 13 figures. Accepted in "Knowledge and Information Systems", 201

Haplotype variation in the ACE gene in global populations, with special reference to India, and an alternative model of evolution of haplotypes

Angiotensin-I-converting enzyme (ACE) is known to be associated with human cardiovascular and psychiatric pathophysiology. We have undertaken a global survey of the haplotypes in ACE gene to study diversity and to draw inferences on the nature of selective forces that may be operating on this gene. We have investigated the haplotype profiles reconstructed using polymorphisms in the regulatory (rs4277405, rs4459609, rs1800764, rs4292, rs4291), exonic (rs4309, rs4331, rs4343), and intronic (rs4340; Alu [I/D]) regions covering 17.8 kb of the ACE gene. We genotyped these polymorphisms in a large number of individuals drawn from 15 Indian ethnic groups and estimated haplotype frequencies. We compared the Indian data with available data from other global populations. Globally, five major haplotypes were observed. High-frequency haplotypes comprising mismatching alleles at the loci considered were seen in all populations. The three most frequent haplotypes among Africans were distinct from the major haplotypes of other world populations. We have studied the evolution of the two major haplotypes (TATATTGIA and CCCTCCADG), one of which contains an Alu insertion (I) and the other a deletion (D), seen most frequently among Caucasians (68%), non-African HapMap populations (65–88%), and Indian populations (70–95%) in detail. The two major haplotypes among Caucasians are reported to represent two distinct clades A and B. Earlier studies have postulated that a third clade C (represented by the haplotypes TACATCADG and TACATCADA) arose from an ancestral recombination event between A and B. We find that a more parsimonious explanation is that clades A and B have arisen by recombination between haplotypes belonging to clade C and a high-frequency African haplotype CCCTTCGIA. The haplotypes, which according to our hypothesis are the putative non-recombinants (PuNR), are uncommon in all non-African populations (frequency range 0–12%). Conversely, the frequencies of the putative recombinant haplotypes (PuR) are very low in the Africans populations (2–8%), indicating that the recombination event is likely to be ancient and arose before, perhaps shortly prior to, the global dispersal of modern humans. The global frequency spectrum of the PuR and the PuNR is difficult to explain only by drift. It appears likely that the ACE gene has been undergoing a combination of different selective pressures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11568-011-9153-6) contains supplementary material, which is available to authorized users