Lalji Singh

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

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

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.

Evolution of sex-chromosomes and formation of W-chromatin in snakes

The analysis of sex-chromosome complexes and formation of W-chromatin in 16 species of snakes of the families Boidae, Colubridae, Elapidae, and Hydrophiidae, reveal three very pertinent facts. First, the snakes exhibit various states of the differentiation of the Z and W chromosomes, apparently according to the evolutionary status of the families, being homomorphic in primitive families and well differentiated in highly evolved ones. Second, the demonstration of a heteropycnotic body in the interphase nuclei of the families of a large number of species of snakes has definitely shown that the nuclear sexing is possible not only in those species of snakes where the W chromosome is morphologically distinguishable from the Z, but also in those species where it is not so, but shows an asynchrony in the replicating pattern of W. It is suggested that development of allocycly rather than establishment of structural changes is the first step in the differentiation of the W from the Z in snakes. Third, the absence of coexistence of nucleolus and W-chromatin in a condensed state in the interphase nuclei of different tissues in a few species of snakes reported in this paper suggests that the W-chromatin is responsible for the synthesis of the nucleolus in these snakes.

Evolution of karyotypes in snakes

Karyotype analysis and morphometric measurement of the chromosomes of 17 species of snakes have been done. Chromosomes of different species so far worked out in each family have been compared using quantitative methods to derive chromosomal affinities between species of different taxonomic categories. The following conclusions have been drawn: (i) It is suggested that the retention of Xenopeltidae as a separate family is unnecessary and the only species Xenopeltis unicolor referred to in that group should be included in the family Boidae. (ii) The subfamilies, Boinae and Pythoninae cannot be distinguished chromosomally. (iii) On the basis of chromosomal similarities, the cytologically known species of Colubridae. have been put into 13 different groupings which do not always correspond to the views of the present day colubrid taxonomists. (iv) In Hydrophiidae, speciation seems to have occurred through changes in the 4th pair of autosomes and sex chromosomes in general and the W chromosome in particular. Evidences are presented to show that fission and inversion have played an important role in bringing about the structural rearrangements in this group. (v) Family Viperidae according to taxonomists is divided into two subfamilies. Both the subfamilies are chromosomally very similar.

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.

Importance of short-lived components of a dry tropical forest for biomass production and nutrient cycling

Short-lived components in a dry tropical forest ecosystem in India - tree foliage, fine roots and herbaceous plants - are shown to be important for biomass production and nutrient cycling. With 62 % they contribute much more to the dry matter production than the long-lived components- tree boles, branches and coarse roots - which make up only 38 %. The contribution of short-lived components to the total uptake of different nutrients was also high: 18 - 30 % for tree foliage, 26 - 34 % for fine roots and 6 - 19 % for herbs; their share in the total nutrient storage is less: 6 - 19 % for tree foliage, 4 -8 % for fine roots and 0.6 - 1.3 % for herbs. The transfer of nutrients by the short-lived components was also substantial: 31 - 46 % for foliage, 7- 24 % for herbs and 33 -45 % for fine roots. The results indicate that the short-lived components play a signifi- cant role in the functioning of a dry tropical forest.

Sexual dimorphism in somatic interphase nuclei of snakes

Somatic interphase nuclei of different tissues of heterogametic females of various species of snakes with a differentiated W chromosome possess a distinct, darkly stained chromocenter comparable to th

Complex genetic origin of Indian populations and its implications.

Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000xa0years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.

The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations

Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India.

IL-4 Haplotype-590T,-34T and Intron-3 VNTR R2 Is Associated with Reduced Malaria Risk among Ancestral Indian Tribal Populations

Background Interleukin 4 (IL-4) is an anti-inflammatory cytokine, which regulates balance between TH1 and TH2 immune response, immunoglobulin class switching and humoral immunity. Polymorphisms in this gene have been reported to affect the risk of infectious and autoimmune diseases. Methods We have analyzed three regulatory IL-4 polymorphisms; -590C>T, -34C>T and 70 bp intron-3 VNTR, in 4216 individuals; including: (1) 430 ethnically matched case-control groups (173 severe malaria, 101 mild malaria and 156 asymptomatic); (2) 3452 individuals from 76 linguistically and geographically distinct endogamous populations of India, and (3) 334 individuals with different ancestry from outside India (84 Brazilian, 104 Syrian, and 146 Vietnamese). Results The -590T, -34T and intron-3 VNTR R2 alleles were found to be associated with reduced malaria risk (P<0.001 for -590C>T and -34C>T, and Pu200a=u200a0.003 for VNTR). These three alleles were in strong LD (r2>0.75) and the TTR2 (-590T, -34T and intron-3 VNTR R2) haplotype appeared to be a susceptibility factor for malaria (Pu200a=u200a0.009, ORu200a=u200a0.552, 95% CIu200a=u200a0.356 –0.854). Allele and genotype frequencies differ significantly between caste, nomadic, tribe and ancestral tribal populations (ATP). The distribution of protective haplotype TTR2 was found to be significant (χ2 3u200a=u200a182.95, p-value <0.001), which is highest in ATP (40.5%); intermediate in tribes (33%); and lowest in caste (17.8%) and nomadic (21.6%). Conclusions Our study suggests that the IL-4 polymorphisms regulate host susceptibility to malaria and disease progression. TTR2 haplotype, which gives protection against malaria, is high among ATPs. Since they inhabited in isolation and mainly practice hunter-gatherer lifestyles and exposed to various parasites, IL-4 TTR2 haplotype might be under positive selection.