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1.  Population Genetic Structure in Indian Austroasiatic Speakers: The Role of Landscape Barriers and Sex-Specific Admixture 
Molecular biology and evolution  2010;28(2):1013-1024.
The geographic origin and time of dispersal of Austroasiatic (AA) speakers, presently settled in south and southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. The first of these places the origin of Austroasiatic speakers in southeast Asia with a later dispersal to south Asia during the Neolithic, whereas the second hypothesis advocates pre-Neolithic origins and dispersal of this language family from south Asia. To test the two alternative models, this study combines the analysis of uniparentally inherited markers with 610,000 common single nucleotide polymorphism loci from the nuclear genome. Indian AA speakers have high frequencies of Y chromosome haplogroup O2a; our results show that this haplogroup has significantly higher diversity and coalescent time (17–28 thousand years ago) in southeast Asia, strongly supporting the first of the two hypotheses. Nevertheless, the results of principal component and “structure-like” analyses on autosomal loci also show that the population history of AA speakers in India is more complex, being characterized by two ancestral components—one represented in the pattern of Y chromosomal and EDAR results and the other by mitochondrial DNA diversity and genomic structure. We propose that AA speakers in India today are derived from dispersal from southeast Asia, followed by extensive sex-specific admixture with local Indian populations.
doi:10.1093/molbev/msq288
PMCID: PMC3355372  PMID: 20978040
Austroasiatic; mtDNA; Y chromosome; autosomes; admixture
2.  Nepalese populations show no association between the distribution of malaria and protective alleles 
Malaria is perhaps the most important parasitic infection and strongest known force for selection in the recent evolutionary history of the human genome. Genetically-determined resistance to malaria has been well-documented in some populations, mainly from Africa. The disease is also endemic in South Asia, the world’s second most populous region, where resistance to malaria has also been observed, for example in Nepal. The biological basis of this resistance, however, remains unclear. We have therefore investigated whether known African resistance alleles also confer resistance in Asia. We typed seven single nucleotide polymorphisms (SNPs) from the genes HBB, FY, G6PD, TNFSF5, TNF, NOS2 and FCGR2A in 928 healthy individuals from Nepal. Five loci were found to be fixed for the non-resistant allele (HBB, FY, G6PD, TNFSF5 and NOS2). The remaining two (rs1800629 and rs1801274) showed the presence of the resistant allele at a frequency of 93% and 27% in TNF and FCGR2A, respectively. However, the frequencies of these alleles did not differ significantly between highland (susceptible) and lowland (resistant) populations. The observed differences in allele and genotype frequencies in Nepalese populations therefore seem to reflect demographic processes or other selective forces in the Himalayan region, rather than malaria selection pressure actin on these alleles.
PMCID: PMC2684443  PMID: 19461987
Malaria; Himalayas; Nepal; single nucleotide polymorphisms; selection; resistance
3.  Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: isolation and drift in the Himalayas 
Forensic science international  2006;166(2-3):176-181.
26 Y-chromosomal short tandem repeat (STR) loci were amplified in a sample of 769 unrelated males from Nepal, using two multiplex polymerase chain reaction (PCR) assays. The 26 loci gave a discriminating power of 0.997, with 59% unique haplotypes, and the highest frequency haplotype occurring 12 times. We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%). Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan. Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database.
doi:10.1016/j.forsciint.2006.05.007
PMCID: PMC2627361  PMID: 16781103
Y chromosome; STRs; microsatellites; Haplotype; Nepal; Bhutan; Himalayas
4.  Diversity of 26-locus Y-STR haplotypes in a Nepalese population sample: Isolation and drift in the Himalayas 
Forensic Science International  2007;166(2-3):176-181.
Twenty-six Y-chromosomal short tandem repeat (STR) loci were amplified in a sample of 769 unrelated males from Nepal, using two multiplex polymerase chain reaction (PCR) assays. The 26 loci gave a discriminating power of 0.997, with 59% unique haplotypes, and the highest frequency haplotype occurring 12 times. We identified novel alleles at four loci, microvariants at a further two, and nine examples of amelogenin-Y deletions (1.2%). Comparison with a similarly sized Bhutanese sample typed with the same markers suggested histories of isolation and drift, with drift having a greater effect in Bhutan. Extended (11-locus) haplotypes for the Nepalese samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).
doi:10.1016/j.forsciint.2006.05.007
PMCID: PMC2627361  PMID: 16781103
Y chromosome; STRs; Microsatellites; Haplotype; Nepal; Bhutan; Himalayas
5.  Nepalese populations show no association between the distribution of malaria and protective alleles 
Malaria is perhaps the most important parasitic infection and strongest known force for selection in the recent evolutionary history of the human genome. Genetically-determined resistance to malaria has been well-documented in some populations, mainly from Africa. The disease is also endemic in South Asia, the world's second most populous region, where resistance to malaria has also been observed, for example in Nepal. The biological basis of this resistance, however, remains unclear. We have therefore investigated whether known African resistance alleles also confer resistance in Asia. We typed seven single nucleotide polymorphisms (SNPs) from the genes HBB, FY, G6PD, TNFSF5, TNF, NOS2 and FCGR2A in 928 healthy individuals from Nepal. Five loci were found to be fixed for the non-resistant allele (HBB, FY, G6PD, TNFSF5 and NOS2). The remaining two (rs1800629 and rs1801274) showed the presence of the resistant allele at a frequency of 93% and 27% in TNF and FCGR2A, respectively. However, the frequencies of these alleles did not differ significantly between highland (susceptible) and lowland (resistant) populations. The observed differences in allele and genotype frequencies in Nepalese populations therefore seem to reflect demographic processes or other selective forces in the Himalayan region, rather than malaria selection pressure acting on these alleles.
PMCID: PMC2684443  PMID: 19461987
Malaria; Himalayas; Nepal; single nucleotide polymorphisms; selection; resistance
6.  A Linguistically Informed Autosomal STR Survey of Human Populations Residing in the Greater Himalayan Region 
PLoS ONE  2014;9(3):e91534.
The greater Himalayan region demarcates two of the most prominent linguistic phyla in Asia: Tibeto-Burman and Indo-European. Previous genetic surveys, mainly using Y-chromosome polymorphisms and/or mitochondrial DNA polymorphisms suggested a substantially reduced geneflow between populations belonging to these two phyla. These studies, however, have mainly focussed on populations residing far to the north and/or south of this mountain range, and have not been able to study geneflow patterns within the greater Himalayan region itself. We now report a detailed, linguistically informed, genetic survey of Tibeto-Burman and Indo-European speakers from the Himalayan countries Nepal and Bhutan based on autosomal microsatellite markers and compare these populations with surrounding regions. The genetic differentiation between populations within the Himalayas seems to be much higher than between populations in the neighbouring countries. We also observe a remarkable genetic differentiation between the Tibeto-Burman speaking populations on the one hand and Indo-European speaking populations on the other, suggesting that language and geography have played an equally large role in defining the genetic composition of present-day populations within the Himalayas.
doi:10.1371/journal.pone.0091534
PMCID: PMC3948894  PMID: 24614536
7.  The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations 
PLoS ONE  2012;7(11):e48477.
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.
doi:10.1371/journal.pone.0048477
PMCID: PMC3509117  PMID: 23209554

Results 1-7 (7)