Showing papers by "Ranjan Deka published in 1999"

Y-Chromosome Evidence for a Northward Migration of Modern Humans into Eastern Asia during the Last Ice Age

Abstract: Summary The timing and nature of the arrival and the subsequent expansion of modern humans into eastern Asia remains controversial. Using Y-chromosome biallelic markers, we investigated the ancient human-migration patterns in eastern Asia. Our data indicate that southern populations in eastern Asia are much more polymorphic than northern populations, which have only a subset of the southern haplotypes. This pattern indicates that the first settlement of modern humans in eastern Asia occurred in mainland Southeast Asia during the last Ice Age, coinciding with the absence of human fossils in eastern Asia, 50,000–100,000 years ago. After the initial peopling, a great northward migration extended into northern China and Siberia.

Genomic diversity : applications in human population genetics

Abstract: Contents. Preface. Classical to Molecular Polymorphisms: Population Genetic Studies from the Indian Sub-Continent S.S. Papiha, S.S. Mastana Variability in nDNA, mtDNA, and Proteins - A Test Case M.H. Hutz, et al. Genetic Diversity among Five Native American Tribes of Colombia: Evidence from Nine Autosomal Microsatellites F. D. Guarino, et al. Trinucleotide Repeats, Genetic Instability, and Variation in the Human Genome R. Deka, R. Chakraborty Y-Chromosomal DNA Markers C. Tyler-Smith. On the Genetic Origin of the Turks: Study of Six Y-Chromosomal Short Tandem Repeats B. Rolf, A. Rohl, et al. The Origins of Pakistani Populations: Evidence from Y Chromosome Markers S. Q. Mehdi, et al. The Use of Y-Chromosomal DNA Variation to Investigate Population History: Recent Male Spread in Asia and Europe T. Zerjal, et al. A Mitochondrial DNA Database: Applications to Problems of Nomenclature and Population Genetics P. Francalacci, et al. The Tras-Caucasus and the Expansion of the Caucasoid-Specific Human Mitochondrial DNA Lineages E. Metspalu, et al. The Place of the Indian Mitochondrial DNA Variants in the Global Network of Maternal Lineages and the Peopling of the Old World T. Kivisild, et al. Mitochondrial DNA Variation in the Southwest Pacific D.A. Merriwether, et al. Molecular Anthropology: Progress and Perspectives on Ancient DNA Technology C.J. Kolman. Interspersed Repeat Insertion Polymorphisms for Studies of Human Molecular Anthropology P.L. Deininger, et al. Statistical Issues Regarding the Use of Microsatellite Loci for Molecular Anthropological Studies R. Chakraborty. Epilogue.

Genetic variation at twentythree microsatellite loci in sixteen human populations

Abstract: We have analysed genetic variation at 23 microsatellite loci in a global sample of 16 ethnically and geographically diverse human populations. On the basis of their ancestral heritage and geographic locations, the studied populations can be divided into five major groups, viz. African, Caucasian, Asian Mongoloid, American Indian and Pacific Islander. With respect to the distribution of alleles at the 23 loci, large variability exists among the examined populations. However, with the exception of the American Indians and the Pacific Islanders, populations within a continental group show a greater degree of similarity. Phylogenetic analyses based on allele frequencies at the examined loci show that the first split of the present-day human populations had occurred between the Africans and all of the non-African populations, lending support to an African origin of modern human populations. Gene diversity analyses show that the coefficient of gene diversity estimated from the 23 loci is, in general, larger for populations that have remained isolated and probably of smaller effective sizes, such as the American Indians and the Pacific Islanders. These analyses also demonstrate that the component of total gene diversity, which is attributed to variation between groups of populations, is significantly larger than that among populations within each group. The empirical data presented in this work and their analyses reaffirm that evolutionary histories and the extent of genetic variation among human populations can be studied using microsatellite loci.

Rate and directionality of mutations and effects of allele size constraints at anonymous, gene-associated, and disease-causing trinucleotide loci.

Abstract: We studied the patterns of within- and between-population variation at 29 trinucleotide loci in a random sample of 200 healthy individuals from four diverse populations: Germans, Nigerians, Chinese, and New Guinea highlanders. The loci were grouped as disease-causing (seven loci with CAG repeats), gene-associated (seven loci with CAG/CCG repeats and eight loci with AAT repeats), or anonymous (seven loci with AAT repeats). We used heterozygosity and variance of allele size (expressed in units of repeat counts) as measures of within-population variability and GST (based on heterozygosity as well as on allele size variance) as the measure of genetic differentiation between populations. Our observations are: (1) locus type is the major significant factor for differences in within-population genetic variability; (2) the disease-causing CAG repeats (in the nondisease range of repeat counts) have the highest within-population variation, followed by the AAT-repeat anonymous loci, the AAT-repeat gene-associated loci, and the CAG/CTG-repeat gene-associated loci; (3) an imbalance index beta, the ratio of the estimates of the product of effective population size and mutation rate based on allele size variance and heterozygosity, is the largest for disease-causing loci, followed by AAT- and CAG/CCG-repeat gene-associated loci and AAT-repeat anonymous loci; (4) mean allele size correlates positively with allele size variance for AAT- and CAG/CCG-repeat gene-associated loci and negatively for anonymous loci; and (5) GST is highest for the disease-causing loci. These observations are explained by specific differences of rates and patterns of mutations in these four groups of trinucleotide loci, taking into consideration the effects of the past demographic history of the modern human population.

Analysis of five Y-specific microsatellite loci in Asian and Pacific populations.

Abstract: We have analyzed five Y-specific microsatellite loci (DYS388, DYS390, DYS391, DYS394, DYS395) in 17 Asian and Pacific populations representing a broad geographical area and different linguistic families, with an emphasis on populations from mainland and insular Southeast Asia. Analysis of gene diversity indicates that several of the studied populations have experienced substantial genetic isolation, and a reduction in male effective sizes (viz. the Northeast Indian populations Nishi, Adi and the Taiwanese aboriginals). The average values of the F(ST) and ((ST) statistics indicate a high degree of genetic differentiation among these populations at the five Y-specific markers (F(ST) =0.21 and ((ST) = 0.33, based on individual loci; F(ST) = 0.09 and ((ST) = 0.36, based on haplotypes), which conform to the expectation of a fourfold smaller effective size of the Y-linked loci compared with the autosomal loci. Dendrogram and principal coordinates analysis, with few exceptions, show a major separation between mainland and insular populations. Among the mainland populations, the Tibeto-Burman speakers from Northeast India cluster in a well-defined group, supported by high bootstrap values. The Southern Chinese, Northern Thai, So, and Cambodian also are integral to this cluster. The other major cluster is rather heterogeneous and includes, among others, the Austronesian-speaking populations. The Samoans of the Pacific, with a distinctive pattern of allelic distributions, stand as an outlier in the tree and PC representations. Although trends of genetic affinities among ethnically and geographically related populations are evident from the Y-specific microsatellite data, microsatellites are not optimal for deciphering complex migratory patterns of human populations, which could possibly be clarified by using additional and more stable genetic markers.

Patterns of Instability of Expanded CAG Repeats at the ERDA1 Locus in General Populations

Abstract: Summary A highly polymorphic CAG repeat locus, ERDA1 , was recently described on human chromosome 17q21.3, with alleles as large as 50–90 repeats and without any disease association in the general population. We have studied allelic distribution at this locus in five human populations and have characterized the mutational patterns by direct observation of 731 meioses. The data show that large alleles (≥40 CAG repeats) are generally most common in Asian populations, less common in populations of European ancestry, and least common among Africans. We have observed a high intergenerational instability (46.3%±5.1%) of the large alleles. Although the mutation rate is not dependent on parental sex, paternal transmissions have predominantly resulted in contractions, whereas maternal transmissions have yielded expansions. Within this class of large alleles, the mutation rate increases concomitantly with increasing allele size, but the magnitude of repeat size change does not depend on the size of the progenitor allele. Sequencing of specific alleles reveals that the intermediate-sized alleles (30–40 repeats) have CAT/CAC interruptions within the CAG-repeat array. These results indicate that expansion and instability of trinucleotide repeats are not exclusively disease-associated phenomena. The implications of the existence of massively expanded alleles in the general populations are not yet understood.

Genetic variation at 9 autosomal microsatellite loci in Asian and Pacific populations.

Abstract: Genetic variation at 9 autosomal microsatellite loci (CFS1R, TH01, PLA2A, F13A1, CYP19, LPL, D20S481, D20S473, and D20S604) has been characterized in 16 Asian and Oceanic populations, mostly from mainland and insular Southeast Asia. The neighbor-joining tree and the principal coordinates analysis of the genetic relationships of these populations show a clear separation of Papua New Guinea Highlanders and, to a lesser extent, Malayan aborigines (Orang Asli or Semai) from the rest of the populations. Although the number of markers used in this study appears to be inadequate for clarifying the patterns of genetic relationships among the studied populations, in the principal coordinates analysis a geographic trend is observed in the mainland and insular Southeast Asian populations. Furthermore, in an attempt to contrast the extent of variation between autosomal and Y-chromosome-specific microsatellite loci and to reveal potential differences in the patterns of male and female migrations, we have also compared genetic variation at these 9 autosomal loci with variation observed at 5 Y-chromosome-specific microsatellites in a common set of 14 Asian populations.

Trinucleotide Repeats, Genetic Instability and Variation in the Human Genome

Abstract: Trinucleotide repeats have been implicated in the genesis of over a dozen human diseases. These repeats are normally polymorphic in human populations. However, disease manifests when the repeat arrays become longer than a certain threshold. The expanded repeats are meiotically unstable. Recently, two other trinucleotide repeat loci have been reported with very large and unstable alleles in the general population without being associated with any known disease. These findings imply that the process of instability is not exclusively a disease-associated phenomenon. In this chapter, we discuss some of the population genetic properties of these loci, with a general emphasis on questions relating to maintenance of the expanded alleles in human populations.