Gene Frequency Data Research Articles

Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

BackgroundThe genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes.ResultsWe discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a ‘two-haplotype genomic hybridization model’ for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations.ConclusionsThe yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.

Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs.

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.

Luigi Luca Cavalli-Sforza. 25 January 1922—31 August 2018

Though it was as a bacteriologist that Luca Cavalli-Sforza first flourished scientifically, it was the subject of human population genetics that he dominated for the second half of the twentieth century. He pioneered both genetical demography and the construction of the genetical evolutionary tree of man, initially from gene-frequency data and ultimately from tracing the paths of descent of individual DNA sequences. He was among the first to apply the new computers to the problems he encountered, using his self-taught knowledge of mathematics and statistics. He conducted expeditions to the Pygmies of the African rainforest and studied the spread of agriculture in Europe, demonstrating the similarity between its wave of advance and the contours of population gene frequency. He noted the correspondence between the descent tree of languages and the human evolutionary tree.Cavalli headed university departments in Pavia and then Stanford, surrounding himself with young colleagues and driving forward research with vigorous discussion and unceasing enthusiasm. His knowledge was spread across medicine and genetics, anthropology and linguistics, archaeology and history, and he expressed himself fluently in speech and writing in Italian, English and French. A true Renaissance man.His published work in human population genetics and cultural evolution over more than 50 years constituted ‘one long argument’, as Darwin said ofThe origin of species. The villages of the Parma valley were his Galapagos Islands, and random genetic drift his adjunct to natural selection for the case of man. His demonstration of the importance of drift in recent human evolution informed the model for constructing evolutionary trees from gene-frequency data. On this one long argument he wrote and lectured ceaselessly, not only for other scientists but also for a wider audience, always mindful of a responsibility to promote an understanding of man's biology and evolutionary history for society's benefit. In so doing he brought an informed and rational approach to the problem of human diversity and the problems of human diversity.

HLA Polymorphisms and Haplotype Diversity in Transylvania, Romania.

Transylvania is a historical region in the northwestern part of Romanian with a rather heterogeneous population. Our study is the first to determine human leukocyte antigen (HLA) profiles in a large population sample from this region and to compare them with other European population groups. HLA genes were examined in 2,794 individuals using the Single Specific Primer-Polymerase Chain Reaction (SSP-PCR) and Polymerase Chain Reaction Sequence-Specific Oligonucleotide (PCR-SSO) methods. All samples were tested for the HLA-A locus, 2,773 for HLA-B, 1,847 for HLA-C, and 2,719 for HLA-DRB1 loci. HLA gene frequency data from several European population groups (as presented in studies involving more than 1,000 individuals) served as reference in comparison with the local sample. The distribution of HLA genes in the studied population group was heterogeneous, as the Hardy-Weinberg equilibrium was statistically significant (P value < 0.01). The most common genes found in our sample group were A∗02 (0.27%), B∗35 (0.14%), C∗07 (0.25%), and DRB1∗11 (0.19%). The most common haplotype was A∗01~B∗08~C∗07~DRB1∗03 (1.26% in 1,770 individuals with complete data). This analysis confirmed the known heterogeneity of the Transylvanian population. The study indicates that the European population groups located in close vicinity (those from Serbia, Hungary, Wallachia, and Croatia) are genetically closest to the Transylvanian population.

Distribution of Blood Types and ABO Gene Frequencies in Egypt

Abstract ABO blood group was first discovered by Landsteiner in 1901. Currently, there are more than 30 blood group systems, but ABO system remains the most clinically important of all blood groups in transfusion practice. The ABO blood group system antibodies are naturally occurring without any exposure to RBCs through transfusion or pregnancy, unlike the other blood group systems. Method The study was performed on a total of 40,591 healthy blood donors in Egypt. ABO and Rh (D) groupings were performed on all donors’ samples. Data on the frequency of ABO and Rh(D) blood groups were reported in numbers and percentages. Results The study showed that type A is the most common blood group (35.12%) in Egypt followed by O at 31.94%, followed by B at 23.12%, while AB had the least prevalence at 9.74%; A &gt; O &gt; B &gt; AB. Our study showed that 91.78% of the donor population were Rh positive and 8.22% were Rh negative. The frequencies of the IA, IB, and IO alleles were calculated using the Hardy-Weinberg law of equilibrium. The calculated gene frequencies are 0.2537 for IA (p), 0.1812 for IB (q), and 0.5651 for IO (r). In the Egyptian population, O (r) records the highest value, followed by B (q) and A (p); O &gt; B &gt; A. The homozygous types were as follows: OO, 31.94%; AA, 6.43%; and BB, 3.28%. The heterozygous types were AO, 28.67%; BO, 20.47%; and AB, 9.78%. Conclusions The study provides the first accurate ABO gene frequency data as well as information on the distribution of ABO blood group Rh groups of various alleles in the Egyptian population. This information is very helpful in the effective management of the blood bank inventory. It will help transfusion services planning for future health challenge and improve blood transfusion practice.

Status of insecticide resistance and its biochemical and molecular mechanisms in Anopheles stephensi (Diptera: Culicidae) from Afghanistan

BackgroundInsecticide resistance of Anopheles stephensi, the main malaria vector in eastern Afghanistan, has been reported previously. This study describes the biochemical and molecular mechanisms of resistance to facilitate effective vector control and insecticide resistance management.MethodsMosquito larvae were collected from the provinces of Kunar, Laghman and Nangarhar from 2014 to 2017. The susceptibility of the reared 3–4 days old adults was tested with deltamethrin 0.05%, bendiocarb 0.1%, malathion 5%, permethrin 0.75% and DDT 4%. Cytochrome P450 content and general esterase, glutathione S-transferase (GST) and acetylcholinesterase (AChE) activities were measured in the three field populations and the results were compared with those of the laboratory susceptible An. stephensi Beech strain. Two separate allele-specific PCR assays were used to identify L1014, L1014F and L1014S mutations in the voltage gated sodium channel gene of An. stephensi. Probit analysis, ANOVA and Hardy–Weinberg equilibrium were used to analyse bioassay, biochemical assay and gene frequency data respectively.ResultsThe population of An. stephensi from Kunar was susceptible to bendiocarb, apart from this, all populations were resistant to all the other insecticides tested. The differences between all values for cytochrome P450s, general esterases, GSTs and AChE inhibition rates in the Kunar, Laghman and Nangarhar populations were statistically significant when compared to the Beech strain, excluding GST activities between Kunar and Beech due to the high standard deviation in Kunar. The three different sodium channel alleles [L1014 (wild type), L1014F (kdr west) and L1014S (kdr east)] were all segregated in the Afghan populations. The frequencies of kdr east mutation were 22.9%, 32.7% and 35% in Kunar, Laghman and Nangarhar populations respectively. Kdr west was at the lowest frequency of 4.44%.ConclusionsResistance to different groups of insecticides in the field populations of An. stephensi from Kunar, Laghman and Nangarhar Provinces of Afghanistan is caused by a range of metabolic and site insensitivity mechanisms, including esterases, cytochrome P450s and GSTs combined with AChE and sodium channel target site insensitivity. The intensity and frequency of these mechanisms are increasing in these populations, calling for urgent reorientation of vector control programmes and implementation of insecticide resistance management strategies.

Defining Genetic, Taxonomic, and Geographic Boundaries Among Species of the Psorophora confinnis (Diptera: Culicidae) Complex in North and South America.

The Psorophora confinnis complex is currently composed of three species--Psorophora confinnis sensu stricto (Lynch Arribalzaga) in South America, Psorophora columbiae (Dyar and Knab) in North America, and Psorophora jamaicensis (Theobald) in the Caribbean. Members of the complex are of considerable importance as vectors of arboviruses, for example, Venezuelan equine encephalitis virus, and are significant biting pests throughout their range. The biological and geographic boundaries of Ps. confinnis and Ps. columbiae are unclear. In fact, the name Ps. columbiae is presently designated as "provisional." In this article, we aim to clarify the taxonomy and geographic distributions of species within the Ps. confinnis complex. A population genetics approach was employed using gene and genotypic frequency data at 26 isozyme loci. The results suggest that the Ps. confinnis complex in North and South America is composed of four species. Ps. confinnis s.s. and Ps. columbiae are distinct species in South and North America, respectively. Populations in Colombia, South America, formally designated as Ps. funiculus (Dyar) and populations in the southwestern United States and western Mexico, formally designated Ps. toltecum (Dyar and Knab), are distinct species. Psorophora toltecum and Psorophora funiculus species names should be resurrected from synonymy. In addition we identified a Ps. columbiae and Ps. toltecum hybrid zone in central Texas in a region described as being one of 13 North American suture zones, being geographical areas in which closely related species occur in sympatry and frequently hybridize.

Detecting and Measuring Selection from Gene Frequency Data

The recent advent of high-throughput sequencing and genotyping technologies makes it possible to produce, easily and cost effectively, large amounts of detailed data on the genotype composition of populations. Detecting locus-specific effects may help identify those genes that have been, or are currently, targeted by natural selection. How best to identify these selected regions, loci, or single nucleotides remains a challenging issue. Here, we introduce a new model-based method, called SelEstim, to distinguish putative selected polymorphisms from the background of neutral (or nearly neutral) ones and to estimate the intensity of selection at the former. The underlying population genetic model is a diffusion approximation for the distribution of allele frequency in a population subdivided into a number of demes that exchange migrants. We use a Markov chain Monte Carlo algorithm for sampling from the joint posterior distribution of the model parameters, in a hierarchical Bayesian framework. We present evidence from stochastic simulations, which demonstrates the good power of SelEstim to identify loci targeted by selection and to estimate the strength of selection acting on these loci, within each deme. We also reanalyze a subset of SNP data from the Stanford HGDP-CEPH Human Genome Diversity Cell Line Panel to illustrate the performance of SelEstim on real data. In agreement with previous studies, our analyses point to a very strong signal of positive selection upstream of the LCT gene, which encodes for the enzyme lactase-phlorizin hydrolase and is associated with adult-type hypolactasia. The geographical distribution of the strength of positive selection across the Old World matches the interpolated map of lactase persistence phenotype frequencies, with the strongest selection coefficients in Europe and in the Indus Valley.

Trans-National Genetic Distance and Genetic Identity of Barak Valley Hindus en Route the Journey of Mankind from Africa for ABO Gene

The present study aimed at estimating the genetic distance and genetic identity between Barak Valley Hindus and other twenty four nations for ABO blood group gene along the route of historic journey of mankind from Africa as proposed by Stephen Oppenheimer to gain insights on the evolutionary relationship and genetic closeness of the Hindus with other nations. Barak Valley Zone, located in southern part of Assam state in North East India, has inhabited the major endogamous group, the Hindus, for several centuries. Over the last few decades, they have maintained distinct culture and life style. This study used ABO gene frequency data of these populations to estimate Nei’s standard genetic distance and genetic identity of population genetics between Barak Valley Hindus and other nations. The historic journey of mankind commenced from Africa about 200,000 years ago ( www.bradshawfoundation.com). Genetic distance estimate ranged from 0.07 to 5.18%. Barak Valley Hindus (BVH) showed relatively low genetic distance for ABO gene with the populations of Saudi Arabia (0.07%), India (0.13%), Borneo (0.40%), Russia (0.59%), Central Asia (0.60%), Siberia (0.60%), South China (0.71%) and Sri Lanka (0.93%) suggesting high genetic identity and possible evolutionary relationship of BVH during migration with these nations. But the BVH showed highest genetic distance with Australia (5.18%) followed by Norway (4.13%), Sudan (3.89%) and Sweden (3.60%) indicating low genetic identity of BVH with these nations. Migration was not the key determining factor in changing the ABO gene frequency in human populations.

Genetic polymorphism analysis of killer cell immunoglobulin-like receptor genes in the Chinese Uygur population

Human killer cell immunoglobulin-like receptors are expressed in natural killer cells and subsets of T lymphocytes. They regulate these cells upon interaction with human leukocyte antigen class I molecules and other ligands presented by target cells. KIR gene frequencies and haplotype distributions have been shown to differ significantly between populations from different geographical regions and ethnic origins, which relates to functional variations in the immune response. We have investigated KIR gene frequencies and genotype diversities of 15 KIR genes (KIR2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 2DS1, 2DS2, 2DS3, 2DS4, ID, 2DS5, 3DL1, 3DL2, 3DL3, 3DS1) and two pseudogenes (KIR3DP1 and 2DP1) in 120 unrelated healthy individuals of the Uygur population living in the Xinjiang autonomous region of China. All individuals were typed positive for the four framework loci KIR3DL3, 2DL4, 3DL2 and KIR3DP1, while activating genes (KIR2DS1, 2DS2, 2DS3, 2DS5 and KIR3DS1) indicated some variation in this population. KIR3DS1 was found in a higher frequency in the studied population than in other groups from China. Linkage disequilibrium among KIR genes displayed a wide range. χ(2) analysis, conducted among non-ubiquitous genes, based on the KIR gene frequency data from our study population and previously published population data, revealed significant differences in the KIR2DL1, 2DL2, 2DL3, 2DL5, 3DL1, 2DS1, 2DS2, 2DS3, 2DS5, and 3DS1 genes. A neighbor-joining phylogenic tree, built using the observed carrier frequencies data of 13 KIR loci (KIR2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 3DL1, 3DL2, 3DL3, 2DS1, 2DS2, 2DS3, 2DS5, and 3DS1), showed relationships between the population studied and other previously reported populations. The present study can therefore be valuable for enriching the ethnical gene information resources of the KIR gene pool, for population origin studies and for KIR-related clinical practice.

Heterozygosity and Fixation Index for ABO Gene in Barak Valley Populations vis-a-vis a Few Exotic Populations

In a genetic study of 26 human populations including 2 major endogamous populations (Hindus and Muslims) of Barak Valley in Assam and 24 exotic populations, observed heterozygosity (Ho), fixation index (F) and Panmictic index (P) for ABO gene were estimated from gene frequency data to reveal the extent of inbreeding that has taken place in each population during evolution. Observed heterozygosity, a measure of genetic variation, ranged from 0.3254 to 0.6086 in these populations. Expected Hardy-Weinberg heterozygosity of ABO gene was estimated as 0.6666 assuming the occurrence of all the three alleles in equal frequency. Fixation index was the highest in the population of Sudan (51.18%) followed by Australia (48.51%) and Iceland (38.28%) indicating the occurrence of high inbreeding and the presence of more homozygosity in these populations during evolution. But the fixation index was the lowest in the population of South China (8.70%) followed by Central Asia (11.82%) and Russia (12.96%). It suggested the occurrence of low inbreeding and hence more outbreeding in these populations resulting in the existence of more heterozygosity (high genetic variation) in these populations. Panmictic index, a measure of outbreeding, is the opposite of fixation index and it varied from 48.82 (Sudan) to 91.30% (South China). The population showing the highest fixation index recorded the lowest panmictic index and vice-versa. In evolutionary context, outbreeding in human populations would be more desirable to reduce the incidence of genetic diseases caused by recessive genes and to enhance heterozygosity for those loci for better adaptation of future generations, possibly at the cost of gradually increasing genetic load in the population.

Diversity of Killer Cell Immunoglobulin-like Receptor Genes in the Bai Ethnic Minority of Yunnan, China

Killer cell immunoglobulin-like receptors (KIRs), expressed in both natural killer (NK) cells and a subset of T cells, represent a family of both inhibitory and activating receptors that can regulate NK and T cells upon interacting with human leucocyte antigen (HLA) class I molecules on target cells. The number and distribution of KIR genes vary between individuals and populations from different geographical regions and ethnic origins. In this study, we investigated KIR gene frequencies and genotype diversities of 13 KIR genes, 2 pseudogenes, expressed and non-expressed forms of KIR2DL5 and the two subtypes, full-length and deleted forms, of KIR2DS4 in 100 unrelated healthy individuals of the Bai population, living in the Dali Bai autonomous prefecture in the Yunnan province. All individuals were typed positive for the three framework loci KIR3DL3, 2DL4 and 3DL2, as well as for three non-framework genes KIR2DL1, 2DL3 and the pseudogene KIR2DP1. The gene frequencies of the other KIR genes ranged from 7%-95%. The results of tested linkage disequilibrium (LD) among KIR genes demonstrated that they display a wide range of LD. χ² analysis among non-ubiquitous genes, using the KIR gene frequency data from our study population, as well as from previously published population data, was conducted and revealed significant differences in the KIR2DL1, 2DL2, 3DL1 and KIR2DS1 genes. The results of the present study can be valuable for enriching the Chinese ethnic gene information resources of the KIR gene pool, for anthropological studies, as well as for KIR-related disease research.

Comparative Study of Various Genetic Distance Measures between Populations for the ABO Gene

Quantification of the genetic distance between populations is essential in many genetic research programs. Several formulae have been proposed for the estimation of the genetic distance between populations using gene frequency data. Nei’s D has been the most widely used genetic distance measure in different research programs. But the selection of a suitable measure to estimate genetic distance between real-world human populations is a very difficult task. The present study was undertaken to estimate the genetic distance between Barak Valley Muslims (BVM) and other twenty four nations with the ABO blood group gene frequency data using seven different formulae, as well as to estimate the correlation coefficients between distance measures and to work out the regression equations. Seven genetic distance measures namely Nei’s D, Nei’s Nm, La, Nei’s Da, Dc, Re and Nei’s Ne were calculated between BVM and other 24 nations. Correlation coefficients of Nei’s D with other measures were determined to find out which other genetic distance measures were similar to Nei’s D. Linear regression equations of Nei’s D with other distance measures were determined. Nei’s D showed a highly significant (p=0.01) positive correlation with Cavalli-Sforza and Edwards chord distance Dc (0.90), Reynolds Re (0.90), Nei’s Da (0.74) and Nei’s Ne (0.63) but a negative correlation with Nei’s Nm and La. Since Nei’s D had very high positive correlation with Dc and Re distance measures, any one of these measures could be reliably used in genetic analysis instead of all the three measures for estimating genetic distance between populations.

The diversity of a distributed genome in bacterial populations

The distributed genome hypothesis states that the set of genes in a population of bacteria is distributed over all individuals that belong to the specific taxon. It implies that certain genes can be gained and lost from generation to generation. We use the random genealogy given by a Kingman coalescent in order to superimpose events of gene gain and loss along ancestral lines. Gene gains occur at a constant rate along ancestral lines. We assume that gained genes have never been present in the population before. Gene losses occur at a rate proportional to the number of genes present along the ancestral line. In this infinitely many genes model we derive moments for several statistics within a sample: the average number of genes per individual, the average number of genes differing between individuals, the number of incongruent pairs of genes, the total number of different genes in the sample and the gene frequency spectrum. We demonstrate that the model gives a reasonable fit with gene frequency data from marine cyanobacteria.

Large scale screening for haemoglobin disorders in southern Vietnam: implications for avoidance and management

In order to obtain an approximate assessment of the public health burden that will be posed by the inherited disorders of haemoglobin in southern Vietnam, several thousand individuals were screened for these conditions. A smaller sample was screened for glucose-6-phosphate dehydrogenase (G6PD) deficiency. The important haemoglobin disorders identified were beta thalassaemia, haemoglobin E and a variety of different forms of alpha thalassaemia. There were sufficient G6PD-deficient individuals to materially affect malaria control programme design. The most remarkable finding was wide variation in the gene frequencies of these conditions among the ethnic groups sampled. The approximate number of babies expected to be born with clinically significant haemoglobin disorders in Vietnam was estimated from the gene-frequency data. This study emphasizes the importance of wide-scale population screening, including ethnic subgroups, to establish the requirements for inherited haemoglobin disorder programmes in resource-limited settings.

Hierarchical gene diversity analysis and its application to brown trout population data

A generalized FORTRAN IV computer program (NEGST) for nested gene diversity analysis and its application to brown trout gene frequency data are presented. In its present shape the program handles up to five hierarchical levels of subdivision, 70 operational units (subpopulations), and 50 polymorphic loci with 20 alleles per locus.

Population history of the Dniester–Carpathians: evidence from Alu markers

The area between the Dniester and the eastern Carpathian mountain range is at a geographical crossroads between eastern Europe and the Balkans. Little is known about the genetics of the population of this region. We performed an analysis of 12 binary autosomal markers in samples from six Dniester-Carpathian populations: two Moldavian, one Romanian, one Ukrainian and two Gagauz populations. The results were compared with gene frequency data from culturally and linguistically related populations from Southeast Europe and Central Asia. Small genetic differences were found among southeastern European populations (in particular those of the Dniester-Carpathian region). The observed homogeneity suggests either a very recent common ancestry of all southeastern European populations or strong gene flow between them. Despite this low level of differentiation, tree reconstruction and principle component analyses allowed a distinction between Balkan-Carpathian (Macedonians, Romanians, Moldavians, Ukrainians and Gagauzes) and eastern Mediterranean (Turks, Greeks and Albanians) population groups. The genetic affinities among Dniester-Carpathian and southeastern European populations do not reflect their linguistic relationships. The results indicate that the ethnic and genetic differentiations occurred in these regions to a considerable extent independently of each other. In particular, Gagauzes, a Turkic-speaking population, show closer affinities to their geographical neighbors than to other Turkic populations.

Study of Genetic Relationships of Indian Gurkha Population on the Basis of HLA - A and B Loci Antigens

KEYWORDS Population genetics; HLA antigens; genetic relationship; Gurkha population ABSTRACT Indian population is well known for its genetic diversity. Among the numerous endogamous ethnic groups of North Bengal, we have collected blood samples from 50 unrelated Nepali speaking individuals, belonging to Gurkha community. In the present investigation, the frequency of HLA-A and B loci antigens has been analyzed serologically and compared with few major world populations. The frequency of A2, A11, A33, B18 and B51 showed increased frequency and several haplotypes including A3-B35, A33-B44, A68-B35 have significant linkage disequilibrium values. The standard genetic distances of the Gurkha population were calculated on the basis of gene frequency data of HLA antigens and when compared with other populations, it has revealed that Gurkha population is genetically closer to the population of Mongoloid origin. It can be considered that the Gurkha population may have been originated from Mongolians and/or Tibetan stocks.

Y-chromosome STR haplotype diversity in Brazilian populations

A sample of 198 unrelated males distributed among the five geopolitical regions in Brazil were typed for the minimal Y-STR haplotype composed of microsatellite loci DYS19, DYS385I/II, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393. Gene frequency data, gene diversity, haplotype diversity and power of discrimination were estimated. An AMOVA indicated that 99.97% of the haplotypic variation is found within regions and only a small 0.03% and non significant variation is found among the five regions (Fst = 0.00031, P-value = 0.43). This result suggests that a single national database of Y-STR haplotypes can be used in the quantitative assessment of matches in forensic casework in the Brazilian population. A significant haplotype diversity of 99.8% was found and 172 different haplotypes were observed in 198 chromosomes. Haplotype (14–11, 14–13–29–24–11–13–13) with five occurrences in 198 chromosomes was the most frequent in Brazil.

Genetic heterogeneity in northeastern India: reflection of Tribe-Caste continuum in the genetic structure.

We critically examined the gene frequency data for 11 genetic markers commonly available in the literature for 22 populations of northeastern India in the light of their geographic, linguistic, and ethnic affiliations. The markers investigated were three blood groups (A1A2BO, MNS, and Rh), four serum proteins (KM, Gc, Hp, and Tf), and four enzyme systems (AP, AK, EsD, and Hb). The neighbor-joining tree and multidimensional scaling of the distance matrix suggest relatively high genetic differentiation among the Mongoloid groups, with probably diverse origins when compared to the Caucasoid Indo-European populations, which had probably come from relatively more homogeneous backgrounds. Broadly speaking, the pattern of population affinities conforms to the ethno-historic, linguistic, and geographic backgrounds. An interesting and important feature that emerges from this analysis is the reflection of the effect of the sociological process of a Tribe-Caste continuum on genetic structure. While on one end we have the cluster of Caucasoid caste populations, the other end consists of Mongoloid tribal groups. In between are the populations which were originally tribes but now have become semi-Hinduized caste groups, viz., Rajbanshi, Chutiya, and Ahom. These groups have currently assumed caste status and speak Indo-European languages. Therefore, one may infer that what appears to be a purely sociological phenomenon of a Tribe-Caste continuum may well reflect in their genetic structure.