Apolipoprotein B 3'-VNTR polymorphism in Eastern European populations

Apolipoprotein B 3' (3' ApoB) minisatellite polymorphism was studied in healthy unrelated individuals from the Russian Federation and the Republic of Belarus, in 10 populations from five ethnic groups: Russians, Byelorussians, Adygeis, Kalmyks and Yakuts. The analysis was carried out using PCR and electrophoresis followed by silver staining. Overall, 25 alleles of the 3' ApoB minisatellite, ranging from 25 to 55 repeats, were detected. Heterozygosity indices were high and varied from 0.73 to 0.84. The distributions of alleles of this minisatellite in the Caucasoid populations (Russians, Byelorussians and Adygeis) had a bimodal character, whereas that for Mongoloid populations (Kalmyks and Yakuts) had a unimodal distribution. Nei's genetic distances between the populations studied and some reference populations of Europe and Asia were estimated. Despite their allele distribution homogeneity, different East Slavonic ethnic groups were clearly resolved by multidimensional analyses. The East Slavonic and Adygei populations revealed a high similarity with European Caucasoids. The Mongoloid populations (Kalmyks and Yakuts) were considerably different from those of the European Caucasoid populations, but were similar to other Asian Mongoloid populations. The results demonstrate the variability of 3' ApoB minisatellite polymorphism not only in distant populations but also, to a certain extent, in genetically relative ones.     

HLA in the Azores Archipelago: possible presence of Mongoloid genes

The HLA profile of the Azoreans has been compared with those of other world populations in order to provide additional information regarding the history of their origins. The allele frequencies, genetic distances between populations, correspondence analyses and most frequent haplotypes were calculated. Our results indicate that the Azorean population most likely contains an admixture of high-frequency Caucasoid, Mongoloid and, to a lesser degree, Negroid HLA genes. The middle Atlantic Azores Archipelago was officially colonized by the Portuguese after 1439 and historical records are concordant with the existence of Caucasoid and Negroid population. However, Mongoloid genes were not suspected, but the Oriental HLA haplotypes A24-B44-DR6-DQ1, A29-B21-DR7-DQ2 and A2-B50-DR7-DQ2 are the fourth, fifth and sixth most frequent ones in Azores. A correspondence analysis shows that the Azorean population is equidistant from Asian and European populations and genetic distances are in some cases closer to the Asian than to European ethnic groups, and never are significantly different; also, B*2707 subtype is found in Asians and Azoreans (but not in Europeans) and the same Machado-Joseph Disease founder haplotypes (Chr 14) are found in both Japanese and Azoreans. It is proposed that a Mongoloid population exists in Azores; whether, the arrival occurred prior to discovery is undetermined.     

Genetic variation observed at three tetrameric short tandem repeat loci HumTHO1, TPOX,and CSF1PO— in five ethnic population groups of northeastern India

This paper portrays the genetic variation observed at three tetrameric short tandem repeat (STR) loci HumTHO1, TPOX, and CSF1PO in five ethnic population groups from northeastern India. The study also specifies the suitability of use of these markers for forensic testing. The populations studied included three tribal groups (Kuki, Naga and Hmar), one Mongoloid caste group (Meitei), and a religious caste group (Manipuri Muslims). The loci were highly polymorphic in the populations, and all loci met Hardy–Weinberg expectations. No evidence for association of alleles among the loci was detected. The probability of match for the three loci of the most frequent genotype in the five population groups ranged between 2.6 × 10⁻⁴ and 6.6 × 10⁻⁵. The average heterozygosity among the population groups was approximately 70% with the overall extent of gene differentiation among the five groups being high (G_st = 0.046). Genetic affinity among the populations reveal very close association between the Kuki, Hmar, Naga, and Meitei. The Manipuri Muslims, despite being found in the same region, have had no admixture with these populations and maintain a substantial distance with the other groups. The genetic polymorphism data suggest that the studied systems can be used for human identity testing to estimate the frequency of a multiple locus STR DNA profile in population groups of northeastern India. Am. J. Hum. Biol. 13:23–29, 2001. © 2001 Wiley‐Liss, Inc.     

Genetic profile based upon 15 microsatellites of four caste groups of the eastern Indian state,Bihar

Background: The formation of caste groups among the Hindu community and the practice of endogamy exert a great impact on the genetic structure and diversity of the Indian population. Allele frequency data of 15 microsatellite loci clearly portray the genetic diversity and relatedness among four socio-culturally advanced caste groups: Brahmin, Bhumihar, Rajput and Kayasth of Caucasoid ethnicity of Bihar. Aim: The study seeks to understand the impact of the man-made caste system on the genetic profile of the four major caste groups of Bihar. Methods and procedure: Computation of average heterozygosity, most frequent allele, allele diversity and coefficient of gene differentiation (Gst), along with genetic distance (D_A) and principal coordinate analysis were performed to assess intra-population and inter-population diversity. Main outcomes and results: The average Gst value for all the loci was 0.012 ± 0.0033, and the level of average heterozygosity was ?75.5%, indicating genetic similarity and intra-population diversity. Genetic distance (D_A) values and the phylogenetic tree along with other higher caste groups of India indicate the relative distance between them. Conclusion: The present study clearly depicts the genetic profile of these caste groups, their inherent closeness in the past, and the impact of the imposed caste system that later restricted the gene flow. The study highlights the status of Bhumihar and Kayasth in the Hindu caste system. The former was found clustering with the Brahmin group (as expected, since Bhumihar is known to be a subclass of Brahmin), whereas the distance between the Brahmin and Kayasth caste groups was found to be large. North-eastern Indian Mongoloids form a separate cluster.     

Genetic relationships of the populations in eastern India.

The genetic relationships for four sets of populations in eastern India have been studied by using gene frequency data available in the literature. The Caucasoid populations in Assam and West Bengal are genetically close but different from the Mongoloid populations in the neighbourhood. The genetic distance analysis shows that the Mongoloid populations in Assam and West Bengal cluster according to their states of residence, indicating a correlation between genetic and geographical distances.     

Genetic structure and affinity among eight ethnic populations of Eastern India: based on 22 polymorphic DNA loci.

The nature and extent of genetic variation at 22 polymorphic DNA loci, belonging to three distinct classes, especially, 12 STR loci (D3S1358, vWA, FGA, D5S818, D13S317, D7S820, D8S1179, D21S11, D18S51, HPRTB, F13B, LPL), four VNTR loci (D1S7, D4S139, D5S110, D17S79), and six coding loci (HLDQA1, LDLR, GYPA, HBGG, D7S8, GC) were investigated among eight population groups of West Bengal and Manipur regions of India. Of these, two groups from West Bengal belong to Caucasoid and six (one in WB and five in Manipur) belong to Mongoloid stock. Both STR and the expressed loci show wide diversity among the eight populations. For example, Manipur Muslims show differences in allele frequency when compared to four other regional populations. Similarly, Garo, one of the Mongoloid populations of West Bengal, differ in allele frequency from their counterparts in the Manipur region. Departure from Hardy-Weinberg expectations was observed at certain loci in a few populations (e.g., D21S1137 in Kayastha and Brahmin, HUM F13B in Meitei). Heterozygosity values were higher for Caucasoid than Mongoloid groups. The overall gene differentiation (GST) for STR loci is higher (5.3%) than for those at the expressed region (4.6%). The clustering pattern of the eight populations differs with respect to different classes of genetic markers used. The dendrograms based on six coding loci (HLDQA1, LDLR, GYPA, HBGG, D7S8, GC) differs from those based on STR and VNTR markers. Caucasoid and Mongoloid groups form different clusters and Manipur Muslims are distinct from others. The clustering pattern corresponded with the spatial and ethnic affiliations of the populations. Using different classes of DNA loci at the coding and noncoding region will help to better understand the influence of population structure variables on the genetic structure of populations.     

中国汉族两群体HLA-DQA1基因的遗传构成及有关15群体DQA1基因频率的比较分析

以HLA基因的PCR-RFLP分型方法研究了哈尔滨地区(Hans-H,71例)和上海地区(Hans-S,98例)两个汉族群体HLA-DQA1座位的遗传多态性。共检出8种等位基因。两群体均以DQA1*0301频率最高,而*0401最低(哈尔滨群体未检出),频率分布符合Hardy-Weinberg平衡。综合分析华人12群体及日本人、高加索人和尼格鲁人等3群体的HLA-DQA1的基因频率显示:卡方总体检验Hans-H及Hans-S与北方华人其它4群体(除维族)间相互无显著差异(P>0.05)),但逐项检验群体间多存在一个至几个基因频率的显著差异(P<0.05～0.001)。总体检验北方华人6群体(包括Hans-S)与南方5群体间均有显著差异(P<0.05～0.001),但满族与南方汉人3群体总体检验无显著差异(P>0.05),而维族与北方华人6群体则有显著差异(P<0.05～0.001)。另外,华人与异族间总体均有非常显著差异(P<0.001),但相对而言,华人(尤其是北方人)与日本人最为接近,华人与高加索人相似性较大,与尼格鲁人差异最大,而高加索人与尼格鲁人差异也较小。并对上述结果进行了讨论。     

Mitochondrial DNA variation and substructure among the tribal populations of Andhra Pradesh,India

We analyzed mtDNA HVR‐I variation among six tribal populations—Andh, Pardan, Gond, Naikpod, Kolam and Chenchu—from Andhra Pradesh. These tribes belong to the Dravidian and Indo‐European linguistic group. Except for Chenchu, the rest of the tribal samples were collected from two or more than two locations. The analysis of molecular variance (AMOVA) of the sequences yields a significant F_ST value (0.045), suggesting a fair degree of genetic differentiation among these tribes. When the tribal samples collected from different locations were considered as subpopulations in AMOVA, it is found that the variation among the subunits within the tribal groups is smaller than among the tribes. However, when Chenchu is removed from the analysis, the magnitude of within and between groups diversity becomes similar. In the multidimensional scaling plot based on F_ST distances the Chenchu is found to be the extreme outlier. Exclusion of Chenchu from AMOVA analysis and multidimensional scaling plot does not result in any specific pattern of population clustering. Mismatch distribution suggest that Chenchu might have undergone a bottleneck effect and does not show evidence of past demographic expansion as shown by the other five tribal groups. A comparison of AP tribes with some other caste and tribal populations of India suggests common maternal genetic heritage. Am. J. Hum. Biol., 2008. © 2008 Wiley‐Liss, Inc.     

Immunoglobulin (Gm and Km) allotypes in nine endogamous groups of West Bengal, India

Blood samples from 898 individuals of nine endogamous groups of West Bengal, India were typed for determining the haplotypic structure in the gamma-light chain (Gm) and kappa-light chain (Km) of immunoglobulin (IgG). The Gm haplotype frequencies detected by Glm (1), Glm (2) and G3m (5) markers suggest that in this eastern state of India there is considerable variation of frequencies of the typical Mongoloid haplotype Gm1,5, which shows a high incidence in Rajbanshi, Rabha, Garo and Lodha groups. On the contrary, this haplotype is probably absent in the high caste groups, Rarhi Brahmin and Vaidya, and is relatively infrequent in Jalia Kaibarta, a scheduled caste of the south-western part of the state. The Km1 allele is also high in frequency among Rajbanshi, Rabha, Garo and Munda in comparison with Rarhi Brahmin and Vaidya, suggesting the former four groups' strong Mongoloid affiliation. This survey signifies that there is considerable variation in the extent of Mongoloid admixture in Bengali populations. Such admixture is not restricted in specific social class either. It further demonstrates that heterogeneity of the genetic structure of Bengali populations do not correspond to the present social ranking on the basis of caste hierarchy.     

Y Chromosome and Mitochondrial DNA Variation in Lithuanians

The genetic composition of the Lithuanian population was investigated by analysing mitochondrial DNA hypervariable region 1, RFLP polymorphisms and Y chromosomal biallelic and STR markers in six ethnolinguistic groups of Lithuanians, to address questions about the origin and genetic structure of the present day population. There were no significant genetic differences among ethnolinguistic groups, and an analysis of molecular variance confirmed the homogeneity of the Lithuanian population. MtDNA diversity revealed that Lithuanians are close to both Slavic (Indo‐European) and Finno‐Ugric speaking populations of Northern and Eastern Europe. Y‐chromosome SNP haplogroup analysis showed Lithuanians to be closest to Latvians and Estonians. Significant differences between Lithuanian and Estonian Y chromosome STR haplotypes suggested that these populations have had different demographic histories. We suggest that the observed pattern of Y chromosome diversity in Lithuanians may be explained by a population bottleneck associated with Indo‐European contact. Different Y chromosome STR distributions in Lithuanians and Estonians might be explained by different origins or, alternatively, be the result of some period of isolation and genetic drift after the population split.     

The Gagauz, a Linguistic Enclave, are not a Genetic Isolate

The Gagauz are a Turkic‐speaking group that migrated from Turkey to their present location in the southern part of the Republic of Moldova about 150 years ago. Surrounded by Indo‐European‐speaking populations, they thus form a linguistic enclave, which raises the following question: to what extent have they remained in genetic isolation from their geographic neighbours? Analyses of mtDNA and Y chromosome variation indicate that despite their linguistic differences, the Gagauz have admixed extensively with neighbouring groups. Our data suggest that there has been more mtDNA than Y chromosome admixture, in keeping with the patrilocal nature of these groups. Moreover, when compared with another linguistic enclave, the Kalmyks there appears to be a correlation between the amount of genetic admixture and the amount of linguistic influence that these two linguistic enclaves have experienced from neighbouring groups.     

Diversity and Divergence Among the Tribal Populations of India

Tribal populations of the Indian subcontinent have been of longstanding interest to anthropologists and human geneticists. To investigate the relationship of Indian tribes to Indian castes and continental populations, we analyzed 45 unlinked autosomal STR loci in 9 tribal groups, 8 castes, and 18 populations from Africa, Europe and East Asia. South Indian tribal populations demonstrate low within‐population heterozygosity (range: 0.54 – 0.69), while tribal populations sampled further north and east have higher heterozygosity (range: 0.69 – 0.74). Genetic distance estimates show that tribal Indians are more closely related to caste Indians than to other major groups. Between‐tribe differentiation is high and exceeds that for eight sub‐Saharan African populations (4.8% vs. 3.7%). Telugu‐speaking populations are less differentiated than non‐Telugu speakers (F_ST: 0.029 vs. 0.079), but geographic distance was not predictive of genetic affinity between tribes. South Indian tribes show significant population structure, and individuals can be clustered statistically into groups that correspond with their tribal affiliation. These results are consistent with high levels of genetic drift and isolation in Indian tribal populations, particularly those of South India, and they imply that these populations may be potential candidates for linkage disequilibrium and association mapping.     

HLA gene and haplotype frequencies in Russians, Bashkirs and Tatars, living in the Chelyabinsk Region (Russian South Urals)

We have characterized the HLA‐A, ‐B, ‐DRB1, ‐DQA1 and ‐DQB1 profiles of three major ethnic groups living in Chelyabinsk Region of Russian South Urals, viz., Russians (n = 207), Bashkirs (n = 146) and Tatars (n = 135). First field level typing was performed by PCR using sequence‐specific primers. Estimates included carriage and gene frequencies, linkage disequilibrium and its significance and related values. Population comparisons were made between the allele family frequencies of the three populations and between these populations and 20 others using a dendrogram. Chelyabinsk Region Russians demonstrate all the features typical of a Caucasoid population, but also have some peculiarities. Together with Tatars, Russians have high frequencies of allele families and haplotypes characteristic of Finno‐Ugric populations. This presupposes a Finno‐Ugric impact on Russian and Tatar ethnogenesis. However, this was not apparent in Bashkirs, the first of the three populations to live in this territory, and implies admixture with populations of a Finno‐Ugric origin with precursors of Russians and Tatars before they came to the South Urals. The Bashkirs appear close to Mongoloids in allele and haplotype distribution. However, Bashkirs cannot be labelled either as typical Mongoloids or as Caucasoids. Thus, Bashkirs possess some alleles and haplotypes frequent in Mongoloids, which supports the Turkic impact on Bashkir ethnogenesis, but also possess the AH 8.1 haplotype, which could evidence an ancient Caucasoid population that took part in their ethnic formation or of recent admixture with adjacent populations (Russians and Tatars). Bashkirs showed no features of populations with a substantial Finno‐Ugric component, for example Chuvashes or Russian Saami. This disputes the commonly held belief of a Finno‐Ugric origin for Bashkirs. Tatars appeared close to many European populations. However, they possessed some characteristics of Asiatic populations possibly reflecting a Mongoloid influence on Tatar ethnogenesis. Some aspects of HLA in Tatars appeared close to Chuvashes and Bulgarians, thus supporting the view that Tatars may be descendents of ancient Bulgars.     

HLA molecular markers in Tuvinians: a population with both Oriental and Caucasoid characteristics

HLA class I and class II alleles have been studied for the first time in the Turkish-speaking Tuvinian population, which lives in Russia, North of Mongolia and close to the Altai mountains. Comparisons have been done with about 11000 chromosomes from other worldwide populations, and extended haplotypes, genetic distances, neighbor joining dendrograms and correspondence analyses have been calculated. Tuvinians show an admixture of Mongoloid and Caucasoid characters, the latter probably coming from the ancient Kyrgyz background or, less feasibly, more recent Russian Caucasoid admixture. However, Siberian population traits are not found and thus Tuvinians are closer to Central Asian populations. Siberians are more related to Na-Dene and Eskimo American Indians; Amerindians (from nowadays Iberian–America) are not related to any other group, including Pacific Islanders, Siberians or other American Indians. The 'more than one wave' model for the peopling of the Americas is supported.     

Population genetics of coagulation factor XIIIB in three ethnic groups of Singapore.

The distribution of plasma coagulation factor XXIIB polymorphism was determined by PAG isoelectric focusing and immunoblotting in a group of 670 subjects comprising 375 Chinese, 110 Malays and 185 Indians. The frequencies of FXIIIB*1, FXIIIB*2, and FXIIIB*3 were found to be 0.27, 0.03 and 0.70 in the Chinese; 0.33, 0.05 and 0.64 in the Malays and 0.58, 0.08 and 0.33 in the Indians. The phenotypic distribution of FXIIIB alleles was at Hardy-Weinberg equilibrium in all three populations. A two-dimensional principal-components analysis on the basis of three common alleles at the FXIIIB locus among 19 populations, so far studied, clearly differentiates the Negroid, Mongoloid and Caucasoid populations into three major groups with the exception of Amerindians (Minnesota) and US Blacks showing some Caucasoid influence.     

Presence of three different paternal lineages among North Indians: A study of 560 Y chromosomes

Background: The genetic structure, affinities, and diversity of the 1 billion Indians hold important keys to numerous unanswered questions regarding the evolution of human populations and the forces shaping contemporary patterns of genetic variation. Although there have been several recent studies of South Indian caste groups, North Indian caste groups, and South Indian Muslims using Y-chromosomal markers, overall, the Indian population has still not been well studied compared to other geographical populations. In particular, no genetic study has been conducted on Shias and Sunnis from North India.

Aim: This study aims to investigate genetic variation and the gene pool in North Indians.

Subjects and methods: A total of 32 Y-chromosomal markers in 560 North Indian males collected from three higher caste groups (Brahmins, Chaturvedis and Bhargavas) and two Muslims groups (Shia and Sunni) were genotyped.

Results: Three distinct lineages were revealed based upon 13 haplogroups. The first was a Central Asian lineage harbouring haplogroups R1 and R2. The second lineage was of Middle-Eastern origin represented by haplogroups J2*, Shia-specific E1b1b1, and to some extent G* and L*. The third was the indigenous Indian Y-lineage represented by haplogroups H1*, F*, C* and O*. Haplogroup E1b1b1 was observed in Shias only.

Conclusion: The results revealed that a substantial part of today's North Indian paternal gene pool was contributed by Central Asian lineages who are Indo-European speakers, suggesting that extant Indian caste groups are primarily the descendants of Indo-European migrants. The presence of haplogroup E in Shias, first reported in this study, suggests a genetic distinction between the two Indo Muslim sects. The findings of the present study provide insights into prehistoric and early historic patterns of migration into India and the evolution of Indian populations in recent history.     

Immunoglobulin allotypes in Southwest Asia: Populations at the Crossroads

Southwest Asia has a long history of contact with Central Asian and with Sub‐Saharan African populations. Is the genetic structure of these populations reflective of these historical facts? To study this, data was generated on the immunoglobulin heavy chain (GM) and light chain (KM) allotypes from seven Arab and three non‐Arab populations in SW Asia to examine the relationship of these populations to SE European, NW Indian, Sub‐Saharan African, and Central Asian populations. Like mtDNA and Y chromosome markers, the GM haplotypes are largely continent specific making them an excellent tool for the detection of gene flow whereas the KM markers are less informative. Six of the nine GM haplotypes detected in SW Asians are Indo‐European, Sub‐Saharan African, or East Asian specific. The allotype results indicate variable but significantly higher Sub‐Saharan African gene flow in Arab populations (average 26.9%; 15.0–61.6%) vs. the non‐Arab populations (average 7.3%; 9.0–13.4%), but higher levels of Central Asian gene flow in the non‐Arab populations (average 28.8%; 10.5–48.8%) vs. the Arab populations (average 9.0%; 0.0–26.4%). Principal components analysis and hierarchical cluster analysis based on the immunoglobulin allotypes are consistent with the historical population contacts of this part of the world and reflect the power of the GM haplotypes in dissecting population relationships. However, the KM*1 frequencies were only correlated with the degree of African gene flow (Pearson r = 0.69, P = 0.026) in SW Asian populations. Am. J. Hum. Biol., 2008. © 2008 Wiley‐Liss, Inc.     

Diversity of Killer Cell Immunoglobulin‐Like Receptor Genes in the Bengali Population of Northern West Bengal,India

The Indian Subcontinent exhibits extensive diversity in its culture, religion, ethnicity and linguistic heritage, which symbolizes extensive genetic variations within the populations. The highly polymorphic Killer cell Immunoglobulin‐like Receptor (KIR) family plays an important role in tracing genetic differentiation in human population. In this study, we aimed to analyse the KIR gene polymorphism in the Bengali population of northern West Bengal, India. To our knowledge, this is the first report on the KIR gene polymorphism in the Bengalis of West Bengal, India. Herein, we have studied the distribution of 14 KIR genes (KIR3DL1‐3DL3, KIR2DL1‐2DL5, KIR2DS1‐2DS5 AND KIR3DS1) and two pseudogenes (KIR3DP1 and 2DP1) in the Bengalis. Apart from the framework genes (KIR2DL4, 3DL2, 3DL3 and 3DP1), which are present in all the individuals, the gene frequencies of other KIR genes varied between 0.34 and 0.88. Moreover, upon comparing the KIR polymorphism of the Bengalis with the available published data of other world populations, it has been found that the Indo‐European‐speaking Bengalis from the region share both Dravidian and Indo‐Aryan gene pool with considerable influences of mongoloid and European descents. Furthermore, evidences from previously published data on human leucocyte antigen and Y‐chromosome haplogroup diversity support the view. Our results will help to understand the genetic background of the Bengali population, in illustrating the population migration events in the eastern and north‐eastern part of India, in explaining the extensive genetic admixture amongst the different linguistic groups of the region and also in KIR‐related disease researches.     

Genetic profile based upon 15 microsatellites of four caste groups of the eastern Indian state,Bihar

BACKGROUND: The formation of caste groups among the Hindu community and the practice of endogamy exert a great impact on the genetic structure and diversity of the Indian population. Allele frequency data of 15 microsatellite loci clearly portray the genetic diversity and relatedness among four socio-culturally advanced caste groups: Brahmin, Bhumihar, Rajput and Kayasth of Caucasoid ethnicity of Bihar. AIM: The study seeks to understand the impact of the man-made caste system on the genetic profile of the four major caste groups of Bihar. METHODS AND PROCEDURE: Computation of average heterozygosity, most frequent allele, allele diversity and coefficient of gene differentiation (Gst), along with genetic distance (DA)and principal coordinate analysis were performed to assess intra-population and inter-population diversity. MAIN OUTCOMES AND RESULTS: The average Gst value for all the loci was 0.012 +/- 0.0033, and the level of average heterozygosity was approximately 75.5%, indicating genetic similarity and intra-population diversity. Genetic distance (DA) values and the phylogenetic tree along with other higher caste groups of India indicate the relative distance between them. CONCLUSION: The present study clearly depicts the genetic profile of these caste groups, their inherent closeness in the past, and the impact of the imposed caste system that later restricted the gene flow. The study highlights the status of Bhumihar and Kayasth in the Hindu caste system. The former was found clustering with the Brahmin group (as expected, since Bhumihar is known to be a subclass of Brahmin), whereas the distance between the Brahmin and Kayasth caste groups was found to be large. North-eastern Indian Mongoloids form a separate cluster.