Population structure and genetic differentiation among the substructured Vysya caste population in comparison to the other populations of Andhra Pradesh,India

OBJECTIVES: The present paper focuses on the study of the patterns of genetic microdifferentiation among one of the substructured caste populations of Andhra Pradesh, namely Vysya, with reference to 17 other Telugu speaking populations from the same region of India. SUBJECTS AND METHODS: A total of 302 individuals from the three Vysya subgroups (101 of Arya Vysya, 100 from Kalinga Vysya and 101 from Thrivarnika) were typed in 17 blood groups and protein polymorphisms. Nei's gene diversity analysis, as well as neighbour-joining tree and UPGMA cluster diagrams, derived from standard genetic distances, R-matrix analysis and a regression model for investigating the patterns of external gene flow and genetic drift due to isolation under the island model, were done at two levels: (1) considering only the three Vysya populations and (2) considering common loci among 20 populations of Andhra Pradesh. RESULTS: Seven of the 17 systems investigated were found to be monomorphic among all the three Vysya groups. The UPGMA tree and bidimensional scaling of the D(2) distances derived from R-matrix analysis show a very distinct cluster of Vysya populations. Application of the model of regression of average heterozygosity versus the distance of populations from the centroid shows the three Vysya populations placed as clear outliers above the theoretical regression line. CONCLUSIONS: Different approaches employed in this study give support to the hypothesis of different origin and/or demographic story for the three Vysya groups compared with other populations of Andhra Pradesh.     

Genetic affinities between the migrant and parental populations of fishermen,East coast,India

Genetic affinities between the migrant groups of fishermen from Puri and their parental counterparts in the Southern areas were examined using 11 genetic loci: four blood groups, five red cell enzymes, and two serum proteins. The samples for the parental populations (about 430 subjects) were drawn from 34 villages spread along the 400 km coast in Ganjam district of Orissa and the contiguous Srikakulam, Vishakhapatnam, and East Godavari districts of Andhra Pradesh. Significant departures between the migrant groups and their parental counterparts were observed at some loci, although the configuration of interpopulation distances among the migrants mimicked that of the parental populations. While the observed differences may be due to a founder effect and subsequent random genetic drift in at least two of the three small populations, given high child mortality and the systematic nature of differences observed, the role of selection cannot be totally ruled out. © 1995 Wiley-Liss, Inc.     

Genetic affinity of two south Indian ethnic groups with other populations

Humans appear to have spread to several parts of the Indian subcontinent by the middle Paleolithic period. It also provided a major passage for the distribution of modern humans. For the first time generic human leucocyte antigen (HLA) class II (DRB1) genotyping was performed using polymerase chain reaction-sequence-specific primer (PCR-SSP) (low-resolution) technique in two endogamous groups (Hindu-Brahmins and Sunni-Muslims) from the southern state of Andhra Pradesh in order to decipher the genetic affinity between them and with other populations. Calculation of genetic distances, construction of neighbour-joining dendograms and principal-component (P-C) maps were executed using HLA allelic frequencies. The present study reveals the genetic affinity of the Brahmin and Muslim populations from the state of Andhra Pradesh. The dendograms demonstrated that Indian populations form a separate cluster with oriental populations on one side and the eastern and the western Mediterranean populations on the other side. The principal component maps showed the clustering of Indian populations in the lower-right quadrant, where in the Sunni-Muslims occupied a position more closely to the north Indian Brahmins and the Bhargavas than to the geographically related south Hindu-Brahmin group. The study hypothesizes that unlike Brahmins who can be considered as an immediate stock of the Caucasians, the ancestors of Muslims might have been the result of an admixture between the Indo-Europeans and proto-Dravidians.     

Genetic variation at three VNTR loci (D1S80, APOB, and D17S5) in two tribal populations of Andhra Pradesh, India

This study reports the genetic variation at three variable number of tandem repeat (VNTR) loci (APOB, D17S5 and D1S80) in two tribes (Thoti and Kolam) of Andhra Pradesh, India. Kolams constitute 1% of the total scheduled tribal population of Andhra Pradesh, while Thoti is a numerically small tribe. All three genetic loci were genotyped using the polymerase chain reaction (PCR) technique and were polymorphic in both populations. At the D1S80 locus, both populations showed higher frequencies of allele *31 (9-14%) than other Indian populations. In the APOB system, Thoti showed a very high frequency of allele *37 (54%) and for D17S5 system allele *4 was the most common in Thoti (32%) and allele *2 in Kolam (28%). Both tribes differed statistically significantly from other tribal populations of the region. The level of gene differentiation was low (GST = 0.038) for Indian tribal populations. The allele frequency distribution, heterozygosity and genetic diversity analysis shows that the observed genetic variation is socially and geographically structured.     

Quantitative dermatoglyphics and population structure in Northwest India

The nature and extent of dermatoglyphic variation in northwest India is examined with the help of 28 quantitative variables—20 finger ridge counts and 8 palmar pattern ridge counts—among 12 endogamous populations. These populations represent the entire spectrum of ethnic and socioeconomic variation of the region and are presently distributed in three different states—Rajasthan, Punjab, and Himachal Pradesh. Of a total sample of 1,160 adult males, about 100 from each group were considered. Multiple discriminant analysis and R-matrix analysis were used to derive population relationships and patterns of external gene flow, respectively. Published data on genetic markers were reanalyzed to make the comparative evaluation of the patterns with reference to dermatoglyphs. Both the discriminant analysis and the F_ST from R-matrix analysis suggest highly significant discrimination among the northwestern groups, whether one uses only 20 finger ridge count variables or all 28 variables, including the 8 palmar pattern ridge counts. The 8 palmar variables add very little to the variation explained by the 20 finger ridge count variables. F_ST values suggest that the populations of Punjab are most homogeneous and those of Himachal Pradesh most heterogeneous. However, the levels of differentiation are similar for dermatoglyphs and genetic markers. The pattern of external gene flow as inferred through R-matrix analysis is consistent with the breeding and population structure of the groups, although genetic markers portray a relatively more realistic picture. Overall, the patterns of variation observed in dermatoglyphs and genetic markers are consistent with different dimensions of population structure; whereas dermatoglyphs conform more to the geographic pattern and less to ethnic resemblance, the reverse is true in the case of genetic markers. Am. J. Hum. Biol. 12:315–326, 2000. © 2000 Wiley-Liss, Inc.     

Dermatoglyphic affinities among the Telugu populations with contrasting ethnohistorical backgrounds

Using 22 finger dermatoglyphic variables (radial and ulnar ridge counts on each of the 10 fingers, total number of whorls and total number of loops per individual), affinities among the five endogamous populations of Andhra Pradesh with contrasting ethnohistorical backgrounds were examined. The samples constitute rolled fingerprints of 1,334 individuals of all ages, 736 males and 598 females, and were drawn from the three southern districts of Andhra Pradesh. Univariate analysis of variance, cluster analysis of Mahalanobis' D²-values, and stepwise discriminant analysis were employed to study the extent of population heterogeneity and nature of relationships among them. The observed dermatoglyphic affinities conform to the known ethnohistorical and geographical backgrounds. The smallest set of 9 most discriminating variables gives the best configuration expected under ethnohistorical backgrounds. Addition of more variables, although further augmenting the dispersion among the group centroids, distrots the picture of known ethnohistorical relatiohships. © 1992 Wiley-Liss, Inc.     

Proceedings of the Society for the Study of Human Biology

This study reports the genetic variation at three variable number of tandem repeat (VNTR) loci (APOB, D17S5 and D1S80) in two tribes (Thoti and Kolam) of Andhra Pradesh, India. Kolams constitute 1% of the total scheduled tribal population of Andhra Pradesh, while Thoti is a numerically small tribe. All three genetic loci were genotyped using the polymerase chain reaction (PCR) technique and were polymorphic in both populations. At the D1S80 locus, both populations showed higher frequencies of allele *31 (9–14%) than other Indian populations. In the APOB system, Thoti showed a very high frequency of allele *37 (54%) and for D17S5 system allele *4 was the most common in Thoti (32%) and allele *2 in Kolam (28%). Both tribes differed statistically significantly from other tribal populations of the region. The level of gene differentiation was low (G_ST = 0.038) for Indian tribal populations. The allele frequency distribution, heterozygosity and genetic diversity analysis shows that the observed genetic variation is socially and geographically structured.     

Inbreeding effects on reproductive outcome among seven tribes of Andhra Pradesh,India

The effects of inbreeding on reproductive outcome in terms of fertility and mortality were analyzed in seven tribal populations from Andhra Pradesh, India. The effect on mortality at both prenatal and prereproductive postnatal stages was further verified after estimating genetic load by an exponential regression model. Relatively higher fertility and mortality rates were recorded among consanguineous marriages than nonconsanguineous unions in the majority of tribes. The regression analysis indicated a positive, nonsignificant association between inbreeding and mortality in five tribes. Low B/A ratios were found in five tribes. © 1995 Wiley-Liss, Inc.     

应用D7S820基因座研究中国8个地区汉族人群的亲缘关系

收集D7S820基因座的8个不同地区汉族的相关遗传资料。应用亲缘系数(I)和遗传距离(D)研究八个汉族群体间的遗传关系，并根据遗传距离绘制遗传树。结果显示，成都、贵州和浙江汉族为一群，西安、太原、河北和长白山汉族为一群，而北京汉族为独立的一群。     

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.     

Detection of genetic variation in Indian population groups using a novel minisatellite probe and finding relationships through tree construction

Genetic variation in HaeIII-digested genomic DNA samples from different individuals belonging to population groups from Bengal, Uttar Pradesh (UP), Punjab, and South India was assessed at hypervariable loci, using a minisatellite probe, pBA1.2 (accession number, AF 157691), the repeat unit of which was 24 mer long and rich in G-bases. Comparison of DNA profiles between individuals showed a very low probability of band sharing, which ranged from 0.18 to 0.24. A dendrogram, based on Nei's genetic distance, constructed by the neighbor-joining method, showed the formation of separate clusters by both South Indian and non-Indian samples, whereas the construction of a dendrogram based on the Unweighted pair group method arithmetic average (UPGMA) method with Jaccard's similarity coefficient at the individual level led to the formation of several small clusters which were interleaved; also, the subgroups for each of the populations were intermingled with the subgroups for the other populations. A separate analysis was carried out to check the consistency of the proximity between different individuals forming a cluster and between those individuals who were in the vicinity of two clusters. The dendrograms thus obtained did not change the relationship between the individuals from all the populations studied. Despite the distinct clustering observed in the population group comparison, a probable admixture was reflected in the finding that some individuals belonging to one population group were dispersed or embedded within a cluster generated by the individuals of another population group, when a minute dissection of the data for generating a tree at the individual level was carried out. Received: December 27, 1999 / Accepted: March 13, 2000     

Antiquity, geographic contiguity and genetic affinity among Tibeto-Burman populations of India: a microsatellite study

BACKGROUND: The Tibeto-Burman (TB) populations are one of the four major linguistic population groups of India. They are considered belonging to different stocks and show wide variation in culture and language; however, their genetic relationship, antiquity and migration history among the regional populations has been little investigated. Molecular genetic studies are expected to clearly show the antiquity and genetic diversity of these populations. AIM: This paper seeks to understand the extent and magnitude of genetic affinities and diversities among 14 TB populations (12 Indian and two global groups), investigate the findings based on classical genetic markers and verify the historical accounts of their migration and genetic history based on 12 microsatellite markers. SUBJECTS AND METHODS: The allele frequency data for 12 STR loci of 13 Asian (Tibeto-Burman) populations were obtained from the literature and the Adi Pasi data was obtained by microsatellite typing of their blood samples. The 12 loci studied are D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, vWa, TPOX, D18S51. Three different distance measures, two phylogenetic trees and PCA plot have been employed to understand the genetic relationship of the studied populations. RESULTS: Average heterozygosity values range from 68 to 79% and the average G(ST) value is 4.7%. The dendrogram, based on the D(A) distance, shows the clustering of populations based on their diversities and geographical contiguity; the Mizoram and Arunachal Pradesh populations especially cluster together, populations from Sikkim form a separate subcluster and Manipur populations along with the Garo of West Bengal separate out from the other clusters. The Harpending and Ward regression model shows isolated populations positioned below the regression line and others, who experience external gene flow, placed above the line. The results support folklore migration accounts of their possible antiquity with the Tibetan and southern Chinese populations. CONCLUSIONS: Overall, geographic contiguity, punctuated by isolating barriers, is a major influencing factor of genetic affinity among the TB population; contiguous populations within a region show greater genetic relationship than with distant TB populations over a wide geographical area. The results of the microsatellite study also support the history of diverse routes of migration of these populations.     

Size and shape components of anthropometric differences among the Yanadis

Size and shape components of Mahalanobis D2 were computed from a set of anthropometric characters among the Yanadis, a tribe in the south eastern part of Andhra Pradesh, India. These people are in a transitional stage of development and show differences in sociocultural variables between different geographical regions. From the study it appears that the pattern of differences due to size and shape is the same as that of general distance, irrespective of whether the distances were computed for male, female or pooled data, with some exceptions for females. The noteworthy finding is that the shape components for men and women dominate and are more similar than corresponding size components, thereby indicating that males and females are morphologically similar with respect to their relative measurements. The association of the morphological distances for the five breeding populations with the corresponding road, map and migrational distances were also investigated using simple and partial correlations. The results suggest that the migrational distance among the three is the strongest influencing factor for the morphological differences. The road distance also maintains a very high degree of association, especially with shape components.     

Blood pressure levels among cross-cultural populations of Visakhapatnam district,Andhra Pradesh,India

BACKGROUND: Elevated blood pressure is a leading cause of morbidity and mortality throughout the world, as a major contributor to cardiovascular diseases. Blood pressure tends to vary cross-culturally and studies to address the influence of acculturization/modernization on blood pressure are limited from India, particularly from Andhra Pradesh. AIM: To provide information on blood pressure levels and variability across population groups from the State of Andhra Pradesh, India, and to examine the influence of acculturization/modernization on blood pressure levels. SUBJECTS AND METHODS: The blood pressure levels among 1316 individuals (646 men and 670 women) belonging to two tribal (Khondh and Valmiki) and two caste groups (Wadabalija and Settibalija) from rural and urban areas from Andhra Pradesh were collected. Analysis of covariance (ANCOVA) was used to examine the effect of age and sex, and population differences. RESULTS: The distribution of blood pressure showed significant variability among these population groups. Higher levels of blood pressure were noticed in an acculturizing tribe, the Valmiki, than among the Khondh, a traditional tribal population. The results indicate that age had significant effect on both systolic and diastolic blood pressure levels. Also, the systolic blood pressure was relatively more sensitive than diastolic blood pressure to the effect of age. The sex did not contribute significantly to the variability of blood pressure. CONCLUSIONS: The study revealed significant population differences in the variability of blood pressure, with higher levels among acculturizing tribal population than the non-acculturizing group. But no significant variation was noticed between rural and urban slum dwellers. Age had a significant effect on blood pressure levels.     

Blood pressure levels among cross-cultural populations of Visakhapatnam district,Andhra Pradesh,India

Background : Elevated blood pressure is a leading cause of morbidity and mortality throughout the world, as a major contributor to cardiovascular diseases. Blood pressure tends to vary cross-culturally and studies to address the influence of acculturization/modernization on blood pressure are limited from India, particularly from Andhra Pradesh. Aim : To provide information on blood pressure levels and variability across population groups from the State of Andhra Pradesh, India, and to examine the influence of acculturization/modernization on blood pressure levels. Subjects and methods : The blood pressure levels among 1316 individuals (646 men and 670 women) belonging to two tribal (Khondh and Valmiki) and two caste groups (Wadabalija and Settibalija) from rural and urban areas from Andhra Pradesh were collected. Analysis of covariance (ANCOVA) was used to examine the effect of age and sex, and population differences. Results : The distribution of blood pressure showed significant variability among these population groups. Higher levels of blood pressure were noticed in an acculturizing tribe, the Valmiki, than among the Khondh, a traditional tribal population. The results indicate that age had significant effect on both systolic and diastolic blood pressure levels. Also, the systolic blood pressure was relatively more sensitive than diastolic blood pressure to the effect of age. The sex did not contribute significantly to the variability of blood pressure. Conclusions : The study revealed significant population differences in the variability of blood pressure, with higher levels among acculturizing tribal population than the non-acculturizing group. But no significant variation was noticed between rural and urban slum dwellers. Age had a significant effect on blood pressure levels.     

人类短串联重复序列VWA基因座的群体遗传学研究

为了解不同群体中ＶＷＡ基因座等位基因和基因频率分布，作者应用自动激光荧光ＤＮＡ序列分析仪分析并构建了人类短串联重复序列ＶＷＡ等位基因分型标准物，用扩增片段长度多态技术分析了ＶＷＡ基因型及等位基因频率在中国和德国群体中的分布。计算了１７个群体间ＶＷＡ的遗传距离，并构建了系统树。结果表明ＶＷＡ系统树分析能够正确反映人种及种族间的遗传差异，为人类起源研究提供了新的参考资料。     

Genetic structure of Algerian populations.

Blood samples were collected in Algeria from 4,444 army recruits and tested for 10 genetic polymorphic systems. These samples were collected from territorial Wilayas (administrative units of Algeria) from which the young soldiers had originated. Based on similar geography and economic and political history, these Wilayas were clustered into 10 regions. These regions, not part of the governmental administrative units, were characterized by allelic frequencies, and analyzed using R-matrix principal components, Wright's F(ST), spatial autocorrelation, and Mantel tests. Hierarchical relationships between the culturally defined regions were examined using two different analytical methods of phylogenetic tree constructions: neighbor-joining, and unweighted pair group average arithmetic (UPGMA). These results indicated the predominance of genetic homogeneity due to the gene flow between regions, but with some migration emanating from sub-Saharan Africa and Mediterranean Europe. Wright's F(ST) value of 0.0063, based on 16 alleles, suggested a relatively small genetic microdifferentiation of the regions. In Algeria, gene flow apparently swamped most of the effects of stochastic processes and disrupted the relationship between geography and genetics, as characterized by the isolation-by-distance model. Some genetic differences and similarities were observed between regions or clusters of regions. The resulting genetic structure of the Algerian populations is best explained by a combination of gene flow, ecology, and history.     

Genetic differentiation of invasive Aedes albopictus by RAPD-PCR: implications for effective vector control

Aedes albopictus is an invasive mosquito species of great concern to public health as it is responsible for the biological transmission of several pathogens causing dengue, chikungunya, yellow fever, etc. In 2009, this mosquito was detected for the first time in Agra City. This study represents the first genetic analysis of A. albopictus from India. Random amplified polymorphic DNA (RAPD) was used to study the genetic structure of A. albopictus in four populations from different larval habitats. Seven RAPD primers produced 141 loci. The results displayed rich genetic variation among larval populations which is evident from high value of genetic differentiation (G _ST), i.e. 0.280, indicating a very great genetic differentiation. Effective migration rates were observed to be 1.28, depicting a limited gene flow. According to analysis of molecular variance (AMOVA), the genetic distance between populations was significant (P?<?0.05), showing a very high intrapopulation variation (96 %) with only 4 % variation among populations. Average genetic distances between populations were also calculated using PopGene software. Nei’s average genetic distance between these populations was 0.112 (0.05–0.18). The cluster analysis technique of unweighted pair-group mean analysis (UPGMA) method of arithmetic averages was used to develop the phylogenetic tree which clearly shows two clusters of different larval habitats. The findings highlight high genetic differentiation indicating a slight migration rate confirming the recent introduction of this species in Agra region.     

The distribution of HLA class II haplotypes reveals that the Sardinian population is genetically differentiated from the other Caucasian populations

In this study we have established the frequencies of the DRB1-DQA1-DQB1 haplotypes in a large cohort of Sardinian new-borns and found that the most frequent haplotypes were detected at frequencies unique to the Sardinians. Other haplotypes, common in other Caucasian populations, are rare or absent across the island. Next, the DRB1-DQA1-DQB1 haplotype frequencies obtained in Sardinians and those reported in other human populations were used to compute genetic distances and construct phylogenetic trees. A clear-cut pattern appeared with a split between the three major human groups: Caucasians, Asians and Blacks. Among the Caucasians there were three major clusters: a group representing the North-Africans, a group including most of the European-derived populations and a group encompassing Bulgaria, Greece and Sardinia. When we increased the resolution of the tree using the genetic distances calculated from both DRB1-DQA1-DQB1 haplotypes and class I HLA A, B, C allelic frequencies, the Sardinians clearly emerged as the major outlier among the various European populations considered in this study. These results indicate that the genetic structure of the present Sardinian population is the result of a fixation of haplotypes, which are very rare elsewhere, and are most likely to have originated from a relatively large group of founders.     

HLA class I and II polymorphisms in the Gujjar population from Pakistan

HLA polymorphisms at the HLA -A, -B, -C, -DRB and -DQB1 loci were investigated in the Gujjar population from the Punjab province of Pakistan. The Gujjars (n?=?97) were genotyped using sequence specific primers for polymerase chain reaction. The allele and haplotype frequencies were calculated and a neighbor-joining (NJ) tree comparing the Gujjar with other populations was constructed. The class I allelic groups with a frequency greater than 10% include A*01, A*02, A*11, A*26 and A*31 at the HLA-A locus, B*08 and B*51 at the HLA-B locus and C*07 and C*14 at the HLA-C locus. Among the 12 allelic groups detected at the DRB1* locus, *03, *13, and *15 were present at frequencies higher than 10% whereas at the DQB1 locus, the allelic groups*06 and *02 accounted for over half of the Gujjar population. HLA-A*31-B*51-DRB1*13 was the most common (8.8%) haplotype in this population. A NJ tree revealed that the Pakistani Gujjar are closely related to the Golla tribe from Andhra Pradesh in India. The two populations are dedicated to the same profession, cattle breeding. HLA analyses of additional Punjab castes would provide valuable information for anthropological, organ transplantation and genetic disease studies.