scholarly journals Integrating linguistics, social structure, and geography to model genetic diversity within India

2017 ◽  
Author(s):  
Aritra Bose ◽  
Daniel E. Platt ◽  
Laxmi Parida ◽  
Petros Drineas ◽  
Peristera Paschou
Keyword(s):  
Genetic Diversity ◽  
Social Structure ◽  
Genetic Drift ◽  
Social Stratification ◽  
Indian Subcontinent ◽  
Caste System ◽  
Population Substructure ◽  
Data Set ◽  
Genetic Substructure ◽  
Shared Genetic

AbstractIndia represents an intricate tapestry of population substructure shaped by geography, language, culture and social stratification. While geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics and demographic factors, we developed COGG (Correlation Optimization of Genetics and Geodemographics) to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure highlighted by COGG. Integrating data from India with a data set of additional 1,323 individuals from 50 populations we find that Europeans show shared genetic drift with the Indo-European and Dravidian speakers of India, whereas the East Asians have the maximum shared genetic drift with Tibeto-Burman speaking tribal groups.

scholarly journals Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India

2021 ◽  
Author(s):  
Aritra Bose ◽  
Daniel E Platt ◽  
Laxmi Parida ◽  
Petros Drineas ◽  
Peristera Paschou
Keyword(s):  
Genetic Diversity ◽  
Social Structure ◽  
Genetic Drift ◽  
Social Stratification ◽  
Indian Subcontinent ◽  
Caste System ◽  
Population Substructure ◽  
Shared Language ◽  
Genetic Substructure ◽  
Shared Genetic

Abstract India represents an intricate tapestry of population substructure shaped by geography, language, culture and social stratification. While geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a dataset of 891 individuals from 90 well-defined groups. Bringing together geography, genetics and demographic factors, we developed COGG (Correlation Optimization of Genetics and Geodemographics) to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a dataset of additional 1,323 individuals from 50 Eurasian populations we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.

scholarly journals EVALUATION OF GENETIC DIVERSITY IN SELECTED BEEF BREEDS

AGROFOR ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Kristína LEHOCKÁ ◽  
Radovan KASARDA ◽  
Barbora OLŠANSKÁ ◽  
Nina MORAVČÍKOVÁ
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Beef Cattle ◽  
Genetic Drift ◽  
High Linkage Disequilibrium ◽  
Snp Markers ◽  
Data Set ◽  
Population Structure Analysis ◽  
Red Angus

The aim of the study was to estimate genetic drift and gene flow related to population structure and genetic diversity in selected beef cattle. For the evaluation of the genetic drift and gene flow among analysed populations, the Bayesian Population Structure Analysis and software Treemix were used. The genetic analysis included two cattle breeds bred in Slovakia (Charolais and Limousine). In addition to the Limousine and Charolais breeds, other beef cattle (Angus N = 90, Belgian Blue N = 4, Blonde d'Aquitaine N= 5, Hereford N = 98 and Red Angus N = 15) were analysed. The 50k Bead chip was used; the dataset consisted of 34,834 SNPs. To avoid detection bias, SNPs with high linkage disequilibrium (r2 = 0.05) were pruned from the database; the final data set consisted of 296 animals and 2,539 SNP markers. Our results reflected four modes of gene flow between Angus, Red Angus, Charolais, Limousine and Hereford. Analysed breeds were not confirmed to influence genetic make-up of Belgian Blue and Blonde d'Aquitaine populations. All migration edges reached weight values below 0.2. The only two migration edges higher in weight was observed, first between the ancestor of Limousine breed into Blond d'Aquitaine, and second among historical ancestor of Hereford breed into Red Angus. Our results reflect that the donor population has made a significant contribution to the recipient population.

scholarly journals Trees, Population Structure, F-statistics!

2015 ◽  
Author(s):  
Benjamin M Peter
Keyword(s):  
Population Structure ◽  
Genetic Drift ◽  
Phylogenetic Trees ◽  
Population Substructure ◽  
Methodological Framework ◽  
Genetic Theory ◽  
Genetic History ◽  
Branch Lengths ◽  
Shared Genetic ◽  
F Statistics

Many questions about human genetic history can be addressed by examining the patterns of shared genetic variation between sets of populations. A useful methodological framework for this purpose are F-statistics, that measure shared genetic drift between sets of two, three and four populations, and can be used to test simple and complex hypotheses about admixture between populations. Here, we put these statistics in context of phylogenetic and population genetic theory. We show how measures of genetic drift can be interpreted as branch lengths, paths through an admixture graph or in terms of the internal branches in coalescent trees. We show that the admixture tests can be interpreted as testing general properties of phylogenies, allowing us to generalize applications for arbitrary phylogenetic trees. Furthermore, we derive novel expressions for the F-statistics, which enables us to explore the behavior of F-statistic under population structure models. In particular, we show that population substructure may complicate inference.

scholarly journals Population Substructure Has Implications in Validating Next-Generation Cancer Genomics Studies with TCGA

2019 ◽  
Vol 20 (5) ◽  
pp. 1192 ◽  
Author(s):  
Marina Miller ◽  
Eric Devor ◽  
Erin Salinas ◽  
Andreea Newtson ◽  
Michael Goodheart ◽  
...  
Keyword(s):  
Cancer Genomics ◽  
The Cancer Genome Atlas ◽  
Population Substructure ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
University Of Iowa ◽  
Data Set ◽  
Using Data ◽  
Genetic Substructure

In the era of large genetic and genomic datasets, it has become crucially important to validate results of individual studies using data from publicly available sources, such as The Cancer Genome Atlas (TCGA). However, how generalizable are results from either an independent or a large public dataset to the remainder of the population? The study presented here aims to answer that question. Utilizing next generation sequencing data from endometrial and ovarian cancer patients from both the University of Iowa and TCGA, genomic admixture of each population was analyzed using STRUCTURE and ADMIXTURE software. In our independent data set, one subpopulation was identified, whereas in TCGA 4–6 subpopulations were identified. Data presented here demonstrate how different the genetic substructures of the TCGA and University of Iowa populations are. Validation of genomic studies between two different population samples must be aware of, account for and be corrected for background genetic substructure.

THE CONTRIBUTION OF THE AMARNA LETTERS TOWARDS A STUDY OF SYRO-PALESTINIAN SOCIAL STRUCTURE (1). TERMINOLOGY FOR GOVERNMENT OFFICIALS

2017 ◽  
Vol 25 (2) ◽  
pp. 788-832
Author(s):  
Lukas M. Muntingh
Keyword(s):  
Social Structure ◽  
Bronze Age ◽  
Social Stratification ◽  
Social Life ◽  
Upper Class ◽  
Government Officials ◽  
The Social ◽  
Amarna Letters ◽  
Free People ◽  
Shed Light

Egyptian domination under the 18th and 19th Dynasties deeply influenced political and social life in Syria and Palestine. The correspondence between Egypt and her vassals in Syria and Palestine in the Amarna age, first half of the fourteenth century B.C., preserved for us in the Amarna letters, written in cuneiform on clay tablets discovered in 1887, offer several terms that can shed light on the social structure during the Late Bronze Age. In the social stratification of Syria and Palestine under Egyptian rule according to the Amarna letters, three classes are discernible:1) government officials and military personnel, 2) free people, and 3) half-free people and slaves. In this study, I shall limit myself to the first, the upper class. This article deals with terminology for government officials.

Caste and Untouchability in Jawaharlal Nehru’s Literary Masterpieces

2021 ◽  
pp. 2455328X2110093
Author(s):  
Tahira Tashneem
Keyword(s):  
Social Structure ◽  
Caste System ◽  
Indian Culture ◽  
Complete Eradication ◽  
Political Discourses ◽  
The World

As one of the major pillars of Indian social structure, the caste system distinguishes Indian culture from all other cultures of the world. Though the Constitution of India assures equality of status and opportunity for all citizens and various academic and political discourses also appealed for the complete eradication of the caste system, it has not been eradicated even after five decades of democracy. In this context, it becomes really interesting to re-examine the views on caste as reflected in Jawaharlal Nehru’s prose writings. Nehru’s major prose works unquestionably delineate his concern for caste. Focusing mainly on An Autobiography and the Discovery of India, this article seeks to examine the different representations of caste in his prose works and will also try to locate the gaps and the shifts underlying his views on caste.

scholarly journals Heterozygous Trees Rebound the Fastest after Felling by Beavers to Positively Affect Arthropod Community Diversity

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 694
Author(s):  
Faith M. Walker ◽  
Rachel Durben ◽  
Stephen M. Shuster ◽  
Richard L. Lindroth ◽  
Thomas G. Whitham
Keyword(s):  
Genetic Diversity ◽  
Genetic Relatedness ◽  
Castor Canadensis ◽  
High Stress ◽  
Underlying Mechanism ◽  
Community Level ◽  
Community Diversity ◽  
Population Substructure ◽  
Individual Plant ◽  
Arthropod Community

Although genetic diversity within stands of trees is known to have community-level consequences, whether such effects are present at an even finer genetic scale is unknown. We examined the hypothesis that genetic variability (heterozygosity) within an individual plant would affect its dependent community, which adds a new dimension to the importance of genetic diversity. Our study contrasted foliar arthropod community diversity and microsatellite marker-derived measures of genetic diversity of cottonwood (Populus fremontii) trees that had been felled by beavers (Castor canadensis) and were resprouting, relative to adjacent standing, unfelled trees. Three patterns emerged: 1. Productivity (specific leaf area), phytochemical defenses (salicortin), and arthropod community richness, abundance, and diversity were positively correlated with the heterozygosity of individual felled trees, but not with that of unfelled trees; 2. These relationships were not explained by population substructure, genetic relatedness of the trees, or hybridization; 3. The underlying mechanism appears to be that beaver herbivory stimulates increased productivity (i.e., 2× increase from the most homozygous to the most heterozygous tree) that is the greatest in more heterozygous trees. Salicortin defenses in twigs were also expressed at higher concentrations in more heterozygous trees (i.e., 3× increase from the most homozygous to the most heterozygous tree), which suggests that this compound may dissuade further herbivory by beavers, as has been found for other mammalian herbivores. We suggest that high stress to trees as a consequence of felling reveals a heterozygosity–productivity linkage, which in turn is attractive to arthropods. Although experiments are required to demonstrate causality, these results link the genetic diversity of individual trees to community diversity, supporting the hypothesis that interactions among foundation species (beavers and trees) have community-level effects, and underscores the importance of genetic diversity for biodiversity, conservation, and restoration.

scholarly journals Effect of social structure and introduction history on genetic diversity and differentiation

2021 ◽  
Author(s):  
Sylvia M. Flucher ◽  
Patrick Krapf ◽  
Wolfgang Arthofer ◽  
Andrew V. Suarez ◽  
Ross H. Crozier ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Social Structure ◽  
Introduction History

scholarly journals Microsatellite analysis reveals low genetic diversity in managed populations of the critically endangered gharial (Gavialis gangeticus) in India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Surya Prasad Sharma ◽  
Mirza Ghazanfarullah Ghazi ◽  
Suyash Katdare ◽  
Niladri Dasgupta ◽  
Samrat Mondol ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Indian Subcontinent ◽  
Population Decline ◽  
Mitochondrial Control Region ◽  
Critically Endangered ◽  
Term Survival ◽  
Low Level ◽  
Genetic Status ◽  
In The Wild ◽  
Gavialis Gangeticus

AbstractThe gharial (Gavialis gangeticus) is a critically endangered crocodylian, endemic to the Indian subcontinent. The species has experienced severe population decline during the twentieth century owing to habitat loss, poaching, and mortalities in passive fishing. Its extant populations have largely recovered through translocation programmes initiated in 1975. Understanding the genetic status of these populations is crucial for evaluating the effectiveness of the ongoing conservation efforts. This study assessed the genetic diversity, population structure, and evidence of genetic bottlenecks of the two managed populations inhabiting the Chambal and Girwa Rivers, which hold nearly 80% of the global gharial populations. We used seven polymorphic nuclear microsatellite loci and a 520 bp partial fragment of the mitochondrial control region (CR). The overall mean allelic richness (Ar) was 2.80 ± 0.40, and the observed (Ho) and expected (He) heterozygosities were 0.40 ± 0.05 and 0.39 ± 0.05, respectively. We observed low levels of genetic differentiation between populations (FST = 0.039, P < 0.05; G’ST = 0.058, P < 0.05 Jost’s D = 0.016, P < 0.05). The bottleneck analysis using the M ratio (Chambal = 0.31 ± 0.06; Girwa = 0.41 ± 0.12) suggested the presence of a genetic bottleneck in both populations. The mitochondrial CR also showed a low level of variation, with two haplotypes observed in the Girwa population. This study highlights the low level of genetic diversity in the two largest managed gharial populations in the wild. Hence, it is recommended to assess the genetic status of extant wild and captive gharial populations for planning future translocation programmes to ensure long-term survival in the wild.

scholarly journals Spatial pattern and genetic diversity estimates are linked in stochastic models of population differentiation

2000 ◽  
Vol 23 (3) ◽  
pp. 541-544 ◽  
Author(s):  
José Alexandre Felizola Diniz-Filho ◽  
Mariana Pires de Campos Telles
Keyword(s):  
Genetic Diversity ◽  
Spatial Pattern ◽  
Stochastic Models ◽  
Population Differentiation ◽  
Real Data ◽  
Population Heterogeneity ◽  
Data Set ◽  
Mantel’S Test ◽  
The Relationship ◽  
Diversity Estimates

In the present study, we used both simulations and real data set analyses to show that, under stochastic processes of population differentiation, the concepts of spatial heterogeneity and spatial pattern overlap. In these processes, the proportion of variation among and within a population (measured by G ST and 1 - G ST, respectively) is correlated with the slope and intercept of a Mantel's test relating genetic and geographic distances. Beyond the conceptual interest, the inspection of the relationship between population heterogeneity and spatial pattern can be used to test departures from stochasticity in the study of population differentiation.

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