Journal articles on the topic 'Genetic structure of Indian populations'
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Bose, Aritra, Daniel E. Platt, Laxmi Parida, Petros Drineas, and Peristera Paschou. "Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India." Molecular Biology and Evolution 38, no. 5 (January 22, 2021): 1809–19. http://dx.doi.org/10.1093/molbev/msaa321.
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Abstract India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although 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 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 data set 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.
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Padwal, K. G., S. Chakravarty, and C. P. Srivastava. "Genetic variability and population structure of Leucinodes orbonalis (Guenée), a severe insect pest of brinjal in India." Journal of Environmental Biology 43, no. 1 (January 7, 2022): 59–65. http://dx.doi.org/10.22438/jeb/43/1/mrn-1868.
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Aim: The present study was undertaken to provide valuable insights regarding population genetic structure of Leucinodes orbonalis from diverse agro-ecologies of India. Methodology: Molecular characterization of L. orbonalis populations collected from five major agro-climatic zones of India was carried out using mitochondrial cytochrome oxidase I (COI) gene. Collected specimens were subjected to DNA extractions, partial PCR amplification and sequencing of the target gene, and multiple sequence alignments. Results: The results showed very less diversity in the nucleotide positions of the COI sequences of 79 studied specimens, with a low number of segregating sites (30), nucleotide diversity (0.00438) and overall mean genetic distance (0.004 ± 0.001). The significant negative values of neutrality tests and unimodal mismatch distribution supported the demographic expansion theory in Indian L. orbonalis. Analysis of the molecular variance revealed that 93.13% of the genetic variation was within populations, and the variation among populations was only 6.87%. The pairwise genetic differentiation was also found to be low to moderate between most of the populations. Multiple haplotypes were recorded from all the populations, and both neighbour-joining tree as well as the haplotype network showed that clustering of the haplotypes was independent of the geographical location. Interpretation: Thus, it can be inferred that Indian populations of L. orbonalis have very low genetic variation levels concerning the COI gene. There is a possible occurrence of stable inherited gene flow among populations, thereby reducing genetic variation in India.
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Long, J. C. "The genetic structure of admixed populations." Genetics 127, no. 2 (February 1, 1991): 417–28. http://dx.doi.org/10.1093/genetics/127.2.417.
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Abstract A method for simultaneously estimating the admixture proportions of a hybrid population and Wright's fixation index, FST, for that hybrid is presented. It is shown that the variance of admixture estimates can be partitioned into two components: (1) due to sample size, and (2) due to evolutionary variance (i.e., genetic drift). A chi-square test used to detect heterogeneity of admixture estimates from different alleles, or loci, can now be corrected for both sources of random errors. Hence, its value for the detection of natural selection from heterogeneous admixture estimates is improved. The estimation and testing procedures described above are independent of the dynamics of the admixture process. However, when the admixture dynamics can be specified, FST can be predicted from genetic principles. Two admixture models are considered here, gene flow and intermixture. These models are of value because they lead to very different predictions regarding the accumulation of genes from the parental populations and the accumulation of variance due to genetic drift. When there is not evidence for natural selection, and it is appropriate to apply these models to data, the variance effective size (Ne) of the hybrid population can be estimated. Applications are made to three human populations: two of these are Afro-American populations and one is a Yanomamö Indian village. Natural selection could not be detected using the chi-square test in any of these populations. However, estimates of effective population sizes do lead to a richer description of the genetic structure of these populations.
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Adeola, Adeniyi C., Foluke E. Sola-Ojo, Yusuf A. Opeyemi, Abel O. Oguntunji, Lotanna Micah Nneji, Muslim K. Ewuola, Semiu F. Bello, et al. "Genetic diversity and population structure of muscovy duck (Cairina moschata) from Nigeria." PeerJ 10 (April 15, 2022): e13236. http://dx.doi.org/10.7717/peerj.13236.
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The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (FST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene.
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Das, Sofia P., Subrat K. Swain, Lakshman Sahoo, Joy Krushna Jena, and Paramananda Das. "Single Genetic Stock Revealed by Microsatellite Markers Among Wild Populations of Cirrhinus mrigala from Peninsular India." Turkish Journal of Fisheries and Aquatic Sciences 21, no. 09 (May 26, 2021): 425–33. http://dx.doi.org/10.4194/1303-2712-v21_9_01.
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Cirrhinus mrigala (mrigal) is one of the Indian major carps widely cultured in the whole Indian subcontinent. Population genetic structure of this species from Peninsular Rivers of India is lacking. Among DNA markers, microsatellites are excellent tools to evaluate genetic variation of populations. In this study, genetic variation of six peninsular riverine mrigal populations was evaluated using seventeen microsatellite loci. In analyzing 288 samples, the number of alleles ranged from 4 to 27; observed heterozygosity from 0.595 to 1.00, expected heterozygosity from 0.586 to 0.959 and inbreeding coefficient (FIS) ranged from -0.034 to 0.02. Exact test for Hardy Weinberg disequilibrium revealed that one locus was not in equilibrium across the rivers except one. The AMOVA analysis revealed the main source of genetic variation to be within the population (94.54%) than among the populations (5.46%). The Nei’s genetic distance and structure analysis depict river Narmada and Mahi populations are different from the four east coast rivers. The overall Fst (0.05462) data showed moderate differentiation among the six populations. The results of this study provide essential information to resource recovery and help in delineating populations for fishery management. Besides, the data will provide a valuable baseline for further investigations on the geographic distribution of this commercially important fish species.
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Bamshad, Michael, Toomas Kivisild, W. Scott Watkins, Mary E. Dixon, Chris E. Ricker, Baskara B. Rao, J. Mastan Naidu, et al. "Genetic Evidence on the Origins of Indian Caste Populations." Genome Research 11, no. 6 (May 8, 2001): 994–1004. http://dx.doi.org/10.1101/gr.173301.
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The origins and affinities of the ∼1 billion people living on the subcontinent of India have long been contested. This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in ∼265 males from eight castes of different rank to ∼750 Africans, Asians, Europeans, and other Indians. For maternally inherited mtDNA, each caste is most similar to Asians. However, 20%–30% of Indian mtDNA haplotypes belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans, particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1 and 39 Aluelements) in all of the caste and continental populations (∼600 individuals). Analysis of these data demonstrated that the upper castes have a higher affinity to Europeans than to Asians, and the upper castes are significantly more similar to Europeans than are the lower castes. Collectively, all five datasets show a trend toward upper castes being more similar to Europeans, whereas lower castes are more similar to Asians. We conclude that Indian castes are most likely to be of proto-Asian origin with West Eurasian admixture resulting in rank-related and sex-specific differences in the genetic affinities of castes to Asians and Europeans.
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Mukherjee, B. N., K. C. Malhotra, M. Roy, S. banerjee, H. Walter, and R. Chakraborty. "Genetic heterogeneity and population structure in eastern India: Red cell enzyme variability in ten Assamese populations." Zeitschrift für Morphologie und Anthropologie 77, no. 3 (May 3, 1989): 287–96. http://dx.doi.org/10.1127/zma/77/1989/287.
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Tripathi, Manorama, Piyush Tripathi, Ugam Kumari Chauhan, Rene J. Herrera, and Suraksha Agrawal. "Alu Polymorphic Insertions Reveal Genetic Structure of North Indian Populations." Human Biology 80, no. 5 (October 2008): 483–99. http://dx.doi.org/10.3378/1534-6617-80.5.483.
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PANDEY, Anamika, Mohd Kamran KHAN, George THOMAS, Erdogan E. HAKKI, Seyit Ali KAYIS, Mehmet HAMURCU, Sait GEZGIN, Ali TOPAL, and Mahinur S. AKKAYA. "Estimation of Indian and Turkish Hexaploid Wheat Population Structure to be a Part of Improved Breeding Program." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 43, no. 1 (May 31, 2015): 70–78. http://dx.doi.org/10.15835/nbha4319835.
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Bread wheat (Triticum aestivum) is the most commonly grown crop due to its adaptation in a wide range of eco-geographical conditions and providing enhanced food assurance to the modern world. A diverse and rich collection is the foundation of each successful wheat improvement program. Therefore, major efforts are in progress worldwide to boost wheat production by broadening genetic diversity. Accepting this issue as a target, present study gives an overview of the major progress in the diversity and population evaluation of Indian and Turkish hexaploid wheat employing ISSR and RAPD primers. Various statistical analyses were employed for determining the hexaploid wheat population structure of India and Turkey. Results of dendrogram, scatterplots, Analysis of Molecular Variance (AMOVA) and population structure analysis were found in accordance with each other. All the experimental genotypes were clustered in two main groups, one group containing Indian varieties and another group containing both Indian and Turkish varieties reflecting the direct or indirect interbreeding among the populations of the two countries. Utilizing the genetic association of Indian and Turkish hexaploid wheat population, based on genetic distance estimated in the study, researchers worldwide may include Indian and Turkish hexaploid varieties in the wheat improvement programs and can evade the likelihood of selected germplasm becoming hereditarily consistent.
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THANGARAJ, Muthusamy, Aron Premnath LIPTON, Lijo JOHN, and Achamveetil GOPALAKRISHNAN. "Genetic Diversity of Three Spotted Seahorse, Hippocampus trimaculatus (Leach, 1814 ) in India Using Four Microsatellite Loci." Notulae Scientia Biologicae 4, no. 4 (November 6, 2012): 07–13. http://dx.doi.org/10.15835/nsb448021.
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Seahorse populations are declining year by year not only in India but also throughout the world, because of over-fishing and increasing demand in Chinese market. The three spotted seahorse, Hippocampus trimaculatus is one of the dominant species and distributed all along the Indian coast. To study the genetic structure is very essential to conserve these species effectively. Hippocampus trimaculatus samples (n = 60/population) were collected from Mullimunai in Palk Bay, Tuticorin in Gulf of Mannar and Vizhinjam in south Malabar in India as by-catch in small trawlnets. Microsatellites are being widely applied in animal genome mapping and phylogenetic analysis because of their co-dominant inheritance and high degree of polymorphism. The molecular polymorphism of microsatellite DNA has proved to be a potent tool in the analysis of several aspects of population genetics. In the present study, four microsatellite primers were used to investigate the genetic difference and structure of three selected populations of H. trimaculatus. The result showed the overall FST value (0.0989) of the microsatellite loci between Mullimunai and Vizhinjam was significantly different. The genetic distance between Mullimunai and Tuticorin was 0.183; between Tuticorin and Vizhinjam was 0.461; and Mullimunai and Vizhinjam was 0.837. There was no statistical evidence of recent severe bottlenecks in any of the three populations. Continuous monitoring of microsatellite variations within the populations of all the three locations was suggested to determine whether genetic variation within the populations is stabilized between year classes.
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Acharya, Aditya P., Annam Pavan-Kumar, Pathakota Gireesh-Babu, Chaitanya G. Joshi, Aparna Chaudhari, and Gopal Krishna. "Population genetics of Indian giant river-catfish, Sperata seenghala (Sykes, 1839) using microsatellite markers." Aquatic Living Resources 32 (2019): 4. http://dx.doi.org/10.1051/alr/2019002.
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The giant river-catfish Sperata seenghala is one of the commercially important freshwater catfishes of India with wide distribution in all major rivers and reservoirs. This fish has huge demand in domestic market due to high nutritional value and low number of intramuscular bones. Conversely, the culture practices for this fish have not yet been standardized and capture fisheries is the only source to meet the demand. This may lead to over exploitation of resources and subsequent population reduction. Knowledge on genetic structure of populations is prerequisite to formulate sustainable management and conservation measures. In the present study, 15 microsatellites were used to characterize population genetics of S. seenghala collected from river Brahmaputra, Ganga, Godavari, Mahanadi and Narmada. Locus-wise, the number of alleles varied from 8 to 19 with an average of 12 alleles per locus. The mean observed and expected heterozygosity values varied from 0.622 to 0.699 and 0.733 to 0.774, respectively. Several loci have shown deviation from Hardy–Weinberg equilibrium and no significant linkage disequilibrium between pairs of loci was detected. Pair-wise FST values between populations ranged from 0.135 (Brahmaputra–Ganga) to 0.173 (Brahmaputra–Narmada) and confirmed the moderate to high genetic differentiation among the populations. AMOVA, Structure and Principal Co-ordinate analyses showed significant genetic differentiation among the sampled populations of S. seenghala. A total of 65 private alleles were recorded across populations. This study confirmed the distinctiveness of each population of S. seenghala from five major rivers of India. These populations could be treated as distinct management units (MUs) for assessment and management purpose.
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THIRUMARAISELVI, Ramakrishnan, and Muthusamy THANGARAJ. "Genetic Diversity Analysis of Indian Salmon, Eleutheronema tetradactylum from South Asian Countries Based on Mitochondrial COI Gene Sequences." Notulae Scientia Biologicae 7, no. 4 (December 13, 2015): 417–22. http://dx.doi.org/10.15835/nsb749668.
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Eleutheronema tetradactylum is an important commercial fish species exposed to intense exploitation both in Southeast Asian countries and Northern parts of Australia. Research on the population structure of E. tetradactylum in these coastal waters is substantial in order to ensure sustainable use and appropriate resource management. In this study, genetic variation, diversity and population structure of E. tetradactylum among four FAO fishing areas, along South Asian countries, were evaluated using cytochrome c oxidase subunit I (COI) gene. Totally 30 sequences of COI gene were collected from four FAO fishing areas. Among these 30 individuals, 18 distinct haplotypes were defined. High levels of haplotype diversity (hd = 0.952 ± 0.096) and nucleotide diversity (π = 0.01536 ± 0.00312) were observed in the population within the Bay of Bengal. No haplotype and nucleotide diversity were observed in South China Sea population. Hierarchical analysis of molecular variance (AMOVA) indicated that 0.81% of the genetic variation occurred within the populations, while 7.09% variation occurred among populations. Significant genealogical branches were recognized in North Australian populations (one clade), South China Sea populations (one clade), Arabian Sea and Bay of Bengal populations (one clade) on the neighbor-joining tree. These results suggested that E. tetradactylum populations in FAO fishing areas 51, 57 and 61 have developed different genetic structures. Tests of neutral evolution and mismatch distribution suggest that a population growth of E. tetradactylum may take place in these fishing areas.
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Bhatt, Supriya, Suvankar Biswas, Krithi Karanth, Bivash Pandav, and Samrat Mondol. "Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across the Indian subcontinent." PeerJ 8 (February 4, 2020): e8482. http://dx.doi.org/10.7717/peerj.8482.
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Background Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. Methods We collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. Results Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75–90% population decline between ∼120–200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. Conclusions Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.
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Nadeem, Mohammad, Salim Khan, Mohammad Akmal, Mauji Ram, Fahad Alâ€Qurainy, and Malik Zainul Abdin. "Genetic diversity and podophyllotoxin analysis of Podophyllum hexandrum from Indian central Himalaya." South Asian Journal of Experimental Biology 2, no. 2 (May 10, 2012): 51–56. http://dx.doi.org/10.38150/sajeb.2(2).p51-56.
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Genetic diversity among and within 10 populations of Podophyllum hexandrum was analyzed for precise assessments of genetic structure for conservation planning of wild Indian May apple (Podophyllum hexandrum) in the Central region of Himalayas. Random Amplified Polymorphic DNA (RAPD) studies revealed variability among and within population. Twenty primer sets were evaluated, 18 primers resulted in low and poor polymorphism,where as two gave better results which were counted for final analysis. We found a higher podophyllotoxin levels among the populations. However, the existing variation in podophyllotoxin content among the populations may be due to geographical location, altitude and habitat. It was difficult to ascertain these variations as genetic variations. Whereas morphological variations may have impact on podophyllotoxin content detected in different populations of P. hexandrum. Hence we recommend that any further cultivation of this species require optimization of environmental factors in order to increase the rate of production of podophyllotoxin from any collected population.
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Williams, Samuel M., Michael B. Bennett, Julian G. Pepperell, Jess A. T. Morgan, and Jennifer R. Ovenden. "Spatial genetic subdivision among populations of the highly migratory black marlin Istiompax indica within the central Indo-Pacific." Marine and Freshwater Research 67, no. 8 (2016): 1205. http://dx.doi.org/10.1071/mf14370.
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The black marlin Istiompax indica is a highly migratory species and as a result is expected to show little genetic population structure throughout its broad geographic range. Tissue samples from 183 I. indica were collected from three geographic regions within the central Indo-Pacific and analysed using mitochondrial and nuclear DNA markers. Nuclear genetic heterogeneity was found among populations in the south-western Pacific Ocean, eastern Indian Ocean and South China Sea (significant FST values of 0.013–0.037). Combining information from nuclear markers with published movement and reproductive data suggests that reproductive philopatry plays a role in maintaining contemporary I. indica population structure. Analyses of the mitochondrial control region did not reflect this pattern; however, it identified historical population structure. Differing patterns of genetic population structure revealed by mitochondrial and nuclear markers demonstrated that a transition must have occurred between historical and contemporary population structures. This restructuring presumably reflects a species whose populations have become genetically isolated before experiencing a period of secondary contact. The spatial subdivision evident among populations indicates that I. indica in this central Indo-Pacific region should be managed as three independent stocks, to guide the sustainability of this fisheries resource.
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Yadav, Sweta Kumari U., Jyotsna Singh, B. Padmanaban, and Lalitha Sunil Kumar. "Genetic variability in Indian populations of banana corm weevil [Cosmopolites sordidus (Coleoptera: Curculionidae)] assessed by RAPDs and AFLPs." International Journal of Tropical Insect Science 37, no. 03 (August 17, 2017): 149–62. http://dx.doi.org/10.1017/s1742758417000108.
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AbstractCosmopolites sordidus(Germar), commonly known as banana corm weevil, is an important economic pest in Asia that can cause severe yield loss depending upon the stage at which infestation occurs. In spite of its economic importance, little is known about the population structure of this pest in India. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) were used to characterize the population genetic structure ofC. sordiduscollected from five hot spot locations in India. Nineteen RAPD primers and five selective AFLP primer combinations generated 147 and 304 amplification products, respectively. UPGMA dendrograms generated with both marker systems failed to reveal populations clustered based on geographic distance, which was confirmed by the Mantel test, which did not show a strong correlation between genetic distance and geographic distance. Values of indices of genetic identity showed that the populations were closely related. Though the gene flow estimate (Nm) between the populations was 0.469, suggesting restricted gene flow, the populations are not genetically distinct. These observations suggest that the range expansion of this banana pest in India has taken place through transport of infested corms and plant material, resulting in genetically close populations that are geographically distinct. These results provide important information on the population structure of this pest in India, which will aid in designing suitable strategies for its control and management, especially with respect to insecticide resistance.
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Archak, S., A. B. Gaikwad, K. R. M. Swamy, and J. L. Karihaloo. "Genetic analysis and historical perspective of cashew (Anacardium occidentale L.) introduction into India." Genome 52, no. 3 (March 2009): 222–30. http://dx.doi.org/10.1139/g08-119.
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Cashew ( Anacardium occidentale L.), introduced into India about 400 years ago, is distributed widely in the coastal regions as spontaneous populations as well as in cultivation. Despite the plant’s commercial exploitation, little is known about its actual introduction and diversification. We attempted to construct these events by investigating the level of genetic variation and genetic structure of cashew populations collected from different geographical regions of India. A total of 91 individuals from four populations were analysed using AFLP markers and morphometric data. AFLP analysis based on 354 polymorphic loci revealed Indian cashew to have low but relatively substantial genetic diversity for an introduced species (HE = 0.262 and IS = 0.404). Twenty-seven qualitative and quantitative traits also revealed the existence of considerable morphometric variation (24% around the mean values). Bayesian cluster analysis based on AFLP data did not indicate the existence of definite population differentiation. Morphometric analysis allocated 12% variation among all four populations, whereas AFLP variation observed in cashew individuals was entirely within populations. The results, supporting the possibility of cashew having been introduced into India repeatedly over a period of time but at a single location (west coast), are discussed and their implications for germplasm management are described.
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Salas, E. M., G. Bernardi, M. L. Berumen, M. R. Gaither, and L. A. Rocha. "RADseq analyses reveal concordant Indian Ocean biogeographic and phylogeographic boundaries in the reef fish Dascyllus trimaculatus." Royal Society Open Science 6, no. 5 (May 2019): 172413. http://dx.doi.org/10.1098/rsos.172413.
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Population genetic analysis is an important tool for estimating the degree of evolutionary connectivity in marine organisms. Here, we investigate the population structure of the three-spot damselfish Dascyllus trimaculatus in the Red Sea, Arabian Sea and Western Indian Ocean, using 1174 single nucleotide polymorphisms (SNPs). Neutral loci revealed a signature of weak genetic differentiation between the Northwestern (Red Sea and Arabian Sea) and Western Indian Ocean biogeographic provinces. Loci potentially under selection (outlier loci) revealed a similar pattern but with a much stronger signal of genetic structure between regions. The Oman population appears to be genetically distinct from all other populations included in the analysis. While we could not clearly identify the mechanisms driving these patterns (isolation, adaptation or both), the datasets indicate that population-level divergences are largely concordant with biogeographic boundaries based on species composition. Our data can be used along with genetic connectivity of other species to identify the common genetic breaks that need to be considered for the conservation of biodiversity and evolutionary processes in the poorly studied Western Indian Ocean region.
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Kashyap, Abhijeet Shankar, Nazia Manzar, Avantika Maurya, Deendayal Das Mishra, Ravinder Pal Singh, and Pawan Kumar Sharma. "Development of Diagnostic Markers and Applied for Genetic Diversity Study and Population Structure of Bipolaris sorokiniana Associated with Leaf Blight Complex of Wheat." Journal of Fungi 9, no. 2 (January 23, 2023): 153. http://dx.doi.org/10.3390/jof9020153.
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Bipolaris sorokiniana, a key pathogenic fungus in the wheat leaf blight complex, was the subject of research that resulted in the development of fifty-five polymorphic microsatellite markers. These markers were then used to examine genetic diversity and population structure in Indian geographical regions. The simple sequence repeat (SSR) like trinucleotides, dinucleotides, and tetranucleotides accounted for 43.37% (1256), 23.86% (691), and 16.54% (479) of the 2896 microsatellite repeats, respectively. There were 109 alleles produced by these loci overall, averaging 2.36 alleles per microsatellite marker. The average polymorphism information content value was 0.3451, with values ranging from 0.1319 to 0.5932. The loci’s Shannon diversity varied from 0.2712 to 1.2415. These 36 isolates were divided into two main groups using population structure analysis and unweighted neighbour joining. The groupings were not based on where the isolates came from geographically. Only 7% of the overall variation was found to be between populations, according to an analysis of molecular variance. The high amount of gene flow estimate (NM = 3.261 per generation) among populations demonstrated low genetic differentiation in the entire populations (FST = 0.071). The findings indicate that genetic diversity is often minimal. In order to examine the genetic diversity and population structure of the B. sorokiniana populations, the recently produced microsatellite markers will be helpful. This study’s findings may serve as a foundation for developing improved management plans for the leaf blight complex and spot blotch of wheat diseases in India.
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Simón, Belén, José Luis Cenis, Francisco Beitia, Saif Khalid, Ignacio M. Moreno, Aurora Fraile, and Fernando García-Arenal. "Genetic Structure of Field Populations of Begomoviruses and of Their Vector Bemisia tabaci in Pakistan." Phytopathology® 93, no. 11 (November 2003): 1422–29. http://dx.doi.org/10.1094/phyto.2003.93.11.1422.
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The genetic structure of field populations of begomoviruses and their whitefly vector Bemisia tabaci in Pakistan was analyzed. Begomoviruses and B. tabaci populations were sampled from different crops and weeds in different locations in Punjab and Sindh provinces, in areas where cotton leaf curl disease (CLCuD) occurs or does not occur. Phylogenetic analysis based on nucleotide sequences of the intergenic region in the viral DNA-A provided evidence of two clusters of isolates: viruses isolated from species in the family Malvaceae, and viruses isolated from other dicotyledon families. Analysis of the capsid protein (CP) open reading frame grouped isolates into three geographical clusters, corresponding to isolates collected in Punjab, Sindh, or both provinces. Random amplified polymorphic DNA analyses of the B. tabaci population showed that intrapopulation diversity was high at both the local and regional scales. Sequence analysis of the mitocondrial cytochrome oxydase I (mt COI) gene showed that the B. tabaci population was structured into at least three genetic lineages corresponding to the previously described Indian, Southeast Asian, and Mediterranean-African clades. The Indian clade was present only in Punjab, the Mediterranean-African only in Sindh, and the Southeast Asian in both provinces. B. tabaci haplotypes of the Indian clade were found only in the Punjab, where CLCuD occurs. Hence, the geographical distribution of virus and vector genotypes may be correlated, because similar phylogenetic relationships were detected for the viral CP and the vector mt COI genes.
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Kumar, J., R. J. Nelson, and R. S. Zeigler. "Population Structure and Dynamics of Magnaporthe grisea in the Indian Himalayas." Genetics 152, no. 3 (July 1, 1999): 971–84. http://dx.doi.org/10.1093/genetics/152.3.971.
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Abstract The population genetics of Magnaporthe grisea, the rice blast pathogen, were analyzed in a center of rice diversity (the Uttar Pradesh hills of the Indian Himalayas) using multilocus and single-, or low-copy, DNA markers. Based on DNA fingerprinting with the multilocus probe MGR586 and single-locus probes, 157 haplotypes clustered into 56 lineages (at ≥70% MGR586 band similarity, each with unique single-locus profiles) and high diversity indices were detected among 458 isolates collected from 29 sites during 1992–1995. Most valleys sampled had distinct populations (73% of the lineages were site specific) with some containing one or a few lineages, confirming the importance of clonal propagation, and others were very diverse. Widely distributed lineages suggested that migration occurs across the region and into the Indo-Gangetic plains. Repeated sampling at one site, Matli, (170 isolates, 1992–1995) yielded 19 lineages and diversity significantly greater than that reported from similar samples from Colombia and the Philippines. Analysis of allelic associations using pairwise comparisons and multilocus variance analysis failed to reject the hypothesis of gametic phase equilibrium. The Matli population shifted from highly diverse in 1992 to almost complete dominance by one lineage in 1995. Such population dynamics are consistent with recombination followed by differential survival of clonal descendants of recombinant progeny. At another site, Ranichauri, population (n = 84) composition changed from 2 to 11 lineages over 2 yr and yielded additional evidence for equilibrium. Sexually fertile and hermaphrodite isolates of both mating types were recovered from rice in both Matli and Ranichauri. We demonstrate that Himalayan M. grisea populations are diverse and dynamic and conclude that the structure of some populations may be affected to some extent by sexual recombination.
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Vijh, Ramesh Kumar, Upasna Sharma, Priyanka Banerjee, Jyoti Joshi, Tirumala Bharani Kumar Settypalli, S. B. Gokhale, Uma Gaur, Dinesh Kumar Yadav, Sonika Ahlawat, and Reena Arora. "New insights into the spatial genetic structure of the Indian riverine buffalo populations." Livestock Science 216 (October 2018): 227–32. http://dx.doi.org/10.1016/j.livsci.2018.09.003.
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Roberts, Mark A., Tonia S. Schwartz, and Stephen A. Karl. "Global Population Genetic Structure and Male-Mediated Gene Flow in the Green Sea Turtle (Chelonia mydas): Analysis of Microsatellite Loci." Genetics 166, no. 4 (April 1, 2004): 1857–70. http://dx.doi.org/10.1093/genetics/166.4.1857.
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Abstract We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model.
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Sukumaran, Sandhya, Wilson Sebastian, and A. Gopalakrishnan. "Population genetic structure of Indian oil sardine, Sardinella longiceps along Indian coast." Gene 576, no. 1 (January 2016): 372–78. http://dx.doi.org/10.1016/j.gene.2015.10.043.
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Akbar, Nebuchad Nezzar, Dian Pertiwi, Neviaty P. Zamani, Beginer Subhan, and Hawis H. Madduppa. "Studi pendahuluan genetika populasi ikan tuna sirip kuning (thunnus albacares) dari dua populasi di laut Kepulauan Maluku, Indonesia." Depik 9, no. 1 (March 23, 2020): 95–106. http://dx.doi.org/10.13170/depik.9.1.10585.
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Abstract. Yellowfin tuna (Thunnus albacares) is a large pelagic fish that have high economic value and inhabits the Moluccas Sea, Indonesia. Tuna catches in the Moluccas sea was very high and might decrease the yellowfin tuna population in this region. The research on population genetic of yellowfin tuna is fundamental to answer the problem. This information can be used as baseline data for future management, utilization, and basis of genetic conservation. The objective of this research was to infer the genetic population structure of two populations (North Maluku and Ambon) in the Moluccas Sea, Indonesia. In total, 41 tissue samples from pectoral fins of yellowfin tuna were collected in this study (North Maluku 33 samples and Ambon 8 samples). The results showed that genetic distances were low between the two populations. Additionally, the comparison of genetic distance between the Moluccas population and Indian Ocean waters also showed no significant differences. The Fst analysis showed the high gene flow between these two populations. Furthermore, haplotype network analysis showed that these two populations were the panmixia population. The overall result showed that no refraction genetic in the yellowfin tuna population from two populations in the Moluccas Sea.Keywords: Haplotype, genetic distance, Moluccas Sea, index fixation analysis, yellowfin tuna, population genetic structure. Abstrak. Tuna sirip kuning (Thunnus albacares) merupakan jenis pelagis besar bernilai ekonomis tinggi yang hidup di perairan Laut Maluku, Indonesia. Tangkapan ikan tuna di Laut Maluku berstatus tinggi, sehingga dapat menurunkan jumlah populasi. Penelitian tentang genetika populasi ikan tuna sirip kuning penting dilakukan untuk menjawab permasalahan ini. Informasi ini dapat menjadi sumber data untuk pengelolaan, pemanfaatan dan pelestarian untuk konservasi genetik. Tujuan penelitian untuk mengetahui struktur populasi genetik pada dua populasi di Laut Maluku (Maluku Utara dan Ambon). Secara total, 41 sampel jaringan dari sirip pectoral Tuna sirip kuning dikumpulkan dalam penelitian ini (Maluku Utara 33 sampel dan Ambon 8 sampel). Hasil penelitian menemukan jarak genetik yang dekat antar kedua populasi. Perbandingan jarak genetik pada populasi Perairan Maluku dan Samudera Hindia tidak menunjukan perbedaan signifikan. Analisis fiksasi indeks (Fst) memperlihatkan aliran genetik kuat antar populasi. Analisis jaringan haplotipe menunjukan kedua populasi merupakan populasi panmiksia. Penelitian ini secara umum menunjukkan belum terjadi perubahan struktur genetik populasi ikan tuna sirip kuning pada dua populasi di Laut Maluku.Kata kunci: Haplotipe, jarak genetik, Laut Maluku, analisis fiksasi indeks, tuna sirip kuning, struktur populasi genetik.
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Mukhopadhyay, Tanmay, and Soumen Bhattacharjee. "Genetic Diversity and Population Structure Analyses of Threatened Amblyceps mangois from Sub-Himalayan West Bengal, India Through Rapd and ISSR Fingerprinting." Croatian Journal of Fisheries 77, no. 1 (March 1, 2019): 33–50. http://dx.doi.org/10.2478/cjf-2019-0004.
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Abstract Amblyceps mangois or the “Indian torrent catfish” is a tropical, freshwater, hill-stream species that has ornamental-commercial value and has been included within the “Endangered” category in the list of threatened freshwater fishes of India. A total fourteen populations from the Terai and Dooars region of northern West Bengal, India were analyzed to study the genetic architecture of this species with the help of RAPD and ISSR markers. The observed number of alleles (S), Nei’s gene diversity (H) and Shannon’s information index (H´ or I) showed the highest values in the Teesta river system and the lowest values in the Mahananda river system. The UPGMA-based dendrogram and PCoA, based on RAPD and ISSR fingerprints, showed that the Mahananda and the Teesta river populations formed a group distinct from the remaining Jaldhaka river population. We further considered the fourteen riverine populations into nine groups according to the continuity of the water flow for SHE analysis. It was found that the three components, i.e. the pattern of diversity (H´), richness (S) and evenness (E), have varied and fluctuated across all fourteen populations from higher to lower altitude as the river flows downstream. AMOVA, PhiPT and genetic hierarchical analyses showed that a distinct hierarchical structure is present in Amblyceps populations in the study region. Low levels of genetic diversity/variation and genetic hierarchical structure with high genetic divergence were found in the present study as an indicator of the recent picture of threatened status of this species. This study is the initial attempt to characterize and evaluate the genetic architecture of the species from this region and there is a scope to manage the evolutionary significant units (ESU) for conservation purpose.
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Singh, B. N., and Seema Sisodia. "The Drosophila ananassae species complex: Evolutionary relationships among different members." Genetika 45, no. 1 (2013): 273–88. http://dx.doi.org/10.2298/gensr1301273s.
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Information about genetic structure and historical demography of natural populations is central to understanding how natural selection changes genomes. Drosophila ananassae is a widespread species occurring in geographically isolated or partially isolated populations and provides a unique opportunity to investigate population structure and molecular variation. D. ananassae and its closely related species serve as a widely used model in population and evolutionary genetics. The ananassae subgroup belongs to the melanogaster species group. This subgroup contains 22 described species distributed mainly throughout Southeast Asia, with some species expanding into northeastern Australia, South Pacific and Indian subcontinent and Africa. Within the ananassae subgroup, three species complexes-ananassae, bipectinata and ercepeae have been recognized based on male genital morphology. D. ananassae and its relatives have many advantages as a model of genetic differentiation and speciation. In this review, distribution, phylogenies, hybridization, sexual isolation among D. ananassae complex have been discussed. The complex of several cryptic island species provides a useful model for evolutionary studies dealing with the mechanisms of speciation.
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Parvatheesam, C., and M. C. Babu. "Genetic structure of Rajaka caste and affinities with other caste populations of Andhra Pradesh, India." Zeitschrift für Morphologie und Anthropologie 81, no. 3 (November 13, 1997): 365–71. http://dx.doi.org/10.1127/zma/81/1997/365.
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Mukherjee, Sabyasachi, Anupama Mukherjee, Sanjeev Kumar, Harendra Verma, Shivam Bhardwaj, Oshin Togla, Siddhartha Narayan Joardar, et al. "Genetic Characterization of Endangered Indian Mithun (Bos frontalis), Indian Bison/Wild Gaur (Bos gaurus) and Tho-Tho Cattle (Bos indicus) Populations Using SSR Markers Reveals Their Diversity and Unique Phylogenetic Status." Diversity 14, no. 7 (July 7, 2022): 548. http://dx.doi.org/10.3390/d14070548.
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Mithun (Bos frontalis) or gayal and Indian Bison or wild gaur (Bos gaurus) are listed among the rare and endangered bovine species of India. The remote location of mithun in four North Eastern Hill states (Arunachal Pradesh, Nagaland, Manipur, and Mizoram), scattered population size, and non-availability of genetic diversity status are major limitations towards devising a suitable breeding and conservation policy of these species. Since several studies have demonstrated the successful applicability of microsatellite/SSR markers across related genera/families in both crop plants and animal species, 30 FAO recommended cattle microsatellites were utilized for the assessment of the genetic diversity of Indian mithun, bison, and local Tho-tho cattle. Mitochondrial transmembrane protein coding cytochrome B (CYTB) complete sequence data of 71 bovine samples from India were also used to reinforce the study. Population structuring clustered the all bovines into three subgroups as per geographical location and species. Bottleneck analysis indicated a mode shift in the allelic frequency distribution of gaur, indicating minor genetic bottleneck events in the past, while no bottleneck was found in mithun and Tho-tho cattle. To our knowledge, this study represents the first report of molecular genetic characterization showing the population structure and status of genetic diversity in rare Indian bovines, namely, Mithun, Gaur, and Tho-tho cattle.
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Sahu, P. K., B. Das, L. Sahoo, S. Senapati, and G. D. Nayak. "Genetic relationship and population structure of three Indian local chicken populations as revealed by mtDNA D-loop." Mitochondrial DNA Part A 27, no. 4 (July 10, 2015): 2986–88. http://dx.doi.org/10.3109/19401736.2015.1060474.
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Das, Priyanka, Pranabesh Sarkar, Diptendu Chatterjee, and Arup Ratan Bandyopadhyay. "Genetic Variation and Population structure: A study on four populations of Tripura, North East India." Asian Journal of Medical Sciences 9, no. 3 (May 1, 2018): 46–49. http://dx.doi.org/10.3126/ajms.v9i3.19492.
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Back Ground: Genetic polymorphisms of ABO and RhD blood group and Haptoglobin (HP) types have already been widely used to understand variation and population structure. The present study attempted to understand the variation and population structure on the basis of ABO and RhD blood group polymorphisms and Haptoglobin (HP) as serum protein polymorphism of four Tibeto-Burman speaker groups considered as aboriginal tribes of Tripura. Genetic studies on populations in north-east Indian have been performed less frequently than in the other parts of India, in spite of diversity among these populations. Aims and Objective: Best of the knowledge the present study is the first attempt on the variation and population genetic structure concerning the ABO, RhD and HP polymorphism of the four endogamous populations – Tripuri, Hrangkhawl, Rupini and Kolui tribal population of Tripura.Materials and Methods: Present study consisted of four hundred (400) participants 100 each from above mentioned population groups. ABO and RhD blood groups were done by antigen-antisera agglutination test and HP types were ascertained by Polyacrylamide Gel Electrophoresis (PAGE) following standard techniques. Allele frequencies and Fst were calculated by using standard method.Results: Examination on ABO blood group revealed higher O allele among the two groups Tripuri and Hrangkhawl followed by A and B alleles. Among the other two groups, Rupini and Kolui, revealed higher A allele and B allele respectively. Higher D allele frequency in the RHD Blood group system has been found for each of the population group. On the other hand, Serum protein marker - HP types demonstrated higher HP*2 allele frequency than HP*1 alleles. Calculated very low Fst value (0.02-0.08) of three polymorphic markers (ABO, RhD and HP) were suggestive for low differentiation among these groups, indicating less admixture and prevailing endogamous nature of these population.Conclusion: Very low Fst values of three polymorphic markers were suggestive for low differentiation among these groups, indicating least admixture and prevailing endogamous nature of these population. The overall genetic difference revealed highest distance between Tripuri and Hrangkhwal and least distance between Rupini and Kolui.Asian Journal of Medical Sciences Vol.9(3) 2018 46-49
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Bharti, Neeraj, Ruma Banerjee, Archana Achalere, Sunitha Manjari Kasibhatla, and Rajendra Joshi. "Genetic diversity of ‘Very Important Pharmacogenes’ in two South-Asian populations." PeerJ 9 (November 10, 2021): e12294. http://dx.doi.org/10.7717/peerj.12294.
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Objectives Reliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response. Methods Joint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni’s multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score. Results Population stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be ‘deleterious’. Conclusions Analysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.
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Rajkumar, Subramani, Sunil Kumar Singh, Akshay Nag, and Paramvir S. Ahuja. "Genetic Structure of Indian Valerian (Valeriana jatamansi) Populations in Western Himalaya Revealed by AFLP." Biochemical Genetics 49, no. 9-10 (June 17, 2011): 674–81. http://dx.doi.org/10.1007/s10528-011-9448-2.
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Ge, Yu, Teng Zhang, Bin Wu, Lin Tan, Funing Ma, Minghong Zou, Haihong Chen, et al. "Genome-Wide Assessment of Avocado Germplasm Determined from Specific Length Amplified Fragment Sequencing and Transcriptomes: Population Structure, Genetic Diversity, Identification, and Application of Race-Specific Markers." Genes 10, no. 3 (March 13, 2019): 215. http://dx.doi.org/10.3390/genes10030215.
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Genomic data is a powerful tool. However, the phylogenetic relationships among different ecological races of avocado remain unclear. Here, we used the results from specific length amplified fragment sequencing (SLAF-seq) and transcriptome data to infer the population structure and genetic diversity of 21 avocado cultivars and reconstructed the phylogeny of three ecological races and two interracial hybrids. The results of the three analyses performed (unweighted pair-group methods with arithmetic means (UPGMA) cluster, Principal coordinate analysis (PCoA), and STRUCTURE) based on single nucleotide polymorphisms (SNPs) from SLAF-seq all indicated the existence of two populations based on botanical race: Mexican–Guatemalan and West Indian genotype populations. Our results based on SNPs from SLAF-seq indicated that the Mexican and Guatemalan races were more closely related to each other than either was to the West Indian race, which also was confirmed in the UPGMA cluster results based on SNPs from transcriptomic data. SNPs from SLAF-seq provided strong evidence that the Guatemalan, Mexican, and Guatemalan × Mexican hybrid accession possessed higher genetic diversity than the West Indian races and Guatemalan × West Indian hybrid accessions. Six race-specific Kompetitive allele specific PCR (KASP) markers based on SNPs from SLAF-seq were then developed and validated.
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Radhakrishnan, Divya Prema, Vineesh Nedumpally, Ayyathurai Kathirvelpandian, Basheer Valaparambil Saidmuhammed, and Achamveettil Gopalakrishnan. "Population structure of Spanish mackerelScomberomorus commerson(Lacepede 1800) in the Northern Indian Ocean determined using microatellite markers." Aquatic Living Resources 31 (2018): 22. http://dx.doi.org/10.1051/alr/2018011.
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Narrow barred Spanish mackerel,Scomberomorus commerson(Lacepede, 1800) is one of the economically important marine fish species in the Northern Indian Ocean. Genetic stock structuring is reported inS. commersonfrom Arabian Peninsula, Indo-West Pacific, Northern Australian, Southeast Asia and Northern Australia. The present study utilized microsatellite markers to elucidate the population structure ofS. commerson(Lacepede, 1800) in the Arabian Sea and Bay of Bengal. A total of 12 polymorphic microsatellite loci were amplified in 250 samples collected from five different geographic locations. LowFSTvalues (0.0023–0.027), AMOVA, PCoA and the Bayesian analysis of genetic structure indicated unit stock of the species in Indian waters. Bottleneck analysis using Wilcoxon signed rank tests and Mode shift test indicated lack of recent bottleneck events across populations ofS. commerson. The findings of the present study could be used in managing the commercially important species,S. commersonas a unit stock in Arabian Sea and Bay of Bengal of Northern Indian Ocean and reinforces the need for regional cooperation on fisheries management.
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Renuka, G., and G. Shamitha. "Studies on Genetic Diversity and Population Structure of Tasar Silkworm, Antheraeamylitta.Drury." Research Journal of Biotechnology 16, no. 7 (June 25, 2021): 101–13. http://dx.doi.org/10.25303/167rjbt10121.
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The populations of Indian tropical Tasar silkworm, Antheraeamylitta Drury, the semi-wild, sericigenous, lepidopteran insect are distributed in eco pockets of various States. These ecoraces vary in geography, topography, ecology, food plant flora and frequency of life cycle in latitudinal and altitudinal gradients. They exhibit diversity in phenotypic, behavioural, physiogenetic and commercial characters. In the present study, the SSR amplification of 7 silkworm strains/ecoraces (16 individuals in each, with seven primers which generated polymorphism) yielded a total of 887 bands, out of which 420 were (47.3 %) polymorphic. Most of the bands were observed within the range 130 to 500 base pairs which is in accordance with the allelic size of the primers taken for studies. The subsequent analysis of its population structure using these alleles revealed the formation of population clusters. The study suggests that these markers could be effectively utilized for identifying the genetic variability among tasar ecoraces.
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Permana, Gusti Ngurah, Bedjo Slamet, Bagus Arya Permana, Ayu Krisna Dewi, and Gusti Ngurah Mahardika. "POPULATION GENETIC STRUCTURE OF SPINY LOBSTERS, Panulirus homarus AND Panulirus ornatus, IN THE INDIAN OCEAN, CORAL TRIANGLE, AND SOUTH CHINA SEA." Indonesian Aquaculture Journal 14, no. 1 (May 31, 2019): 7. http://dx.doi.org/10.15578/iaj.14.1.2019.7-14.
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Populations of spiny lobsters worldwide are threatened by overfishing, while its supply from aquaculture is currently insufficient to meet the market demand. This current study investigated the genetic structure of two economically important spiny lobsters, P. homarus and P. ornatus sourced from the Indian Ocean and South China Sea. Fragments of the cytochrome oxidase subunit-I (COI) gene of the mitochondrial DNA of 71 P. homarus and 42 P. ornatus collected from 6 and 5 fish landing sites in Indonesia, respectively, were sequenced. Homologous sequences from the Indian Ocean and South China Sea available at GenBank were included in the analysis. No genetic differences were observed in P. ornatus populations from the two geographic regions (xST = -0.005) while a diminutive difference was found in the populations of P. homarus (xST = -0.002 and 0.009). These results, combined with a negative Tajima’s D estimates, points to a deficit of nucleotide variation relative to the expectations from the mutation/drift equilibrium. Reconstruction of the phylogeny of P. homarus demonstrates that all Indonesian samples of P. homarus are grouped in one cluster and share the common cluster with GenBank data originated from Taiwan, Vietnam, India, Sri Lanka, Oman, and Iran. The phylogeny of P. ornatus indicates that there are two separated lineages existing in Indonesia.
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Akbar, Nebuchadnezzar, M. Irfan, and Muhammad Aris. "Population Genetics and Phylogeography of Bigeye Tuna in Moluccas Seas, Indonesia." ILMU KELAUTAN: Indonesian Journal of Marine Sciences 23, no. 4 (January 4, 2019): 145. http://dx.doi.org/10.14710/ik.ijms.23.4.145-155.
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The bigeye tuna (Thunnus obesus) is a migratory fish which can be found in the Atlantic, Indian and Pacific oceans. This fish has a commercial value and has been exploited worldwide including in Indonesia. The exploitation might affect the genetic diversity and population structure. The fact that the population stock resource is abundant and following fishing activities are increasing, study on population genetic and phylogeography canbe used as information to determine the status of the fish population based on genetic data. The study was conducted to investigate population genetic, and phylogeography of bigeye tuna in the North Moluccas and South Mollucas Seas, Indonesia. A total of 60 tissue bigeye tuna samples were collected from two study sites. The samples were amplified using mitochondrial DNA control region. Within population genetic diversity was revealed of 0.985 and 1.00 in North Moluccas and in south Moluccas, respectively, while between populations was 0.989. The genetic distance within population of North Moluccas (0.029) and South Mollucas (0.24) was very low, and all population was 0.027. The genetic distance between population of North Mollucas and South Mollucas was 0.025, South Mollucas and all population was 0.023, and all population with Norht Mollucas was 0.027. The genetic distance of North Mollucas and Pacific Ocean was 0.029, South Mollucas and Pacific Ocean was 0.023, North Mollucas, South Mollucas and Indian Ocean was 0.32. The Fst value between populations (0.990) showed that the two populations were not genetically different. A similar result showed from the phylogenetic trees analysis which individual of bigeye tuna was randomly clustred between North Moluccas and South Mollucas population, indicating that they were genetically close and from the same population. The population bigeye tuna from the North Mollucas and the South Mollucas exhibits no apparent phylogeographic distribution.
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Chauhan, Mamta, Ashok Kumar Gupta, and Santosh Dhillon. "Genetic diversity and population structure of three Indian horse breeds." Molecular Biology Reports 38, no. 5 (November 21, 2010): 3505–11. http://dx.doi.org/10.1007/s11033-010-0461-z.
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Sahoo, Lakshman, Ashoktaru Barat, Sangram Ketan Sahoo, Bismay Sahoo, Gargee Das, Paramananda Das, Jitendra Kumar Sundaray, and Saroj Kumar Swain. "Genetic Diversity and Population Structure of Endangered Indian Catfish, Clarias magur as Revealed by mtDNA D-loop Marker." Turkish Journal of Fisheries and Aquatic Sciences 21, no. 01 (November 12, 2020): 9–18. http://dx.doi.org/10.4194/1303-2712-v21_1_02.
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Clarias magur, popularly known as magur, is one of the economically important catfish species having high aquaculture potential in India due to its efficient food conversion, taste, and nutritional benefits. Due to habitat degradation, over exploitation, lack of resources, indiscriminate use of agricultural pesticides and introduction of competitor exotic species, the wild populations are dwindling day by day. According to IUCN, it is listed as endangered species. In the present study, the population genetic structure of 206 magur samples collected from seven different geographical regions was examined using partial mitochondrial D-loop (control region) sequence variation. In total of 17 haplotypes were observed with high number of private alleles, number of haplotypes ranged from 2 to 6 and maximum number of haplotypes was observed in UP population. Haplotype diversity and nucleotide diversity ranged from 0.06897 to 0.76322 and 0.00019 to 0.00208, respectively. Pairwise FST values ranged from 0.01383 to 0.62069 and highest genetic differentiation was observed between AP and AS population. Low genetic diversity and significant population genetic differentiation was observed in the present study. The information generated in the present investigation would facilitate formulating appropriate strategy for management, conservation, and genetic improvement program of this commercially important aquaculture species.
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Campos, João Carlos, Asghar Mobaraki, Elham Abtin, Raquel Godinho, and José Carlos Brito. "Preliminary assessment of genetic diversity and population connectivity of the Mugger Crocodile in Iran." Amphibia-Reptilia 39, no. 1 (2018): 126–31. http://dx.doi.org/10.1163/15685381-16000173.
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The Mugger Crocodile (Crocodylus palustris) is a threatened reptile inhabiting the Indian Sub-continent and Western Asia. Despite its “Vulnerable” conservation status, data about population genetic structure and connectivity are unavailable. This study makes a preliminary assessment of the genetic diversity, population structure and habitat connectivity ofC. palustrisin Iran. Ten tissue samples collected along the Sarbaz-Bahukalat basins were analysed and a set of 12 microsatellites was genotyped. Genetic diversity indices were estimated and population substructuring was assessed through Bayesian clustering analysis. Potential connectivity was verified through Remote Sensing water indexes, further implemented in a circuit analysis. Low genetic diversity was observed (mean observed heterozygosity = 0.35; mean expected heterozygosity = 0.43) and no population structure was found (K = 1). Water index and circuit analysis suggested possible connection among sites. This study highlights the potential vulnerability of crocodile populations and the importance of habitat connectivity for their persistence in the arid regions of Iran.
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Marquardt, Paula E., Craig S. Echt, Bryan K. Epperson, and Dan M. Pubanz. "Genetic structure, diversity, and inbreeding of eastern white pine under different management conditions." Canadian Journal of Forest Research 37, no. 12 (December 2007): 2652–62. http://dx.doi.org/10.1139/x07-114.
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Resource sustainability requires a thorough understanding of the influence of forest management programs on the conservation of genetic diversity in tree populations. To observe how differences in forest structure affect the genetic structure of eastern white pine ( Pinus strobus L.), we evaluated six eastern white pine sites across the 234 000 acre (1 acre = 0.4046856 ha) Menominee Indian Reservation in northeastern Wisconsin (45°00′N, 88°45′W). The six sites sampled for nuclear and chloroplast DNA microsatellite markers were of contrasting densities and managed by different management systems: shelterwood, pine release, plantation, and old growth. Three of the sites had natural regeneration, which was also sampled. Mean values of spatial genetic autocorrelation were positive in all mature populations and variable; the strongest spatial structuring of genes occurred in the least disturbed old-growth site (I – E(I) = 0.031). Genetic structuring at the historical old-growth site fit the isolation-by-distance model for a neighborhood size of 130 individuals. Significant inbreeding occurred in five populations, but the seedling or sapling populations as a group (f = 0.088) are significantly less inbred than the local mature populations (f = 0.197). The increase in heterozygosity between generations was attributed to harvesting having reduced the spatial genetic structure of the mature trees.
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McCallum, John, Susan Thomson, Meeghan Pither-Joyce, Fernand Kenel, Andrew Clarke, and Michael J. Havey. "Genetic Diversity Analysis and Single-nucleotide Polymorphism Marker Development in Cultivated Bulb Onion Based on Expressed Sequence Tag–Simple Sequence Repeat Markers." Journal of the American Society for Horticultural Science 133, no. 6 (November 2008): 810–18. http://dx.doi.org/10.21273/jashs.133.6.810.
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Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.
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Glass, Jessica R., Scott R. Santos, John SK Kauwe, and Brandon D. Pickett. "Phylogeography of two marine predators, giant trevally (Caranx ignobilis) and bluefin trevally (Caranx melampygus), across the Indo-Pacific." Bulletin of Marine Science 97, no. 2 (April 1, 2021): 257–80. http://dx.doi.org/10.5343/bms.2019.0114.
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For economically valuable marine fishes, identifying biogeographic barriers and estimating the extent of gene flow are critical components of fisheries management. We examined the population genetic structure of two commercially important reef-associated predators, the giant trevally ( Caranx ignobilis) and bluefin trevally (Caranx melampygus). We sampled 225 individuals and 32,798 single nucleotide polymorphisms (SNPs) of C. ignobilis, and 74 individuals and 43,299 SNPs of C. melampygus. Analyses of geographic population structure indicate the two species display subtly different phylogeographic patterns. Caranx ignobilis comprises two to three putative populations—one in the Central Pacific, one inhabiting the Western Pacific and Eastern Indian oceans, and one in the Western Indian Ocean—with some restricted gene flow between them. Caranx melampygus shows evidence of restricted gene flow from Hawaii to the West Pacific and Indian oceans, as well as limited genetic connectivity across the Indo- Pacific Barrier. Both species exhibit patterns characteristic of other large, reef-associated predators such as deepwater snappers and the great barracuda. This study contributes to ongoing assessments of the role of the Indo-Pacific Barrier in shaping patterns of phylogeography for large reef-associated fishes. Furthermore, by identifying putative populations of C. ignobilis and C. melampygus in the Central Pacific, our findings serve to improve future management measures for these economically important, data-limited species, particularly in light of historic and contemporary overfishing in Hawaii.
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Mahalle, Rashmi Manohar, Snehel Chakravarty, and Chandra Prakash Srivastava. "Population Genetic Differentiation and Structure of Maruca vitrata (Lepidoptera: Crambidae) in India." Diversity 14, no. 7 (July 7, 2022): 546. http://dx.doi.org/10.3390/d14070546.
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Maruca vitrata is one of the primary biotic constraints for pigeon pea production in India. The present study assessed the genetic variation and population structure of M. vitrata from diverse agro-ecologies in India using the mitochondrial cytochrome c oxidase I gene. A low number of segregating sites (10), haplotypes (13), nucleotide diversity (0.00136), and overall mean genetic distance (0.0013) were observed among the populations. The negative values of the neutrality tests and unimodal mismatch distribution supported its demographic expansion in the country. The analysis of molecular variance (AMOVA) revealed that the variation among populations or groups was only 13.91%, and the geographical distance did not significantly contribute to the genetic differentiation (R2 = 0.0024, p = 0.280). The clustering of haplotypes was also independent of the geographical location. Overall, our results suggest the existence of low genetic variation and high gene flow among populations of M. vitrata in India.
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Nugraha, Budi, Dian Novianto, and Abram Barata. "KERAGAMAN GENETIK IKAN TUNA MATA BESAR (Thunnus obesus) DI SAMUDERA HINDIA." Jurnal Penelitian Perikanan Indonesia 17, no. 4 (January 30, 2017): 277. http://dx.doi.org/10.15578/jppi.17.4.2011.277-284.
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Informasi kondisi populasi ikan tuna mata besar di perairan Samudera Hindia belum banyak diketahui. Hal ini dapat diprediksi melalui pendekatan dengan menggunakan analisis DNA. Penelitian ini bertujuan untuk mendapatkan informasi keragaman genetik dan struktur populasi ikan tuna mata besar dari perairan Samudera Hindia sebelah selatan Jawa dan Nusa Tenggara, dan barat Sumatera. Pengambilan sampel ikan tuna mata besar dilakukan pada bulan Maret sampai November 2010 berlokasi di perairan Samudera Hindia sebelah selatan Jawa dan Nusa Tenggara, dan barat Sumatera. Pengumpulan sampel jaringan (sirip) ikan tuna mata besar dilakukan oleh observer di atas kapal tuna longline. Nilai keragaman haplotipe (genetik) yang diperoleh adalah 0,8267 untuk kelompok sampel 1 dan 0,7766 untuk kelompok sampel 2 dengan nilai rata-rata keragaman genetik adalah 0,8017. Jarak genetik antara kelompok sampel ikan tuna mata besar di Samudera Hindia adalah 0,0038. Dendrogram yang dibentuk berdasarkan jarak genetik menunjukkan bahwa kelompok sampel ikan tuna mata besar yang diamati dapat dibagi menjadi dua kelompok populasi (subpopulasi), yaitu kelompok pertama terdiri dari ikan tuna mata besar yang berasal dari Samudera Hindia selatan Jawa dan Nusa Tenggara, sedangkan kelompok kedua yang berasal dari Samudera Hindia barat Sumatera. Information of bigeye tuna population condition in Indian Ocean has been not known. This can be predicted through the approach of using DNA analysis. This study aimes to obtain information on genetic diversity and population structure of the bigeye tuna from the Indian Ocean south of Java and Nusa Tenggara, and West Sumatra. Sampling bigeye tuna conducted in March until November 2010 is located in the Indian Ocean south of Java and Nusa Tenggara, and West Sumatra. The samples (fin) of bigeye tuna was collected by the observers on board tuna longline. Value of haplotype diversity (genetic) obtained was 0.8267 for the sample group 1 and 0.7766 for sample group 2 with an average was 0.8017. Genetic distance between sample groups of bigeye tuna in the Indian Ocean was 0.0038. Dendrogram established based on genetic distance shows that the group of bigeye tuna observed can be divided into two groups of populations (subpopulations), the first group consisted of bigeye tuna from the Indian Ocean south of Java and Nusa Tenggara, while the second group was from the Indian Ocean west of Sumatra.
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Karl, S. A., B. W. Bowen, and J. C. Avise. "Global population genetic structure and male-mediated gene flow in the green turtle (Chelonia mydas): RFLP analyses of anonymous nuclear loci." Genetics 131, no. 1 (May 1, 1992): 163–73. http://dx.doi.org/10.1093/genetics/131.1.163.
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Abstract We introduce an approach for the analysis of Mendelian polymorphisms in nuclear DNA (nDNA), using restriction fragment patterns from anonymous single-copy regions amplified by the polymerase chain reaction, and apply this method to the elucidation of population structure and gene flow in the endangered green turtle, Chelonia mydas. Seven anonymous clones isolated from a total cell DNA library were sequenced to generate primers for the amplification of nDNA fragments. Nine individuals were screened for restriction site polymorphisms at these seven loci, using 40 endonucleases. Two loci were monomorphic, while the remainder exhibited a total of nine polymorphic restriction sites and three size variants (reflecting 600-base pair (bp) and 20-bp deletions and a 20-bp insertion). A total of 256 turtle specimens from 15 nesting populations worldwide were then scored for these polymorphisms. Genotypic proportions within populations were in accord with Hardy-Weinberg expectations. Strong linkage disequilibrium observed among polymorphic sites within loci enabled multisite haplotype assignments. Estimates of the standardized variance in haplotype frequency among global collections (FST = 0.17), within the Atlantic-Mediterranean (FST = 0.13), and within the Indian-Pacific (FST = 0.13), revealed a moderate degree of population substructure. Although a previous study concluded that nesting populations appear to be highly structured with respect to female (mitochondrial DNA) lineages, estimates of Nm based on nDNA data from this study indicate moderate rates of male-mediated gene flow. A positive relationship between genetic similarity and geographic proximity suggests historical connections and/or contemporary gene flow between particular rookery populations, likely via matings on overlapping feeding grounds, migration corridors or nonnatal rookeries.
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Abdul Kareem, V. K., P. E. Rajasekharan, S. Mini, and T. Vasantha Kumar. "Genetic diversity and structure of the threatened anti-cancerous plantNothapodytes nimmonianaas revealed by ISSR analysis." Plant Genetic Resources 9, no. 4 (July 22, 2011): 506–14. http://dx.doi.org/10.1017/s1479262111000803.
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Inter simple sequence repeat markers were used to assess the genetic diversity and population genetic structure in 12 populations ofNothapodytes nimmonianafrom Western Ghats of India. A total of 16 selected primers produced 103 discernible bands, with 76 (73.7%) being polymorphic. The Nei's gene diversity (h) ranged from 0.1166 to 0.2124, with an average of 0.1518 at the population level and 0.2965 at the species level indicating high genetic diversity. The Shannon's index (I) was estimated to be 0.2189 within populations (range 0.1703–0.2947) and 0.4352 at the species level. The analysis of molecular variance showed that the genetic variation was found mainly within populations (73%), but variance among populations was only 27% and its value, ΦPT = 0.271,P < 0.001, implied that high genetic differentiation among populations. In addition, Nei's differentiation coefficient (GST) was found to be high (0.4882) and the gene flow (Nm) was low (0.5242), confirming the high population genetic differentiation. The unweighted pair-group method using arithmetic average clustering elicited similar results. Based on this, we propose conservation strategy for this plant species.
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Al-Hamidhi, Salama, Asia Parveen, Furhan Iqbal, Muhammad Asif, Naheed Akhtar, Elshafie I. Elshafie, Albano Beja-Pereira, and Hamza A. Babiker. "Diversity and Genetic Structure of Theileria annulata in Pakistan and Other Endemic Sites." Pathogens 11, no. 3 (March 10, 2022): 334. http://dx.doi.org/10.3390/pathogens11030334.
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Background: Theileria annulata is a tick-borne protozoan parasite responsible for bovine theileriosis, a disease that impacts cattle population in many developing countries. Development and deployment of effective control strategies, based on vaccine or therapy, should consider the extent of diversity of the parasite and its population structure in different endemic areas. In this study, we examined T. annulata in Pakistan and carried out a comparative analysis with similar data garneted in other areas, to provide further information on the level of parasite diversity and parasite genetic structure in different endemic areas. Methods: The present study examined a set of 10 microsatellites/minisatellites and analyzed the genetic structure of T. annulata in cattle breeds from Pakistan (Indian sub-continent) and compared these with those in Oman (Middle East), Tunisia (Africa), and Turkey (Europe). Result: A high level of genetic diversity was observed among T. annulata detected in cattle from Pakistan, comparable to that in Oman, Tunisia, and Turkey. The genotypes of T. annulata in these four countries form genetically distinct groups that are geographically sub-structured. The T. annulata population in Oman overlapped with that in the Indian Subcontinent (Pakistan) and that in Africa (Tunisia). Conclusions: The T. annulata parasite in Pakistan is highly diverse, and genetically differentiated. This pattern accords well and complements that seen among T. annulata representing the global endemic site. The parasite population in the Arabian Peninsula overlapped with that in the Indian-Subcontinent (India) and that in Africa (Tunisia), which shared some genotypes with that in the Near East and Europe (Turkey). This suggests some level of parasite gene flow, indicative of limited movement between neighboring countries.
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Manomohan, Vandana, Ramasamy Saravanan, Rudolf Pichler, Nagarajan Murali, Karuppusamy Sivakumar, Krovvidi Sudhakar, Raja K. Nachiappan, and Kathiravan Periasamy. "Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin." PLOS ONE 16, no. 5 (May 24, 2021): e0246497. http://dx.doi.org/10.1371/journal.pone.0246497.
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The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.