Population genetics of Indian giant river-catfish, Sperata seenghala (Sykes, 1839) using microsatellite markers

2019 ◽  
Vol 32 ◽  
pp. 4 ◽  
Author(s):  
Aditya P. Acharya ◽  
Annam Pavan-Kumar ◽  
Pathakota Gireesh-Babu ◽  
Chaitanya G. Joshi ◽  
Aparna Chaudhari ◽  
...  
Keyword(s):  
Population Genetics ◽  
Genetic Differentiation ◽  
Wide Distribution ◽  
Genetic Structure Of Populations ◽  
Population Reduction ◽  
Hardy Weinberg Equilibrium ◽  
Commercially Important ◽  
Sperata Seenghala ◽  
Over Exploitation ◽  
Significant Linkage

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.

Contrasting patterns of genetic structure and disequilibrium in populations of a stone-cased caddisfly (Tasimiidae) from northern and southern Australia

2008 ◽  
Vol 59 (3) ◽  
pp. 235 ◽  
Author(s):  
Alicia Slater Schultheis ◽  
Richard Marchant ◽  
Jane Margaret Hughes
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Adult Emergence ◽  
Conclusive Evidence ◽  
Emergence Patterns ◽  
Freshwater Invertebrate ◽  
Gene Coi ◽  
Hardy Weinberg Equilibrium ◽  
New Recruits ◽  
Genetic Patchiness

In marine and freshwater invertebrate populations, microscale genetic differentiation or ‘genetic patchiness’ is thought to result from variation in the abundance and genetic composition of new recruits at a particular location. In the present study, the role of the adult emergence patterns in genetic patchiness was examined using mtDNA and two microsatellite loci to compare patterns of genetic differentiation in asynchronously (subtropical) and synchronously emerging (temperate) populations of the stone-cased caddisfly Tasimia palpata. A 550 base pair region of the mitochondrial cytochrome c oxidase subunit I gene (COI) was sequenced in at least 14 individuals from each population. Genetic structure was detected only at the reach scale in the subtropical populations and no genetic differentiation was detected in temperate populations. There were more deviations from Hardy–Weinberg equilibrium (HWE) in subtropical populations than in temperate populations where 44% and 12.5%, respectively, of tests for deviations from HWE were significant. Although distinct patterns of genetic structure and deviations from HWE were observed in the subtropical and temperate populations of T. palpata, no conclusive evidence was found to suggest that the differences are caused by differences in emergence patterns. We hypothesise that genetic patchiness must be caused by post-recruitment processes, most likely the preservation of oviposition ‘hotspots’ in subtropical streams.

scholarly journals Pesticides and the evolution of the genetic structure of Anopheles coluzzii populations in some localities in Benin (West Africa)

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Arsène Jacques Y. H. Fassinou ◽  
Come Z. Koukpo ◽  
Razaki A. Ossè ◽  
Fiacre R. Agossa ◽  
Roseric Azondékon ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Anopheles Coluzzii ◽  
Natural Habitats ◽  
Chi Square ◽  
Agroecological Zones ◽  
Chi Square Test ◽  
Hardy Weinberg Equilibrium ◽  
Study Sites ◽  
Homozygous Resistant

Abstract Background Changes in the natural habitats of insect groups are determined the genetic polymorphisms between individuals. The objective of this study was to establish the genetic structure of the Anopheles coluzzii populations in four localities of Benin. Methods Insecticide surveys and larval sampling were conducted on 4 study localities, including Cotonou, Ketou, Zagnanado, and Sô-Ava. Molecular characterizations were performed on the Anopheles mosquitoes collected with the allelic and genotypic frequencies of kdr gene determined. The multiple comparison Chi square test for proportions was performed with R version 3.3.3. Next, the observed heterozygosity, expected heterozygosity, and indices of fixation, and genetic differentiation were estimated. Finally, the Hardy–Weinberg equilibrium (EHW) was determined to assess whether panmixia exists in the different populations of mosquitoes of the agroecological zones under study. Results Carbamates, pyrethroids, organophosphorus and organochlorines use have been reported in all localities except Sô-Ava. Anopheles coluzzii was strongly represented across all study localities. The L1014F allele was observed in the localities of Kétou, Cotonou and Zagnanado. Likewise, insecticide selection pressure of homozygous resistant individuals (L1014F/L1014F) was significantly higher in Kétou, Cotonou and Zagnanado (p value < 0.05). Surprisingly in Sô-Ava, a relatively high frequency of the L1014F allele despite the reported absence of pesticide use was observed. All mosquito populations were found to be deficient in heterozygosity across the study sites (FIS< 0). No genetic differentiation (FST< 0) was observed in the localities of Zagnanado and Kétou. Conclusion The survey on the use of insecticides showed that insecticide selection pressures differ across the investigated localities. It would be desirable to rotate or apply formulations of combined products with different modes of action. Doing so would enable a better management of resistant homozygous individuals, and mitigate the resistance effect of commonly used insecticides.

scholarly journals Microsatellite loci development and population genetics in Neotropical fish Curimata mivartii (Characiformes: Curimatidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5959 ◽  
Author(s):  
Ricardo M. Landínez-García ◽  
Edna J. Marquez
Keyword(s):  
Population Genetics ◽  
Microsatellite Loci ◽  
Molecular Tools ◽  
Migratory Species ◽  
Lower Section ◽  
Neotropical Fish ◽  
International Union ◽  
Commercially Important ◽  
Species Specific ◽  
Near Threatened

The Curimatidae family plays an ecological role in the recycling and distribution of nutrients and constitutes a major food source for several commercially important fishes. Curimata mivartii, a member of this family, is considered a short-distance migratory species (≤100 km), categorized by the International Union for Conservation of Nature as a near threatened species, based on its declining population densities and habitat disturbance and fragmentation. Since population genetics and species-specific molecular tools remain unknown for all members of the Curimatidae family, this study developed a set of microsatellite loci and studied the population genetics of C. mivartii in the lower section of the Colombian Magdalena-Cauca basin. The results showed high levels of genetic diversity and evidence of gene flow even between locations separated over 350 km. This information provides a baseline for designing conservation and management programs for C.mivartii and constitutes the first study of population genetics in Curimatidae.

Genetic structure of marginal populations of white spruce (Piceaglauca) at its northern limit of distribution in Nouveau-Québec

1989 ◽  
Vol 19 (11) ◽  
pp. 1371-1379 ◽  
Author(s):  
Monique Tremblay ◽  
Jean-Pierre Simon
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Geographic Distance ◽  
White Spruce ◽  
Gene Exchange ◽  
Northern Limit ◽  
Marginal Populations ◽  
Subarctic Region ◽  
Hardy Weinberg Equilibrium ◽  
Or Gene

The genetic structure of six marginal populations of white spruce (Piceaglauca (Moench) Voss) located at Richmond Gulf in the subarctic region of Nouveau-Québec, and one southern population located at Kuujjuaraapik (Poste-de-la-Baleine) were analyzed by acrylamide gel electrophoresis for seven enzyme systems. The analysis of 27 loci disclosed an average polymorphism of 76.2% and a level of heterozygosity of 0.319. Data based on Wright's; statistics: indicated a deficiency of heterozygotes for 60% of the loci, as calculated from the Hardy–Weinberg equilibrium. These results, coupled with the very low percentage of filled seeds in cones of all populations, suggest that a certain level of inbreeding or gene exchange among near-neighbour relatives influences the genetic structure of these populations. The genetic differentiation among populations is relatively high for a conifer [Formula: see text] and is not correlated with geographic distance. The age of trees, covering a period of 400 years affected by climatic changes, does not contribute to the genetic differentiation of the populations.

scholarly journals Best Practices for Population Genetic Analyses

2017 ◽  
Vol 107 (9) ◽  
pp. 1000-1010 ◽  
Author(s):  
N. J. Grünwald ◽  
S. E. Everhart ◽  
B. J. Knaus ◽  
Z. N. Kamvar
Keyword(s):  
Population Genetics ◽  
Population Genetic ◽  
Sampling Strategy ◽  
Population Data ◽  
Practical Experience ◽  
Population Genetic Analysis ◽  
Genetic Structure Of Populations ◽  
Web Of Data ◽  
R Programming ◽  
Pathogen Populations

Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.

Genetic differentiation among various populations of the diamondback moth, Plutella xylostella Lepidoptera Yponomeutidae

2006 ◽  
Vol 96 (2) ◽  
pp. 137-144 ◽  
Author(s):  
A. Pichon ◽  
L. Arvanitakis ◽  
O. Roux ◽  
A.A. Kirk ◽  
C. Alauzet ◽  
...  
Keyword(s):  
South Africa ◽  
New York ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Plutella Xylostella ◽  
Diamondback Moth ◽  
The Philippines ◽  
Fixation Index ◽  
Geographical Distance ◽  
Hardy Weinberg Equilibrium

AbstractGenetic variation among 14 populations of Plutella xylostella (Linnaeus) from USA (Geneva, New York), Brazil (Brasilia), Japan (Okayama), The Philippines (Caragan de Oyo), Uzbekistan (Tashkent), France (Montpellier), Benin (Cotonou), South Africa (Johannesburg), Réunion Island (Montvert), and five localities in Australia (Adelaide, Brisbane, Mareeba, Melbourne, Sydney) were assessed by analysis of allozyme frequencies at seven polymorphic loci. Most of the populations were not in Hardy–Weinberg equilibrium and had a deficit in heterozygotes. The global differentiation among populations was estimated by the fixation index (Fst) at 0.103 for the 14 populations and at 0.047 when populations from Australia and Japan, which differed most and had a strong genetic structure, were excluded from the analysis. By contrast, the populations from Benin (West Africa) and Brazil (South America) were very similar to each other. Genetic differentiation among the populations was not correlated with geographical distance.

scholarly journals Analysis of population genetic structure from Bucaramanga (Colombia) based on gene polymorphisms associated with regulation of blood pressure

2012 ◽  
pp. 154-161
Author(s):  
Francisco Javier León ◽  
Fernando Rondón González ◽  
Clara Inés Vargas Castellanos ◽  
Myriam Oróstegui ◽  
Leonelo Bautista ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Genetic Structure ◽  
Fragment Length Polymorphism ◽  
Association Studies ◽  
Genetic Structure Of Populations ◽  
Hardy Weinberg Equilibrium ◽  
Endothelial Nitric Oxide ◽  
Intron 4 ◽  
Regulation Of Blood Pressure ◽  
Genetic Equilibrium

Introduction: In spite nearly 40% of the variability in blood pressure can be explained by genetic factors, the identifi­cation of genes associated to essential high blood pressure is difficult in populations where individuals have different genetic precedents; in these circumstances it is necessary to determinate whether the population is sub-structured because this can bias studies associated with this disease. Objectives: To determine the genetic structure of the population in Bucaramanga from genetic polymorphisms asso­ciated with the regulation of blood pressure: 448G>T, 679C>T y 1711C>T from the gene kinase 4 of the dopaminergic receptor linked to the protein G and Glu298Asp, -786T>C and the VNTR of the intron 4 of the gene of endothelial nitric oxide. Methodology: A sample of 552 unrelated individuals was studied through analysis of Restriction fragment length polymorphism. The allelic, haplotypic and genotypic frequencies were calculated, the Hardy-Weinberg equilibrium was determined and a molecular analysis of variance was performed to determine the genetic structure. Results: 38 Haplotypes were identified, with GCCTG4b as the most frequent (21.2%). The most diverse polymorphism was 448G>T with a frequency of 49.9% for heterozygous. The six polymorphisms were found in genetic equilibrium and genetic structure of populations was not evidenced (FST = 0,0038). Conclusion: The population studied does not present a genetic sub-structure and the polymorphisms analyzed were found in genetic equilibrium, this indicates that the population mixes randomly and there are no sub-groups capable of affecting the results of the association studies

scholarly journals Genetic structure of Antioquia Holstein from two SNPs and association with dairy traits

2015 ◽  
pp. 4974-4988
Author(s):  
Stephania Madrid G ◽  
Albeiro López H ◽  
Julián Echeverri Z
Keyword(s):  
Genetic Differentiation ◽  
Marker Assisted Selection ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Reproductive Traits ◽  
Phenotypic Selection ◽  
Milk Traits ◽  
Dairy Traits ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium

ABSTRACT Objective. Analyze the structure and genetic differentiation of a population of Antioquia Holstein cows from the polymorphisms A192G of INHA and A-320T of FSHR, and explore the association of the genotypic combinations with milk traits. Materials and methods. 1240 lactations of 356 animals from 9 herds in 6 municipalities of Antioquia were analyzed. Genotyping was performed by PCR-RFLP. Structure and genetic diversity parameters were determined using GenAlex software. The association of genotypes combinations with productive and reproductive traits was explored through a linear mixed model. Results. SNP A192G showed a frequency of 0.534 and 0.466 for A and G alleles respectively and SNP A-320T had a frequency of 0.660 far A allele and 0.339 for T allele, this way the population is in HWE. The FST, FIS and FIT values were 0.059, 0.285 and 0.328 respectively indicating a moderate genetic differentiation between subpopulations. The A-320T SNP showed significant effect on milk yield. Fat and protein percentage, calving interval and services per conception were not affected by these polymorphisms or their interaction. Conclusions. Phenotypic selection made on this population has not been strong enough to generate noticeable changes in allele frequencies of these polymorphisms or deviations from Hardy-Weinberg equilibrium. The interaction of these polymorphisms has no significant effect on the characteristics of zootechnical interest, so its use in programs of molecular marker assisted selection is not recommended.

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