Polymorphic microsatellites in Simulium damnosum s.l. and their use for differentiating two savannah populations: implications for epidemiological studies

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 154-161 ◽  
Author(s):  
Valérie Dumas ◽  
Stéphane Herder ◽  
Aïcha Bebba ◽  
Cécile Cadoux-Barnabé ◽  
Christian Bellec ◽  
...  
Keyword(s):  
Population Structure ◽  
Microsatellite Markers ◽  
Intraspecific Variability ◽  
Epidemiological Studies ◽  
Null Alleles ◽  
Population Subdivision ◽  
Structure Population ◽  
Polymorphic Microsatellites ◽  
Simulium Damnosum ◽  
Two Populations

In West Africa, Onchocerca volvulus, the cause of human onchocerciasis, is transmitted by sibling species of the Simulium damnosum complex. Little is known about blackfly intraspecific variability and its consequences on vectorial capacity. This study reports the use of microsatellite markers for differentiating populations of S. damnosum s.l. Five microsatellite loci were characterized and used to analyze individuals from two savannah populations in Mali, 120 km apart. Four loci were highly polymorphic, having 8-12 alleles per locus and gene diversities ranging from 77.9 to 88.2%. A significant heterozygote deficiency was observed in the two populations. This may arise from inbreeding, population structure (the Walhund effect), or the presence of null alleles. To test this last hypothesis, new primers were designed for two loci and used to analyze homozygous individuals. After correcting for null alleles, heterozygote deficit persisted. Population subdivision in the two foci remains the most likely explanation. Our results indicate that microsatellite markers could differentiate fly populations, making them valuable tools for the study of population genetic structure.Key words: Simulium damnosum s.l., microsatellites, polymorphism, population structure, population genetics, null alleles.

Microsatellite population structure of Newfoundland black bears (Ursus americanus hamiltoni)

2011 ◽  
Vol 89 (9) ◽  
pp. 831-839 ◽  
Author(s):  
H. Dawn Marshall ◽  
Edward S. Yaskowiak ◽  
Casidhe Dyke ◽  
Elizabeth A. Perry
Keyword(s):  
Population Structure ◽  
Ursus Americanus ◽  
Intraspecific Variability ◽  
Black Bears ◽  
Postglacial Colonization ◽  
Correct Assignment ◽  
Hair Samples ◽  
Males And Females ◽  
Two Populations ◽  
F Statistics

We investigated population structure of black bears ( Ursus americanus hamiltoni Cameron, 1957) from insular Newfoundland using the microsatellite profiles of 12 loci from three broadly distributed areas (Northern, Baie Verte, and Bonavista peninsulas). Our goals were to revisit earlier findings of low heterozygosity in Newfoundland and increase knowledge of intraspecific variability in black bears, and make inferences about postglacial colonization and contemporary movements of island black bears. Ninety-three individuals (42 males) were identified among 543 hair samples: 21 from Bonavista, 25 from Northern Peninsula, and 47 from Baie Verte. Genetic diversity is relatively low (HE = 0.42) and decreases from northwest to southeast. Small but significant subpopulation differentiation revealed by F statistics is greatest between Northern and Baie Verte peninsulas; it is lower and comparable in the remaining pairwise comparisons. We hypothesize that postglacial colonization proceeded from the Northern Peninsula southeastward. Bears migrated from the Northern Peninsula to Baie Verte at some more distant time in the past, then diverged by genetic drift. More recently, migration occurred from these two populations to Bonavista, characterized by positive FIS indicative of admixture. Tests of biased dispersal and posterior probability of correct assignment to locality reveal contemporary movements of both males and females with historical dispersal attributable to males.

Genetic Diversity and Population Structure in Two Captive Rhesus Monkey (Macaca Mulatta) Populations as Revealed by Microsatellite Markers

2021 ◽  
Author(s):  
Chao Du ◽  
Bai Mo ◽  
Wujiao Li ◽  
Wencong Liu ◽  
Zongxiu Hu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Macaca Mulatta ◽  
Psychological Research ◽  
Effect Analysis ◽  
Bottleneck Effect ◽  
Genetic Lineages ◽  
Captive Populations ◽  
Two Populations

Abstract Rhesus monkeyss (Macaca mulatta) are extensively used in the field of medical and psychological research as valuable experimental animals. 15 polymorphic chromosome-specific microsatellite markers were used to analyze the genetic diversity and population structure in two captive individuals. A total of 155 alleles were identified, with the number of alleles per locus ranging from 7 to 15, giving an average number of 10.3 alleles per locus. The mean number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were 5.602, 0.7297, 0.8016, and 0.7716, respectively. The populations HS and XJ shared partial common alleles, however, the remaining in XJ were not detected. Structure analysis indicated that two populations belong to three genetic lineages. AMOVA showed that the genetic variance was 91% among individuals, while it was 9% among populations, respectively. The bottleneck effect analysis revealed that the two captive populations were in accordance with mutation-drift equilibrium. In the comparison of the genetic parameters and structure between the HS and XJ, we speculated that the genetic diversity was higher, which may be attributed to the exchange of germplasm resources and the input of new individuals from wild populations.

Polymorphic microsatellites in Simulium damnosum s.l. and their use for differentiating two savannah populations: implications for epidemiological studies

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 154-161 ◽  
Author(s):  
Valérie Dumas ◽  
Stéphane Herder ◽  
Aïcha Bebba ◽  
Cécile Cadoux-Barnabé ◽  
Christian Bellec ◽  
...  
Keyword(s):  
Epidemiological Studies ◽  
Polymorphic Microsatellites ◽  
Simulium Damnosum

scholarly journals Isolation and Characterization of Microsatellite Markers for Soybean Looper (Lepidoptera: Noctuidae)

2019 ◽  
Vol 19 (5) ◽  
Author(s):  
C S Silva ◽  
E M G Cordeiro ◽  
A S Corrêa
Keyword(s):  
Population Structure ◽  
Microsatellite Markers ◽  
Null Alleles ◽  
Isolation And Characterization ◽  
Hardy Weinberg Equilibrium ◽  
High Degree ◽  
Soybean Looper ◽  
Lepidoptera Noctuidae ◽  
F Statistics

Abstract We constructed 13 microsatellite markers for Chrysodeixis includens (Walker), a serious crop pest in the Americas. All SSR (Simple Sequence Repeat) markers were polymorphic, with no evidence of linkage disequilibrium between any loci in any population. The total number of alleles per locus ranged from 5 for L3, L9, and L11 to 26 for L6; the mean number of alleles per locus in three populations of C. includens ranged from 2.33 for L3 to 14.67 for L6. Hardy–Weinberg equilibrium (HWE) deviation was not observed in four loci for at least one population (L3, L5, L9, L10). Markers L6, L7, L8, L10, L11, L12, and L13 showed a frequency of null alleles > 0.2 for at least one population. STRUCTURE and F-statistics revealed low population structure among the populations (FST = 0.013) and a high degree of inbreeding (FIS = 0.658). The SSR markers developed here will be useful in future studies on the ecology, demography, host dynamics, and gene flow of C. includens. This information is essential to understand the recent status of C. includens as a key pest in South America.

scholarly journals Average Number of Nucleotide Differences in a Sample From a Single Subpopulation: A Test for Population Subdivision

Genetics ◽  
1987 ◽  
Vol 117 (1) ◽  
pp. 149-153
Author(s):  
Curtis Strobeck
Keyword(s):  
Monte Carlo Simulation ◽  
Population Structure ◽  
Random Mating ◽  
Population Subdivision ◽  
Expected Number ◽  
Migration Rates ◽  
Mating Population ◽  
Unbiased Estimates ◽  
Increasing Function ◽  
Stepping Stone Model

ABSTRACT Unbiased estimates of θ = 4Nµ in a random mating population can be based on either the number of alleles or the average number of nucleotide differences in a sample. However, if there is population structure and the sample is drawn from a single subpopulation, these two estimates of θ behave differently. The expected number of alleles in a sample is an increasing function of the migration rates, whereas the expected average number of nucleotide differences is shown to be independent of the migration rates and equal to 4N  Tµ for a general model of population structure which includes both the island model and the circular stepping-stone model. This contrast in the behavior of these two estimates of θ is used as the basis of a test for population subdivision. Using a Monte-Carlo simulation developed so that independent samples from a single subpopulation could be obtained quickly, this test is shown to be a useful method to determine if there is population subdivision.

scholarly journals Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Information Content ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Mean Value ◽  
Date Palms ◽  
Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

scholarly journals Identification of a new Indian camel germplasm by microsatellite markers based genetic diversity and population structure of three camel populations

2020 ◽  
Vol 27 (7) ◽  
pp. 1699-1709
Author(s):  
Rekha Sharma ◽  
Sonika Ahlawat ◽  
Himani Sharma ◽  
Ved Prakash ◽  
Shilpa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers

The effect of population structure on growth patterns in the woody goldenrod Solidago pauciflosculosa

1983 ◽  
Vol 61 (7) ◽  
pp. 1955-1958 ◽  
Author(s):  
Marvin P. Pritts ◽  
James F. Hancock
Keyword(s):  
Population Structure ◽  
Seedling Establishment ◽  
Reproductive Output ◽  
Plant Biomass ◽  
Growth Patterns ◽  
Dispersion Pattern ◽  
Allocation Patterns ◽  
Total Plant Biomass ◽  
Total Plant ◽  
Two Populations

The population structure and growth patterns of two populations of Solidago pauciflosculosa, a woody goldenrod, were investigated. Populations consisted of even-aged contagious patches of individuals, a dispersion pattern likely caused by the periodic appearance of microsites suitable for seedling establishment. The density of individuals within the even-aged clumps varied considerably and was correlated with total plant biomass and reproductive output. Density was not correlated with either reproductive or nonreproductive allocation patterns.

Genetic diversity and population structure of Korean wild soybean ( Glycine soja Sieb. and Zucc.) inferred from microsatellite markers

2017 ◽  
Vol 71 ◽  
pp. 87-96 ◽  
Author(s):  
Muhammad Amjad Nawaz ◽  
Seung Hwan Yang ◽  
Hafiz Mamoon Rehman ◽  
Faheem Shehzad Baloch ◽  
Jeong Dong Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Glycine Soja ◽  
Wild Soybean
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