Insertional polymorphism of a non-LTR mobile element (NLRCth1) in European populations of Chironomus riparius (Diptera, Chironomidae) as detected by transposon insertion display

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1154-1163 ◽  
Author(s):  
G Zampicinini ◽  
A Blinov ◽  
P Cervella ◽  
V Guryev ◽  
G Sella
Keyword(s):  
Natural Populations ◽  
Mobile Element ◽  
Genetic Distances ◽  
Chironomus Riparius ◽  
Allozyme Polymorphism ◽  
Transposon Insertion ◽  
Random Samples ◽  
Order Of Magnitude ◽  
Specific Amplification ◽  
Insertional Polymorphism

The midge Chironomus riparius is distributed all over the Palearctic region and is well characterized both at the morphological and cytogenetic levels. Here we describe a population study based on the insertional polymorphism of the retroposon NLRCth1, by means of a S-SAP (sequence-specific amplification polymorphism) derived technique (transposon insertion display; TID). While a previous study of allozyme polymorphism in Russian samples showed little variability, all the amplicons we identified are polymorphic. Genetic distances between 6 natural populations were calculated according to Nei and did not show a positive correlation with geographic distances. The genetic diversity detected among individuals of a given population was one order of magnitude higher than that among populations. However, the value of ΦST was significant (p < 0.001) and indicates that natural populations are more genetically differentiated than random samples of individuals.Key words: retrotransposable elements, genetic differentiation, Chironomus riparius, sequence-specific amplification polymorphism.

scholarly journals On the Rate and Linearity of Viability Declines in Drosophila Mutation-Accumulation Experiments: Genomic Mutation Rates and Synergistic Epistasis Revisited

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 797-806 ◽  
Author(s):  
James D Fry
Keyword(s):  
Mutation Rate ◽  
Average Rate ◽  
Natural Populations ◽  
Mutation Accumulation ◽  
High Rate ◽  
Deleterious Mutations ◽  
Order Of Magnitude ◽  
Contamination Event ◽  
Genomic Mutation ◽  
The 1960S

Abstract High rates of deleterious mutations could severely reduce the fitness of populations, even endangering their persistence; these effects would be mitigated if mutations synergize each others’ effects. An experiment by Mukai in the 1960s gave evidence that in Drosophila melanogaster, viability-depressing mutations occur at the surprisingly high rate of around one per zygote and that the mutations interact synergistically. A later experiment by Ohnishi seemed to support the high mutation rate, but gave no evidence for synergistic epistasis. Both of these studies, however, were flawed by the lack of suitable controls for assessing viability declines of the mutation-accumulation (MA) lines. By comparing homozygous viability of the MA lines to simultaneously estimated heterozygous viability and using estimates of the dominance of mutations in the experiments, I estimate the viability declines relative to an appropriate control. This approach yields two unexpected conclusions. First, in Ohnishi’s experiment as well as in Mukai’s, MA lines showed faster-than-linear declines in viability, indicative of synergistic epistasis. Second, while Mukai’s estimate of the genomic mutation rate is supported, that from Ohnishi’s experiment is an order of magnitude lower. The different results of the experiments most likely resulted from differences in the starting genotypes; even within Mukai’s experiment, a subset of MA lines, which I argue probably resulted from a contamination event, showed much slower viability declines than did the majority of lines. Because different genotypes may show very different mutational behavior, only studies using many founding genotypes can determine the average rate and distribution of effects of mutations relevant to natural populations.

scholarly journals Genetic structure and gene flow of Eugenia dysenterica natural populations

2005 ◽  
Vol 40 (10) ◽  
pp. 975-980 ◽  
Author(s):  
Maria Imaculada Zucchi ◽  
José Baldin Pinheiro ◽  
Lázaro José Chaves ◽  
Alexandre Siqueira Guedes Coelho ◽  
Mansuêmia Alves Couto ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Variability ◽  
Pearson Correlation ◽  
Natural Populations ◽  
Similarity Index ◽  
Genetic Distances ◽  
Strong Positive Correlation ◽  
Randomly Amplified Polymorphic Dna ◽  
Jaccard Similarity ◽  
Eugenia Dysenterica

This study was carried out to assess the genetic variability of ten "cagaita" tree (Eugenia dysenterica) populations in Southeastern Goiás. Fifty-four randomly amplified polymorphic DNA (RAPD) loci were used to characterize the population genetic variability, using the analysis of molecular variance (AMOVA). A phiST value of 0.2703 was obtained, showing that 27.03% and 72.97% of the genetic variability is present among and within populations, respectively. The Pearson correlation coefficient (r) among the genetic distances matrix (1 - Jaccard similarity index) and the geographic distances were estimated, and a strong positive correlation was detected. Results suggest that these populations are differentiating through a stochastic process, with restricted and geographic distribution dependent gene flow.

scholarly journals GENE CONVERSION AND TRANSFER OF GENETIC INFORMATION WITHIN THE INVERTED REGION OF INVERSION HETEROZYGOTES

Genetics ◽  
1973 ◽  
Vol 75 (1) ◽  
pp. 123-131
Author(s):  
Arthur Chovnick
Keyword(s):  
Information Transfer ◽  
Logical Consequence ◽  
Natural Populations ◽  
Inverted Region ◽  
Order Of Magnitude ◽  
Inversion Heterozygote ◽  
Gene Complexes ◽  
Reciprocal Transfer ◽  
Comparison Of The Results ◽  
Transfer Of Information

ABSTRACT Prior studies of recombination which monitor exchange events in exceedingly short intervals (i.e., separable sites within a cistron) reveal that the basic event in recombination involves a non-reciprocal transfer of information, termed conversion. As a logical consequence of the model suggested by the work in Drosophila, the present investigation examined recombination between rosy mutant alleles (ry:3-52.0) in Drosophila melanogaster in a paracentric inversion (In(3R)P18) heterozygote, which placed the rosy region approximately at the center of the inverted region. Comparison of the results of this study with experiments carried out in standard chromosome homozygotes reveals a dramatic suppression of classical crossovers between the rosy mutant alleles in the inversion heterozygote. However, conversions continue to occur for all rosy mutant alleles in all heterozygous combinations in the inversion heterozygote. Moreover, the order of magnitude of conversion frequencies seen in the inversion heterozygote does not change from that seen in the standard chromosome homozygote study. The significance of these observations with reference to the role of rearrangements as barriers of information transfer is discussed. Particular attention is directed to the elaborate inversion polymorphisms seen in natural populations, and to notions concerning their role in the evolution of adaptive gene complexes.

scholarly journals Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2936 ◽  
Author(s):  
Caroline E. Dubé ◽  
Serge Planes ◽  
Yuxiang Zhou ◽  
Véronique Berteaux-Lecellier ◽  
Emilie Boissin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
454 Sequencing ◽  
Genetic Distances ◽  
Null Alleles ◽  
Future Research ◽  
Significant Linkage ◽  
Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Investigating heritability of cadmium tolerance in Chironomus riparius natural populations: A physiological approach

Chemosphere ◽  
2017 ◽  
Vol 170 ◽  
pp. 83-94 ◽  
Author(s):  
João Pedrosa ◽  
Carlos Gravato ◽  
Diana Campos ◽  
Paulo Cardoso ◽  
Etelvina Figueira ◽  
...  
Keyword(s):  
Natural Populations ◽  
Chironomus Riparius ◽  
Cadmium Tolerance ◽  
Physiological Approach

Genetic structure and variability in Pinusstrobus in Quebec

1994 ◽  
Vol 24 (8) ◽  
pp. 1726-1733 ◽  
Author(s):  
J. Beaulieu ◽  
J.-P. Simon
Keyword(s):  
Genetic Diversity ◽  
Statistical Tests ◽  
Natural Populations ◽  
Genetic Distances ◽  
White Pine ◽  
Eastern White Pine ◽  
Improvement Program ◽  
Bonferroni Procedure ◽  
Natural Range ◽  
Very High

The level of genetic diversity of natural populations of eastern white pine (Pinusstrobus L.) from Quebec was estimated from allozyme variants of 18 loci coding 12 enzyme systems. On average, a white pine population was polymorphic at 50.6% of loci, had 1.96 alleles and 1.22 effective alleles per locus, and observed and expected heterozygosities of 0.176 and 0.180, respectively. The level of genetic diversity was lower in the populations of the St. Lawrence lowlands than in those of western Quebec. This observation will help in guiding the selection program of the eastern white pine improvement program under way in Quebec. Genetic differentiation among sampled populations was weak and accounted for only 2% of the total diversity. The estimate of gene flow was very high, resulting in low values for genetic distances among populations. Only one locus showed a heterogeneity of allelic frequencies among populations after the Bonferroni procedure was applied for simultaneous statistical tests. A cluster analysis based on genetic distances among populations revealed that the Anticosti and Abitibi populations, located at the limit of the natural range of white pine, were similar to populations from regions that were geographically the most distant.

scholarly journals Satellite RNA of Cucumber Mosaic Cucumovirus Spreads Epidemically in Natural Populations of Its Helper Virus

1998 ◽  
Vol 88 (6) ◽  
pp. 520-524 ◽  
Author(s):  
José Luis Alonso-Prados ◽  
Miguel A. Aranda ◽  
José M. Malpica ◽  
Fernando García-Arenal ◽  
Aurora Fraile
Keyword(s):  
Natural Populations ◽  
Helper Virus ◽  
Genetic Distances ◽  
Ribonuclease Protection Assay ◽  
Satellite Rna ◽  
Nucleotide Substitutions ◽  
Single Population ◽  
Cucumber Mosaic Cucumovirus ◽  
Ribonuclease Protection ◽  
Dynamics Of Populations

Three hundred thirty-eight isolates of cucumber mosaic cucumovirus (CMV), sampled from natural populations in six areas of Spain between 1989 and 1996, were screened for the presence of satellite RNA (satRNA). The frequency of CMV isolates with satRNA approached 1.00 in Valencia (east Spain) between 1990 and 1994 where a tomato necrosis epidemic induced by CMV+satRNA had started in 1986 and was smaller north and west of this area in 1992 and 1993. After 1994, satRNA almost disappeared from all CMV populations. Genetic typing of satRNA variantswas done by ribonuclease protection assay, and from these data, genetic distances were estimated for any pair of satRNA variants. CMV-satRNA populations were highly diverse, containing 0.07865 nucleotide substitutions per site on average. Data also showed that the whole compared set of 100 satRNA variants form a single population that is not structured according to place, year, host plant, or strain of helper virus (HV). This is in sharp contrast with the metapopulation structure of the Spanish CMV population. Thus, the genetic structure and dynamics of populations of CMV and its satRNA are not coupled. This shows that CMV-satRNA spreads epidemically, as a hyperparasite, in the population of its HV. This conclusion is relevant to the use of CMV-satRNA as a biocontrol agent of CMV.

scholarly journals THE EFFECT OF COMBINING ALLELES INTO ELECTROPHORETIC CLASSES ON DETECTING LINKAGE DISEQUILIBRIUM

Genetics ◽  
1977 ◽  
Vol 85 (3) ◽  
pp. 543-556
Author(s):  
E Zouros ◽  
G B Golding ◽  
Trudy F C MacKay
Keyword(s):  
Linkage Disequilibrium ◽  
Sample Size ◽  
Natural Populations ◽  
Epistatic Interactions ◽  
Detection Power ◽  
Linkage Disequilibria ◽  
Allelic Distribution ◽  
Order Of Magnitude ◽  
Actual Degree

ABSTRACT When alleles are combined into few detectable classes, linkage correlations are underestimated most of the time. The probability that the linkage correlation will be underestimated is a function of the actual degree of correlation and the evenness of the allelic distribution, but is mainly determined by the distribution of alleles into distinguishable classes. With only two alleles per class this probability will usually be higher than 0.7. Also, the consistency in the sign of the linkage disequilibrium over many populations may escape detection. An increase of sample size by one order of magnitude or more may be required to compensate for the loss in detection power. It follows that the available electrophoretic studies of linkage correlations, although negative in their majority, do not suggest that epistatic interactions and linkage disequilibria are rare in natural populations.

scholarly journals Active learning of deep surrogates for PDEs: application to metasurface design

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Raphaël Pestourie ◽  
Youssef Mroueh ◽  
Thanh V. Nguyen ◽  
Payel Das ◽  
Steven G. Johnson
Keyword(s):  
Machine Learning ◽  
Active Learning ◽  
Large Scale ◽  
Learning Algorithm ◽  
Engineering Optimization ◽  
Optical Surface ◽  
Optical Wavelength ◽  
Random Samples ◽  
Training Cost ◽  
Order Of Magnitude

Abstract Surrogate models for partial differential equations are widely used in the design of metamaterials to rapidly evaluate the behavior of composable components. However, the training cost of accurate surrogates by machine learning can rapidly increase with the number of variables. For photonic-device models, we find that this training becomes especially challenging as design regions grow larger than the optical wavelength. We present an active-learning algorithm that reduces the number of simulations required by more than an order of magnitude for an NN surrogate model of optical-surface components compared to uniform random samples. Results show that the surrogate evaluation is over two orders of magnitude faster than a direct solve, and we demonstrate how this can be exploited to accelerate large-scale engineering optimization.

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