scholarly journals The Effects of Multilocus Balancing Selection on Neutral Variability

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 849-863 ◽  
Author(s):  
Arcadio Navarro ◽  
Nick H Barton
Keyword(s):  
Linkage Disequilibrium ◽  
Balancing Selection ◽  
Gametic Disequilibrium ◽  
Nucleotide Variability ◽  
Large Populations ◽  
Simulation Results ◽  
Structured Coalescent ◽  
Neutral Mutations ◽  
Random Fluctuations ◽  
Neutral Case

Abstract We studied the effect of multilocus balancing selection on neutral nucleotide variability at linked sites by simulating a model where diallelic polymorphisms are maintained at an arbitrary number of selected loci by means of symmetric overdominance. Different combinations of alleles define different genetic backgrounds that subdivide the population and strongly affect variability. Several multilocus fitness regimes with different degrees of epistasis and gametic disequilibrium are allowed. Analytical results based on a multilocus extension of the structured coalescent predict that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. Our simulation results show that although variability increases with the number of genetic backgrounds that are maintained in the population, it is reduced by random fluctuations in the frequencies of those backgrounds and does not reach high levels even in very large populations. We also show that previous results on balancing selection in single-locus systems do not extend to the multilocus scenario in a straightforward way. Different patterns of linkage disequilibrium and of the frequency spectrum of neutral mutations are expected under different degrees of epistasis. Interestingly, the power to detect balancing selection using deviations from a neutral distribution of allele frequencies seems to be diminished under the fitness regime that leads to the largest increase of variability over the neutral case. This and other results are discussed in the light of data from the Mhc.

scholarly journals Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Christelle Vangenot ◽  
José Manuel Nunes ◽  
Gaby M. Doxiadis ◽  
Estella S. Poloni ◽  
Ronald E. Bontrop ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Molecular Diversity ◽  
Selective Sweep ◽  
Balancing Selection ◽  
Substantial Effect ◽  
Human Populations ◽  
Large Set ◽  
Large Populations ◽  
Population Sizes

Abstract Background Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations’ survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. Results Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. Conclusions We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations – like that ascribed to a viral epidemic – exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans’ peopling history. We thus propose a model where chimpanzees’ MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.

scholarly journals Recombination and Selection at Brassica Self-Incompatibility Loci

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 413-425 ◽  
Author(s):  
Philip Awadalla ◽  
Deborah Charlesworth
Keyword(s):  
Linkage Disequilibrium ◽  
Balancing Selection ◽  
Brassica Species ◽  
Selective Constraint ◽  
Intragenic Recombination ◽  
Self Incompatibility ◽  
History Of ◽  
Unknown Gene ◽  
Slg Gene ◽  
High Diversity

Abstract In Brassica species, self-incompatibility is controlled genetically by haplotypes involving two known genes, SLG and SRK, and possibly an as yet unknown gene controlling pollen incompatibility types. Alleles at the incompatibility loci are maintained by frequency-dependent selection, and diversity at SLG and SRK appears to be very ancient, with high diversity at silent and replacement sites, particularly in certain “hypervariable portions of the genes. It is important to test whether recombination occurs in these genes before inferences about function of different parts of the genes can be made from patterns of diversity within their sequences. In addition, it has been suggested that, to maintain the relationship between alleles within a given S-haplotype, recombination is suppressed in the S-locus region. The high diversity makes many population genetic measures of recombination inapplicable. We have analyzed linkage disequilibrium within the SLG gene of two Brassica species, using published coding sequences. The results suggest that intragenic recombination has occurred in the evolutionary history of these alleles. This is supported by patterns of synonymous nucleotide diversity within both the SLG and SRK genes, and between domains of the SRK gene. Finally, clusters of linkage disequilibrium within the SLG gene suggest that hypervariable regions are under balancing selection, and are not merely regions of relaxed selective constraint.

scholarly journals The coalescent process in models with selection, recombination and geographic subdivision

1991 ◽  
Vol 57 (1) ◽  
pp. 83-91 ◽  
Author(s):  
Norman Kaplan ◽  
Richard R. Hudson ◽  
Masaru Iizuka
Keyword(s):  
Genetic Variation ◽  
Population Genetic ◽  
Genetic Model ◽  
Sequence Data ◽  
Balancing Selection ◽  
Similar Model ◽  
Proposed Model ◽  
Coalescent Approach ◽  
Neutral Mutations ◽  
Better Than

SummaryA population genetic model with a single locus at which balancing selection acts and many linked loci at which neutral mutations can occur is analysed using the coalescent approach. The model incorporates geographic subdivision with migration, as well as mutation, recombination, and genetic drift of neutral variation. It is found that geographic subdivision can affect genetic variation even with high rates of migration, providing that selection is strong enough to maintain different allele frequencies at the selected locus. Published sequence data from the alcohol dehydrogenase locus of Drosophila melanogaster are found to fit the proposed model slightly better than a similar model without subdivision.

Population and quantitative genetics of many linked loci in finite populations

1983 ◽  
Vol 219 (1216) ◽  
pp. 253-264 ◽  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Dna Sequence ◽  
Quantitative Genetics ◽  
Quantitative Traits ◽  
Theoretical Studies ◽  
Population Surveys ◽  
Finite Populations ◽  
Simulation Results ◽  
New Mutations

Theoretical studies on the effects of linkage on variability of quantitative traits and response to directional selection in finite populations are reviewed. Emphasis is given to predictions that can be based on observable parameters, such as population size, chromosome lengths and the increment in variance from new mutations. Although truncation selection produces negative linkage disequilibrium in infinite populations, simulation results show that the effects of linkage on response are more pronounced in finite populations. Substantial linkage disequilibrium at the DNA sequence level is being found in population surveys. Some of the results and their interpretation are discussed.

scholarly journals Extensive Linkage Disequilibrium, a Common 16.7-Kilobase Deletion, and Evidence of Balancing Selection in the Human Protocadherin α Cluster

2003 ◽  
Vol 72 (3) ◽  
pp. 621-635 ◽  
Author(s):  
James P. Noonan ◽  
Jun Li ◽  
Loan Nguyen ◽  
Chenier Caoile ◽  
Mark Dickson ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Balancing Selection

scholarly journals Structured Coalescent Processes on Different Time Scales

Genetics ◽  
1997 ◽  
Vol 146 (4) ◽  
pp. 1501-1514 ◽  
Author(s):  
Magnus Nordborg
Keyword(s):  
Local Adaptation ◽  
Time Scales ◽  
Balancing Selection ◽  
Background Selection ◽  
Selfing Rate ◽  
Local Selection ◽  
Structured Coalescent ◽  
High Degree ◽  
Different Time Scales ◽  
Coalescence Times

It is demonstrated that the structured coalescent model can readily be extended to include phenomena such as partial selfing and background selection through the use of an approximation based on separation of time scales. A model that includes these phenomena, as well as geographic subdivision and linkage to a polymorphism maintained either by local adaptation or by balancing selection, is derived, and the expected coalescence time for a pair of genes is calculated. It is found that background selection reduces coalescence times within subpopulations and allelic classes, leading to a high degree of apparent differentiation. Extremely high levels of subpopulation differentiation are also expected for regions of the genome surrounding loci important in local adaptation. These regions will be wider the stronger the local selection, and the higher the selfing rate.

Nucleotide variability and linkage disequilibrium patterns at the porcineFABP5gene

2008 ◽  
Vol 39 (5) ◽  
pp. 468-473 ◽  
Author(s):  
A. Ojeda ◽  
J. Estellé ◽  
J. M. Folch ◽  
M. Pérez-Enciso
Keyword(s):  
Linkage Disequilibrium ◽  
Nucleotide Variability

scholarly journals The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations

1997 ◽  
Vol 70 (2) ◽  
pp. 155-174 ◽  
Author(s):  
BRIAN CHARLESWORTH ◽  
MAGNUS NORDBORG ◽  
DEBORAH CHARLESWORTH
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Balancing Selection ◽  
Polymorphic Locus ◽  
Stochastic Simulations ◽  
Population Subdivision ◽  
Background Selection ◽  
Balanced Polymorphism ◽  
Local Selection ◽  
Species Population

Levels of neutral genetic diversity in populations subdivided into two demes were studied by multi-locus stochastic simulations. The model includes deleterious mutations at loci throughout the genome, causing ‘background selection’, as well as a single locus at which a polymorphism is maintained, either by frequency-dependent selection or by local selective differences. These balanced polymorphisms induce long coalescence times at linked neutral loci, so that sequence diversity at these loci is enhanced at statistical equilibrium. We study how equilibrium neutral diversity levels are affected by the degree of population subdivision, the presence or absence of background selection, and the level of inbreeding of the population. The simulation results are compared with approximate analytical formulae, assuming the infinite sites neutral model. We discuss how balancing selection can be distinguished from local selection, by determining whether peaks of diversity in the region of the polymorphic locus are seen within or between demes. The width of such diversity peaks is shown to depend on the total species population size, rather than local deme sizes. We show that, with population subdivision, local selection enhances between-deme diversity even at neutral sites distant from the polymorphic locus, producing higher FST values than with no selection; very high values can be generated at sites close to a selected locus. Background selection also increases FST, mainly because of decreased diversity within populations, which implies that its effects may be distinguishable from those of local selection. Both effects are stronger in selfing than outcrossing populations. Linkage disequilibrium between neutral sites is generated by both balancing and local selection, especially in selfing populations, because of linkage disequilibrium between the neutral sites and the selectively maintained alleles. We discuss how these theoretical results can be related to data on genetic diversity within and between local populations of a species.

Noise Based Independent Component Analysis Model for Harmonic Current Estimation

2012 ◽  
Vol 433-440 ◽  
pp. 2551-2555
Author(s):  
P. Supriya ◽  
T.N. Padmanabhan Nambiar
Keyword(s):  
Independent Component Analysis ◽  
Component Analysis ◽  
Independent Component ◽  
Analysis Model ◽  
Noise Elimination ◽  
Interconnected Power System ◽  
Harmonic Currents ◽  
Current Estimation ◽  
Simulation Results ◽  
Random Fluctuations

In a deregulating environment, Independent Component Analysis (ICA) is used to estimate the harmonic currents of non linear loads as it does not require information about the topology of the network. However, analysis is done by ignoring the effect of various noises that creep into the measurement system. In the present work, the effect of environmental noise on a simple interconnected power system with five buses is taken up. The two algorithms namely Fast ICA (FICA) and Efficient Variant Fast ICA(EFICA) are used for the analysis. A fixed noise is added and it is eliminated using whitening technique The simulation results of both algorithms show that noise elimination by whitening technique is highly successful. However, EFICA gives better results than FICA when random fluctuations of load exist rather than when fixed variations exist.

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