Selection in a Subdivided Population With Local Extinction and Recolonization

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 789-795 ◽  
Author(s):  
Joshua L Cherry
Keyword(s):  
Natural Selection ◽  
Local Extinction ◽  
Fixation Probability ◽  
Selection Coefficient ◽  
Additional Source ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Theoretical Predictions ◽  
Fixation Probabilities ◽  
Do So

Abstract In a subdivided population, local extinction and subsequent recolonization affect the fate of alleles. Of particular interest is the interaction of this force with natural selection. The effect of selection can be weakened by this additional source of stochastic change in allele frequency. The behavior of a selected allele in such a population is shown to be equivalent to that of an allele with a different selection coefficient in an unstructured population with a different size. This equivalence allows use of established results for panmictic populations to predict such quantities as fixation probabilities and mean times to fixation. The magnitude of the quantity Nese, which determines fixation probability, is decreased by extinction and recolonization. Thus deleterious alleles are more likely to fix, and advantageous alleles less likely to do so, in the presence of extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.

scholarly journals Selection, Subdivision and Extinction and Recolonization

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 1105-1114 ◽  
Author(s):  
Joshua L Cherry
Keyword(s):  
Frequency Dependence ◽  
Allele Frequency ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Theoretical Predictions ◽  
Subdivided Populations ◽  
Fixation Probabilities ◽  
Selection Parameters ◽  
To Come ◽  
Do So

Abstract In a subdivided population, the interaction between natural selection and stochastic change in allele frequency is affected by the occurrence of local extinction and subsequent recolonization. The relative importance of selection can be diminished by this additional source of stochastic change in allele frequency. Results are presented for subdivided populations with extinction and recolonization where there is more than one founding allele after extinction, where these may tend to come from the same source deme, where the number of founding alleles is variable or the founders make unequal contributions, and where there is dominance for fitness or local frequency dependence. The behavior of a selected allele in a subdivided population is in all these situations approximately the same as that of an allele with different selection parameters in an unstructured population with a different size. The magnitude of the quantity Nese, which determines fixation probability in the case of genic selection, is always decreased by extinction and recolonization, so that deleterious alleles are more likely to fix and advantageous alleles less likely to do so. The importance of dominance or frequency dependence is also altered by extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.

scholarly journals Fixation probabilities in graph-structured populations under weak selection

2021 ◽  
Vol 17 (2) ◽  
pp. e1008695
Author(s):  
Benjamin Allen ◽  
Christine Sample ◽  
Patricia Steinhagen ◽  
Julia Shapiro ◽  
Matthew King ◽  
...  
Keyword(s):  
Natural Selection ◽  
Search Algorithm ◽  
Weighted Graph ◽  
Structured Populations ◽  
Death Process ◽  
Fixation Probability ◽  
Graph Structure ◽  
Weak Selection ◽  
Arbitrary Graph ◽  
Fixation Probabilities

A population’s spatial structure affects the rate of genetic change and the outcome of natural selection. These effects can be modeled mathematically using the Birth-death process on graphs. Individuals occupy the vertices of a weighted graph, and reproduce into neighboring vertices based on fitness. A key quantity is the probability that a mutant type will sweep to fixation, as a function of the mutant’s fitness. Graphs that increase the fixation probability of beneficial mutations, and decrease that of deleterious mutations, are said to amplify selection. However, fixation probabilities are difficult to compute for an arbitrary graph. Here we derive an expression for the fixation probability, of a weakly-selected mutation, in terms of the time for two lineages to coalesce. This expression enables weak-selection fixation probabilities to be computed, for an arbitrary weighted graph, in polynomial time. Applying this method, we explore the range of possible effects of graph structure on natural selection, genetic drift, and the balance between the two. Using exhaustive analysis of small graphs and a genetic search algorithm, we identify families of graphs with striking effects on fixation probability, and we analyze these families mathematically. Our work reveals the nuanced effects of graph structure on natural selection and neutral drift. In particular, we show how these notions depend critically on the process by which mutations arise.

scholarly journals Fixation probability in spatially changing environments

1991 ◽  
Vol 58 (3) ◽  
pp. 243-251 ◽  
Author(s):  
Hidenori Tachida ◽  
Masaru Iizuka
Keyword(s):  
Local Population ◽  
Fixation Probability ◽  
Two Dimensional ◽  
Selection Coefficient ◽  
Changing Environments ◽  
Subdivided Population ◽  
Subdivided Populations ◽  
Varying Environments ◽  
And Migration ◽  
Spatially Varying

SummaryThe fixation probability of a mutant in a subdivided population with spatially varying environments is investigated using a finite island model. This probability is different from that in a panmictic population if selection is intermediate to strong and migration is weak. An approximation is used to compute the fixation probability when migration among subpopulations is very weak. By numerically solving the two-dimensional partial differential equation for the fixation probability in the two subpopulation case, the approximation was shown to give fairly accurate values. With this approximation, we show in the case of two subpopulations that the fixation probability in subdivided populations is greater than that in panmictic populations mostly. The increase is most pronounced when the mutant is selected for in one subpopulation and is selected against in the other subpopulation. Also it is shown that when there are two types of environments, further subdivision of subpopulations does not cause much change of the fixation probability in the no dominance case unless the product of the selection coefficient and the local population size is less than one. With dominance, the effect of subdivision becomes more complex.

scholarly journals The Effect of Deleterious Alleles on Adaptation in Asexual Populations

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 395-411 ◽  
Author(s):  
Toby Johnson ◽  
Nick H Barton
Keyword(s):  
Selective Sweep ◽  
Deleterious Mutation ◽  
Short Interval ◽  
Selective Advantage ◽  
Asexual Population ◽  
Restrictive Assumption ◽  
Deleterious Alleles ◽  
Fixation Probabilities ◽  
Asexual Populations ◽  
Beneficial Allele

Abstract We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.

scholarly journals The Population Genetics of Synthetic Lethals

Genetics ◽  
1998 ◽  
Vol 150 (1) ◽  
pp. 449-458 ◽  
Author(s):  
Patrick C Phillips ◽  
Norman A Johnson
Keyword(s):  
Double Mutant ◽  
Single Locus ◽  
Single Mutation ◽  
Hybrid Breakdown ◽  
Selection Coefficient ◽  
Deleterious Alleles ◽  
Synthetic Lethals ◽  
Mutant Homozygote ◽  
Diploid Model

Abstract Synthetic lethals are variants at different loci that have little or no effect on viability singly but cause lethality in combination. The importance of synthetic lethals and, more generally, of synthetic deleterious loci (SDL) has been controversial. Here, we derive the expected frequencies for SDL under a mutation-selection balance for the complete haploid model and selected cases of the diploid model. We have also obtained simple approximations that demonstrate good fit to exact solutions based on numerical iterations. In the haploid case, equilibrium frequencies of carrier haplotypes (individuals with only a single mutation) are comparable to analogous single-locus results, after allowing for the effects of linkage. Frequencies in the diploid case, however, are much higher and more comparable to the square root of the single-locus results. In particular, when selection operates only on the double-mutant homozygote and linkage is not too tight, the expected frequency of the carriers is approximately the quartic root of the ratio between the mutation rate and the selection coefficient of the synthetics. For a reasonably wide set of models, the frequencies of carriers can be on the order of a few percent. The equilibrium frequencies of these deleterious alleles can be relatively high because, with SDL, both dominance and epistasis act to shield carriers from exposure to selection. We also discuss the possible role of SDL in maintaining genetic variation and in hybrid breakdown.

scholarly journals Selection, Load and Inbreeding Depression in a Large Metapopulation

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1191-1202 ◽  
Author(s):  
Michael C Whitlock
Keyword(s):  
Population Structure ◽  
Inbreeding Depression ◽  
Population Subdivision ◽  
Response To Selection ◽  
Mutation Load ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Soft Selection ◽  
Mean Fitness ◽  
The Mean

Abstract The subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient FST and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.

Adaptation and Natural Selection

2021 ◽  
pp. 125-154
Author(s):  
Áki J. Láruson ◽  
Floyd A. Reed
Keyword(s):  
Natural Selection ◽  
Allele Frequency ◽  
Levels Of Selection ◽  
Frequency Data ◽  
Selection Coefficient ◽  
Frequency Distributions ◽  
Single Allele ◽  
Selection Strength ◽  
The Difference ◽  
Over Time

Here non-random shifts in allele frequencies over time are introduced, as well as how to incorporate varying levels of selection into a model of a single population through time. This chapter highlights the difference between weak and strong selection, the dynamics of single allele versus genotype-level selection, and how selection strength and population size affect allele frequency distributions over time. Finally the inference of the selection coefficient from allele frequency data is discussed, alongside the concepts of overdominance and underdominance.

scholarly journals Sexual Selection Does Not Increase the Rate of Compensatory Adaptation to a Mutation Influencing a Secondary Sexual Trait in Drosophila melanogaster

2020 ◽  
Vol 10 (5) ◽  
pp. 1541-1551
Author(s):  
Christopher H. Chandler ◽  
Anna Mammel ◽  
Ian Dworkin
Keyword(s):  
Drosophila Melanogaster ◽  
Sexual Selection ◽  
Natural Selection ◽  
Spontaneous Mutation ◽  
Phenotypic Expression ◽  
Theoretical Work ◽  
Phenotypic Suppression ◽  
Compensatory Adaptation ◽  
Deleterious Alleles ◽  
Sex Comb

Theoretical work predicts that sexual selection can enhance natural selection, increasing the rate of adaptation to new environments and helping purge harmful mutations. While some experiments support these predictions, remarkably little work has addressed the role of sexual selection on compensatory adaptation—populations’ ability to compensate for the costs of deleterious alleles that are already present. We tested whether sexual selection, as well as the degree of standing genetic variation, affect the rate of compensatory evolution via phenotypic suppression in experimental populations of Drosophila melanogaster. These populations were fixed for a spontaneous mutation causing mild abnormalities in the male sex comb, a structure important for mating success. We fine-mapped this mutation to an ∼85 kb region on the X chromosome containing three candidate genes, showed that the mutation is deleterious, and that its phenotypic expression and penetrance vary by genetic background. We then performed experimental evolution, including a treatment where opportunity for mate choice was limited by experimentally enforced monogamy. Although evolved populations did show some phenotypic suppression of the morphological abnormalities in the sex comb, the amount of suppression did not depend on the opportunity for sexual selection. Sexual selection, therefore, may not always enhance natural selection; instead, the interaction between these two forces may depend on additional factors.

Genetic load and biological changes to extant humans

2020 ◽  
pp. 1-4
Author(s):  
Arthur Saniotis ◽  
Maciej Henneberg ◽  
Kazhaleh Mohammadi
Keyword(s):  
Natural Selection ◽  
Current Knowledge ◽  
Genetic Load ◽  
Differential Fertility ◽  
Medical Interventions ◽  
Deleterious Alleles ◽  
Gradual Process ◽  
Genetic Complexity ◽  
Sexual Recombination ◽  
Improved Sanitation

Abstract Extant humans are currently increasing their genetic load, which is informing present and future human microevolution. This has been a gradual process that has been rising over the last centuries as a consequence of improved sanitation, nutritional improvements, advancements in microbiology and medical interventions, which have relaxed natural selection. Moreover, a reduction in infant and child mortality and changing societal attitudes towards fertility have led to a decrease in total fertility rates (TFRs) since the 19th century. Generally speaking, decreases in differential fertility and mortality have meant that there is less opportunity for natural selection to eliminate deleterious mutations from the human gene pool. It has been argued that the average human may carry ~250–300 mutations that are mostly deleterious, as well as several hundred less-deleterious variants. These deleterious alleles in extant humans mean that our fitness is being constrained. While such alleles are viewed as reducing human fitness, they may also have had an adaptive function in the past, such as assisting in genetic complexity, sexual recombination and diploidy. Saying this, our current knowledge on these fitness compromising alleles is still lacking.

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