scholarly journals SIMULATION OF X-LINKED SELECTION IN DROSOPHILA

Genetics ◽  
1976 ◽  
Vol 83 (3) ◽  
pp. 551-571
Author(s):  
Philip W Hedrick
Keyword(s):  
Gene Frequency ◽  
Frequency Change ◽  
Wild Type ◽  
Weak Selection ◽  
Gene Frequencies ◽  
Linked Gene ◽  
Males And Females ◽  
Genetic Simulation ◽  
Linked Selection ◽  
Best Fit

ABSTRACT The change in gene frequency for two X-linked mutants, y and w, in a number of experiments was compared to that predicted from a genetic simulation program which utilized estimated differences in relative mating ability, fecundity, and viability. The simulation gave excellent predictions of gene frequency change even when experiments were started with different initial gene frequencies in the males and females or when the two loci were segregating simultaneously. The rate of elimination was slower when there were unequal initial gene frequencies than when males and females had equal initial gene frequencies. Simulation demonstrated that this was a general phenomenon when there is strong selection but that the opposite is true for weak selection. In two other experiments, the mating advantage of wild-type males was balanced by a fecundity advantage in mutant females. In all four replicates of both experiments, the mutant was maintained for several generations at the high initial frequency but then decreased quickly and was eliminated. Results obtained restarting one of these experiments with flies from a generation after the decline in gene frequency indicated that a linked gene and not frequency-dependent selection was responsible for the unpredictable gene-frequency change in the mutant. Using a least squares technique, it was found that a recessive fecundity locus 15 map units from the w locus gave the best fit for bothexperiments.

scholarly journals Maximum likelihood estimation of fitness components in experimental evolution

2018 ◽  
Author(s):  
Jingxian Liu ◽  
Jackson Champer ◽  
Chen Liu ◽  
Joan Chung ◽  
Riona Reeves ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Likelihood Estimation ◽  
Loss Of Function ◽  
Wild Type ◽  
Fitness Components ◽  
Linked Gene ◽  
Males And Females

AbstractEstimating fitness differences between allelic variants is a central goal of experimental evolution. Current methods for inferring selection from allele frequency time series typically assume that evolutionary dynamics at the locus of interest can be described by a fixed selection coefficient. However, fitness is an aggregate of several components including mating success, fecundity, and viability, and distinguishing between these components could be critical in many scenarios. Here we develop a flexible maximum likelihood framework that can disentangle different components of fitness and estimate them individually in males and females from genotype frequency data. As a proof-of-principle, we apply our method to experimentally-evolved cage populations of Drosophila melanogaster, in which we tracked the relative frequencies of a loss-of-function and wild-type allele of yellow. This X-linked gene produces a recessive yellow phenotype when disrupted and is involved in male courtship ability. We find that the fitness costs of the yellow phenotype take the form of substantially reduced mating preference of wild-type females for yellow males, together with a modest reduction in the viability of yellow males and females. Our framework should be generally applicable to situations where it is important to quantify fitness components of specific genetic variants, including quantitative characterization of the population dynamics of CRISPR gene drives.

scholarly journals Maximum Likelihood Estimation of Fitness Components in Experimental Evolution

Genetics ◽  
2019 ◽  
Vol 211 (3) ◽  
pp. 1005-1017 ◽  
Author(s):  
Jingxian Liu ◽  
Jackson Champer ◽  
Anna Maria Langmüller ◽  
Chen Liu ◽  
Joan Chung ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Experimental Evolution ◽  
Likelihood Estimation ◽  
Loss Of Function ◽  
Wild Type ◽  
Fitness Components ◽  
Linked Gene ◽  
Males And Females ◽  
Gene Drives

Estimating fitness differences between allelic variants is a central goal of experimental evolution. Current methods for inferring such differences from allele frequency time series typically assume that the effects of selection can be described by a fixed selection coefficient. However, fitness is an aggregate of several components including mating success, fecundity, and viability. Distinguishing between these components could be critical in many scenarios. Here, we develop a flexible maximum likelihood framework that can disentangle different components of fitness from genotype frequency data, and estimate them individually in males and females. As a proof-of-principle, we apply our method to experimentally evolved cage populations of Drosophila melanogaster, in which we tracked the relative frequencies of a loss-of-function and wild-type allele of yellow. This X-linked gene produces a recessive yellow phenotype when disrupted and is involved in male courtship ability. We find that the fitness costs of the yellow phenotype take the form of substantially reduced mating preference of wild-type females for yellow males, together with a modest reduction in the viability of yellow males and females. Our framework should be generally applicable to situations where it is important to quantify fitness components of specific genetic variants, including quantitative characterization of the population dynamics of CRISPR gene drives.

scholarly journals Geographical patterns of gene frequencies in Italian populations of Ornithogalum montanum (Liliaceae)

1991 ◽  
Vol 58 (2) ◽  
pp. 95-104 ◽  
Author(s):  
Massimo Pigliucci ◽  
Guido Barbujani
Keyword(s):  
Gene Frequency ◽  
Genetic Relationships ◽  
Environmental Parameter ◽  
Allele Frequencies ◽  
Population Subdivision ◽  
Restricted Gene Flow ◽  
Frequency Change ◽  
Gene Frequencies ◽  
Unit Distance ◽  
Geographical Patterns

SummaryGeographic variation was studied at 15 electrophoretic loci (40 alleles) in Italian populations of Ornithogalum montanum Cyr. ex Ten. (Liliaceae). Homogeneity of allele frequencies was assessed by G tests; gene-frequency patterns were described by spatial autocorrelation statistics; matrices of genetic and environmental distance were compared through a series of Mantel's tests, and the zones of highest overall gene-frequency change per unit distance (steep multi-locus clines, or genetic boundaries) were identified. Nineteen allele frequencies appear heterogeneously distributed, but only 3 of them show significant spatial structure. Only 2 allele frequencies are correlated with 1 environmental parameter. Large genetic differences are observed between spatially close populations. These findings support a model of differentiation in which the genetic relationships between isolates do not depend on their spatial distances, but reflect mainly population subdivision and restricted gene flow.

scholarly journals Evolution under Fertility and Viability Selection

Genetics ◽  
1987 ◽  
Vol 115 (2) ◽  
pp. 367-375
Author(s):  
Thomas Nagylaki
Keyword(s):  
Gene Frequency ◽  
Geometric Mean ◽  
Rate Of Change ◽  
Frequency Change ◽  
Weak Selection ◽  
Significant Gene ◽  
Explicit Time Dependence ◽  
Mean Fitness ◽  
The Mean ◽  
Dioecious Populations

ABSTRACT Evolution at a single multiallelic locus under arbitrary weak selection on both fertility and viability is investigated. Discrete, nonoverlapping generations are posited for autosomal and X-linked loci in dioecious populations, but monoecious populations are studied in both discrete and continuous time. Mating is random. The results hold after several generations have elapsed. With an error of order s [i.e., O(s)], where s represents the selection intensity, the population evolves in Hardy-Weinberg proportions. Provided the change per generation of the fertilities and viabilities due to their explicit time dependence (if any) is O(s  2), the rate of change of the deviation from Hardy-Weinberg proportions is O(s  2). If the change per generation of the viabilities and genotypic fertilities is smaller than second order [i.e., o(s  2)], then to O(s  2) the rate of change of the mean fitness is equal to the genic variance. The mean fitness is the product of the mean fertility and the mean viability; in dioecious populations, the latter is the unweighted geometric mean of the mean viabilities of the two sexes. Hence, as long as there is significant gene frequency change, the mean fitness increases. If it is the fertilities of matings that change slowly [at rate o(s  2)], the above conclusions apply to a modified mean fitness, defined as the product of the mean viability and the square root of the mean fertility.

scholarly journals A MARKOV PROCESS OF GENE FREQUENCY CHANGE IN A GEOGRAPHICALLY STRUCTURED POPULATION

Genetics ◽  
1974 ◽  
Vol 76 (2) ◽  
pp. 367-377
Author(s):  
Takeo Maruyama
Keyword(s):  
Genetic Variation ◽  
Markov Process ◽  
Diffusion Process ◽  
Gene Frequency ◽  
Transition Probabilities ◽  
Large Population ◽  
Sample Path ◽  
Time Parameter ◽  
Frequency Change ◽  
Structured Population

ABSTRACT A Markov process (chain) of gene frequency change is derived for a geographically-structured model of a population. The population consists of colonies which are connected by migration. Selection operates in each colony independently. It is shown that there exists a stochastic clock that transforms the originally complicated process of gene frequency change to a random walk which is independent of the geographical structure of the population. The time parameter is a local random time that is dependent on the sample path. In fact, if the alleles are selectively neutral, the time parameter is exactly equal to the sum of the average local genetic variation appearing in the population, and otherwise they are approximately equal. The Kolmogorov forward and backward equations of the process are obtained. As a limit of large population size, a diffusion process is derived. The transition probabilities of the Markov chain and of the diffusion process are obtained explicitly. Certain quantities of biological interest are shown to be independent of the population structure. The quantities are the fixation probability of a mutant, the sum of the average local genetic variation and the variation summed over the generations in which the gene frequency in the whole population assumes a specified value.

scholarly journals A comparison of two methods for predicting changes in the distribution of gene frequency when selection is applied repeatedly to a finite population

1969 ◽  
Vol 13 (2) ◽  
pp. 117-126 ◽  
Author(s):  
Derek J. Pike
Keyword(s):  
Iterative Procedure ◽  
Gene Frequency ◽  
Finite Population ◽  
Transition Matrices ◽  
Single Cycle ◽  
Gene Frequencies ◽  
Mean And Variance ◽  
The Mean ◽  
The One ◽  
Selection Of

Robertson (1960) used probability transition matrices to estimate changes in gene frequency when sampling and selection are applied to a finite population. Curnow & Baker (1968) used Kojima's (1961) approximate formulae for the mean and variance of the change in gene frequency from a single cycle of selection applied to a finite population to develop an iterative procedure for studying the effects of repeated cycles of selection and regeneration. To do this they assumed a beta distribution for the unfixed gene frequencies at each generation.These two methods are discussed and a result used in Kojima's paper is proved. A number of sets of calculations are carried out using both methods and the results are compared to assess the accuracy of Curnow & Baker's method in relation to Robertson's approach.It is found that the one real fault in the Curnow-Baker method is its tendency to fix too high a proportion of the genes, particularly when the initial gene frequency is near to a fixation point. This fault is largely overcome when more individuals are selected. For selection of eight or more individuals the Curnow-Baker method is very accurate and appreciably faster than the transition matrix method.

scholarly journals exrB: amalB-linked gene inEscherichia coliB involved in sensitivity to radiation and filament formation

1974 ◽  
Vol 23 (2) ◽  
pp. 175-184 ◽  
Author(s):  
Joseph Greenberg ◽  
Leonard J. Berends ◽  
John Donch ◽  
Michael H. L. Green
Keyword(s):  
Escherichia Coli ◽  
Normal Growth ◽  
Filament Formation ◽  
Wild Type ◽  
Sensitive Mutant ◽  
Γ Radiation ◽  
Linked Gene ◽  
Derivatives Of

SUMMARYPAM 26, a radiation-sensitive mutant ofEscherichia colistrain B, is described. Its properties are attributable to a mutation in a gene,exrB, which is cotransducible withmalB. It differs fromuvrA(alsomalB-linked) derivatives of strain B in being sensitive to 1-methyl-3-nitro-1-nitroso-guanidine and γ-radiation, and in being able to reactivate UV-irradiated phage T3. It differs fromexrA(alsomalB-linked) derivatives of strain B in forming filaments during the course of normal growth as well as after irradiation. WhenexrBwas transduced into a K12 (lon+) strain, filaments did not form spontaneously. Three-point transductions established the order of markers asmet A malB exrB. Based on an analysis of the frequency of wild-type recombinants in a reciprocal transduction betweenexrAandexrBstrains, it was inferred that they are not isogenic and that the order of markers ismalB exrA exrB.

scholarly journals Linking Genes to Traits in Fungi

2021 ◽  
Author(s):  
A. L. Romero-Olivares ◽  
E. W. Morrison ◽  
A. Pringle ◽  
S. D. Frey
Keyword(s):  
Organic Matter ◽  
Nitrogen Uptake ◽  
Brown Rot ◽  
Terrestrial Ecosystems ◽  
Organic Matter Decomposition ◽  
Gene Frequencies ◽  
Ecological Processes ◽  
Linked Gene ◽  
Carbon Cycles ◽  
Brown Rot Fungi

AbstractFungi are mediators of the nitrogen and carbon cycles in terrestrial ecosystems. Examining how nitrogen uptake and organic matter decomposition potential differs in fungi can provide insight into the underlying mechanisms driving fungal ecological processes and ecosystem functioning. In this study, we assessed the frequency of genes encoding for specific enzymes that facilitate nitrogen uptake and organic matter decomposition in 879 fungal genomes with fungal taxa grouped into trait-based categories. Our linked gene-trait data approach revealed that gene frequencies vary across and within trait-based groups and that trait-based categories differ in trait space. We present two examples of how this linked gene-trait approach can be used to address ecological questions. First, we show that this type of approach can help us better understand, and potentially predict, how fungi will respond to environmental stress. Specifically, we found that trait-based categories with high nitrogen uptake gene frequency increased in relative abundance when exposed to high soil nitrogen enrichment. Second, by comparing frequencies of nitrogen uptake and organic matter decomposition genes, we found that most ectomycorrhizal fungi in our dataset have similar gene frequencies to brown rot fungi. This demonstrates that gene-trait data approaches can shed light on potential evolutionary trajectories of life history traits in fungi. We present a framework for exploring nitrogen uptake and organic matter decomposition gene frequencies in fungal trait-based groups and provide two concise examples on how to use our framework to address ecological questions from a mechanistic perspective.

scholarly journals MALE-SPECIFIC LETHAL MUTATIONS OF DROSOPHILA MELANOGASTER. II. PARAMETERS OF GENE ACTION DURING MALE DEVELOPMENT

Genetics ◽  
1983 ◽  
Vol 105 (4) ◽  
pp. 881-896
Author(s):  
John M Belote
Keyword(s):  
Growth Patterns ◽  
Gene Products ◽  
Wild Type ◽  
Linked Gene ◽  
Lethal Mutations ◽  
Male Specific Lethal ◽  
A Cell ◽  
Type Gene ◽  
Diploid Cells ◽  
Male Specific

ABSTRACT The male-specific lethal mutations (msl's) identify loci whose wild-type gene products are essential for male, but not female, viability. Earlier studies in which X-linked gene activities were monitored in msl/msl male larvae demonstrated that these genes are responsible for setting and/or maintaining the level of X chromosome transcription in males (i.e., they are necessary for proper dosage compensation). The present study examines several important questions concerning their mode of action during development—The results of an examination of the effects of an msl-1 deficiency on male-lethal phase and female viability suggest that this mutation is an amorph, or a severe hypomorph. The effects of rendering a fly mutant for more than one male-lethal mutation were also examined. Multiply mutant flies were no more severely affected than singly mutant ones. A gynandromorph analysis revealed that the male-limited lethality associated with msl-2 has no single lethal focus. Somatic clones of homozygous msl-2 cells were initiated at various times during development by X-ray-induced mitotic recombination. An examination of the viability, growth patterns and morphology of marked clones demonstrated that: (1) msl-2  + acts in a cell autonomous manner, (2) msl-2  + function is required not only in larval (polytene) cells as was shown in previous work but is also needed in the diploid cells that give rise to adult structures, (3) the msl-2  + gene is needed fairly late in development and perhaps continuously, (4) the msl-2 mutation does not affect sexual differentiation.

scholarly journals On sojourn times at particular gene frequencies

1975 ◽  
Vol 25 (2) ◽  
pp. 89-94 ◽  
Author(s):  
Edward Pollak ◽  
Barry C. Arnold
Keyword(s):  
Markov Chains ◽  
Gene Frequency ◽  
Overlapping Generations ◽  
Finite Population ◽  
Diffusion Method ◽  
Gene Frequencies ◽  
Sojourn Times ◽  
The Mean ◽  
Number Of Visits ◽  
Finite Markov Chains

SUMMARYThe distribution of visits to a particular gene frequency in a finite population of size N with non-overlapping generations is derived. It is shown, by using well-known results from the theory of finite Markov chains, that all such distributions are geometric, with parameters dependent only on the set of bij's, where bij is the mean number of visits to frequency j/2N, given initial frequency i/2N. The variance of such a distribution does not agree with the value suggested by the diffusion method. An improved approximation is derived.

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