Random Genetic Drift in Small Populations

2020 ◽  
pp. 147-178
Author(s):  
Daniel L. Hartl
Keyword(s):  
Amino Acid ◽  
Allele Frequency ◽  
Genetic Drift ◽  
Diffusion Processes ◽  
Natural Populations ◽  
Small Populations ◽  
Random Genetic Drift ◽  
Diffusion Approximations ◽  
Sampling Formula ◽  
Allozyme Polymorphisms

Chapter 6 deals with the consequences of random genetic drift in finite populations and includes details of the diffusion approximations and their solutions as well as conditional diffusion processes. It includes probabilities of fixation and conditional times to fixation for neutral and nonneutral alleles. Various scenarios of mutation, migration, and selection are examined with regard to the stationary distributions of allele frequency. The Ewens sampling formula and its importance is discussed, as well as its implications for the distribution of the number of alleles in samples. An analysis of allozyme polymorphisms supports the hypothesis that most amino acid polymorphisms in natural populations are slightly deleterious.

On Some Theoretical Studies on Gene Differentiation in Natural Populations

1975 ◽  
Vol 24 (1-2) ◽  
pp. 111-117
Author(s):  
Ranajit Chakraborty
Keyword(s):  
Genetic Variation ◽  
Genetic Drift ◽  
Molecular Level ◽  
Gene Diversity ◽  
Natural Populations ◽  
Simultaneous Action ◽  
Present Moment ◽  
Theoretical Studies ◽  
Random Genetic Drift ◽  
Approaches To Study

Different mathematical approaches to study the extent of genetic variation of natural populations are reviewed. The modern understanding of the gene structure permits new interpretations of existing concepts like fixation or inbreeding. A more recent measure of genie divergence, which at molecular level is designed to measure net codon differences is also seen to be related with gene diversity in a substructed population. It is argued that such variations are produced and preserved possibly by simultaneous action of migration, mutation, selection, and random genetic drift. At the present moment it is very difficult to isolate out the effect of each factor because of varying degrees of variation at the different gene sites and between different sets of populations.

scholarly journals Constraints on Allele Size at Microsatellite Loci: Implications for Genetic Differentiation

Genetics ◽  
1996 ◽  
Vol 143 (2) ◽  
pp. 1021-1032 ◽  
Author(s):  
Maarten J Nauta ◽  
Franz J Weissing
Keyword(s):  
Genetic Drift ◽  
Time Perspective ◽  
Sequence Data ◽  
Distance Measures ◽  
Population Divergence ◽  
Small Populations ◽  
Random Genetic Drift ◽  
Microsatellite Data ◽  
Mutation Pressure ◽  
History Of

Abstract Microsatellites are promising genetic markers for studying the demographic structure and phylogenetic history of populations. We present theoretical arguments indicating that the usefulness of microsatellite data for these purposes may be limited to a short time perspective and to relatively small populations. The evolution of selectively neutral markers is governed by the interaction of mutation and random genetic drift. Mutation pressure has the inherent tendency to shift different populations to the same distribution of alleles. Hence, mutation pressure is a homogenizing force, and population divergence is caused by random genetic drift. In case of allozymes or sequence data, the diversifying effect of drift is typically orders of magnitude larger than the homogenizing effect of mutation pressure. By a simple model, we demonstrate that the situation may be different for microsatellites where mutation rates are high and the range of alleles is limited. With the help of computer simulations, we investigate to what extent genetic distance measures applied to microsatellite data can nevertheless yield useful estimators for phylogenetic relationships or demographic parameters. We show that predictions based on microsatellite data are quite reliable in small populations, but that already in moderately sized populations the danger of misinterpretation is substantial.

scholarly journals The genetic structure of natural populations of Drosophila melanogaster. XXII. Comparative study of DNA polymorphisms in northern and southern natural populations.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 753-761
Author(s):  
T S Takano ◽  
S Kusakabe ◽  
T Mukai
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Drift ◽  
Nucleotide Diversity ◽  
Restriction Site ◽  
Natural Populations ◽  
Dna Polymorphisms ◽  
Restriction Map ◽  
Random Genetic Drift ◽  
Two Populations ◽  
Restriction Site Polymorphisms

Abstract Restriction map variation in four gene regions (Adh, Amy, Pu and Gpdh) was surveyed for 86 second chromosomes from northern (Aomori) and southern (Ogasawara) Japanese populations of Drosophila melanogaster (43 chromosomes from each population). The regions examined cover a total of 62 kilobases. Estimates of nucleotide diversity (pi) were approximately constant across the gene regions and populations examined. The distribution of restriction site polymorphisms was compatible with the expectation from the neutral mutation-random genetic drift hypothesis, but insertion/deletion polymorphisms were not consistent with it. While the two populations shared a majority of restriction site polymorphisms, frequencies of individual restriction site variants were significantly different between the two populations at 7 out of 35 segregating sites. In addition, an insertion in the Amy region was found in 15 chromosomes from the Ogasawara sample but absent in the Aomori sample. A considerable difference was observed in the number of rare insertions and deletions between the two populations. The numbers of aberrations uniquely represented were 16 in the Ogasawara sample and only 3 in the Aomori sample. These findings suggest that the two populations were differentiated from each other to some degree by means of random genetic drift and/or other factors.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals Recombination Can Evolve in Large Finite Populations Given Selection on Sufficient Loci

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2249-2258 ◽  
Author(s):  
Mark M Iles ◽  
Kevin Walters ◽  
Chris Cannings
Keyword(s):  
Experimental Evidence ◽  
Genetic Drift ◽  
Finite Population ◽  
Selective Advantage ◽  
Indirect Selection ◽  
Small Populations ◽  
Finite Populations ◽  
Population Sizes ◽  
Population Recombination

AbstractIt is well known that an allele causing increased recombination is expected to proliferate as a result of genetic drift in a finite population undergoing selection, without requiring other mechanisms. This is supported by recent simulations apparently demonstrating that, in small populations, drift is more important than epistasis in increasing recombination, with this effect disappearing in larger finite populations. However, recent experimental evidence finds a greater advantage for recombination in larger populations. These results are reconciled by demonstrating through simulation without epistasis that for m loci recombination has an appreciable selective advantage over a range of population sizes (am, bm). bm increases steadily with m while am remains fairly static. Thus, however large the finite population, if selection acts on sufficiently many loci, an allele that increases recombination is selected for. We show that as selection acts on our finite population, recombination increases the variance in expected log fitness, causing indirect selection on a recombination-modifying locus. This effect is enhanced in those populations with more loci because the variance in phenotypic fitnesses in relation to the possible range will be smaller. Thus fixation of a particular haplotype is less likely to occur, increasing the advantage of recombination.

CYTO-NUCLEAR EPISTASIS: TWO-LOCUS RANDOM GENETIC DRIFT IN HERMAPHRODITIC AND DIOECIOUS SPECIES

Evolution ◽  
2006 ◽  
Vol 60 (4) ◽  
pp. 643 ◽  
Author(s):  
Michael J. Wade ◽  
Charles J. Goodnight
Keyword(s):  
Genetic Drift ◽  
Random Genetic Drift ◽  
Dioecious Species

scholarly journals Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1envEvolution During Chronic Infection

Genetics ◽  
2004 ◽  
Vol 166 (3) ◽  
pp. 1155-1164 ◽  
Author(s):  
Daniel Shriner ◽  
Raj Shankarappa ◽  
Mark A. Jensen ◽  
David C. Nickle ◽  
John E. Mittler ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Genetic Drift ◽  
Chronic Infection ◽  
Random Genetic Drift ◽  
Immunodeficiency Virus

NUMERICAL ANALYSIS OF RANDOM DRIFT IN A CLINE

Genetics ◽  
1980 ◽  
Vol 94 (2) ◽  
pp. 497-517
Author(s):  
Thomas Nagylaki ◽  
Bradley Lucier
Keyword(s):  
Natural Populations ◽  
The Other ◽  
Random Genetic Drift ◽  
Gene Frequencies ◽  
Random Drift ◽  
Linear Habitat ◽  
Asymptotic Formulae ◽  
A Chain ◽  
Average Position ◽  
Uniform Population

ABSTRACT The equilibrium state of a diffusion model for random genetic drift in a cline is analyzed numerically. The monoecious organism occupies an unbounded linear habitat with constant, uniform population density. Migration is homogeneouq symmetric and independent of genotype. A single diallelic locus with a step environment is investigated in the absence of dominance and mutation. The flattening of the expected cline due to random drift is very slight in natural populations. The ratio of the variance of either gene frequency to the product of the expected gene frequencies decreases monotonically to a nonzero constant. The correlation between the gene frequencies at two points decreases monotonically to zero as the separation is increased with the average position fixed; the decrease is asymptotically exponential. The correlation decreases monotonically to a positive constant depending on the separation as the average position increasingly deviates from the center of the cline with the separation fixed. The correlation also decreases monotonically to zero if one of the points is fixed and the other is moved outward in the habitat, the ultimate decrease again being exponential. Some asymptotic formulae are derived analytically.—The loss of an allele favored in an environmental pocket is investigated by simulating a chain of demes exchanging migrants, the other assumptions being the same as above. For most natural populations, provided the allele would be maintained in the population deterministically, this process is too slow to have evolutionary importance.

scholarly journals A General Solution of the Wright–Fisher Model of Random Genetic Drift

2016 ◽  
Vol 27 (4) ◽  
pp. 467-492 ◽  
Author(s):  
Tat Dat Tran ◽  
Julian Hofrichter ◽  
Jürgen Jost
Keyword(s):  
General Solution ◽  
Genetic Drift ◽  
Random Genetic Drift ◽  
Fisher Model

scholarly journals Evolution of gene regulatory networks by means of selection and random genetic drift

2018 ◽  
Author(s):  
Antonios Kioukis ◽  
Pavlos Pavlidis
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Genetic Drift ◽  
Regulatory Networks ◽  
Fitness Landscape ◽  
Random Genetic Drift ◽  
Maturation Period ◽  
Evolutionary Forces ◽  
Gene Regulatory

The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. Furthermore, it is not known if existing tools that identify recent and strong positive selection from genomic sequences, in simple models of evolution, can detect recent positive selection when it operates on GRNs. Here, we propose a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. Since the population size is finite, random genetic drift is explicitly applied. The fitness of a mutation is not constant, but we evaluate the fitness of each individual by measuring its genetic distance from an optimal genotype. Mutations and recombination may take place from generation to generation, modifying the genotypic composition of the population. Each individual goes through a maturation period, where its GRN reaches equilibrium. At the next step, individuals compete to produce the next generation. As time progresses, the beneficial genotypes push the population higher in the fitness landscape. We examine properties of the GRN evolution such as robustness against the deleterious effect of mutations and the role of genetic drift. We confirm classical results from Andreas Wagner’s work that GRNs show robustness against mutations and we provide new results regarding the interplay between random genetic drift and natural selection.

Sign in / Sign up

Export Citation Format

Share Document