scholarly journals Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models

2016 ◽  
Author(s):  
Zhangyi He ◽  
Mark Beaumont ◽  
Feng Fu
Keyword(s):  
Population Dynamics ◽  
Life Cycle ◽  
Natural Selection ◽  
Population Regulation ◽  
Genetic Research ◽  
Natural Populations ◽  
Gene Migration ◽  
Local Selection ◽  
Fisher Model ◽  
Regulation Mechanisms

AbstractThe Wright-Fisher model and its extensions are of central importance in population genetics, and so far, they have formed the basis of most theoretical and applied population genetic research. In the present work, we explore the effect that the ordering of natural selection and population regulation in the life cycle has on the resulting population dynamics under the Wright-Fisher model, especially for the evolution of one- and two-locus systems. With weak natural selection, the details of how to order natural selection and population regulation in the life cycle do not matter in the Wright-Fisher model and its diffusion approximation. By contrast, we show that when there is strong natural selection and the population is in linkage disequilibrium, there can be appreciable differences in the resulting population dynamics under the Wright-Fisher model, depending on whether natural selection occurs before or after population regulation in the life cycle. We argue that this effect may be of significance in natural populations subject to gene migration and local selection.F.Y. supported in part by EPSRC Grant EP/I028498/1.

scholarly journals Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models

2017 ◽  
Vol 7 (7) ◽  
pp. 2095-2106 ◽  
Author(s):  
Zhangyi He ◽  
Mark Beaumont ◽  
Feng Yu
Keyword(s):  
Linkage Disequilibrium ◽  
Natural Selection ◽  
Population Regulation ◽  
Genetic Recombination ◽  
Gene Migration ◽  
Fisher Model ◽  
Fecundity Selection ◽  
Regulation Mechanisms ◽  
The Difference ◽  
Significant Linkage

Abstract We explore the effect of different mechanisms of natural selection on the evolution of populations for one- and two-locus systems. We compare the effect of viability and fecundity selection in the context of the Wright-Fisher model with selection under the assumption of multiplicative fitness. We show that these two modes of natural selection correspond to different orderings of the processes of population regulation and natural selection in the Wright-Fisher model. We find that under the Wright-Fisher model these two different orderings can affect the distribution of trajectories of haplotype frequencies evolving with genetic recombination. However, the difference in the distribution of trajectories is only appreciable when the population is in significant linkage disequilibrium. We find that as linkage disequilibrium decays the trajectories for the two different models rapidly become indistinguishable. We discuss the significance of these findings in terms of biological examples of viability and fecundity selection, and speculate that the effect may be significant when factors such as gene migration maintain a degree of linkage disequilibrium.

Laboratory comparison of the relative success of Biomphalaria glabrata stocks which are susceptible and insusceptible to infection with Schistosoma mansoni

Parasitology ◽  
1983 ◽  
Vol 86 (2) ◽  
pp. 335-344 ◽  
Author(s):  
D. J. Minchella ◽  
P. T. Loverde
Keyword(s):  
Life Cycle ◽  
Natural Selection ◽  
Reproductive Success ◽  
Natural Populations ◽  
Biomphalaria Glabrata ◽  
Selective Advantage ◽  
Controlled Conditions ◽  
Plausible Answer ◽  
Major Objection ◽  
Transmit Disease

SUMMARYA method of interrupting the life-cycle of the human blood fluke Schistosoma by increasing the proportion of genetically insusceptible intermediate host snails in natural populations was first proposed nearly 25 years ago. The method assumes that insusceptible snails will be at a selective advantage over susceptible snails when the schistosome parasite is present, and therefore natural selection will act to increase the proportion of alleles for insusceptibility. A major objection to the proposed technique is ‘If insusceptible snails are at a selective advantage, then why are they not predominant in natural populations that transmit disease?’ One explanation of this paradox is that insusceptibility may be associated with a disadvantageous character or a physiological defect. This study tests this hypothesis by measuring the relative reproductive success of susceptible and insusceptible snails under controlled conditions. Results indicate that insusceptible (unsuitable) snails are negatively affected in the presence of either susceptible snails or schistosome parasites. Furthermore, in the presence of both susceptible snails and schistosome parasites, insusceptible snails are selectively disadvantaged compared to susceptible snails. These results obtained under laboratory-controlled conditions suggest a plausible answer as to why insusceptible snails are not predominant in natural populations that transmit disease.

scholarly journals Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data

2021 ◽  
Author(s):  
Wenyang Lyu ◽  
Xiaoyang Dai ◽  
Mark Beaumont ◽  
Feng Yu ◽  
Zhangyi He
Keyword(s):  
Natural Selection ◽  
Ancient Dna ◽  
Natural Populations ◽  
Genetic Evolution ◽  
Ecological Context ◽  
Gene Migration ◽  
Monte Carlo Techniques ◽  
New Information ◽  
Statistical Approaches ◽  
Detection And Quantification

With the rapid growth of the number of sequenced ancient genomes, there has been increasing interest in using this new information to study past and present adaptation. Such an additional temporal component has the promise of providing improved power for the estimation of natural selection. Over the last decade, statistical approaches for detection and quantification of natural selection from ancient DNA (aDNA) data have been developed. However, most of the existing methods do not allow us to estimate the timing of natural selection along with its strength, which is key to understanding the evolution and persistence of organismal diversity. Additionally, most methods ignore the fact that natural populations are almost always structured, which can result in overestimation of the effect of natural selection. To address these issues, we propose a novel Bayesian framework for the inference of natural selection and gene migration from aDNA data with Markov chain Monte Carlo techniques, co-estimating both timing and strength of natural selection and gene migration. Such an advance enables us to infer drivers of natural selection and gene migration by correlating genetic evolution with potential causes such as the changes in the ecological context in which an organism has evolved. The performance of our procedure is evaluated through extensive simulations, with its utility shown with an application to ancient chicken samples.

scholarly journals Moment-based approximations for the Wright-Fisher model of population dynamics under natural selection at two linked loci

2021 ◽  
Author(s):  
Zhangyi He ◽  
Wenyang Lyu ◽  
Mark Beaumont ◽  
Feng Yu
Keyword(s):  
Population Dynamics ◽  
Natural Selection ◽  
Probability Distribution ◽  
Diffusion Approximation ◽  
Normal Approximation ◽  
Genetic Recombination ◽  
Transition Probability ◽  
Computational Cost ◽  
Fisher Model ◽  
Support Issue

AbstractProperly modelling genetic recombination and local linkage has been shown to bring a significant improvement to the inference of natural selection from time series genetic data under a Wright-Fisher model. Existing approaches that can take genetic recombination effect and local linkage information into account are built upon either the diffusion approximation or the moment-based approximation of the Wright-Fisher model. However, such approximations are either limited to the increased computational cost like the diffusion approximation or suffer from the distribution support issue like the normal approximation, which can seriously affect computational efficiency and accuracy. In this work, we propose two novel moment-based approximations for the Wright-Fisher model of population dynamics subject to natural selection at a pair of linked loci. Our key innovation is that we extend existing approaches to calculate the mean and (co)variance of the two-locus Wright-Fisher model with selection and suggest a logistic normal distribution or a hierarchical beta distribution as a parametric continuous probability distribution to approximate the Wright-Fisher model by matching its first two moments to those of the Wright-Fisher model. Compared with the diffusion approximation, our approximations enable the computation of the transition probability distribution of the Wright-Fisher model at a far smaller computational cost and also allow us to avoid the distribution support issue found in the normal approximation.

scholarly journals Polymorphism for Y-Linked Suppressors of sex-ratio in Two Natural Populations of Drosophila mediopunctata

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 891-902 ◽  
Author(s):  
Antonio Bernardo Carvalho ◽  
Suzana Casaccia Vaz ◽  
Louis Bernard Klaczko
Keyword(s):  
Population Genetics ◽  
Population Dynamics ◽  
Natural Selection ◽  
Sex Ratio ◽  
Numerical Simulations ◽  
Natural Populations ◽  
Meiotic Drive ◽  
X Chromosomes ◽  
Variable Expression ◽  
Y Chromosomes

In several Drosophila species there is a trait known as “sex-ratio”: males carrying certain X chromosomes (called “SR”) produce female biased progenies due to X-Y meiotic drive. In Drosophila mediopunctata this trait has a variable expression due to Y-linked suppressors of sex-ratio expression, among other factors. There are two types of Y chromosomes (suppressor and nonsuppressor) and two types of SR chromosomes (suppressible and unsuppressible). Sex-ratio expression is suppressed in males with the SRsuppressible/Ysuppressor genotype, whereas the remaining three genotypes produce female biased progenies. Now we have found that ∼10–20% of the Y chromosomes from two natural populations 1500 km apart are suppressors of sex-ratio expression. Preliminary estimates indicate that Ysuppressor has a meiotic drive advantage of 6% over Ynonsuppressor. This Y polymorphism for a nonneutral trait is unexpected under current population genetics theoly. We propose that this polymorphism is stabilized by an equilibrium between meiotic drive and natural selection, resulting from interactions in the population dynamics of X and Y alleles. Numerical simulations showed that this mechanism may stabilize nonneutral Y polymorphisms such as we have found in D. mediopunctata.

scholarly journals Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data

2021 ◽  
Author(s):  
Wenyang Lyu ◽  
Xiaoyang Dai ◽  
Mark Beaumont ◽  
Feng Yu ◽  
Zhangyi He
Keyword(s):  
Natural Selection ◽  
Ancient Dna ◽  
Natural Populations ◽  
Genetic Evolution ◽  
Ecological Context ◽  
Gene Migration ◽  
Monte Carlo Techniques ◽  
New Information ◽  
Statistical Approaches ◽  
Detection And Quantification

With the rapid growth of the number of sequenced ancient genomes, there has been increasing interest in using this new information to study past and present adaptation. Such an additional temporal component has the promise of providing improved power for the estimation of natural selection. Over the last decade, statistical approaches for detection and quantification of natural selection from ancient DNA (aDNA) data have been developed. However, most of the existing methods do not allow us to estimate the timing of natural selection along with its strength, which is key to understanding the evolution and persistence of organismal diversity. Additionally, most methods ignore the fact that natural populations are almost always structured. This can result in overestimation of the effect of natural selection. To address these issues, we propose a novel Bayesian framework for the inference of natural selection and gene migration from aDNA data with Markov chain Monte Carlo techniques, co-estimating both timing and strength of natural selection and gene migration. Such an advance enables us to infer drivers of natural selection and gene migration by correlating genetic evolution with potential causes such as the changes in the ecological context in which an organism has evolved. The performance of our procedure is evaluated through extensive simulations, with its utility shown with an application to ancient chicken samples.

Specific features of long-term domestication of australian crayfish Cherax quadricarinatus in conditions of the western part of Russian Federation

2018 ◽  
Vol 194 ◽  
pp. 188-192
Author(s):  
D. I. Shokasheva
Keyword(s):  
Natural Selection ◽  
Russian Federation ◽  
Natural Populations ◽  
Cherax Quadricarinatus ◽  
Local Environments ◽  
Local Species ◽  
Adaptive Ability

Natural populations of crayfish are in depression in Russia and local species are not cultivated. In this situation, experimental cultivation of allochtonous australian crayfish Cherax quadricarinatus is conducted. This species is distinguished by high reproductive abilities and good consumer properties. It has domesticated in Russia spontaneously and produced 9–10 generations in Astrakhan Region. Certain natural selection in the process of domestication provides adaptive ability of this species to local environments and its capabil­ity to reproduce a viable progeny, so there is no doubts in good prospects of its cultivation in industrial conditions.

scholarly journals GENETIC LOAD IN NATURAL POPULATIONS: IS IT COMPATIBLE WITH THE HYPOTHESIS THAT MANY POLYMORPHISMS ARE MAINTAINED BY NATURAL SELECTION?

Genetics ◽  
1974 ◽  
Vol 77 (3) ◽  
pp. 569-589
Author(s):  
Martin L Tracey ◽  
Francisco J Ayala
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Natural Population ◽  
Natural Populations ◽  
Genetic Load ◽  
Structural Genes ◽  
Invertebrate Species ◽  
Average Proportion ◽  
Mean Fitness ◽  
The Mean

ABSTRACT Recent studies of genetically controlled enzyme variation lead to an estimation that at least 30 to 60% of the structural genes are polymorphic in natural populations of many vertebrate and invertebrate species. Some authors have argued that a substantial proportion of these polymorphisms cannot be maintained by natural selection because this would result in an unbearable genetic load. If many polymorphisms are maintained by heterotic natural selection, individuals with much greater than average proportion of homozygous loci should have very low fitness. We have measured in Drosophila melanogaster the fitness of flies homozygous for a complete chromosome relative to normal wild flies. A total of 37 chromosomes from a natural population have been tested using 92 experimental populations. The mean fitness of homozygous flies is 0.12 for second chromosomes, and 0.13 for third chromosomes. These estimates are compatible with the hypothesis that many (more than one thousand) loci are maintained by heterotic selection in natural populations of D. melanogaster.

scholarly journals Evolutionary dynamics of spore killers.

Genetics ◽  
1993 ◽  
Vol 135 (3) ◽  
pp. 923-930 ◽  
Author(s):  
M J Nauta ◽  
R F Hoekstra
Keyword(s):  
Life Cycle ◽  
Segregation Distortion ◽  
Population Genetic ◽  
Field Data ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Additional Advantage ◽  
Genetic Modeling ◽  
Spore Killing ◽  
Ascospore Formation

Abstract Spore killing in ascomycetes is a special form of segregation distortion. When a strain with the Killer genotype is crossed to a Sensitive type, spore killing is expressed by asci with only half the number of ascospores as usual, all surviving ascospores being of the Killer type. Using population genetic modeling, this paper explores conditions for invasion of Spore killers and for polymorphism of Killers, Sensitives and Resistants (which neither kill, nor get killed), as found in natural populations. The models show that a population with only Killers and Sensitives can never be stable. The invasion of Killers and stable polymorphism only occur if Killers have some additional advantage during the process of spore killing. This may be due to the effects of local sib competition or some kind of "heterozygous" advantage in the stage of ascospore formation or in the short diploid stage of the life cycle. This form of segregation distortion appears to be essentially different from other, well-investigated forms, and more field data are needed for a better understanding of spore killing.

scholarly journals Signatures of natural selection between life cycle stages separated by metamorphosis in European eel

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
J. M. Pujolar ◽  
M. W. Jacobsen ◽  
D. Bekkevold ◽  
J. Lobón-Cervià ◽  
B. Jónsson ◽  
...  
Keyword(s):  
Life Cycle ◽  
Natural Selection ◽  
European Eel ◽  
Life Cycle Stages
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