scholarly journals Selfish Genes, Pleiotropy and the Origin of Recombination

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2089-2097 ◽  
Author(s):  
Jody Hey
Keyword(s):  
Natural Selection ◽  
Simple Model ◽  
Computer Simulations ◽  
Recombination Rate ◽  
Evolutionary Origin ◽  
Deleterious Mutations ◽  
Beneficial Mutations ◽  
Selfish Genes ◽  
Simple Interaction

Abstract If multiple linked polymorphisms are under natural selection, then conflicts arise and the efficiency of natural selection is hindered relative to the case of no linkage. This simple interaction between linkage and natural selection creates an opportunity for mutations that raise the level of recombination to increase in frequency and have an enhanced chance of fixation. This important finding by S. Otto and N. Barton means that mutations that raise the recombination rate, but are otherwise neutral, will be selectively favored under fairly general circumstances of multilocus selection and linkage. The effect described by Otto and Barton, which was limited to neutral modifiers, can also be extended to include all modifiers of recombination, both beneficial and deleterious. Computer simulations show that beneficial mutations that also increase recombination have an increased chance of fixation. Similarly, deleterious mutations that also decrease recombination have an increased chance of fixation. The results suggest that a simple model of recombination modifiers, including both neutral and pleiotropic modifiers, is a necessary explanation for the evolutionary origin of recombination.

scholarly journals The Evolution of Recombination: Removing the Limits to Natural Selection

Genetics ◽  
1997 ◽  
Vol 147 (2) ◽  
pp. 879-906 ◽  
Author(s):  
Sarah Perin Otto ◽  
Nick H Barton
Keyword(s):  
Natural Selection ◽  
Mutation Rate ◽  
Recombination Rate ◽  
Evolutionary Change ◽  
Fixation Probability ◽  
Beneficial Mutation ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
Tight Linkage ◽  
Selection For

One of the oldest hypotheses for the advantage of recombination is that recombination allows beneficial mutations that arise in different individuals to be placed together on the same chromosome. Unless recombination occurs, one of the beneficial alleles is doomed to extinction, slowing the rate at which adaptive mutations are incorporated within a population. We model the effects of a modifier of recombination on the fixation probability of beneficial mutations when beneficial alleles are segregating at other loci. We find that modifier alleles that increase recombination do increase the fixation probability of beneficial mutants and subsequently hitchhike along as the mutants rise in frequency. The strength of selection favoring a modifier that increases recombination is proportional to λ2  Sδr/r when linkage is tight and λ2  S  3δr/N when linkage is loose, where λ is the beneficial mutation rate per genome per generation throughout a population of size N, S is the average mutant effect, r is the average recombination rate, and δr is the amount that recombination is modified. We conclude that selection for recombination will be substantial only if there is tight linkage within the genome or if many loci are subject to directional selection as during periods of rapid evolutionary change.

Interactions Between Natural Selection, Recombination and Gene Density in the Genes of Drosophila

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 595-608 ◽  
Author(s):  
Jody Hey ◽  
Richard M Kliman
Keyword(s):  
Gene Expression ◽  
Natural Selection ◽  
Recombination Rate ◽  
Codon Bias ◽  
Gene Density ◽  
Drosophila Genome ◽  
Functional Variation ◽  
Subtle Effect ◽  
Efficiency Of Selection ◽  
The Impact

AbstractIn Drosophila, as in many organisms, natural selection leads to high levels of codon bias in genes that are highly expressed. Thus codon bias is an indicator of the intensity of one kind of selection that is experienced by genes and can be used to assess the impact of other genomic factors on natural selection. Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significant, association with recombination—as expected if recombination allows natural selection to act more efficiently when multiple linked sites segregate functional variation. The same reasoning leads to the expectation that the efficiency of selection, and thus average codon bias, should decline with gene density. However, this prediction is not confirmed. Levels of codon bias and gene expression are highest for those genes in an intermediate range of gene density, a pattern that may be the result of a tradeoff between the advantages for gene expression of close gene spacing and disadvantages arising from regulatory conflicts among tightly packed genes. These factors appear to overlay the more subtle effect of linkage among selected sites that gives rise to the association between recombination rate and codon bias.

scholarly journals Estimation of Parameters of Deleterious Mutations in Partial Selfing or Partial Outcrossing Populations and in Nonequilibrium Populations

Genetics ◽  
2000 ◽  
Vol 154 (4) ◽  
pp. 1893-1906 ◽  
Author(s):  
Jian Li ◽  
Hong-Wen Deng
Keyword(s):  
Computer Simulations ◽  
Natural Populations ◽  
Deleterious Mutations ◽  
Selfing Rate ◽  
Estimation Of Parameters ◽  
Animal Populations ◽  
Rapid Pace ◽  
Dynamics Of Populations ◽  
Mutation And Selection

Abstract The Deng-Lynch method was developed to estimate the rate and effects of deleterious genomic mutations (DGM) in natural populations under the assumption that populations are either completely outcrossing or completely selfing and that populations are at mutation-selection (M-S) balance. However, in many plant and animal populations, selfing or outcrossing is often incomplete in that a proportion of populations undergo inbreeding while the rest are outcrossing. In addition, the degrees of deviation of populations from M-S balance are often not known. Through computer simulations, we investigated the robustness and the applicability of the Deng-Lynch method under different degrees of partial selfing or partial outcrossing and for nonequilibrium populations approaching M-S balance at different stages. The investigation was implemented under constant, variable, and epistatic mutation effects. We found that, generally, the estimation by the Deng-Lynch method is fairly robust if the selfing rate (S) is <0.10 in outcrossing populations and if S > 0.8 in selfing populations. The estimation may be unbiased under partial selfing with variable and epistatic mutation effects in predominantly outcrossing populations. The estimation is fairly robust in nonequilibrium populations at different stages approaching M-S balance. The dynamics of populations approaching M-S balance under various parameters are also studied. Under mutation and selection, populations approach balance at a rapid pace. Generally, it takes 400–2000 generations to reach M-S balance even when starting from homogeneous individuals free of DGM. Our investigation here provides a basis for characterizing DGM in partial selfing or outcrossing populations and for nonequilibrium populations.

scholarly journals The Advantages of Segregation and the Evolution of Sex

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1099-1118 ◽  
Author(s):  
Sarah P Otto
Keyword(s):  
Sexual Reproduction ◽  
Asexual Reproduction ◽  
Deleterious Mutations ◽  
Evolution Of Sex ◽  
Beneficial Mutations ◽  
Selection Regime ◽  
Strong Selection ◽  
Genome Wide ◽  
Low Levels

AbstractIn diploids, sexual reproduction promotes both the segregation of alleles at the same locus and the recombination of alleles at different loci. This article is the first to investigate the possibility that sex might have evolved and been maintained to promote segregation, using a model that incorporates both a general selection regime and modifier alleles that alter an individual’s allocation to sexual vs. asexual reproduction. The fate of different modifier alleles was found to depend strongly on the strength of selection at fitness loci and on the presence of inbreeding among individuals undergoing sexual reproduction. When selection is weak and mating occurs randomly among sexually produced gametes, reductions in the occurrence of sex are favored, but the genome-wide strength of selection is extremely small. In contrast, when selection is weak and some inbreeding occurs among gametes, increased allocation to sexual reproduction is expected as long as deleterious mutations are partially recessive and/or beneficial mutations are partially dominant. Under strong selection, the conditions under which increased allocation to sex evolves are reversed. Because deleterious mutations are typically considered to be partially recessive and weakly selected and because most populations exhibit some degree of inbreeding, this model predicts that higher frequencies of sex would evolve and be maintained as a consequence of the effects of segregation. Even with low levels of inbreeding, selection is stronger on a modifier that promotes segregation than on a modifier that promotes recombination, suggesting that the benefits of segregation are more likely than the benefits of recombination to have driven the evolution of sexual reproduction in diploids.

scholarly journals Mismatch induced speciation in Salmonella : model and data

2006 ◽  
Vol 361 (1475) ◽  
pp. 2045-2053 ◽  
Author(s):  
Daniel Falush ◽  
Mia Torpdahl ◽  
Xavier Didelot ◽  
Donald F Conrad ◽  
Daniel J Wilson ◽  
...  
Keyword(s):  
New Species ◽  
Natural Selection ◽  
Dna Sequence ◽  
Computer Simulations ◽  
De Novo ◽  
Sequence Data ◽  
Biological Species ◽  
Species Boundaries ◽  
Population Subdivision ◽  
Geographical Population

In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations which show that the homology dependence of recombination can cause de novo speciation in a neutrally evolving population once a critical population size has been exceeded. Our model can explain the patterns of divergence and genetic exchange observed in the genus Salmonella , without invoking either natural selection or geographical population subdivision. If this model was validated, based on extensive sequence data, it would imply that the named subspecies of Salmonella enterica correspond to good biological species, making species boundaries objective. However, multilocus sequence typing data, analysed using several conventional tools, provide a misleading impression of relationships within S. enterica subspecies enterica and do not provide the resolution to establish whether new species are presently being formed.

scholarly journals The evolution of superstitious and superstition-like behaviour

2008 ◽  
Vol 276 (1654) ◽  
pp. 31-37 ◽  
Author(s):  
Kevin R Foster ◽  
Hanna Kokko
Keyword(s):  
Popular Culture ◽  
Natural Selection ◽  
Simple Model ◽  
Correct Response ◽  
Evolutionary Biology ◽  
Adaptive Behaviour ◽  
Multiple Events ◽  
Cause And Effect ◽  
Pascal’S Wager ◽  
Hamilton's Rule

Superstitious behaviours, which arise through the incorrect assignment of cause and effect, receive considerable attention in psychology and popular culture. Perhaps owing to their seeming irrationality, however, they receive little attention in evolutionary biology. Here we develop a simple model to define the condition under which natural selection will favour assigning causality between two events. This leads to an intuitive inequality—akin to an amalgam of Hamilton's rule and Pascal's wager—-that shows that natural selection can favour strategies that lead to frequent errors in assessment as long as the occasional correct response carries a large fitness benefit. It follows that incorrect responses are the most common when the probability that two events are really associated is low to moderate: very strong associations are rarely incorrect, while natural selection will rarely favour making very weak associations. Extending the model to include multiple events identifies conditions under which natural selection can favour associating events that are never causally related. Specifically, limitations on assigning causal probabilities to pairs of events can favour strategies that lump non-causal associations with causal ones. We conclude that behaviours which are, or appear, superstitious are an inevitable feature of adaptive behaviour in all organisms, including ourselves.

scholarly journals Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data

2016 ◽  
Author(s):  
Paula Tataru ◽  
Maéva Mollion ◽  
Sylvain Glemin ◽  
Thomas Bataillon
Keyword(s):  
Molecular Evolution ◽  
Evolutionary Genetics ◽  
Deleterious Mutations ◽  
Probabilistic Framework ◽  
Evolutionary Trajectory ◽  
Beneficial Mutations ◽  
Fitness Effects ◽  
Polymorphism Data ◽  
Inference Methods ◽  
Biased Estimates

ABSTRACTThe distribution of fitness effects (DFE) encompasses deleterious, neutral and beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the rate of adaptive molecular evolution (α). Inference of DFE and α from patterns of polymorphism (SFS) and divergence data has been a longstanding goal of evolutionary genetics. A widespread assumption shared by numerous methods developed so far to infer DFE and α from such data is that beneficial mutations contribute only negligibly to the polymorphism data. Hence, a DFE comprising only deleterious mutations tends to be estimated from SFS data, and α is only predicted by contrasting the SFS with divergence data from an outgroup. Here, we develop a hierarchical probabilistic framework that extends on previous methods and also can infer DFE and α from polymorphism data alone. We use extensive simulations to examine the performance of our method. We show that both a full DFE, comprising both deleterious and beneficial mutations, and α can be inferred without resorting to divergence data. We demonstrate that inference of DFE from polymorphism data alone can in fact provide more reliable estimates, as it does not rely on strong assumptions about a shared DFE between the outgroup and ingroup species used to obtain the SFS and divergence data. We also show that not accounting for the contribution of beneficial mutations to polymorphism data leads to substantially biased estimates of the DFE and α. We illustrate these points using our newly developed framework, while also comparing to one of the most widely used inference methods available.

scholarly journals Evolutionary stalling and a limit on the power of natural selection to improve a cellular module

2020 ◽  
Vol 117 (31) ◽  
pp. 18582-18590 ◽  
Author(s):  
Sandeep Venkataram ◽  
Ross Monasky ◽  
Shohreh H. Sikaroodi ◽  
Sergey Kryazhimskiy ◽  
Betul Kacar
Keyword(s):  
Escherichia Coli ◽  
Natural Selection ◽  
Adaptive Evolution ◽  
Genetic Load ◽  
Performance Theory ◽  
Biological Functions ◽  
Beneficial Mutations ◽  
Translation Machinery ◽  
Adaptive Mutations ◽  
Organismal Fitness

Cells consist of molecular modules which perform vital biological functions. Cellular modules are key units of adaptive evolution because organismal fitness depends on their performance. Theory shows that in rapidly evolving populations, such as those of many microbes, adaptation is driven primarily by common beneficial mutations with large effects, while other mutations behave as if they are effectively neutral. As a consequence, if a module can be improved only by rare and/or weak beneficial mutations, its adaptive evolution would stall. However, such evolutionary stalling has not been empirically demonstrated, and it is unclear to what extent stalling may limit the power of natural selection to improve modules. Here we empirically characterize how natural selection improves the translation machinery (TM), an essential cellular module. We experimentally evolved populations ofEscherichia coliwith genetically perturbed TMs for 1,000 generations. Populations with severe TM defects initially adapted via mutations in the TM, but TM adaptation stalled within about 300 generations. We estimate that the genetic load in our populations incurred by residual TM defects ranges from 0.5 to 19%. Finally, we found evidence that both epistasis and the depletion of the pool of beneficial mutations contributed to evolutionary stalling. Our results suggest that cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations.

DIFFUSION OF A POPULATION OF INTERACTING REPLICATORS IN SEQUENCE SPACE

2002 ◽  
Vol 05 (04) ◽  
pp. 457-461 ◽  
Author(s):  
BÄRBEL M. R. STADLER
Keyword(s):  
Simple Model ◽  
Population Size ◽  
Computer Simulations ◽  
Mutation Rate ◽  
Sequence Space ◽  
Finite Population ◽  
Fitness Landscape ◽  
Diffusion Constant ◽  
Sequence Length

We consider a simple model for catalyzed replication. Computer simulations show that a finite population moves in sequence space by diffusion analogous to the behavior of a quasispecies on a flat fitness landscape. The diffusion constant depends linearly on the per position mutation rate and the ratio of sequence length and population size.

A Simplified Bioenergetics Model of a Hammerhead Shark for Teaching Natural Selection

2019 ◽  
Vol 81 (2) ◽  
pp. 115-119
Author(s):  
Jay Y. S. Hodgson
Keyword(s):  
Natural Selection ◽  
Reproductive Success ◽  
Computer Simulations ◽  
Trade Off ◽  
Bioenergetics Model ◽  
Hammerhead Shark ◽  
Differential Reproductive Success ◽  
Evolutionary Consequences ◽  
Successful Predation

Students often have difficulty understanding the underpinning mechanisms of natural selection because they lack the means to directly test hypotheses within the classroom. Computer simulations are ideal platforms to allow students to manipulate variables and observe evolutionary outcomes; however, many available models solve the scenario for the users without revealing the evolutionarily significant calculations. I developed a simplified bioenergetics model of a hammerhead shark for teaching natural selection that allows the users to manipulate variables and see the impacts of modeling while solving for the evolutionary consequences. Students generate variation within the population by controlling cephalofoil widths and swimming speeds of an individual, which affect its ability to detect and capture prey at the expense of energy lost as drag from swimming. The trade-off between energy gained from successful predation and energy lost from metabolic expenditures dictates rates of reproduction. By manipulating a subset of factors that influence differential reproductive success, students gain an improved understanding of natural selection.

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