scholarly journals The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens

2010 ◽  
Vol 7 (1) ◽  
pp. 98-100 ◽  
Author(s):  
Michael J. McDonald ◽  
Tim F. Cooper ◽  
Hubertus J. E. Beaumont ◽  
Paul B. Rainey
Keyword(s):  
Natural Selection ◽  
Normal Distribution ◽  
Pseudomonas Fluorescens ◽  
Genetic Architecture ◽  
Rank Order ◽  
Detailed Knowledge ◽  
Theoretical Studies ◽  
Fitness Effects ◽  
Reference Type ◽  
New Mutations

Theoretical studies of adaptation emphasize the importance of understanding the distribution of fitness effects (DFE) of new mutations. We report the isolation of 100 adaptive mutants—without the biasing influence of natural selection—from an ancestral genotype whose fitness in the niche occupied by the derived type is extremely low. The fitness of each derived genotype was determined relative to a single reference type and the fitness effects found to conform to a normal distribution. When fitness was measured in a different environment, the rank order changed, but not the shape of the distribution. We argue that, even with detailed knowledge of the genetic architecture underpinning the adaptive types (as is the case here), the DFEs remain unpredictable, and we discuss the possibility that general explanations for the shape of the DFE might not be possible in the absence of organism-specific biological details.

scholarly journals The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

2020 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Stefan Zdraljevic ◽  
Daniel E. Cook ◽  
Asher D. Cutter ◽  
Erik C. Andersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Population Size ◽  
Genomic Structure ◽  
Random Mating ◽  
Population Substructure ◽  
C Elegans ◽  
Fitness Effects ◽  
Self Fertilization ◽  
New Mutations

ABSTRACTThe distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection can conspire to compromise estimates of the DFE from extant polymorphisms. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.

scholarly journals Genomics of isolation in hybrids

2012 ◽  
Vol 367 (1587) ◽  
pp. 439-450 ◽  
Author(s):  
Zachariah Gompert ◽  
Thomas L. Parchman ◽  
C. Alex Buerkle
Keyword(s):  
Reproductive Isolation ◽  
Genetic Architecture ◽  
Large Scale ◽  
Empirical Studies ◽  
Hybrid Zones ◽  
Direct Measure ◽  
Fitness Effects ◽  
Outlier Loci ◽  
Admixed Population ◽  
Genome Level

Hybrid zones are common in nature and can offer critical insights into the dynamics and components of reproductive isolation. Hybrids between diverged lineages are particularly informative about the genetic architecture of reproductive isolation, because introgression in an admixed population is a direct measure of isolation. In this paper, we combine simulations and a new statistical model to determine the extent to which different genetic architectures of isolation leave different signatures on genome-level patterns of introgression. We found that reproductive isolation caused by one or several loci of large effect caused greater heterogeneity in patterns of introgression than architectures involving many loci with small fitness effects, particularly when isolating factors were closely linked. The same conditions that led to heterogeneous introgression often resulted in a reasonable correspondence between outlier loci and the genetic loci that contributed to isolation. However, demographic conditions affected both of these results, highlighting potential limitations to the study of the speciation genomics. Further progress in understanding the genomics of speciation will require large-scale empirical studies of introgression in hybrid zones and model-based analyses, as well as more comprehensive modelling of the expected levels of isolation with different demographies and genetic architectures of isolation.

scholarly journals Estimation of Genetic Variance in Fitness, and Inference of Adaptation, When Fitness Follows a Log-Normal Distribution

2019 ◽  
Vol 110 (4) ◽  
pp. 383-395 ◽  
Author(s):  
Timothée Bonnet ◽  
Michael B Morrissey ◽  
Loeske E B Kruuk
Keyword(s):  
Natural Selection ◽  
Animal Models ◽  
Normal Distribution ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Relative Fitness ◽  
Parameter Estimates ◽  
Log Normal ◽  
Change In Mean ◽  
Log Normal Distribution

AbstractAdditive genetic variance in relative fitness (σA2(w)) is arguably the most important evolutionary parameter in a population because, by Fisher’s fundamental theorem of natural selection (FTNS; Fisher RA. 1930. The genetical theory of natural selection. 1st ed. Oxford: Clarendon Press), it represents the rate of adaptive evolution. However, to date, there are few estimates of σA2(w) in natural populations. Moreover, most of the available estimates rely on Gaussian assumptions inappropriate for fitness data, with unclear consequences. “Generalized linear animal models” (GLAMs) tend to be more appropriate for fitness data, but they estimate parameters on a transformed (“latent”) scale that is not directly interpretable for inferences on the data scale. Here we exploit the latest theoretical developments to clarify how best to estimate quantitative genetic parameters for fitness. Specifically, we use computer simulations to confirm a recently developed analog of the FTNS in the case when expected fitness follows a log-normal distribution. In this situation, the additive genetic variance in absolute fitness on the latent log-scale (σA2(l)) equals (σA2(w)) on the data scale, which is the rate of adaptation within a generation. However, due to inheritance distortion, the change in mean relative fitness between generations exceeds σA2(l) and equals (exp⁡(σA2(l))−1). We illustrate why the heritability of fitness is generally low and is not a good measure of the rate of adaptation. Finally, we explore how well the relevant parameters can be estimated by animal models, comparing Gaussian models with Poisson GLAMs. Our results illustrate 1) the correspondence between quantitative genetics and population dynamics encapsulated in the FTNS and its log-normal-analog and 2) the appropriate interpretation of GLAM parameter estimates.

Population and quantitative genetics of many linked loci in finite populations

1983 ◽  
Vol 219 (1216) ◽  
pp. 253-264 ◽  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Dna Sequence ◽  
Quantitative Genetics ◽  
Quantitative Traits ◽  
Theoretical Studies ◽  
Population Surveys ◽  
Finite Populations ◽  
Simulation Results ◽  
New Mutations

Theoretical studies on the effects of linkage on variability of quantitative traits and response to directional selection in finite populations are reviewed. Emphasis is given to predictions that can be based on observable parameters, such as population size, chromosome lengths and the increment in variance from new mutations. Although truncation selection produces negative linkage disequilibrium in infinite populations, simulation results show that the effects of linkage on response are more pronounced in finite populations. Substantial linkage disequilibrium at the DNA sequence level is being found in population surveys. Some of the results and their interpretation are discussed.

The distribution of fitness effects of new mutations

2007 ◽  
Vol 8 (8) ◽  
pp. 610-618 ◽  
Author(s):  
Adam Eyre-Walker ◽  
Peter D. Keightley
Keyword(s):  
Fitness Effects ◽  
New Mutations

scholarly journals What does the Distribution of Fitness Effects of new mutations (DFE) reflect? Insights from plants

2021 ◽  
Author(s):  
Jun Chen ◽  
Thomas Bataillon ◽  
Sylvain Glémin ◽  
Martin Lascoux
Keyword(s):  
Fitness Effects ◽  
New Mutations

scholarly journals EXCURSIONS ALONG THE INTERFACE BETWEEN DISRUPTIVE AND STABILIZING SELECTION

Genetics ◽  
1979 ◽  
Vol 93 (3) ◽  
pp. 773-795
Author(s):  
Joseph Felsenstein
Keyword(s):  
Natural Selection ◽  
Normal Distribution ◽  
Multivariate Normal Distribution ◽  
Normal Approximation ◽  
Breeding Value ◽  
Stabilizing Selection ◽  
Multivariate Normal ◽  
Algebraic Analysis ◽  
Locus Model

ABSTRACT When a polygenic character is exposed to natural selection in which the curve giving fitness as a function of phenotype is a mixture of two Gaussian (normal) curves, the population may respond either by evolving to a specialized phenotype near one of the two optimum phenotypes, or by evolving to a generalized phenotype between them. Using approximate multivariate normal distribution methods, it is demonstrated that the condition for selection to result in a specialized phenotype is that the curve of fitness as a function of breeding value be bimodal. This implies that a specialized phenotype is more likely to result the higher is the heritability of the character. Numerical iterations of four-locus models and algebraic analysis of a symmetric two-locus model generally support the conclusions of the normal approximation.

scholarly journals Endless forms of sexual selection

2019 ◽  
Author(s):  
Willow R Lindsay ◽  
Staffan Andersson ◽  
Badreddine Bererhi ◽  
Jacob Höglund ◽  
Arild Johnsen ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Natural Selection ◽  
Mate Choice ◽  
Sexual Conflict ◽  
Genetic Architecture ◽  
Mating Systems ◽  
Population Divergence ◽  
Trait Evolution ◽  
Mating Competition ◽  
Mhc Genes

The field of sexual selection has burgeoned with research into trait evolution in the context of ecology, sociality, phylogeny, natural selection, and sexual conflict. This paper is the product of a “stock-taking” workshop; our aim is to stimulate discussion, not to provide an exhaustive review. We identify outstanding questions organized into four thematic sections. 1) Evolution of mate choice and mating systems. Variation in mate quality can generate mating competition and choice in either sex with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems. Specifically, polyandry evolves in response to the strength of pre- vs. post-copulatory selection. The evolution of polyandry may be related to diversity of pathogens and Major Histocompatibility Complex (MHC) genes. MHC genes are also potential cues of kinship in avoidance of inbreeding. The balance between inbreeding avoidance and inclusive fitness in mating decisions deserves greater attention. 2) Sender and receiver mechanisms shaping signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are a challenge to measure. The neuroethology of sensory and cognitive receiver biases is the main key to signal form and the ‘aesthetic sense’ proposed by Darwin. Since a receiver bias is sufficient to both start and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate ‘null model’ of sexual selection. 3) Genetic architecture of sexual selection. Despite advances in modern molecular techniques, the number and identity of genes underlying performance remain largely unknown. A combination of genomic techniques and long-term field studies that reveal ecological correlates of reproductive success is warranted. In-depth investigations into the genetic basis of sexual dimorphism will reveal constraints and trajectories of sexually selected trait evolution. 4) Sexual selection and conflict as drivers of speciation. Population divergence and speciation is often driven by an interplay between sexual and natural selection. To what extent sexual selection promotes or counteracts population divergence may differ depending on the genetic architecture of traits as well as covariance between mating competition and local adaptation, if traits have multiple functions and if sensory systems used in mate choice are locally adapted. Also, post-copulatory processes, e.g. selection against heterospecific sperm, may influence the importance of sexual selection. Sexual conflict can shape speciation processes, since mate choice selection on females can restrict gene flow whereas selection on males is permissive. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection.

scholarly journals The evolutionary impacts of synonymous mutations

2021 ◽  
Author(s):  
Deepa Agashe
Keyword(s):  
Synonymous Codon ◽  
Analytical Framework ◽  
Synonymous Mutations ◽  
Fitness Effects ◽  
Distinct Category ◽  
Dramatic Shift ◽  
Evolutionary Consequences ◽  
New Mutations

During the 50 years since the genetic code was cracked, our understanding of the evolutionary consequences of synonymous mutations has undergone a dramatic shift. Synonymous codon changes were initially considered selectively neutral, and as such, exemplars of evolution via genetic drift. However, the pervasive and non-negligible fitness impacts of synonymous mutations are now clear across organisms. Despite the accumulated evidence, it remains challenging to incorporate the effects of synonymous changes in studies of selection, because the existing analytical framework was built with a focus on the fitness effects of nonsynonymous mutations. In this chapter, I trace the development of this topic and discuss the evidence that gradually transformed our thinking about the role of synonymous mutations in evolution. I suggest that our evolutionary framework should encompass the impacts of all mutations on various forms of information transmission. Folding synonymous mutations into a common distribution – rather than setting them apart as a distinct category – will allow a more complete and cohesive picture of the evolutionary consequences of new mutations.

Sign in / Sign up

Export Citation Format

Share Document