scholarly journals A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments

Genetics ◽  
2014 ◽  
Vol 196 (3) ◽  
pp. 841-852 ◽  
Author(s):  
Claudia Bank ◽  
Ryan T. Hietpas ◽  
Alex Wong ◽  
Daniel N. Bolon ◽  
Jeffrey D. Jensen
Keyword(s):  
Bayesian Mcmc ◽  
Fitness Effects ◽  
Adaptive Walks ◽  
Mcmc Approach ◽  
New Mutations

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.

A Bayesian MCMC approach to reconstruct spatial vegetation dynamics from sparse vegetation maps

2011 ◽  
Vol 26 (6) ◽  
pp. 805-822
Author(s):  
Imelda Somodi ◽  
Klára Virágh ◽  
István Miklós
Keyword(s):  
Vegetation Dynamics ◽  
Bayesian Mcmc ◽  
Sparse Vegetation ◽  
Vegetation Maps ◽  
Mcmc Approach

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 AGNfitter: A BAYESIAN MCMC APPROACH TO FITTING SPECTRAL ENERGY DISTRIBUTIONS OF AGNs

2016 ◽  
Vol 833 (1) ◽  
pp. 98 ◽  
Author(s):  
Gabriela Calistro Rivera ◽  
Elisabeta Lusso ◽  
Joseph F. Hennawi ◽  
David W. Hogg
Keyword(s):  
Spectral Energy ◽  
Spectral Energy Distributions ◽  
Energy Distributions ◽  
Bayesian Mcmc ◽  
Mcmc Approach

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 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 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.

Climbing Mount Probable

2021 ◽  
pp. 135-164
Author(s):  
Arlin Stoltzfus
Keyword(s):  
Modern Synthesis ◽  
Causal Process ◽  
Gene Frequencies ◽  
Formal Basis ◽  
One Step ◽  
Adaptive Walks ◽  
Per Se ◽  
New Mutations

Chapter 8 provides the formal basis to recognize biases in the introduction of variation as a cause of evolutionary biases. The shifting-gene-frequencies theory of the Modern Synthesis posits a “buffet” view in which evolution is merely a process of shifting the frequencies of pre-existing alleles, without new mutations. Within this theory, mutation is represented like selection or drift, as a “force” that shifts frequencies. Yet, within a broader conception of evolution, a second kind of causal process is required: an introduction process that can shift a frequency upwards from 0, which selection and drift cannot do. Abstract models demonstrate the influence of biases in the introduction process in one-step and multi-step adaptive walks. Such biases do not require mutation biases per se, but may arise from effects of development, and from the differential accessibility of alternative forms in abstract possibility-spaces.

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