scholarly journals Testing the adaptive walk model of gene evolution

2021 ◽  
Author(s):  
Ana Filipa Moutinho ◽  
Adam Eyre-Walker ◽  
Julien Y. Dutheil
Keyword(s):  
Molecular Evolution ◽  
Fitness Landscape ◽  
Gene Evolution ◽  
Molecular Adaptation ◽  
Fitness Effects ◽  
Arduous Task ◽  
Different Ages ◽  
Species Specific ◽  
Gene Age ◽  
Adaptive Walk

AbstractUnderstanding the dynamics of species adaptation to their environments has long been a central focus of the study of evolution. Early adaptive theories proposed that populations evolve by “walking” in a fitness landscape. This “adaptive walk” is characterised by a pattern of diminishing returns, where populations further away from their fitness optimum take larger steps than those closer to their optimal conditions. This theory can also be used to understand molecular evolution in time, particularly across genes of different ages. We expect young genes to evolve faster and experience mutations with stronger fitness effects than older genes because they are further away from their fitness optimum. Testing this hypothesis, however, constitutes an arduous task. Young genes are small, encode proteins with a higher degree of intrinsic disorder, are expressed at lower levels, and are involved in species-specific adaptations. Since all these factors lead to increased protein evolutionary rates, they could be masking the effect of gene age. While controlling for these factors, we fitted models of the distribution of fitness effects to population genomic datasets of animals and plants. We found that a gene’s evolutionary age significantly impacts the molecular adaptive rate. Moreover, we observed that substitutions in young genes tend to have larger fitness effects. Our study, therefore, provides the first evidence of an “adaptive walk” model of molecular evolution in large evolutionary timescales.Significant statementHow does molecular adaptation occur? John Maynard Smith was one of the first to address this question by introducing the notion of “adaptive walk”, which defines the “walk” of a gene towards higher fitness. At the start of this walk, genes tend to experience mutations with larger fitness effects than those closer to their fitness peak. Whilst being well-established, this theory has never been tested on large evolutionary timescales. Here, we achieve this by comparing molecular adaptive rates across genes of different ages in plants and animals. We showed that a gene’s age acts as a significant determinant of molecular adaptation, where young genes adapt faster than old ones. We, therefore, provide evidence for an “adaptive walk” through time.

scholarly journals Differential strengths of molecular determinants guide environment specific mutational fates

2017 ◽  
Author(s):  
Rohan Dandage ◽  
Rajesh Pandey ◽  
Gopal Jayaraj ◽  
Kausik Chakraborty
Keyword(s):  
Protein Folding ◽  
Molecular Evolution ◽  
Protein Stability ◽  
Environmental Effects ◽  
Environmental Conditions ◽  
Fitness Landscape ◽  
Dependent Manner ◽  
The Common ◽  
Physical And Chemical ◽  
Substrate Binding Protein

AbstractUnder the influence of selection pressures imposed by natural environments, organisms maintain competitive fitness through underlying molecular evolution of individual genes across the genome. For molecular evolution, how multiple interdependent molecular constraints play a role in determination of fitness under different environmental conditions is largely unknown. Here, using Deep Mutational Scanning (DMS), we quantitated empirical fitness of ∼2000 single site mutants of Gentamicin-resistant gene (GmR). This enabled a systematic investigation of effects of different physical and chemical environments on the fitness landscape of the gene. Molecular constraints of the fitness landscapes seem to bear differential strengths in an environment dependent manner. Among them, conformity of the identified directionalities of the environmental selection pressures with known effects of the environments on protein folding proves that along with substrate binding, protein stability is the common strong constraint of the fitness landscape. Our study thus provides mechanistic insights into the molecular constraints that allow accessibility of mutational fates in environment dependent manner.Author SummaryEnvironmental conditions play a central role in both organismal adaptations and underlying molecular evolution. Understanding of environmental effects on evolution of genotype is still lacking a depth of mechanistic insights needed to assist much needed ability to forecast mutational fates. Here, we address this issue by culminating high throughput mutational scanning using deep sequencing. This approach allowed comprehensive mechanistic investigation of environmental effects on molecular evolution. We monitored effects of various physical and chemical environments onto single site mutants of model antibiotic resistant gene. Alongside, to get mechanistic understanding, we identified multiple molecular constraints which contribute to various degrees in determining the resulting survivabilities of mutants. Across all tested environments, we find that along with substrate binding, protein stability stands out as the common strong constraints. Remarkable direct dependence of the environmental fitness effects on the type of environmental alteration of protein folding further proves that protein stability is the major constraint of the gene. So, our findings reveal that under the influence of environmental conditions, mutational fates are channeled by various degrees of strengths of underlying molecular constraints.

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 SELVa: Simulator of evolution with landscape variation

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0242225 ◽  
Author(s):  
Elena Nabieva ◽  
Georgii A. Bazykin
Keyword(s):  
Molecular Evolution ◽  
Landscape Change ◽  
Arbitrary Shape ◽  
Fitness Landscape ◽  
Substitution Process ◽  
Individual Site ◽  
Flexible Framework ◽  
Landscape Variation

Organisms evolve to increase their fitness, a process that may be described as climbing the fitness landscape. However, the fitness landscape of an individual site, i.e., the vector of fitness values corresponding to different variants at this site, can itself change with time due to changes in the environment or substitutions at other epistatically interacting sites. While there exist a number of simulators for modeling different aspects of molecular evolution, very few can accommodate changing landscapes. We present SELVa, the Simulator of Evolution with Landscape Variation, aimed at modeling the substitution process under a changing single-position fitness landscape in a set of evolving lineages that form a phylogeny of arbitrary shape. Written in Java and distributed as an executable jar file, SELVa provides a flexible framework that allows the user to choose from a number of implemented rules governing landscape change.

scholarly journals Pineal Gland Morphology in Relation to Age and Season in Three Canidae Species

2019 ◽  
Vol 36 (04) ◽  
pp. 247-254
Author(s):  
Svetlana Kalinina ◽  
Viktor Ilyukha ◽  
Lyudmila Uzenbaeva
Keyword(s):  
Pineal Gland ◽  
Morphological Changes ◽  
Nyctereutes Procyonoides ◽  
Raccoon Dog ◽  
Silver Fox ◽  
Reticular Fibers ◽  
Different Ages ◽  
Blue Fox ◽  
Species Specific ◽  
Insight Into

Abstract Introduction The aim of the present study was to determine the morphological features of the pineal gland in three closely related Canidae species (raccoon dog, Nyctereutes procyonoides Gray, 1834; silver fox, Vulpes vulpes L., 1758; and blue fox, Vulpes lagopus L., 1758) of different ages during the breeding (spring) and nonbreeding (winter) periods. Materials and Methods Histological analysis of the pineal glands of canids was performed. Results The morphological changes in the pineal gland detected in the current study are either age-associated, including increase in the reticular fibers and vascularization in the studied species, as well as increase in the amount of the protruding septae in the blue fox, or seasonally related, including an increase in the number and size of blood vessels. The present work reported two types of pigments: lipofuscin (primarily in the silver fox) and melanin (primarily in the raccoon dog and in the blue fox). The pineal gland in the blue fox is characterized by the ability to form corpora arenacea. Conclusions The present study provides the first insight into the morphological changes of the pineal gland in three closely related Canidae species of different ages during the breeding (spring) and nonbreeding (winter) periods, and showed some species-specific features of gland morphology. The aspects concerning the biogenesis of the calcium concretions and the factors influencing the accumulation of pigments need further investigation.

Neutral theories of molecular evolution

2019 ◽  
pp. 67-84
Author(s):  
Asher D. Cutter
Keyword(s):  
Molecular Evolution ◽  
Dna Sequences ◽  
Neutral Theory ◽  
Null Model ◽  
Sequence Evolution ◽  
Neutral Model ◽  
Frequency Distributions ◽  
Fitness Effects ◽  
Theoretical Predictions ◽  
Dna Sequence Evolution

Chapter 4, “Neutral theories of molecular evolution,” outlines the logic and predictions of the neutral theory of molecular evolution and its derivatives as a simple conceptual framework for understanding DNA sequence evolution. It introduces the standard neutral model as a null model of evolutionary change in DNA sequences to describe patterns of polymorphism within species and divergence between species. An overview is provided for the molecular clock concept and for predictions about the amount of polymorphism and allele frequency distributions within populations. This chapter covers how population size and selection intersect to define nearly neutral fitness effects and their implications, as well as misinterpretations and misapplications of Neutral Theory. This overview provides a foundation for how theoretical predictions offer null models for tests of molecular evolution developed in later chapters.

Species-specific size expansion and molecular evolution of the oleosins in angiosperms

Gene ◽  
2012 ◽  
Vol 509 (2) ◽  
pp. 247-257 ◽  
Author(s):  
Qi Liu ◽  
Yepeng Sun ◽  
Wujie Su ◽  
Jing Yang ◽  
Xiuming Liu ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Species Specific

scholarly journals Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host

2015 ◽  
Vol 370 (1675) ◽  
pp. 20140292 ◽  
Author(s):  
Julia Hillung ◽  
José M. Cuevas ◽  
Santiago F. Elena
Keyword(s):  
Genetic Variation ◽  
Fitness Landscape ◽  
Host Population ◽  
Gene Model ◽  
New Host ◽  
Host Fitness ◽  
Fitness Effects ◽  
Rate Of Spread ◽  
Virus Diversity ◽  
Gene For Gene

The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana —tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host–parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis.

scholarly journals The Changing Geometry of a Fitness Landscape Along an Adaptive Walk

2014 ◽  
Vol 10 (5) ◽  
pp. e1003520 ◽  
Author(s):  
Devin Greene ◽  
Kristina Crona
Keyword(s):  
Fitness Landscape ◽  
Adaptive Walk
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