scholarly journals On the feasibility of saltational evolution

2018 ◽  
Author(s):  
Mikhail I. Katsnelson ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Evolutionary Biology ◽  
Fitness Landscape ◽  
Evolutionary Process ◽  
Analytic Solutions ◽  
Population Bottlenecks ◽  
Effective Population ◽  
Evolutionary Transitions ◽  
Evolutionary Changes ◽  
Saltational Evolution ◽  
As Stress

One of the key tenets of Darwin’s theory that was inherited by the Modern Synthesis of evolutionary biology is gradualism, that is, the notion that evolution proceeds gradually, via accumulation of “infinitesimally small” heritable changes 1,2. However, some of the most consequential evolutionary changes, such as, for example, the emergence of major taxa, seem to occur abruptly rather than gradually, as captured in the concepts of punctuated equilibrium 3,4 and evolutionary transitions 5,6. We examine a mathematical model of an evolutionary process on a rugged fitness landscape 7,8 and obtain analytic solutions for the probability of multi-mutational leaps, that is, several mutations occurring simultaneously, within a single generation in one genome, and being fixed all together in the evolving population. The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multi-mutational leap is low, and accordingly, their contribution to the evolutionary process is minor at best. However, such leaps could become an important factor of evolution in situations of population bottlenecks and elevated mutation rates, such as stress-induced mutagenesis in microbes or tumor progression, as well as major evolutionary transitions and evolution of primordial replicators.

scholarly journals On the feasibility of saltational evolution

2019 ◽  
Vol 116 (42) ◽  
pp. 21068-21075 ◽  
Author(s):  
Mikhail I. Katsnelson ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Fitness Landscape ◽  
Evolutionary Process ◽  
Adaptive Strategy ◽  
Analytic Solutions ◽  
Mutation Rates ◽  
Effective Population ◽  
Single Generation ◽  
Saltational Evolution ◽  
Induced Mutagenesis ◽  
As Stress

Is evolution always gradual or can it make leaps? We examine a mathematical model of an evolutionary process on a fitness landscape and obtain analytic solutions for the probability of multimutation leaps, that is, several mutations occurring simultaneously, within a single generation in 1 genome, and being fixed all together in the evolving population. The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multimutation leap is low, and accordingly the contribution of such leaps is minor at best. However, we show that, taking sign epistasis into account, leaps could become an important factor of evolution in cases of substantially elevated mutation rates, such as stress-induced mutagenesis in microbes. We hypothesize that stress-induced mutagenesis is an evolvable adaptive strategy.

Units and levels of selection

2018 ◽  
Author(s):  
Samir Okasha
Keyword(s):  
Natural Selection ◽  
Kin Selection ◽  
Evolutionary Biology ◽  
Evolutionary Process ◽  
Levels Of Selection ◽  
Evolutionary Transitions ◽  
Individual Organism ◽  
Selection Processes ◽  
Hierarchical Levels ◽  
The Individual

In a standard Darwinian explanation, natural selection takes place at the level of the individual organism, i.e. some organisms enjoy a survival or reproduction advantage over others, which results in evolutionary change. In principle however, natural selection could operate at other hierarchical levels too, above and below that of the organism, for example the level of genes, cells, groups, colonies or even whole species. This possibility gives rise to the ‘levels of selection’ question in evolutionary biology. Group and colony-level selection have been proposed, originally by Darwin, as a means by which altruism can evolve. (In biology, ‘altruism’ refers to behaviour which entails a fitness cost to the individual so behaving, but benefits others.) Though this idea is still alive today, many theorists regard kin selection as a superior explanation for the existence of altruism. Kin selection arises from the fact that relatives share genes, so if an organism behaves altruistically towards its relatives, there is a greater than random chance that the beneficiary of the altruistic action will itself be an altruist. Kin selection is closely bound up with the ‘gene’s eye view’ of evolution, which holds that genes, not organisms, are the true beneficiaries of the evolutionary process. The gene’s eye approach to evolution, though heuristically valuable, does not in itself resolve the levels of selection question, because selection processes that occur at many hierarchical levels can all be seen from a gene’s eye viewpoint. In recent years, the levels of selection discussion has been re-invigorated, and subtly transformed, by the important new work on the ‘major evolutionary transitions’. These transitions occur when a number of free-living biological units, originally capable of surviving and reproducing alone, become integrated into a larger whole, giving rise to a new biological unit at a higher level of organization. Evolutionary transitions are intimately bound up with the levels of selection issue, because during a transition the potential exists for selection to operate simultaneously at two different hierarchical levels.

scholarly journals Inferring long-term effective population size with Mutation-Selection models

2021 ◽  
Author(s):  
T. Latrille ◽  
V. Lanore ◽  
N. Lartillot
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Fitness Landscape ◽  
Evolutionary Process ◽  
Simulated Data ◽  
Effective Population ◽  
Current Form ◽  
Codon Models ◽  
Extant Species

AbstractMutation-selection phylogenetic codon models are grounded on population genetics first principles and represent a principled approach for investigating the intricate interplay between mutation, selection and drift. In their current form, mutation-selection codon models are entirely characterized by the collection of site-specific amino-acid fitness profiles. However, thus far, they have relied on the assumption of a constant genetic drift, translating into a unique effective population size (Ne) across the phylogeny, clearly an unreasonable hypothesis. This assumption can be alleviated by introducing variation in Ne between lineages. In addition to Ne, the mutation rate (μ) is susceptible to vary between lineages, and both should co-vary with life-history traits (LHTs). This suggests that the model should more globally account for the joint evolutionary process followed by all of these lineage-specific variables (Ne, μ, and LHTs). In this direction, we introduce an extended mutation-selection model jointly reconstructing in a Bayesian Monte Carlo framework the fitness landscape across sites and long-term trends in Ne, μ and LHTs along the phylogeny, from an alignment of DNA coding sequences and a matrix of observed LHTs in extant species. The model was tested against simulated data and applied to empirical data in mammals, isopods and primates. The reconstructed history of Ne in these groups appears to correlate with LHTs or ecological variables in a way that suggests that the reconstruction is reasonable, at least in its global trends. On the other hand, the range of variation in Ne inferred across species is surprisingly narrow. This last point suggests that some of the assumptions of the model, in particular concerning the assumed absence of epistatic interactions between sites, are potentially problematic.

scholarly journals Genetic Algorithms as a method to study adaptive walks in biological landscapes

2020 ◽  
Author(s):  
Edith Invernizzi ◽  
Graeme D Ruxton
Keyword(s):  
Genetic Algorithms ◽  
Evolutionary Biology ◽  
Fitness Landscape ◽  
Evolutionary Process ◽  
Simulation Modelling ◽  
Fitness Landscapes ◽  
Mathematical Methods ◽  
Reproductive Process ◽  
Modelling Framework ◽  
Phenotypic Fitness

AbstractThe metaphor of fitness landscapes is common in evolutionary biology, as a way to visualise the change in allele or phenotypic frequencies of a population under selection. Understanding how different factors in the evolutionary process affect the trajectory of the population across the landscape is of interest to both theoretical and empirical evolutionary biologists. However, fitness landscape studies often have to rely heavily on mathematical methods that are not easy to access by biologically trained researchers. Here, we used a method borrowed from engineering - genetic algorithms - to simulate the evolutionary process and study how different components affect the path taken through a phenotypic fitness landscape. In a simple study, we compare five selection models that reflect different degrees of dependency of fitness on trait quality: this includes strengths of selection, trait-quality dependent reproductive hierarchy and the amount of stochasticity in the reproductive process. We include an analysis of other evolutionary variables such as population size and mutation rate. We analyse a game theory problem, as a test landscape, that lends itself to analysis through a deterministic mathematical simulation, which we use for comparison. Our results show that there are differences in the speed with which different models of selection lead to the fitness optimum.Author summaryEvolution and adaptation in biology occurs in fitness landscapes, multidimensional spaces representing all possible genotypic or phenotypic combinations, where population adapt by following the cline of the fitness dimension. The study of adaptation on complex fitness landscapes has so far been limited by the need for mathematically heavy methods. Here, we present a simulation modelling framework, genetic algorithms, that can be used for evolutionary simulations of a population on a fitness landscape of chosen features and with custom evolutionary parameters.

scholarly journals Clownfishes evolution below and above the species level

2018 ◽  
Vol 285 (1873) ◽  
pp. 20171796 ◽  
Author(s):  
Jonathan Rolland ◽  
Daniele Silvestro ◽  
Glenn Litsios ◽  
Laurélène Faye ◽  
Nicolas Salamin
Keyword(s):  
Morphological Evolution ◽  
Empirical Studies ◽  
Evolutionary Process ◽  
Species Level ◽  
Receptor Protein ◽  
Effective Population ◽  
Selective Pressures ◽  
Rates Of Evolution ◽  
Evolutionary Changes ◽  
The Difference

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1 , a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels.

scholarly journals Conflict and cooperation in eukaryogenesis: implications for the timing of endosymbiosis and the evolution of sex

2015 ◽  
Author(s):  
Arunas L Radzvilavicius ◽  
Neil W Blackstone
Keyword(s):  
Cell Fusion ◽  
Mitochondrial Gene ◽  
Evolutionary Process ◽  
Eukaryotic Cell ◽  
Evolutionary Transition ◽  
Evolutionary Transitions ◽  
Conflict And Cooperation ◽  
Conflict Mediation ◽  
Considerable Debate ◽  
History Of

The complex eukaryotic cell is a result of an ancient endosymbiosis and one of the major evolutionary transitions. The timing of key eukaryotic innovations relative to the acquisition of mitochondria remains subject to considerable debate, yet the evolutionary process itself might constrain the order of these events. Endosymbiosis entailed levels-of-selection conflicts, and mechanisms of conflict mediation had to evolve for eukaryogenesis to proceed. The initial mechanisms of conflict mediation were based on the pathways inherited from prokaryotic symbionts and led to metabolic homeostasis in the eukaryotic cell, while later mechanisms (e.g., mitochondrial gene transfer) contributed to the expansion of the eukaryotic genome. Perhaps the greatest opportunity for conflict arose with the emergence of sex involving whole-cell fusion. While early evolution of cell fusion may have affected symbiont acquisition, sex together with the competitive symbiont behaviour would have destabilised the emerging higher-level unit. Cytoplasmic mixing, on the other hand, would have been beneficial for selfish endosymbionts, capable of using their own metabolism to manipulate the life history of the host. Given the results of our mathematical modelling, we argue that sex represents a rather late proto- eukaryotic innovation, allowing for the growth of the chimeric nucleus and contributing to the successful completion of the evolutionary transition.

scholarly journals Testing Host-Plant Driven Speciation in Phytophagous Insects: A Phylogenetic Perspective

2019 ◽  
Author(s):  
Emmanuelle Jousselin ◽  
Marianne Elias
Keyword(s):  
Host Plant ◽  
Evolutionary Biology ◽  
Phylogenetic Analyses ◽  
Evolutionary Process ◽  
Niche Differentiation ◽  
Ecological Speciation ◽  
Model Systems ◽  
Phytophagous Insects ◽  
Ecological Specialization ◽  
Recent Developments

During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation. Phytophagous insects represent model systems for the study of this evolutionary process. The host-plants on which these insects feed and often spend parts of their life cycle constitute ideal agents of divergent selection for these organisms. Adaptation to feeding on different host-plant species can potentially lead to ecological specialization of populations and subsequent speciation. This process is thought to have given birth to the astonishing diversity of phytophagous insects and is often put forward in macroevolutionary scenarios of insect diversification. Consequently, numerous phylogenetic studies on phytophagous insects have aimed at testing whether speciation driven by host-plant adaptation is the main pathway for the diversification of the groups under investigation. The increasing availability of comprehensive and well-resolved phylogenies and the recent developments in phylogenetic comparative methods are offering an unprecedented opportunity to test hypotheses on insect diversification at a macroevolutionary scale, in a robust phylogenetic framework. Our purpose here is to review the contribution of phylogenetic analyses to investigate the importance of plant-mediated speciation in the diversification of phytophagous insects and to present suggestions for future developments in this field.

scholarly journals Memahami Sensionalisme dalam Berita Televisi: Perspektif Evolusi Biologi

2020 ◽  
Vol 16 (2) ◽  
Author(s):  
Gentur Agustinus Naru
Keyword(s):  
Human Brain ◽  
Evolutionary Biology ◽  
Evolutionary Process ◽  
Time Difference ◽  
Evolutionary Perspective ◽  
History Of ◽  
The Relationship

Although there have been many studies regarding sensationalism on television, there have not been enough studies to explain why sensational news always attracts viewers' attention regardless of space or time difference. Encouraged by this background, this research tries to answer the question, "What makes sensational news interesting to television viewers?" Inspired by a biological evolutionary perspective, this article formulates a hypothesis that reads, "Sensationalism can draw the attention of the audience because sensational news arouses the most basic instincts of humans, namely the mode of survival (Gurven, 2017)". In this view, the model has become inherent in humans as a result of the evolutionary process. In other words, this hypothesis also believes that audience interest in sensational news is universal rather than contextual.   This article explores a variety of literature in biology, psychology, and communication to try to answer that hypothesis. In order to that, this article is divided into three main sections. We will first explore the history of sensational journalism on television to show the historicity of sensational topics and techniques on television. Second, we will demonstrate the philosophical roots of an evolutionary biology view that explains the relationship between information stimuli and the workings of the human brain and the basic instincts we have carried since evolution thousands of years ago. Finally, we will show studies that prove empirically how news patterns (both sensational topics and production formats) impact viewing interest.

New Developments in Evolutionary Innovation

2021 ◽  
pp. 1-6
Author(s):  
Gino Cattani ◽  
Mariano Mastrogiorgio
Keyword(s):  
Evolutionary Theory ◽  
Significant Influence ◽  
Evolutionary Biology ◽  
Economic Change ◽  
Evolutionary Process ◽  
Punctuated Equilibrium ◽  
Darwinian Evolution ◽  
New Developments ◽  
Evolutionary Innovation ◽  
Equilibrium Speciation

The publication of ‘An Evolutionary Theory of Economic Change’ by Nelson and Winter has had a major impact on economics and related fields such as innovation and strategy. All of these fields have developed owing to recent re-examinations and extensions of evolutionary theory. A paradigm that underlies several studies in this tradition is the concept of neo-Darwinian evolution—the idea that the unit of the evolutionary process (e.g. a technological artefact) is subject to a dynamic of variation, selection, and retention leading to adaptation to a predefined function. This book refers to the frameworks of punctuated equilibrium, speciation, and exaptation, which, despite their significant influence in evolutionary biology, have been reflected only partially in evolutionary approaches to economics, innovation, and strategy. This chapter introduces the book’s aim to fill this gap, and outlines the approaches and perspectives of each of the chapters.

scholarly journals Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Diversity ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 164 ◽  
Author(s):  
Peter Houde ◽  
Edward L. Braun ◽  
Lawrence Zhou
Keyword(s):  
Evolutionary Biology ◽  
Gene Tree ◽  
Difficult Problem ◽  
Gene Trees ◽  
Effective Population ◽  
Deep Time ◽  
Ecological Release ◽  
Population Sizes ◽  
Demographic Inference ◽  
Gene Tree Discordance

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

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