scholarly journals The evolution of genetic diversity in changing environments

2014 ◽  
Author(s):  
Oana Carja ◽  
Uri Liberman ◽  
Marcus W. Feldman
Keyword(s):  
Phenotypic Variation ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Theoretical Models ◽  
Fluctuating Selection ◽  
Evolutionary Forces ◽  
And Migration ◽  
Compare And Contrast ◽  
Insight Into

The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection and the signatures of environmental and selective volatility in the patterns of genetic and phenotypic variation have been important areas of focus in population genetics. On one hand, stretches of constant selection pull the genetic makeup of populations towards local fitness optima. On the other, in order to cope with changes in the selection regime, populations may evolve mechanisms that create a diversity of genotypes. By tuning the rates at which variability is produced, such as the rates of recombination, mutation or migration, populations may increase their long-term adaptability. Here we use theoretical models to gain insight into how the rates of these three evolutionary forces are shaped by fluctuating selection. We compare and contrast the evolution of recombination, mutation and migration under similar patterns of environmental change and show that these three sources of phenotypic variation are surprisingly similar in their response to changing selection. We show that knowing the shape, size, variance and asymmetry of environmental runs is essential for accurate prediction of genetic evolutionary dynamics.

scholarly journals Evolution with a seed bank: the population genetic consequences of microbial dormancy

2017 ◽  
Author(s):  
WR Shoemaker ◽  
JT Lennon
Keyword(s):  
Seed Bank ◽  
Population Genetic ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Seed Banks ◽  
Hedging Strategy ◽  
Term Survival ◽  
Evolutionary Forces ◽  
Growth And Reproduction

ABSTRACTDormancy is a bet-hedging strategy that allows organisms to persist through conditions that are sub-optimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long-term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence microbial evolutionary dynamics.

scholarly journals Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

2019 ◽  
Author(s):  
Kathryn E. Holt ◽  
Florent Lassalle ◽  
Kelly L. Wyres ◽  
Ryan Wick ◽  
Rafal J. Mostowy
Keyword(s):  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Purifying Selection ◽  
Evolutionary Forces ◽  
Polysaccharide Synthesis ◽  
Surface Polysaccharides ◽  
Surface Polysaccharide ◽  
Selective Preservation ◽  
Multiple Species

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormachei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.

scholarly journals Eco-evolutionary feedbacks promote fluctuating selection and long-term stability of antagonistic networks

2018 ◽  
Vol 285 (1874) ◽  
pp. 20172596 ◽  
Author(s):  
Cecilia Siliansky de Andreazzi ◽  
Paulo R. Guimarães ◽  
Carlos J. Melián
Keyword(s):  
Temporal Variation ◽  
Evolutionary Dynamics ◽  
Species Interaction ◽  
Fluctuating Selection ◽  
Term Stability ◽  
Long Term Stability ◽  
Interacting Species ◽  
Species Abundances ◽  
Antagonistic Interactions

Studies have shown the potential for rapid adaptation in coevolving populations and that the structure of species interaction networks can modulate the vulnerability of ecological systems to perturbations. Although the feedback loop between population dynamics and coevolution of traits is crucial for understanding long-term stability in ecological assemblages, modelling eco-evolutionary dynamics in species-rich assemblages is still a challenge. We explore how eco-evolutionary feedbacks influence trait evolution and species abundances in 23 empirical antagonistic networks. We show that, if selection due to antagonistic interactions is stronger than other selective pressures, eco-evolutionary feedbacks lead to higher mean species abundances and lower temporal variation in abundances. By contrast, strong selection of antagonistic interactions leads to higher temporal variation of traits and on interaction strengths. Our results present a theoretical link between the study of the species persistence and coevolution in networks of interacting species, pointing out the ways by which coevolution may decrease the vulnerability of species within antagonistic networks to demographic fluctuation.

scholarly journals Evolutionary dynamics in structured populations under strong population genetic forces

2019 ◽  
Author(s):  
Alison F. Feder ◽  
Pleuni S. Pennings ◽  
Joachim Hermisson ◽  
Dmitri A. Petrov
Keyword(s):  
Population Differentiation ◽  
Evolutionary Dynamics ◽  
Structured Populations ◽  
Short Term ◽  
Migration Rates ◽  
Neutral Equilibrium ◽  
Demographic Processes ◽  
And Migration ◽  
Approximate Bayesian

AbstractHigh rates of migration between subpopulations result in little population differentiation in the long-term neutral equilibrium. However, in the short-term, even very abundant migration may not be enough for subpopulations to equilibrate immediately. In this study, we investigate dynamical patterns of short-term population differentiation in adapting populations via stochastic and analytical modeling through time. We characterize a regime in which selection and migration interact to create non-monotonic patterns of the population differentiation statistic FST when migration is weaker than selection, but stronger than drift. We demonstrate how these patterns can be leveraged to estimate high migration rates that would lead to panmixia in the long term equilibrium using an approximate Bayesian computation approach. We apply this approach to estimate fast migration in a rapidly adapting intra-host Simian-HIV population sampled from different anatomical locations. Notably, we find differences in estimated migration rates between different compartments, all above Nem = 1. This work demonstrates how studying demographic processes on the timescale of selective sweeps illuminates processes too fast to leave signatures on neutral timescales.

scholarly journals Who is the typical psychedelics user? Methodological challenges for research in psychedelics use and its consequences

2020 ◽  
pp. 145507252096378
Author(s):  
Petter Grahl Johnstad
Keyword(s):  
Mental Health ◽  
Population Studies ◽  
Theoretical Models ◽  
Research Strategies ◽  
Methodological Review ◽  
Patterns Of Use ◽  
Reliable Model ◽  
Usage Patterns ◽  
Insight Into

Aims: This article argues that despite a resurgence in research on psychedelics over the last two decades, we still have little insight into the psychedelics user population. Furthermore, there is currently little agreement between researchers as to the long-term mental health consequences of psychedelics use. Design: In a methodological review of a range of studies in psychedelics use, it is demonstrated that these studies tend to focus on specific segments of the user population while excluding others. These population segments are probably connected to different patterns of use, which in turn are likely to result in different long-term consequences. Results: The divergent findings on the consequences of psychedelics use may be explained, at least in part, by the fact that different research strategies explore different segments of the user population. Studies focusing on user segments with problematic usage patterns tend to find that psychedelics use is negative for mental health, while studies on infrequent users tend to find that psychedelics use is positive for mental health. Conclusion: Because the field of psychedelics studies lacks a reliable model of the user population, it is difficult for researchers to contextualise and assess the broader validity of their findings. To remedy this situation, the article presents three theoretical models of the user population that afford us with tentative means of contextualising findings and thereby may clarify present disagreements.

scholarly journals General Models of Multilocus Evolution

Genetics ◽  
2002 ◽  
Vol 161 (4) ◽  
pp. 1727-1750 ◽  
Author(s):  
Mark Kirkpatrick ◽  
Toby Johnson ◽  
Nick Barton
Keyword(s):  
Sexual Selection ◽  
Natural Selection ◽  
Evolutionary Dynamics ◽  
Linkage Equilibrium ◽  
Sex Linkage ◽  
Genetic Composition ◽  
Evolutionary Forces ◽  
And Migration ◽  
The Web ◽  
Quasi Linkage Equilibrium

Abstract In 1991, Barton and Turelli developed recursions to describe the evolution of multilocus systems under arbitrary forms of selection. This article generalizes their approach to allow for arbitrary modes of inheritance, including diploidy, polyploidy, sex linkage, cytoplasmic inheritance, and genomic imprinting. The framework is also extended to allow for other deterministic evolutionary forces, including migration and mutation. Exact recursions that fully describe the state of the population are presented; these are implemented in a computer algebra package (available on the Web at http://helios.bto.ed.ac.uk/evolgen). Despite the generality of our framework, it can describe evolutionary dynamics exactly by just two equations. These recursions can be further simplified using a “quasi-linkage equilibrium” (QLE) approximation. We illustrate the methods by finding the effect of natural selection, sexual selection, mutation, and migration on the genetic composition of a population.

scholarly journals Transgenerational dispersal plasticity and its fitness consequences are under genetic control

2019 ◽  
Author(s):  
Hugo Cayuela ◽  
Staffan Jacob ◽  
Nicolas Schtickzelle ◽  
Rik Verdonck ◽  
Hervé Philippe ◽  
...  
Keyword(s):  
Genetic Control ◽  
Phenotypic Variation ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Critical Role ◽  
Natural Populations ◽  
Model Species ◽  
Transgenerational Plasticity ◽  
Species Response

AbstractPhenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species’ response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. Here, we examined how genotype determines the TGP of dispersal, a fundamental process in ecology and evolution. We used an experimental approach involving ~200 clonal generations in a model-species of ciliate to determine if and how TGP influences the expression of dispersal-related traits in several genotypes. Our results show that morphological and movement traits associated with dispersal are plastic, and that these modifications are inherited over at least 35 generations. We also highlight that genotype modulates the fitness costs and benefits associated with plastic dispersal strategies. Our study suggests that genotype-dependent TGP could play a critical role in eco-evolutionary dynamics as dispersal determines gene flow and the long-term persistence of natural populations. More generally, it outlines the tremendous importance that genotype-dependent TGP could have in the ability of organisms to cope with current and future environmental changes.SignificanceThe genetic control of the transgenerational plasticity is still poorly understood despite its critical role in species responses to environmental changes. We examined how genotype determines transgenerational plasticity of a complex trait (i.e., dispersal) in a model-species of ciliate across ~200 clonal generations. Our results provide evidence that plastic phenotypic variation linked to dispersal is stably inherited over tens of generations and that cell genotype modulates the expression and fitness cost of transgenerational plasticity.

scholarly journals Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

2015 ◽  
Vol 112 (21) ◽  
pp. 6676-6681 ◽  
Author(s):  
Adriaan van der Graaf ◽  
René Wardenaar ◽  
Drexel A. Neumann ◽  
Aaron Taudt ◽  
Ruth G. Shaw ◽  
...  
Keyword(s):  
Cytosine Methylation ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Population Level ◽  
Genomic Context ◽  
Term Selection ◽  
Comprehensive Picture ◽  
Dynamic Interplay

Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences.

scholarly journals Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces

2019 ◽  
Vol 9 (10) ◽  
pp. 3395-3407 ◽  
Author(s):  
Alison F. Feder ◽  
Pleuni S. Pennings ◽  
Joachim Hermisson ◽  
Dmitri A. Petrov
Keyword(s):  
Population Differentiation ◽  
Evolutionary Dynamics ◽  
Structured Populations ◽  
Short Term ◽  
Migration Rates ◽  
Neutral Equilibrium ◽  
Demographic Processes ◽  
And Migration ◽  
Approximate Bayesian

In the long-term neutral equilibrium, high rates of migration between subpopulations result in little population differentiation. However, in the short-term, even very abundant migration may not be enough for subpopulations to equilibrate immediately. In this study, we investigate dynamical patterns of short-term population differentiation in adapting populations via stochastic and analytical modeling through time. We characterize a regime in which selection and migration interact to create non-monotonic patterns of population differentiation over time when migration is weaker than selection, but stronger than drift. We demonstrate how these patterns can be leveraged to estimate high migration rates using approximate Bayesian computation. We apply this approach to estimate fast migration in a rapidly adapting intra-host Simian-HIV population sampled from different anatomical locations. We find differences in estimated migration rates between different compartments, even though all are above Nem = 1. This work demonstrates how studying demographic processes on the timescale of selective sweeps illuminates processes too fast to leave signatures on neutral timescales.

Turkish Muslims in a German city: Entrepreneurial and residential self-determination

2015 ◽  
Vol 12 (1) ◽  
pp. 1-12
Author(s):  
Sarah Hackett
Keyword(s):  
Residential Patterns ◽  
Academic Literature ◽  
Self Employment ◽  
German City ◽  
Post War ◽  
Oral History Interviews ◽  
The City ◽  
Insight Into ◽  
Term Objective

Drawing upon a collection of oral history interviews, this paper offers an insight into entrepreneurial and residential patterns and behaviour amongst Turkish Muslims in the German city of Bremen. The academic literature has traditionally argued that Turkish migrants in Germany have been pushed into self-employment, low-quality housing and segregated neighbourhoods as a result of discrimination, and poor employment and housing opportunities. Yet the interviews reveal the extent to which Bremen’s Turkish Muslims’ performances and experiences have overwhelmingly been the consequences of personal choices and ambitions. For many of the city’s Turkish Muslim entrepreneurs, self-employment had been a long-term objective, and they have succeeded in establishing and running their businesses in the manner they choose with regards to location and clientele, for example. Similarly, interviewees stressed the way in which they were able to shape their housing experiences by opting which districts of the city to live in and by purchasing property. On the whole, they perceive their entrepreneurial and residential practices as both consequences and mediums of success, integration and a loyalty to the city of Bremen. The findings are contextualised within the wider debate regarding the long-term legacy of Germany’s post-war guest-worker system and its position as a “country of immigration”.

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