scholarly journals Population genetics of polymorphism and divergence in rapidly evolving populations

2021 ◽  
Author(s):  
Matthew J. Melissa ◽  
Benjamin H Good ◽  
Daniel S Fisher ◽  
Michael M. Desai
Keyword(s):  
Traveling Wave ◽  
Population Genetic ◽  
Evolutionary Dynamics ◽  
Frequency Spectra ◽  
Fitness Effects ◽  
Wide Range ◽  
Fixation Probabilities ◽  
Wave Models ◽  
Traditional Population ◽  
Evolving Populations

In rapidly evolving populations, numerous beneficial and deleterious mutations can arise and segregate within a population at the same time. In this regime, evolutionary dynamics cannot be analyzed using traditional population genetic approaches that assume that sites evolve independently. Instead, the dynamics of many loci must be analyzed simultaneously. Recent work has made progress by first analyzing the fitness variation within a population, and then studying how individual lineages interact with this traveling fitness wave. However, these "traveling wave" models have previously been restricted to extreme cases where selection on individual mutations is either much faster or much slower than the typical coalescent timescale T_c. In this work, we show how the traveling wave framework can be extended to intermediate regimes in which the scaled fitness effects of mutations (T_c s) are neither large nor small compared to one. This enables us to describe the dynamics of populations subject to a wide range of fitness effects, and in particular, in cases where it is not immediately clear which mutations are most important in shaping the dynamics and statistics of genetic diversity. We use this approach to derive new expressions for the fixation probabilities and site frequency spectra of mutations as a function of their scaled fitness effects, along with related results for the coalescent timescale T_c and the rate of adaptation or Muller's ratchet. We find that competition between linked mutations can have a dramatic impact on the proportions of neutral and selected polymorphisms, which is not simply summarized by the scaled selection coefficient T_c s. We conclude by discussing the implications of these results for population genetic inferences.

scholarly journals The Role of Clonal Interference in the Evolutionary Dynamics of Plasmid-Host Adaptation

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Julie M. Hughes ◽  
Brian K. Lohman ◽  
Gail E. Deckert ◽  
Eric P. Nichols ◽  
Matt Settles ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Evolutionary Dynamics ◽  
Host Adaptation ◽  
Replication Initiation ◽  
Clonal Interference ◽  
Replication Initiation Protein ◽  
Wide Range ◽  
Resistance Plasmids ◽  
Evolving Populations

ABSTRACT Promiscuous plasmids replicate in a wide range of bacteria and therefore play a key role in the dissemination of various host-beneficial traits, including antibiotic resistance. Despite the medical relevance, little is known about the evolutionary dynamics through which drug resistance plasmids adapt to new hosts and thereby persist in the absence of antibiotics. We previously showed that the incompatibility group P-1 (IncP-1) minireplicon pMS0506 drastically improved its stability in novel host Shewanella oneidensis MR-1 after 1,000 generations under antibiotic selection for the plasmid. The only mutations found were those affecting the N terminus of the plasmid replication initiation protein TrfA1. Our aim in this study was to gain insight into the dynamics of plasmid evolution. Changes in stability and genotype frequencies of pMS0506 were monitored in evolving populations of MR-1 (pMS0506). Genotypes were determined by sequencing trfA1 amplicons from individual clones and by 454 pyrosequencing of whole plasmids from entire populations. Stability of pMS0506 drastically improved by generation 200. Many evolved plasmid genotypes with point mutations as well as in-frame and frameshift deletions and duplications in trfA1 were observed in all lineages with both sequencing methods. Strikingly, multiple genotypes were simultaneously present at high frequencies (>10%) in each population. Their relative abundances changed over time, but after 1,000 generations only one or two genotypes dominated the populations. This suggests that hosts with different plasmid genotypes were competing with each other, thus affecting the evolutionary trajectory. Plasmids can thus rapidly improve their stability, and clonal interference plays a significant role in plasmid-host adaptation dynamics. IMPORTANCE Promiscuous plasmids play an important role in the spread of antibiotic resistance and many other traits between closely and distantly related bacteria. However, little is known about the dynamics by which these broad-host-range antibiotic resistance plasmids adapt to novel bacteria and thereby become more persistent, even in the absence of antibiotics. In this study, we show that after no more than 200 generations of growth in the presence of antibiotics, a plasmid that was initially poorly maintained in a novel bacterial host evolved to become drastically more persistent in the absence of antibiotics. In each of the evolving populations, an unexpectedly large number of bacterial variants arose with distinct mutations in the plasmid’s replication initiation protein. Our results suggest that clonal interference, characterized by competition between variant clones in a population, plays a major role in the evolution of the persistence of drug resistance.

scholarly journals Evolutionary dynamics of spore killers.

Genetics ◽  
1993 ◽  
Vol 135 (3) ◽  
pp. 923-930 ◽  
Author(s):  
M J Nauta ◽  
R F Hoekstra
Keyword(s):  
Life Cycle ◽  
Segregation Distortion ◽  
Population Genetic ◽  
Field Data ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Additional Advantage ◽  
Genetic Modeling ◽  
Spore Killing ◽  
Ascospore Formation

Abstract Spore killing in ascomycetes is a special form of segregation distortion. When a strain with the Killer genotype is crossed to a Sensitive type, spore killing is expressed by asci with only half the number of ascospores as usual, all surviving ascospores being of the Killer type. Using population genetic modeling, this paper explores conditions for invasion of Spore killers and for polymorphism of Killers, Sensitives and Resistants (which neither kill, nor get killed), as found in natural populations. The models show that a population with only Killers and Sensitives can never be stable. The invasion of Killers and stable polymorphism only occur if Killers have some additional advantage during the process of spore killing. This may be due to the effects of local sib competition or some kind of "heterozygous" advantage in the stage of ascospore formation or in the short diploid stage of the life cycle. This form of segregation distortion appears to be essentially different from other, well-investigated forms, and more field data are needed for a better understanding of spore killing.

scholarly journals Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

2018 ◽  
Vol 115 (44) ◽  
pp. E10407-E10416 ◽  
Author(s):  
Benjamin H. Good ◽  
Stephen Martis ◽  
Oskar Hallatschek
Keyword(s):  
Evolutionary Dynamics ◽  
Competitive Exclusion ◽  
Directional Selection ◽  
Ecological Niches ◽  
Ecological Diversification ◽  
Effective Competition ◽  
Uptake Rates ◽  
Wide Range ◽  
Dynamical Features ◽  
Adaptation Limits

Microbial communities can evade competitive exclusion by diversifying into distinct ecological niches. This spontaneous diversification often occurs amid a backdrop of directional selection on other microbial traits, where competitive exclusion would normally apply. Yet despite their empirical relevance, little is known about how diversification and directional selection combine to determine the ecological and evolutionary dynamics within a community. To address this gap, we introduce a simple, empirically motivated model of eco-evolutionary feedback based on the competition for substitutable resources. Individuals acquire heritable mutations that alter resource uptake rates, either by shifting metabolic effort between resources or by increasing the overall growth rate. While these constitutively beneficial mutations are trivially favored to invade, we show that the accumulated fitness differences can dramatically influence the ecological structure and evolutionary dynamics that emerge within the community. Competition between ecological diversification and ongoing fitness evolution leads to a state of diversification–selection balance, in which the number of extant ecotypes can be pinned below the maximum capacity of the ecosystem, while the ecotype frequencies and genealogies are constantly in flux. Interestingly, we find that fitness differences generate emergent selection pressures to shift metabolic effort toward resources with lower effective competition, even in saturated ecosystems. We argue that similar dynamical features should emerge in a wide range of models with a mixture of directional and diversifying selection.

scholarly journals Geography is more important than life history in the recent diversification of the tiger salamander complex

2021 ◽  
Vol 118 (17) ◽  
pp. e2014719118
Author(s):  
Kathryn M. Everson ◽  
Levi N. Gray ◽  
Angela G. Jones ◽  
Nicolette M. Lawrence ◽  
Mary E. Foley ◽  
...  
Keyword(s):  
Life History ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Tiger Salamander ◽  
Life History Variation ◽  
Mexican Axolotl ◽  
Population Genetic Differentiation ◽  
Wide Range ◽  
Lineage Divergence

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

scholarly journals Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation

2020 ◽  
Author(s):  
Dimitra Aggeli ◽  
Yuping Li ◽  
Gavin Sherlock
Keyword(s):  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Single Point ◽  
Relative Fitness ◽  
Single Point Mutation ◽  
Historical Contingency ◽  
Mutational Spectra ◽  
Fitness Effects ◽  
Mutational Step ◽  
Diminishing Returns

AbstractThe fitness effects of random mutations are contingent upon the genetic and environmental contexts in which they occur, and this contributes to the unpredictability of evolutionary outcomes at the molecular level. Despite this unpredictability, the rate of adaptation in homogeneous environments tends to decrease over evolutionary time, due to diminishing returns epistasis, causing relative fitness gains to be predictable over the long term. Here, we studied the extent of diminishing returns epistasis and the changes in the adaptive mutational spectra after yeast populations have already taken their first adaptive mutational step. We used three distinct adaptive clones that arose under identical conditions from a common ancestor, from which they diverge by a single point mutation, to found populations that we further evolved. We followed the evolutionary dynamics of these populations by lineage tracking and determined adaptive outcomes using fitness assays and whole genome sequencing. We found compelling evidence for diminishing returns: fitness gains during the 2nd step of adaptation are smaller than those of the 1st step, due to a compressed distribution of fitness effects in the 2nd step. We also found strong evidence for historical contingency at the genic level: the beneficial mutational spectra of the 2nd-step adapted genotypes differ with respect to their ancestor and to each other, despite the fact that the three founders’ 1st-step mutations provided their fitness gains due to similar phenotypic improvements. While some targets of selection in the second step are shared with those seen in the common ancestor, other targets appear to be contingent on the specific first step mutation, with more phenotypically similar founding clones having more similar adaptive mutational spectra. Finally, we found that disruptive mutations, such as nonsense and frameshift, were much more common in the first step of adaptation, contributing an additional way that both diminishing returns and historical contingency are evident during 2nd step adaptation.

scholarly journals On the spectrum of vertically propagating gravity waves generated by a transient heat source

2004 ◽  
Vol 4 (1) ◽  
pp. 1063-1090 ◽  
Author(s):  
M. J. Alexander ◽  
J. R. Holton
Keyword(s):  
Heat Source ◽  
Gravity Waves ◽  
High Frequency ◽  
Convective Heating ◽  
Frequency Spectra ◽  
Wide Range ◽  
Frequency Components ◽  
High Frequency Waves ◽  
Vertically Propagating ◽  
Group Velocities

Abstract. It is commonly believed that cumulus convection preferentially generates gravity waves with tropospheric vertical wavelengths approximately twice the depth of the convective heating. Individual cumulonimbus, however, act as short term transient heat sources (duration 10 to 30 min). Gravity waves generated by such sources have broad frequency spectra and a wide range of vertical scales. The high-frequency components tend to have vertical wavelengths much greater than twice the depth of the heating. Such waves have large vertical group velocities, and are only observed for a short duration and at short horizontal distances from the convective source. At longer times and longer distances from the source the dominant wave components have short vertical wavelengths and much slower group velocities, and thus are more likely to be observed even though their contribution to the momentum flux in the upper stratosphere and mesosphere may be less than that of the high frequency waves. These properties of convectively generated waves are illustrated by a linear numerical model for the wave response to a specified transient heat source. The wave characteristics are documented through Fourier and Wavelet analysis, and implications for observing systems are discussed.

Phase Drift in Networks of Coupled Colpitts Oscillators

2021 ◽  
Vol 31 (04) ◽  
pp. 2130010
Author(s):  
Lourdes Coria ◽  
Horacio Lopez ◽  
Antonio Palacios ◽  
Visarath In ◽  
Patrick Longhini
Keyword(s):  
Collective Behavior ◽  
Traveling Wave ◽  
Scaling Law ◽  
Industrial Applications ◽  
Basins Of Attraction ◽  
Navigation Systems ◽  
Negative Effects ◽  
Phase Drift ◽  
Wide Range ◽  
Wave Patterns

In modern times, satellite-based global positioning and navigation systems, such as the GPS, include precise time-keeping devices, e.g. atomic clocks, which are crucial for navigation and for a wide range of economic and industrial applications. However, precise timing might not be available when the environment renders satellite equipment inoperable. In response to this critical need, we have been carrying out, over the past three years, theory and preliminary experiments [Buono et al., 2018a; Buono et al., 2018b; Palacios et al., 2020], towards developing a novel and inexpensive precision timing device that can function independently of GPS availability. The fundamental idea is to exploit collective behavior generated by networks of coupled nonlinear oscillators. Common sense may suggest that synchronized oscillations may lead to higher accuracy. Previous works show, however, that it is not synchronization but rather, traveling wave patterns, in which consecutive oscillators are out of phase by a constant amount, that can better reduce the negative effects of noise and material imperfections which cause phase drift. In this work we advance the state-of-art in the network-based concept by studying, mainly computationally, collective behavior in networks of Colpitts oscillators. These type of oscillators are chosen because they offer a wide range of advantages (such as the ability to tune up the oscillations over a broad frequency range). The results highlight the regions of parameter space, including coupling strength, where traveling wave patterns have the largest basins of attraction and the ability to reduce phase drift by a [Formula: see text] scaling law, where [Formula: see text] is the number of oscillators in the network. The results should also provide guidelines for follow-up design and fabrication tasks of a network-based technology for precision timing.

scholarly journals Microbial control of host gene regulation and the evolution of host–microbiome interactions in primates

2020 ◽  
Vol 375 (1808) ◽  
pp. 20190598 ◽  
Author(s):  
Laura Grieneisen ◽  
Amanda L. Muehlbauer ◽  
Ran Blekhman
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Host Species ◽  
Evolutionary Dynamics ◽  
Microbial Control ◽  
Host Gene ◽  
Primate Species ◽  
Microbiome Composition ◽  
Wide Range ◽  
Species Specific

Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

Completing the Study of Traveling Wave Solutions for Three Two-Component Shallow Water Wave Models

2020 ◽  
Vol 30 (03) ◽  
pp. 2050036 ◽  
Author(s):  
Jibin Li ◽  
Guanrong Chen ◽  
Jie Song
Keyword(s):  
Solitary Wave ◽  
Shallow Water ◽  
Traveling Wave ◽  
Water Wave ◽  
Wave System ◽  
Solitary Wave Solutions ◽  
Shallow Water Wave ◽  
Wave Solutions ◽  
Two Component ◽  
Wave Models

For three two-component shallow water wave models, from the approach of dynamical systems and the singular traveling wave theory developed in [Li & Chen, 2007], under different parameter conditions, all possible bounded solutions (solitary wave solutions, pseudo-peakons, periodic peakons, as well as smooth periodic wave solutions) are derived. More than 19 explicit exact parametric representations are obtained. Of more interest is that, for the integrable two-component generalization of the Camassa–Holm equation, it is found that its [Formula: see text]-traveling wave system has a family of pseudo-peakon wave solutions. In addition, its [Formula: see text]-traveling wave system has two families of uncountably infinitely many solitary wave solutions. The new results complete a recent study by Dutykh and Ionescu-Kruse [2016].

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