Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Impact of Dominance on Adaptation in Changing Environments.

ABSTRACT: Natural environments are seldom static and therefore it is important to ask how a population adapts in a changing environment. We consider a finite, diploid population evolving in a periodically changing environment and study how the fixation probability of a rare mutant depends on its dominance coefficient and the rate of environmental change. We find that, in slowly changing environments, the effect of dominance is the same as in the static environment, that is, if a mutant is beneficial (deleterious) when it appears, it is more (less) likely to fix if it is dominant. But, in fast changing environments, the effect of dominance can be different from that in the static environment and is determined by the mutant's fitness at the time of appearance as well as that in the time-averaged environment. We find that, in a rapidly varying environment that is neutral on average, an initially beneficial (deleterious) mutant that arises while selection is decreasing (increasing) has a fixation probability lower (higher) than that for a neutral mutant as a result of which the recessive (dominant) mutant is favored. If the environment is beneficial (deleterious) on average but the mutant is deleterious (beneficial) when it appears in the population, the dominant (recessive) mutant is favored in a fast changing environment. We also find that, when recurrent mutations occur, dominance does not have a strong influence on evolutionary dynamics.

SUBMITTER: Devi A

PROVIDER: S-EPMC7463278 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Probabilistic adaptation in changing microbial environments.

Project description:Microbes growing in animal host environments face fluctuations that have elements of both randomness and predictability. In the mammalian gut, fluctuations in nutrient levels and other physiological parameters are structured by the host's behavior, diet, health and microbiota composition. Microbial cells that can anticipate environmental fluctuations by exploiting this structure would likely gain a fitness advantage (by adapting their internal state in advance). We propose that the problem of adaptive growth in structured changing environments, such as the gut, can be viewed as probabilistic inference. We analyze environments that are "meta-changing": where there are changes in the way the environment fluctuates, governed by a mechanism unobservable to cells. We develop a dynamic Bayesian model of these environments and show that a real-time inference algorithm (particle filtering) for this model can be used as a microbial growth strategy implementable in molecular circuits. The growth strategy suggested by our model outperforms heuristic strategies, and points to a class of algorithms that could support real-time probabilistic inference in natural or synthetic cellular circuits.

| S-EPMC5160922 | biostudies-literature

Evolutionary adaptation of high-diversity communities to changing environments.

Project description:We use adaptive dynamics models to study how changes in the abiotic environment affect patterns of evolutionary dynamics and diversity in evolving communities of organisms with complex phenotypes. The models are based on the logistic competition model, and environmental changes are implemented as a temporal change of the carrying capacity as a function of phenotype. In general, we observe that environmental changes cause a reduction in the number of species, in total population size, and in phenotypic diversity. The rate of environmental change is crucial for determining whether a community survives or undergoes extinction. Until some critical rate of environmental changes, species are able to follow evolutionarily the shifting phenotypic optimum of the carrying capacity, and many communities adapt to the changing conditions and converge to new stationary states. When environmental changes stop, such communities gradually restore their initial phenotypic diversity.

| S-EPMC7663975 | biostudies-literature

The conflict between adaptation and dispersal for maintaining biodiversity in changing environments.

Project description:Dispersal and adaptation both allow species to persist in changing environments. Yet, we have limited understanding of how these processes interact to affect species persistence, especially in diverse communities where biotic interactions greatly complicate responses to environmental change. Here we use a stochastic metacommunity model to demonstrate how dispersal and adaptation to environmental change independently and interactively contribute to biodiversity maintenance. Dispersal provides spatial insurance, whereby species persist on the landscape by shifting their distributions to track favorable conditions. In contrast, adaptation allows species to persist by allowing for evolutionary rescue. But, when species both adapt and disperse, dispersal and adaptation do not combine positively to affect biodiversity maintenance, even if they do increase the persistence of individual species. This occurs because faster adapting species evolve to hold onto their initial ranges (i.e., monopolization effects), thus impeding slower adapting species from shifting their ranges and thereby causing extinctions. Importantly, these differences in adaptation speed emerge as the result of competition, which alters population sizes and colonization success. By demonstrating how dispersal and adaptation each independently and interactively contribute to the maintenance of biodiversity, we provide a framework that links the theories of spatial insurance, evolutionary rescue, and monopolization. This highlights the expectation that the maintenance of biodiversity in changing environments depends jointly on rates of dispersal and adaptation, and, critically, the interaction between these processes.

| S-EPMC6800316 | biostudies-literature

Establishment of new mutations in changing environments.

Project description:Understanding adaptation in changing environments is an important topic in evolutionary genetics, especially in the light of climatic and environmental change. In this work, we study one of the most fundamental aspects of the genetics of adaptation in changing environments: the establishment of new beneficial mutations. We use the framework of time-dependent branching processes to derive simple approximations for the establishment probability of new mutations assuming that temporal changes in the offspring distribution are small. This approach allows us to generalize Haldane's classic result for the fixation probability in a constant environment to arbitrary patterns of temporal change in selection coefficients. Under weak selection, the only aspect of temporal variation that enters the probability of establishment is a weighted average of selection coefficients. These weights quantify how much earlier generations contribute to determining the establishment probability compared to later generations. We apply our results to several biologically interesting cases such as selection coefficients that change in consistent, periodic, and random ways and to changing population sizes. Comparison with exact results shows that the approximation is very accurate.

| S-EPMC3389982 | biostudies-literature

Bacterial rapid adaptation to alkaline environments

Project description:To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.

2024-06-24 | GSE270261 | GEO

Carryover effects drive competitive dominance in spatially structured environments.

Project description:Understanding how changes to the quality of habitat patches affect the distribution of species across the whole landscape is critical in our human-dominated world and changing climate. Although patterns of species' abundances across a landscape are clearly influenced by dispersal among habitats and local species interactions, little is known about how the identity and origin of dispersers affect these patterns. Because traits of individuals are altered by experiences in their natal habitat, differences in the natal habitat of dispersers can carry over when individuals disperse to new habitats and alter their fitness and interactions with other species. We manipulated the presence or absence of such carried-over natal habitat effects for up to eight generations to examine their influence on two interacting species across multiple dispersal rates and different habitat compositions. We found that experimentally accounting for the natal habitat of dispersers significantly influenced competitive outcomes at all spatial scales and increased total community biomass within a landscape. However, the direction and magnitude of the impact of natal habitat effects was dependent upon landscape type and dispersal rate. Interestingly, effects of natal habitats increased the difference between species performance across the landscape, suggesting that natal habitat effects could alter competitive interactions to promote spatial coexistence. Given that heterogeneity in habitat quality is ubiquitous in nature, natal habitat effects are likely important drivers of spatial community structure and could promote variation in species performance, which may help facilitate spatial coexistence. The results have important implications for conservation and invasive species management.

| S-EPMC4922188 | biostudies-literature

Antagonistic pleiotropy conceals molecular adaptations in changing environments.

Project description:The importance of positive selection in molecular evolution is debated. Evolution experiments under invariant laboratory conditions typically show a higher rate of nonsynonymous nucleotide changes than the rate of synonymous changes, demonstrating prevalent molecular adaptations. Natural evolution inferred from genomic comparisons, however, almost always exhibits the opposite pattern even among closely related conspecifics, which is indicative of a paucity of positive selection. Here we hypothesize that this apparent contradiction is at least in part attributable to ubiquitous and frequent environmental changes in nature, causing nonsynonymous mutations that are beneficial at one time to become deleterious soon after because of antagonistic pleiotropy and hindering their fixations relative to synonymous mutations despite continued population adaptations. To test this hypothesis, we performed yeast evolution experiments in changing and corresponding constant environments, followed by genome sequencing of the evolving populations. We observed a lower nonsynonymous to synonymous rate ratio in antagonistic changing environments than in the corresponding constant environments, and the population dynamics of mutations supports our hypothesis. These findings and the accompanying population genetic simulations suggest that molecular adaptation is consistently underestimated in nature due to the antagonistic fitness effects of mutations in changing environments.

| S-EPMC7058517 | biostudies-literature

The evolutionary dynamics of integrons in changing environments.

Project description:Integrons are genetic elements that are common in bacteria and are hotspots for genome evolution. They facilitate the acquisition and reassembly of gene cassettes encoding a variety of functions, including drug resistance. Despite their importance in clinical settings, the selective forces responsible for the evolution and maintenance of integrons are poorly understood. We present a mathematical model of integron evolution within bacterial populations subject to fluctuating antibiotic exposures. Bacteria carrying a functional integrase that mediates reshuffling of cassette genes and thereby modulates gene expression patterns compete with bacteria without a functional integrase. Our results indicate that for a wide range of parameters, the functional integrase can be stably maintained in the population despite substantial fitness costs. This selective advantage arises because gene-cassette shuffling generates genetic diversity, thus enabling the population to respond rapidly to changing selective pressures. We also show that horizontal gene transfer promotes stable maintenance of the integrase and can also lead to de novo assembly of integrons. Our model generates testable predictions for integron evolution, including loss of functional integrases in stable environments and selection for intermediate gene-shuffling rates in changing environments. Our results highlight the need for experimental studies of integron population biology.

| S-EPMC5029196 | biostudies-literature

Adaptive quantum computation in changing environments using projective simulation.

Project description:Quantum information processing devices need to be robust and stable against external noise and internal imperfections to ensure correct operation. In a setting of measurement-based quantum computation, we explore how an intelligent agent endowed with a projective simulator can act as controller to adapt measurement directions to an external stray field of unknown magnitude in a fixed direction. We assess the agent's learning behavior in static and time-varying fields and explore composition strategies in the projective simulator to improve the agent's performance. We demonstrate the applicability by correcting for stray fields in a measurement-based algorithm for Grover's search. Thereby, we lay out a path for adaptive controllers based on intelligent agents for quantum information tasks.

| S-EPMC4531334 | biostudies-other

Evolution of ecological dominance of yeast species in high-sugar environments.

Project description:In budding yeasts, fermentation in the presence of oxygen evolved around the time of a whole genome duplication (WGD) and is thought to confer dominance in high-sugar environments because ethanol is toxic to many species. Although there are many fermentative yeast species, only Saccharomyces cerevisiae consistently dominates wine fermentations. In this study, we use coculture experiments and intrinsic growth rate assays to examine the relative fitness of non-WGD and WGD yeast species across environments to assess when S. cerevisiae's ability to dominate high-sugar environments arose. We show that S. cerevisiae dominates nearly all other non-WGD and WGD species except for its sibling species S. paradoxus in both grape juice and a high-sugar rich medium. Of the species we tested, S. cerevisiae and S. paradoxus have evolved the highest ethanol tolerance and intrinsic growth rate in grape juice. However, the ability of S. cerevisiae and S. paradoxus to dominate certain species depends on the temperature and the type of high-sugar environment. Our results indicate that dominance of high-sugar environments evolved much more recently than the WGD, most likely just prior to or during the differentiation of Saccharomyces species, and that evolution of multiple traits contributes to S. cerevisiae's ability to dominate wine fermentations.

| S-EPMC4751874 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data