scholarly journals Avoiding dead ends: the experimental evolution of constraint as adaptation to environmental variation in Saccharomyces cerevisiae

2022 ◽  
Author(s):  
Shravan Raghu ◽  
Myron Smith ◽  
Andrew Simons
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Experimental Evolution ◽  
Evolutionary Constraint ◽  
Bet Hedging ◽  
Reduced Frequency ◽  
Short Term Adaptation ◽  
Heat Shocks ◽  
Environmental Unpredictability ◽  
Sequential Treatments ◽  
Short Time

Abstract Environmental unpredictability results in the evolution of bet-hedging traits, which maximize long-term fitness but are, by definition, suboptimal over short time scales. However, because suboptimal traits are expected to be purged by selection in the shorter term, the persistence of bet hedging remains perplexing. Here, we test the hypothesis that bet hedging persists through the evolution of constraint on short-term adaptation. We experimentally evolve Saccharomyces cerevisiae across two sequential treatments in which the frequency of extreme heat shocks decreases. We predict that experimental evolution under lower frequency heat shocks will result in greater adaptive constraint, or “purge-resistant” bet hedging. Constraint is assayed as evolutionary persistence of heat shock tolerance (HST) under constant benign conditions. As predicted, we find the retention of HST only in lines evolved under reduced frequency detrimental conditions. Results help explain the evolution of bet hedging, and challenge the traditional view that evolutionary constraint is inherently maladaptive.

Experimental evolution of bet hedging in rotifer diapause traits as a response to environmental unpredictability

Oikos ◽  
2017 ◽  
Vol 126 (8) ◽  
pp. 1162-1172 ◽  
Author(s):  
Eva Tarazona ◽  
Eduardo M. García-Roger ◽  
María José Carmona
Keyword(s):  
Experimental Evolution ◽  
Bet Hedging ◽  
Environmental Unpredictability

scholarly journals RNA sequencing reveals metabolic and regulatory changes leading to more robust fermentation performance during short-term adaptation of Saccharomyces cerevisiae to lignocellulosic inhibitors

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Marlous van Dijk ◽  
Peter Rugbjerg ◽  
Yvonne Nygård ◽  
Lisbeth Olsson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Response ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Lignocellulosic Hydrolysate ◽  
Short Term ◽  
Down Regulation ◽  
Time Resolved ◽  
Second Generation Bioethanol ◽  
Short Term Adaptation

Abstract Background The limited tolerance of Saccharomyces cerevisiae to inhibitors is a major challenge in second-generation bioethanol production, and our understanding of the molecular mechanisms providing tolerance to inhibitor-rich lignocellulosic hydrolysates is incomplete. Short-term adaptation of the yeast in the presence of dilute hydrolysate can improve its robustness and productivity during subsequent fermentation. Results We utilized RNA sequencing to investigate differential gene expression in the industrial yeast strain CR01 during short-term adaptation, mimicking industrial conditions for cell propagation. In this first transcriptomic study of short-term adaption of S. cerevisiae to lignocellulosic hydrolysate, we found that cultures respond by fine-tuned up- and down-regulation of a subset of general stress response genes. Furthermore, time-resolved RNA sequencing allowed for identification of genes that were differentially expressed at 2 or more sampling points, revealing the importance of oxidative stress response, thiamin and biotin biosynthesis. furan-aldehyde reductases and specific drug:H+ antiporters, as well as the down-regulation of certain transporter genes. Conclusions These findings provide a better understanding of the molecular mechanisms governing short-term adaptation of S. cerevisiae to lignocellulosic hydrolysate, and suggest new genetic targets for improving fermentation robustness.

scholarly journals Evolution of simple multicellularity increases environmental complexity

2016 ◽  
Author(s):  
María Rebolleda-Gómez ◽  
William C. Ratcliff ◽  
Jonathon Fankhauser ◽  
Michael Travisano
Keyword(s):  
Fluid Dynamics ◽  
Saccharomyces Cerevisiae ◽  
Experimental Evolution ◽  
Single Cells ◽  
Environmental Complexity ◽  
Major Transitions ◽  
Rapid Diversification ◽  
Ecological Mechanisms ◽  
Major Transitions In Evolution ◽  
Maintenance Of Diversity

AbstractMulticellularity—the integration of previously autonomous cells into a new, more complex organism—is one of the major transitions in evolution. Multicellularity changed evolutionary possibilities and facilitated the evolution of increased complexity. Transitions to multicellularity are associated with rapid diversification and increased ecological opportunity but the potential mechanisms are not well understood. In this paper we explore the ecological mechanisms of multicellular diversification during experimental evolution of the brewer’s yeast, Saccharomyces cerevisiae. The evolution from single cells into multicellular clusters modifies the structure of the environment, changing the fluid dynamics and creating novel ecological opportunities. This study demonstrates that even in simple conditions, incipient multicellularity readily changes the environment, facilitating the origin and maintenance of diversity.

scholarly journals A continuum of biological adaptations to environmental fluctuation

2019 ◽  
Vol 286 (1912) ◽  
pp. 20191623 ◽  
Author(s):  
Ming Liu ◽  
Dustin R. Rubenstein ◽  
Wei-Chung Liu ◽  
Sheng-Feng Shen
Keyword(s):  
Overlapping Generations ◽  
Bet Hedging ◽  
Environmental Fluctuation ◽  
Infinite Population ◽  
Biological Adaptation ◽  
Hedging Strategies ◽  
Wide Range ◽  
Population Sizes ◽  
Environmental Unpredictability ◽  
Per Capita

Bet-hedging—a strategy that reduces fitness variance at the expense of lower mean fitness among different generations—is thought to evolve as a biological adaptation to environmental unpredictability. Despite widespread use of the bet-hedging concept, most theoretical treatments have largely made unrealistic demographic assumptions, such as non-overlapping generations and fixed or infinite population sizes. Here, we extend the concept to consider overlapping generations by defining bet-hedging as a strategy with lower variance and mean per capita growth rate across different environments. We also define an opposing strategy—the rising-tide—that has higher mean but also higher variance in per capita growth. These alternative strategies lie along a continuum of biological adaptions to environmental fluctuation. Using stochastic Lotka–Volterra models to explore the evolution of the rising-tide versus bet-hedging strategies, we show that both the mean environmental conditions and the temporal scales of their fluctuations, as well as whether population dynamics are discrete or continuous, are crucial in shaping the type of strategy that evolves in fluctuating environments. Our model demonstrates that there are likely to be a wide range of ways that organisms with overlapping generations respond to environmental unpredictability beyond the classic bet-hedging concept.

scholarly journals Biological adaptation under fluctuating selection

2018 ◽  
Author(s):  
Ming Liu ◽  
Dustin R. Rubenstein ◽  
Wei-Chung Liu ◽  
Sheng-Feng Shen
Keyword(s):  
Evolutionary Strategy ◽  
Bet Hedging ◽  
Negative Effects ◽  
Fluctuating Selection ◽  
Hedging Strategy ◽  
Biological Adaptation ◽  
Wide Range ◽  
Population Sizes ◽  
Mean And Variance ◽  
Environmental Unpredictability

AbstractBet-hedging—an evolutionary strategy that reduces fitness variance at the expense of lower mean fitness—is the primary explanation for most forms of biological adaptation to environmental unpredictability. However, most applications of bet-hedging theory to biological problems have largely made unrealistic demographic assumptions, such as non-overlapping generations and fixed population sizes. Consequently, the generality and applicability of bet-hedging theory to real world phenomena remains unclear. Here we use continuous-time, stochastic Lotka-Volterra models to relax overly restrictive demographic assumptions and explore a suite of biological adaptations to fluctuating environments. We discover a novel “rising-tide strategy” that—unlike the bet-hedging strategy—generates both a higher mean and variance in fitness. The positive fitness effects of the rising-tide strategy’s specialization to good years can overcome any negative effects of higher fitness variance in unpredictable environments. Moreover, we show not only that the rising-tide strategy will be selected for over a much broader range of environmental conditions than the bet-hedging strategy, but also under more realistic demographic circumstances. Ultimately, our model demonstrates that there are likely to be a wide range of ways that organisms respond to environmental unpredictability.

scholarly journals Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mark A. Phillips ◽  
Ian C. Kutch ◽  
Kaitlin M. McHugh ◽  
Savannah K. Taggard ◽  
Molly K. Burke
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Variation ◽  
Experimental Evolution ◽  
Complex Traits ◽  
Inbred Lines ◽  
Equal Proportion ◽  
Adaptive Potential ◽  
Synthetic Populations ◽  
The Impact ◽  
Isogenic Strains

Abstract“Synthetic recombinant” populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In the latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant Saccharomyces cerevisiae populations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.

scholarly journals Systemic aneuploidization events drive phenotype switching in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Lydia R Heasley ◽  
Juan Lucas Argueso
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Colony Morphology ◽  
Whole Genome Sequence ◽  
Bet Hedging ◽  
Wild Type ◽  
Environmental Pressures ◽  
Hedging Strategies ◽  
Species Evolution ◽  
Phenotype Switching ◽  
New Perspective

How cells leverage their phenotypic potential to adapt and survive in a changing environment is a complex biological problem, with important implications for pathogenesis and species evolution. One particularly fascinating adaptive approach is the bet hedging strategy known as phenotype switching, which introduces phenotypic variation into a population through stochastic processes. Phenotype switching has long been observed in species across the tree of life, yet the mechanistic causes of switching in these organisms have remained difficult to define. Here we describe the causative basis of colony morphology phenotype switching which occurs among cells of the pathogenic isolate of Saccharomyces cerevisiae, YJM311. From clonal populations of YJM311 cells grown in identical conditions, we identified colonies which displayed altered colony architectures, yet could revert to the wild-type morphology after passaging. Whole genome sequence analysis revealed that these variant clones had all acquired whole chromosome copy number alterations (i.e., aneuploidies). Cumulatively, the variant clones we characterized harbored an exceptional spectrum of karyotypic alterations, with individual variants carrying between 1 and 16 aneuploidies. Most variants harbored unique collections of aneuploidies, indicating that numerous distinct karyotypes could manifest in the same morphological variation. Intriguingly, the genomic stability of these newly aneuploid variant clones modulated how often cells reverted back to the wild-type phenotypic state. We found that such revertant switches were also driven by chromosome missegregation events, and in some cases occurred through a return to euploidy. Together, our results demonstrate that colony morphology switching in this yeast strain is driven by stochastic and systemic aneuploidization events. These findings add an important new perspective to our current understanding of phenotype switching and bet hedging strategies, as well as how environmental pressures perpetuate organismal adaption and genome evolution.

scholarly journals Adaptation to temporally fluctuating environments by the evolution of maternal effects

2015 ◽  
Author(s):  
Snigdhadip Dey ◽  
Steve Proulx ◽  
Henrique Teotonio
Keyword(s):  
Maternal Effects ◽  
Experimental Evolution ◽  
Reproductive Strategies ◽  
Correlated Response ◽  
Bet Hedging ◽  
Offspring Performance ◽  
Trade Offs ◽  
Wide Range ◽  
Fluctuating Environments ◽  
Selection For

Most organisms live in ever-challenging temporally fluctuating environments. Theory suggests that the evolution of anticipatory (or deterministic) maternal effects underlies adaptation to environments that regularly fluctuate every other generation because of selection for increased offspring performance. Evolution of maternal bet-hedging reproductive strategies that randomize offspring phenotypes is in turn expected to underlie adaptation to irregularly fluctuating environments. Although maternal effects are ubiquitous their adaptive significance is unknown since they can easily evolve as a correlated response to selection for increased maternal performance. Using the nematode Caenorhabditis elegans, we show the experimental evolution of maternal provisioning of offspring with glycogen, in populations facing a novel anoxia hatching environment every other generation. As expected with the evolution of deterministic maternal effects, improved embryo hatching survival under anoxia evolved at the expense of fecundity and glycogen provisioning when mothers experienced anoxia early in life. Unexpectedly, populations facing an irregularly fluctuating anoxia hatching environment failed to evolve maternal bet-hedging reproductive strategies. Instead, adaptation in these populations should have occurred through the evolution of balancing trade-offs over multiple generations, since they evolved reduced fitness over successive generations in anoxia but did not go extinct during experimental evolution. Mathematical modelling confirms our conclusion that adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that they are generally much more likely to contribute to adaptation than maternal bet-hedging reproductive strategies.

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