No selection for change in polyandry under experimental evolution

ABSTRACTBacteriophages are a major cause of bacterial mortality and impose strong selection on natural bacterial populations, yet their effects on the dynamics of conjugative plasmids have rarely been tested. We combined experimental evolution, mathematical modeling, and individual-based simulations to explain how the ecological and population genetics effects of bacteriophages upon bacteria interact to determine the dynamics of conjugative plasmids and their persistence. The ecological effects of bacteriophages on bacteria are predicted to limit the existence conditions for conjugative plasmids, preventing persistence under weak selection for plasmid accessory traits. Experiments showed that phages drove faster extinction of plasmids in environments where the plasmid conferred no benefit, but they also revealed more complex effects of phages on plasmid dynamics under these conditions, specifically, the temporary maintenance of plasmids at fixation followed by rapid loss. We hypothesized that the population genetic effects of bacteriophages, specifically, selection for phage resistance mutations, may have caused this. Further mathematical modeling and individual-based simulations supported our hypothesis, showing that conjugative plasmids may hitchhike with phage resistance mutations in the bacterial chromosome.IMPORTANCEConjugative plasmids are infectious loops of DNA capable of transmitting DNA between bacterial cells and between species. Because plasmids often carry extra genes that allow bacteria to live in otherwise-inhospitable environments, their dynamics are central to understanding bacterial adaptive evolution. The plasmid-bacterium interaction has typically been studied in isolation, but in natural bacterial communities, bacteriophages, viruses that infect bacteria, are ubiquitous. Using experiments, mathematical models, and computer simulations we show that bacteriophages drive plasmid dynamics through their ecological and evolutionary effects on bacteria and ultimately limit the conditions allowing plasmid existence. These results advance our understanding of bacterial adaptation and show that bacteriophages could be used to select against plasmids carrying undesirable traits, such as antibiotic resistance.

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Adaptation to temporally fluctuating environments by the evolution of maternal effects

10.1101/023044 ◽

2015 ◽

Cited By ~ 1

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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Indirect evolution of social fitness inequalities and facultative social exploitation

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.0054 ◽

2018 ◽

Vol 285 (1875) ◽

pp. 20180054 ◽

Cited By ~ 3

Author(s):

Ramith R. Nair ◽

Francesca Fiegna ◽

Gregory J. Velicer

Keyword(s):

Social Interaction ◽

Experimental Evolution ◽

Natural Populations ◽

Spore Production ◽

Fruiting Bodies ◽

Cooperative Development ◽

Indirect Evolution ◽

Developmental Contexts ◽

Selection For ◽

Mixed Groups

Microbial genotypes with similarly high proficiency at a cooperative behaviour in genetically pure groups often exhibit fitness inequalities caused by social interaction in mixed groups. Winning competitors in this scenario have been referred to as ‘cheaters’ in some studies. Such interaction-specific fitness inequalities, as well as social exploitation (in which interaction between genotypes increases absolute fitness), might evolve due to selection for competitiveness at the focal behaviour or might arise non-adaptively due to pleiotropy, hitchhiking or genetic drift. The bacterium Myxococcus xanthus sporulates during cooperative development of multicellular fruiting bodies. Using M. xanthus lineages that underwent experimental evolution in allopatry without selection on sporulation, we demonstrate that interaction-specific fitness inequalities and facultative social exploitation during development readily evolved indirectly among descendant lineages. Fitness inequalities between evolved genotypes were not caused by divergence in developmental speed, as faster-developing strains were not over-represented among competition winners. In competitions between ancestors and several evolved strains, all evolved genotypes produced more spores than the ancestors, including losers of evolved-versus-evolved competitions, indicating that adaptation in non-developmental contexts pleiotropically increased competitiveness for spore production. Overall, our results suggest that fitness inequalities caused by social interaction during cooperative processes may often evolve non-adaptively in natural populations.

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Evolution in eggs and phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans

Royal Society Open Science ◽

10.1098/rsos.160496 ◽

2016 ◽

Vol 3 (11) ◽

pp. 160496 ◽

Cited By ~ 1

Author(s):

Bradly Alicea

Keyword(s):

Natural Selection ◽

Caenorhabditis Elegans ◽

Experimental Evolution ◽

Specific Gene ◽

Reproductive Timing ◽

Genetic Strains ◽

Selection For ◽

Carry Over ◽

Strain Dependent

To examine the role of natural selection in fecundity in a variety of Caenorhabditis elegans genetic backgrounds, we used an experimental evolution protocol to evolve 14 distinct genetic strains over 15–20 generations. We were able to generate 790 distinct genealogies, which provided information on both the effects of natural selection and the evolvability of each strain. Among these genotypes are a wild-type (N2) and a collection of mutants with targeted mutations in the daf-c, daf-d and AMPK pathways. Differences are observed in reproductive fitness along with related changes in reproductive timing. The majority of selective effects on fecundity occur during the first few generations of evolution, while the negative selection for reproductive timing occurs on longer time scales. In addition, positive selection on fecundity results in positive and negative strain-dependent selection on reproductive timing. A derivative of population size per generation called reproductive carry-over (RCO) may be informative in terms of developmental selection. While these findings transcend mutations in a specific gene, changes in the RCO measure may nevertheless be products of selection. In conclusion, the broader implications of these findings are discussed, particularly in the context of genotype-fitness maps and the role of uncharacterized mutations in individual variation and evolvability.

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Experimental evolution of recombination and crossover interference in Drosophila caused by directional selection for stress-related traits

BMC Biology ◽

10.1186/s12915-015-0206-5 ◽

2015 ◽

Vol 13 (1) ◽

Cited By ~ 21

Author(s):

Dau Dayal Aggarwal ◽

Eugenia Rashkovetsky ◽

Pawel Michalak ◽

Irit Cohen ◽

Yefim Ronin ◽

...

Keyword(s):

Experimental Evolution ◽

Directional Selection ◽

Crossover Interference ◽

Selection For

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A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus

10.1101/309880 ◽

2018 ◽

Author(s):

William Fitzsimmons ◽

Robert J. Woods ◽

John T. McCrone ◽

Andrew Woodman ◽

Jamie J. Arnold ◽

...

Keyword(s):

Mutation Rate ◽

Experimental Evolution ◽

Rna Viruses ◽

Fundamental Problem ◽

Rna Virus ◽

Mutation Rates ◽

Direct Selection ◽

Growth Defect ◽

Infection Model ◽

Selection For

AbstractMutation rates can evolve through genetic drift, indirect selection due to genetic hitchhiking, or direct selection on the physicochemical cost of high fidelity. However, for many systems, it has been difficult to disentangle the relative impact of these forces empirically. In RNA viruses, an observed correlation between mutation rate and virulence has led many to argue that their extremely high mutation rates are advantageous, because they may allow for increased adaptability. This argument has profound implications, as it suggests that pathogenesis in many viral infections depends on rare orde novomutations. Here we present data for an alternative model whereby RNA viruses evolve high mutation rates as a byproduct of selection for increased replicative speed. We find that a poliovirus antimutator, 3DG64S, has a significant replication defect and that wild type and 3DG64Spopulations have similar adaptability in two distinct cellular environments. Experimental evolution of 3DG64Sunder r-selection led to reversion and compensation of the fidelity phenotype. Mice infected with 3DG64Sexhibited delayed morbidity at doses well above the LD50, consistent with attenuation by slower growth as opposed to reduced mutational supply. Furthermore, compensation of the 3DG64Sgrowth defect restored virulence, while compensation of the fidelity phenotype did not. Our data are consistent with the kinetic proofreading model for biosynthetic reactions and suggest that speed is more important than accuracy. In contrast to what has been suggested for many RNA viruses, we find that within host spread is associated with viral replicative speed and not standing genetic diversity.Author SummaryMutation rate evolution has long been a fundamental problem in evolutionary biology. The polymerases of RNA viruses generally lack proofreading activity and exhibit extremely high mutation rates. Since most mutations are deleterious and mutation rates are tuned by natural selection, we asked why hasn’t the virus evolved to have a lower mutation rate? We used experimental evolution and a murine infection model to show that RNA virus mutation rates may actually be too high and are not necessarily adaptive. Rather, our data indicate that viral mutation rates are driven higher as a result of selection for viruses with faster replication kinetics. We suggest that viruses have high mutation rates, not because they facilitate adaption, but because it is hard to be both fast and accurate.

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Experimental evolution of extremophile levels of radiation resistance in Escherichia coli

10.1101/2021.10.18.464883 ◽

2021 ◽

Author(s):

Steven T Bruckbauer ◽

Benjamin B Minkoff ◽

Takeshi Shinohara ◽

Anna Lipzen ◽

Jie Guo ◽

...

Keyword(s):

Escherichia Coli ◽

Experimental Evolution ◽

Deinococcus Radiodurans ◽

Dna Packaging ◽

Cellular Systems ◽

Cell Physiology ◽

Oxygen Species ◽

Iron Sulfur ◽

Selection For ◽

High Level

Recent human development of high-level sources of ionizing radiation (IR) prompts a corresponding need to understand the effects of IR on living systems. One approach has focused on the capacity of some organisms to survive astonishing levels of IR exposure. Using experimental evolution, we have generated populations of Escherichia coli with IR resistance comparable to the extremophile Deinococcus radiodurans. Every aspect of cell physiology is affected. Cellular isolates exhibit approximately 1,000 base pair changes plus major genomic and proteomic alterations. The IR resistance phenotype is stable without selection for at least 100 generations. Defined and probable contributions include alterations in cellular systems involved in DNA repair, amelioration of reactive oxygen species, Fe metabolism and repair of iron-sulfur centers, DNA packaging, and intermediary metabolism. A path to new mechanistic discoveries, exemplified by an exploration of rssB function, is evident. Most important, there is no single molecular mechanism underlying extreme IR resistance.

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Experimental evolution with Drosophila

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.90551.2008 ◽

2009 ◽

Vol 296 (6) ◽

pp. R1847-R1854 ◽

Cited By ~ 26

Author(s):

Molly K. Burke ◽

Michael R. Rose

Keyword(s):

Stress Resistance ◽

Experimental Evolution ◽

Life History Traits ◽

Model Organism ◽

Direct Selection ◽

Genomic Technologies ◽

Drosophila Model ◽

Powerful Approach ◽

Selection For ◽

Insight Into

Experimental evolution is a powerful approach that can be used for the study of adaptation. Evolutionary biologists often use Drosophila as a model organism in experiments that test theories about the evolution of traits related to fitness. Such evolution experiments can take three forms: direct selection for a trait of interest; surveys of traits of interest in populations selected for other traits; and reverse selection. We review some of the Drosophila experiments that have provided insight into both the evolution of particular physiological traits and the correlations between physiological and life history traits, focusing on stress resistance. The most common artifacts that can obscure the results from evolution experiments are discussed. We also include a treatment of genomic technologies that are now available for the Drosophila model. The primary goal of this review is to introduce the kind of experimental evolution strategies and technologies that evolutionary physiologists might use in the future.

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Experimental evolution reveals favored adaptive routes to cell aggregation in yeast

10.1101/091876 ◽

2016 ◽

Author(s):

Elyse A. Hope ◽

Clara J. Amorosi ◽

Aaron W. Miller ◽

Kolena Dang ◽

Caiti Smukowski Heil ◽

...

Keyword(s):

Experimental Evolution ◽

Community Building ◽

Cell Aggregation ◽

Industrial Processes ◽

Clinical Settings ◽

Loss Of Function ◽

Yeast Flocculation ◽

Single Deletion ◽

Genetic Mechanisms ◽

Selection For

AbstractYeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanismsSaccharomyces cerevisiaeuses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones we identified a transposable element insertion in the promoter region of known flocculation geneFLO1, and in an additional five clones we recovered loss-of-function mutations in transcriptional repressorTUP1, which regulatesFLO1and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving aflo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits.

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Division of labor, bet hedging, and the evolution of mixed biofilm investment strategies

10.1101/107102 ◽

2017 ◽

Author(s):

Nick Vallespir Lowery ◽

Luke McNally ◽

William C. Ratcliff ◽

Sam P. Brown

Keyword(s):

Division Of Labor ◽

Experimental Evolution ◽

Cost Effective ◽

Investment Strategies ◽

Bacterial Cells ◽

Bet Hedging ◽

Planktonic Cells ◽

Selection For ◽

Experimental Findings ◽

Slow Growing

ABSTRACTBacterial cells, like many other organisms, face a tradeoff between longevity and fecundity. Planktonic cells are fast growing and fragile, while biofilm cells are often slower growing but stress resistant. Here we ask: why do bacterial lineages invest simultaneously in both fast and slow growing types? We develop a population dynamical model of lineage expansion across a patchy environment, and find that mixed investment is favored across a broad range of environmental conditions, even when transmission is entirely via biofilm cells. This mixed strategy is favored because of a division of labor, where exponentially dividing planktonic cells can act as an engine for the production of future biofilm cells, which grow more slowly. We use experimental evolution to test our predictions, and show that phenotypic heterogeneity is persistent even under selection for purely planktonic or purely biofilm transmission. Furthermore, simulations suggest that maintenance of a biofilm subpopulation serves as a cost-effective hedge against environmental uncertainty, which is also consistent with our experimental findings.

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