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Models of experimental evolution: the role of genetic chance and selective necessity.

Wahl, L M; Krakauer, D C
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /11/2000 EN
Relevância na Pesquisa
45.88%
We present a theoretical framework within which to analyze the results of experimental evolution. Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales. Artificial adaptive radiation is characterized by a list of common observations; we offer a framework in which many of these repeated questions and patterns can be characterized analytically. We allow for stochasticity by including rare mutations and bottleneck effects, demonstrating how these increase variability in the evolutionary trajectory. When the product Np, the population size times the per locus error rate, is small, the rate of evolution is limited by the chance occurrence of beneficial mutations; when Np is large and selective pressure is strong, the rate-limiting step is the waiting time while existing beneficial mutations sweep through the population. We derive the rate of divergence (substitution rate) and rate of fitness increase for the case when Np is large and illustrate our approach with an application to an experimental data set. A minimal assumption of independent additive fitness contributions provides a good fit to the experimental evolution of the bacteriophage phiX174.

Evaluating the impact of population bottlenecks in experimental evolution.

Wahl, Lindi M; Gerrish, Philip J; Saika-Voivod, Ivan
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /10/2002 EN
Relevância na Pesquisa
45.9%
Experimental evolution involves severe, periodic reductions in population size when fresh media are inoculated during serial transfer. These bottlenecks affect the dynamics of evolution, reducing the probability that a beneficial mutation will reach fixation. We quantify the impact of these bottlenecks on the evolutionary dynamics, for populations that grow exponentially between transfers and for populations in which growth is curbed by a resource-limited environment. We find that in both cases, mutations that survive bottlenecks are equally likely to occur, per unit time, at all times during the growth phase. We estimate the total fraction of beneficial mutations that are lost due to bottlenecks during experimental evolution protocols and derive the "optimal" dilution ratio, the ratio that maximizes the number of surviving beneficial mutations. Although more severe dilution ratios are often used in the literature, we find that a ratio of 0.1-0.2 minimizes the chances that rare beneficial mutations are lost. Finally, we provide a number of useful approximate results and illustrate our approach with applications to experimental evolution protocols in the literature.

Using experimental evolution to explore natural patterns between bacterial motility and resistance to bacteriophages

Koskella, Britt; Taylor, Tiffany B; Bates, Jennifer; Buckling, Angus
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.88%
Resistance of bacteria to phages may be gained by alteration of surface proteins to which phages bind, a mechanism that is likely to be costly as these molecules typically have critical functions such as movement or nutrient uptake. To address this potential trade-off, we combine a systematic study of natural bacteria and phage populations with an experimental evolution approach. We compare motility, growth rate and susceptibility to local phages for 80 bacteria isolated from horse chestnut leaves and, contrary to expectation, find no negative association between resistance to phages and bacterial motility or growth rate. However, because correlational patterns (and their absence) are open to numerous interpretations, we test for any causal association between resistance to phages and bacterial motility using experimental evolution of a subset of bacteria in both the presence and absence of naturally associated phages. Again, we find no clear link between the acquisition of resistance and bacterial motility, suggesting that for these natural bacterial populations, phage-mediated selection is unlikely to shape bacterial motility, a key fitness trait for many bacteria in the phyllosphere. The agreement between the observed natural pattern and the experimental evolution results presented here demonstrates the power of this combined approach for testing evolutionary trade-offs.

Cancer in Light of Experimental Evolution

Sprouffske, Kathleen; Merlo, Lauren M.F.; Gerrish, Philip J.; Maley, Carlo C.; Sniegowski, Paul D.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 11/09/2012 EN
Relevância na Pesquisa
45.92%
Cancer initiation, progression, and the emergence of therapeutic resistance are evolutionary phenomena of clonal somatic cell populations. Studies in microbial experimental evolution and the theoretical work inspired by such studies are yielding deep insights into the evolutionary dynamics of clonal populations, yet there has been little explicit consideration of the relevance of this rapidly growing field to cancer biology. Here, we examine how the understanding of mutation, selection, and spatial structure in clonal populations that is emerging from experimental evolution may be applicable to cancer. Along the way, we discuss some significant ways in which cancer differs from the model systems used in experimental evolution. Despite these differences, we argue that enhanced prediction and control of cancer may be possible using ideas developed in the context of experimental evolution, and we point out some prospects for future research at the interface between these traditionally separate areas.

Mainstreaming Caenorhabditis elegans in experimental evolution

Gray, Jeremy C.; Cutter, Asher D.
Fonte: The Royal Society Publicador: The Royal Society
Tipo: Artigo de Revista Científica
Publicado em 07/03/2014 EN
Relevância na Pesquisa
45.97%
Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host–pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.

Experimental evolution alters the rate and temporal pattern of population growth in Batrachochytrium dendrobatidis, a lethal fungal pathogen of amphibians

Voyles, Jamie; Johnson, Leah R; Briggs, Cheryl J; Cashins, Scott D; Alford, Ross A; Berger, Lee; Skerratt, Lee F; Speare, Rick; Rosenblum, Erica Bree
Fonte: BlackWell Publishing Ltd Publicador: BlackWell Publishing Ltd
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.89%
Virulence of infectious pathogens can be unstable and evolve rapidly depending on the evolutionary dynamics of the organism. Experimental evolution can be used to characterize pathogen evolution, often with the underlying objective of understanding evolution of virulence. We used experimental evolution techniques (serial transfer experiments) to investigate differential growth and virulence of Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis. We tested two lineages of Bd that were derived from a single cryo-archived isolate; one lineage (P10) was passaged 10 times, whereas the second lineage (P50) was passaged 50 times. We quantified time to zoospore release, maximum zoospore densities, and timing of zoospore activity and then modeled population growth rates. We also conducted exposure experiments with a susceptible amphibian species, the common green tree frog (Litoria caerulea) to test the differential pathogenicity. We found that the P50 lineage had shorter time to zoospore production (Tmin), faster rate of sporangia death (ds), and an overall greater intrinsic population growth rate (λ). These patterns of population growth in vitro corresponded with higher prevalence and intensities of infection in exposed Litoria caerulea...

Testing the Role of Genetic Background in Parallel Evolution Using the Comparative Experimental Evolution of Antibiotic Resistance

Vogwill, Tom; Kojadinovic, Mila; Furió, Victoria; MacLean, R. Craig
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.88%
Parallel evolution is the independent evolution of the same phenotype or genotype in response to the same selection pressure. There are examples of parallel molecular evolution across divergent genetic backgrounds, suggesting that genetic background may not play an important role in determining the outcome of adaptation. Here, we measure the influence of genetic background on phenotypic and molecular adaptation by combining experimental evolution with comparative analysis. We selected for resistance to the antibiotic rifampicin in eight strains of bacteria from the genus Pseudomonas using a short term selection experiment. Adaptation occurred by 47 mutations at conserved sites in rpoB, the target of rifampicin, and due to the high diversity of possible mutations the probability of within-strain parallel evolution was low. The probability of between-strain parallel evolution was only marginally lower, because different strains substituted similar rpoB mutations. In contrast, we found that more than 30% of the phenotypic variation in the growth rate of evolved clones was attributable to among-strain differences. Parallel molecular evolution across strains resulted in divergent phenotypic evolution because rpoB mutations had different effects on growth rate in different strains. This study shows that genetic divergence between strains constrains parallel phenotypic evolution...

Analysis of genetic systems using experimental evolution and whole-genome sequencing

Kishony, Roy; Hegreness, Matthew
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
55.82%
The application of whole-genome sequencing to the study of microbial evolution promises to reveal the complex functional networks of mutations that underlie adaptation. A recent study of parallel evolution in populations of Escherichia coli shows how adaptation involves both functional changes to specific proteins as well as global changes in regulation.

Improved Use of a Public Good Selects for the Evolution of Undifferentiated Multicellularity

Koschwanez, John H; Foster, Kevin R; Murray, Andrew W.
Fonte: eLife Sciences Publications, Ltd Publicador: eLife Sciences Publications, Ltd
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
55.82%
We do not know how or why multicellularity evolved. We used the budding yeast, Saccharomyces cerevisiae, to ask whether nutrients that must be digested extracellularly select for the evolution of undifferentiated multicellularity. Because yeast use invertase to hydrolyze sucrose extracellularly and import the resulting monosaccharides, single cells cannot grow at low cell and sucrose concentrations. Three engineered strategies overcame this problem: forming multicellular clumps, importing sucrose before hydrolysis, and increasing invertase expression. We evolved populations in low sucrose to ask which strategy they would adopt. Of 12 successful clones, 11 formed multicellular clumps through incomplete cell separation, 10 increased invertase expression, none imported sucrose, and 11 increased hexose transporter expression, a strategy we had not engineered. Identifying causal mutations revealed genes and pathways, which frequently contributed to the evolved phenotype. Our study shows that combining rational design with experimental evolution can help evaluate hypotheses about evolutionary strategies.; Molecular and Cellular Biology

Physiology and Evolution of Methylamine Metabolism across Methylobacterium extorquens strains

Nayak, Dipti Dinkar
Fonte: Harvard University Publicador: Harvard University
Tipo: Thesis or Dissertation
EN_US
Relevância na Pesquisa
55.82%
The interplay between physiology and evolution in microorganisms is extremely relevant from the stand-point of human health, the environment, and biotechnology; yet microbial physiology and microbial evolution largely continue to grow as disjoint fields of research. The goal of this dissertation was to use experimental evolution to study methylamine metabolism in Methylobacterium extorquens species. Methylotrophs like the M. extorquens species grow on reduced single carbon compounds and are the largest biological sink for methane. M. extorquens AM1, the model system for the study of aerobic methylotrophy, has an unstable genome and severe growth defects as a result of laboratory domestication. First, I describe the genomic, genetic, and phenotypic characterization of a new model system for the study of aerobic methylotrophy: M. extorquens PA1. This strain has a stable genome, was recently isolated from a known ecological niche, and is closely related to AM1. Whereas PA1 grew 10-50% faster than AM1on most substrates, it was five-fold slower on methylamine. The PA1 genome encodes a poorly characterized but ecologically relevant N-methylglutamate pathway whereas AM1 also encodes the well-characterized methylamine dehydrogenase for methylamine oxidation. I characterized the genetics of the N-methylglutamate pathway in PA1 to resolve a linear topology that requires the formation of two...

Cooperation, conflict, and experimental evolution in social amoebae

Kuzdzal, Jennie Jo Helene
Fonte: Universidade Rice Publicador: Universidade Rice
ENG
Relevância na Pesquisa
55.82%
Cooperation and cheater control have helped shape life as we know it, but there is still much to learn. A eukaryote microbial model organism, like Dictyostelium discoideum , is an excellent system for advancing our understanding. When faced with starvation, multiple genetically distinct clones of D. discoideum aggregate together to form a chimeric fruiting body with a sterile stalk that holds aloft a sorus of hardy reproductive spores. One clone may be able to cheat and form disproportionately more spores, while forcing others to form more stalk. Here we discuss the impact of genetic relatedness on cooperation, and how social actions are temporally organized and can be affected by environmental conditions. First, we documented a potential strategy for facultative cheating within chimeras. We showed that the first cells to starve, and initiate the social stage, cheat cells that starved later. In another paper, we reviewed recent studies of social microbes, which demonstrate the importance of high relatedness in the evolution of cooperation and cheater resistance. In an experimental evolution study, we tested the hypothesis that de novo cheater mutants readily evolve under low relatedness conditions. We found that the majority of our lines evolved to cheat their ancestor. Further...

Experimental evolution of TetX2: Correlating changes in fitness to their structural and functional origins

Walkiewicz, Katarzyna
Fonte: Universidade Rice Publicador: Universidade Rice
ENG
Relevância na Pesquisa
55.87%
The study of protein evolution and adaptation resides at the junction between the disciplines of biological chemistry and evolutionary biology. We chose the B. thetaiotaomicron tetracycline resistant enzyme TetX2, as our model system to study the biophysical basis for adaptation to antibiotics; a phenomenon that continuously poses global health challenges. In the work presented here, experimental evolution and biophysical characterization were used to identify and link the physicochemical properties of TetX2 and its adaptive mutants to increased resistance to minocycline. Bacteroides thetaiotaomicron TetX2 was previously identified as a novel oxidoreductase with broad activity against tetracyclines. Experimental evolution of E. coli expressing a chromosomal copy of tet(X2) was used to identify an adaptive mutation (TetX2 T280A ) that confers higher resistance to minocycline and tigecycline. In addition to TetX2 T280A , a family of variants of TetX2 with single amino acid changes in TetX2 sequence that conferred equal or higher resistance towards MCN was identified by error-prone mutagenesis. Changes in fitness of E. coli carrying a single chromosomal copy of either wild-type or one of the mutant alleles were assessed by growth rate assays over a range of minocycline concentrations. Despite similar in vivo performances of TetX2 T280A and two other variants (TetX2 N371I and TetX2 N371T )...

The role of hermaphrodites in the experimental evolution of increased outcrossing rates in Caenorhabditis elegans

Carvalho, Sara; Chelo, Ivo M; Goy, Christine; Teotónio, Henrique
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 02/06/2014 N/A
Relevância na Pesquisa
55.85%
Why most organisms reproduce via outcrossing rather than selfing is a central question in evolutionary biology. It has long ago been suggested that outcrossing is favoured when it facilitates adaptation to novel environments. We have previously shown that the experimental evolution of increased outcrossing rates in populations of the male-hermaphrodite nematode Caenorhabditis elegans were correlated with the experimental evolution of increased male fitness. However, it is unknown whether outcrossing led to adaptation, and if so, which fitness components can explain the observed increase in outcrossing rates.; PhD fellowship from Fundação para a Ciência e a Tecnologia (SFRH/BD/ 36726/2007).

Reproductive assurance drives transitions to self-fertilization in experimental Caenorhabditis elegans

Theologidis, Ioannis; Chelo, Ivo M; Goy, Christine; Teotónio, Henrique
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 05/11/2014 ENG
Relevância na Pesquisa
55.76%
Evolutionary transitions from outcrossing between individuals to selfing are partly responsible for the great diversity of animal and plant reproduction systems. The hypothesis of 'reproductive assurance' suggests that transitions to selfing occur because selfers that are able to reproduce on their own ensure the persistence of populations in environments where mates or pollination agents are unavailable. Here we test this hypothesis by performing experimental evolution in Caenorhabditis elegans.

Fold or die: experimental evolution in vitro

Collins, Sinéad; Rambaut, Andrew; Bridgett, Stephen J.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 18/11/2012
Relevância na Pesquisa
55.87%
We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative Polymerase Chain Reaction (qPCR). It is tractable at the genetic, genomic, phenotypic and fitness levels. The Oli system uses DNA hairpins designed to form structures that self-prime under defined conditions. Selection acts on the phenotype of self-priming, after which differences in fitness are amplified and quantified using qPCR. We outline the methodological and bioinformatics tools for the Oli system here, and demonstrate that it can be used as a conventional experimental evolution model system by test-driving it in an experiment investigating adaptive evolution under different rates of environmental change.; Comment: 20 pages, 4 figures, 1 table, 2 supplementary tables

Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution

Kacar, Betul; Gaucher, Eric
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 22/09/2012
Relevância na Pesquisa
55.92%
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs. Combining ancestral sequence reconstruction with synthetic biology allows us to resurrect the past within a modern context and has expanded our understanding of protein functionality within a historical context. Experimental evolution, on the other hand, provides us with the ability to study evolution in action, under controlled conditions in the laboratory. Here we describe a novel experimental setup that integrates two disparate fields - ancestral sequence reconstruction and experimental evolution. This allows us to rewind and replay the evolutionary history of ancient biomolecules in the laboratory. We anticipate that our combination will provide a deeper understanding of the underlying roles that contingency and determinism play in shaping evolutionary processes.; Comment: 8 pages, 4 figures

Gaussian process test for high-throughput sequencing time series: application to experimental evolution

Topa, Hande; Jónás, Ágnes; Kofler, Robert; Kosiol, Carolin; Honkela, Antti
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
55.88%
Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to monitor genomes in great detail. New experiments not only use HTS to measure genomic features at one time point but to monitor them changing over time with the aim of identifying significant changes in their abundance. In population genetics, for example, allele frequencies are monitored over time to detect significant frequency changes that indicate selection pressures. Previous attempts at analysing data from HTS experiments have been limited as they could not simultaneously include data at intermediate time points, replicate experiments and sources of uncertainty specific to HTS such as sequencing depth. Results: We present the beta-binomial Gaussian process (BBGP) model for ranking features with significant non-random variation in abundance over time. The features are assumed to represent proportions, such as proportion of an alternative allele in a population. We use the beta-binomial model to capture the uncertainty arising from finite sequencing depth and combine it with a Gaussian process model over the time series. In simulations that mimic the features of experimental evolution data, the proposed method clearly outperforms classical testing in average precision of finding selected alleles. We also present simulations exploring different experimental design choices and results on real data from Drosophila experimental evolution experiment in temperature adaptation. Availability: R software implementing the test is available at https://github.com/handetopa/BBGP; Comment: 41 pages...

Evolvability of a viral protease: experimental evolution of catalysis, robustness and specificity

Shafee, Thomas
Fonte: University of Cambridge; Department of Biochemistry; Antibody Discovery and Protein Engineering, Medimmune Publicador: University of Cambridge; Department of Biochemistry; Antibody Discovery and Protein Engineering, Medimmune
Tipo: Thesis; doctoral; PhD
EN
Relevância na Pesquisa
65.93%
The aim of this thesis is to investigate aspects of molecular evolution and enzyme engineering using the experimental evolution of Tobacco Etch Virus cysteine protease (TEV) as a model. I map key features of the local fitness landscape and characterise how they affect details of enzyme evolution. In order to investigate the evolution of core active site machinery, I mutated the nucleophile of TEV to serine. The differing chemical properties of oxygen and sulphur force the enzyme into a fitness valley with a >104-fold activity reduction. Nevertheless, directed evolution was able to recover function, resulting in an enzyme able to utilise either nucleophile. High-throughput screening and sequencing revealed how the array of possible beneficial mutations changes as the enzyme evolves. Potential adaptive mutations are abundant at each step along the evolutionary trajectory, enriched around the active site periphery. It is currently unclear how seemingly neutral mutations affect further adaptive evolution. I used high-throughput directed evolution to accumulate neutral variation in large, evolving enzyme populations and deep sequencing to reconstruct the complex evolutionary dynamics within the lineages. Specifically I was able to observe the emergence of robust enzymes with improved mutation tolerance whose descendants overtake later populations. Lastly...

Using experimental evolution to study adaptations for life within the family

Schrader, Matthew; Jarrett, Benjamin J. M.; Kilner, Rebecca M.
Fonte: University of Chicago Press Publicador: University of Chicago Press
Tipo: Article; accepted version
EN
Relevância na Pesquisa
65.88%
This is the author accepted manuscript. The final version is available from the University of Chicago Press via http://dx.doi.org/10.1086/680500; Parents of many species provision their young and the extent of parental provisioning constitutes a major component of the offspring?s social environment. Thus a change in parental provisioning, whether evolved or plastic, can alter the form or strength of selection on offspring and result in the coevolution of parental provisioning and traits expressed in offspring. Although this reasoning is central to our evolutionary understanding of family life, there is little direct evidence that selection by parents causes evolutionary change in their young. Here we use experimental evolution to examine directly how populations of burying beetles, Nicrophorus vespilloides, adapt to a change in post-hatching parental provisioning. We measured the performance of larvae descended from independent lab populations that had been propagated for several generations with and without post-hatching parental care (Full Care and No Care populations respectively). We found that adaptation to the absence of post32 hatching care led to rapid and consistent changes in larval survival in the absence of care. Specifically...

Fundamental shift in vitamin B12 eco-physiology of a model alga demonstrated by experimental evolution

Helliwell, Katherine E.; Collins, Sin?ad; Kazamia, Elena; Purton, Saul; Wheeler, Glen L.; Smith, Alison G.
Fonte: Nature Publishing Group on behalf of the International Society for Microbial Ecology Publicador: Nature Publishing Group on behalf of the International Society for Microbial Ecology
Tipo: Article; accepted version
EN
Relevância na Pesquisa
65.85%
This is the author accepted manuscript. The final version is available from NPG via http://dx.doi.org/10.1038/ismej.2014.230; A widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. Vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism?s metabolism to the environment, but this has never been demonstrated directly. Moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic demand for these important micronutrients has significant implications in terms of nutrient acquisition, and in microbial organisms, can affect community composition and metabolic exchange between coexisting species. Here, we investigate the origins of vitamin dependence, using an experimental evolution approach with the vitamin B12-independent model green alga Chlamydomonas reinhardtii. In fewer than 500 generations of growth in the presence of vitamin B12, we observe the evolution of a B12-dependent clone that rapidly displaces its ancestor. Genetic characterization of this line reveals a type-II Gulliver-related transposable element (GR-TE) integrated into the B12-independent methionine synthase gene (METE)...