1
|
Horton JS, Ali SUP, Taylor TB. Transient mutation bias increases the predictability of evolution on an empirical genotype-phenotype landscape. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220043. [PMID: 37004722 PMCID: PMC10067260 DOI: 10.1098/rstb.2022.0043] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/25/2023] [Indexed: 04/04/2023] Open
Abstract
Predicting how a population will likely navigate a genotype-phenotype landscape requires consideration of selection in combination with mutation bias, which can skew the likelihood of following a particular trajectory. Strong and persistent directional selection can drive populations to ascend toward a peak. However, with a greater number of peaks and more routes to reach them, adaptation inevitably becomes less predictable. Transient mutation bias, which operates only on one mutational step, can influence landscape navigability by biasing the mutational trajectory early in the adaptive walk. This sets an evolving population upon a particular path, constraining the number of accessible routes and making certain peaks and routes more likely to be realized than others. In this work, we employ a model system to investigate whether such transient mutation bias can reliably and predictably place populations on a mutational trajectory to the strongest selective phenotype or usher populations to realize inferior phenotypic outcomes. For this we use motile mutants evolved from ancestrally non-motile variants of the microbe Pseudomonas fluorescens SBW25, of which one trajectory exhibits significant mutation bias. Using this system, we elucidate an empirical genotype-phenotype landscape, where the hill-climbing process represents increasing strength of the motility phenotype, to reveal that transient mutation bias can facilitate rapid and predictable ascension to the strongest observed phenotype in place of equivalent and inferior trajectories. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
Collapse
Affiliation(s)
- James S. Horton
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Shani U. P. Ali
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tiffany B. Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| |
Collapse
|
2
|
Rabitz H, Russell B, Ho TS. The Surprising Ease of Finding Optimal Solutions for Controlling Nonlinear Phenomena in Quantum and Classical Complex Systems. J Phys Chem A 2023; 127:4224-4236. [PMID: 37142303 DOI: 10.1021/acs.jpca.3c01896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This Perspective addresses the often observed surprising ease of achieving optimal control of nonlinear phenomena in quantum and classical complex systems. The circumstances involved are wide-ranging, with scenarios including manipulation of atomic scale processes, maximization of chemical and material properties or synthesis yields, Nature's optimization of species' populations by natural selection, and directed evolution. Natural evolution will mainly be discussed in terms of laboratory experiments with microorganisms, and the field is also distinct from the other domains where a scientist specifies the goal(s) and oversees the control process. We use the word "control" in reference to all of the available variables, regardless of the circumstance. The empirical observations on the ease of achieving at least good, if not excellent, control in diverse domains of science raise the question of why this occurs despite the generally inherent complexity of the systems in each scenario. The key to addressing the question lies in examining the associated control landscape, which is defined as the optimization objective as a function of the control variables that can be as diverse as the phenomena under consideration. Controls may range from laser pulses, chemical reagents, chemical processing conditions, out to nucleic acids in the genome and more. This Perspective presents a conjecture, based on present findings, that the systematics of readily finding good outcomes from controlled phenomena may be unified through consideration of control landscapes with the same common set of three underlying assumptions─the existence of an optimal solution, the ability for local movement on the landscape, and the availability of sufficient control resources─whose validity needs assessment in each scenario. In practice, many cases permit using myopic gradient-like algorithms while other circumstances utilize algorithms having some elements of stochasticity or introduced noise, depending on whether the landscape is locally smooth or rough. The overarching observation is that only relatively short searches are required despite the common high dimensionality of the available controls in typical scenarios.
Collapse
Affiliation(s)
- Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Benjamin Russell
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tak-San Ho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
3
|
Zhou DH, Zhang QG. Fast drug rotation reduces bacterial resistance evolution in a microcosm experiment. J Evol Biol 2023; 36:641-649. [PMID: 36808770 DOI: 10.1111/jeb.14163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/17/2022] [Accepted: 01/16/2023] [Indexed: 02/21/2023]
Abstract
Drug rotation (cycling), in which multiple drugs are administrated alternatively, has the potential for limiting resistance evolution in pathogens. The frequency of drug alternation could be a major factor to determine the effectiveness of drug rotation. Drug rotation practices often have low frequency of drug alternation, with an expectation of resistance reversion. Here we, based on evolutionary rescue and compensatory evolution theories, suggest that fast drug rotation can limit resistance evolution in the first place. This is because fast drug rotation would give little time for the evolutionarily rescued populations to recover in population size and genetic diversity, and thus decrease the chance of future evolutionary rescue under alternate environmental stresses. We experimentally tested this hypothesis using the bacterium Pseudomonas fluorescens and two antibiotics (chloramphenicol and rifampin). Increasing drug rotation frequency reduced the chance of evolutionary rescue, and most of the finally surviving bacterial populations were resistant to both drugs. Drug resistance incurred significant fitness costs, which did not differ among the drug treatment histories. A link between population sizes during the early stages of drug treatment and the end-point fates of populations (extinction vs survival) suggested that population size recovery and compensatory evolution before drug shift increase the chance of population survival. Our results therefore advocate fast drug rotation as a promising approach to reduce bacterial resistance evolution, which in particular could be a substitute for drug combination when the latter has safety risks.
Collapse
Affiliation(s)
- Dong-Hao Zhou
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
4
|
Cirne D, Campos PRA. Rate of environmental variation impacts the predictability in evolution. Phys Rev E 2022; 106:064408. [PMID: 36671169 DOI: 10.1103/physreve.106.064408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
In the two last decades, we have improved our understanding of the adaptive evolution of natural populations under constant and stable environments. For instance, experimental methods from evolutionary biology have allowed us to explore the structure of fitness landscapes and survey how the landscape properties can constrain the adaptation process. However, understanding how environmental changes can affect adaptation remains challenging. Very little progress has been made with respect to time-varying fitness landscapes. Using the adaptive-walk approximation, we survey the evolutionary process of populations under a scenario of environmental variation. In particular, we investigate how the rate of environmental variation influences the predictability in evolution. We observe that the rate of environmental variation not only changes the duration of adaptive walks towards fitness peaks of the fitness landscape, but also affects the degree of repeatability of both outcomes and evolutionary paths. In general, slower environmental variation increases the predictability in evolution. The accessibility of endpoints is greatly influenced by the ecological dynamics. The dependence of these quantities on the genome size and number of traits is also addressed. To our knowledge, this contribution is the first to use the predictive approach to quantify and understand the impact of the speed of environmental variation on the degree of parallelism of the evolutionary process.
Collapse
Affiliation(s)
- Diego Cirne
- Departamento de Física, Universidade Federal de Pernambuco, 50740-560 Recife-PE, Brazil
| | - Paulo R A Campos
- Departamento de Física, Universidade Federal de Pernambuco, 50740-560 Recife-PE, Brazil
| |
Collapse
|
5
|
Zhou D, Zhang Q. Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation. Ecol Evol 2021; 11:9689-9696. [PMID: 34306654 PMCID: PMC8293784 DOI: 10.1002/ece3.7792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbor very low genetic diversity compared with their parental populations. The present study addresses how population size and within-population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment and then imposed a one-individual-size population bottleneck on those surviving the antibiotic stress. During the subsequent compensatory evolution, population size increased and leveled off very rapidly. The increase of diversity was of slower paces and persisted longer. In the very early stage of compensatory evolution, populations of large sizes had a greater chance to diversify; however, this productivity-diversification relationship was not observed in later stages. Population size and diversity from the end of the compensatory evolution was not contingent on initial population growth performance. We discussed the possibility that our results be explained by the emergence of a "holey" fitness landscape under the antibiotic stress.
Collapse
Affiliation(s)
- Dong‐Hao Zhou
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life SciencesBeijing Normal UniversityBeijingChina
| | - Quan‐Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life SciencesBeijing Normal UniversityBeijingChina
| |
Collapse
|
6
|
Freund L, Vasse M, Velicer GJ. Hidden paths to endless forms most wonderful: parasite-blind diversification of host quality. Proc Biol Sci 2021; 288:20210456. [PMID: 33906400 PMCID: PMC8080016 DOI: 10.1098/rspb.2021.0456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/24/2021] [Indexed: 01/21/2023] Open
Abstract
Evolutionary diversification can occur in allopatry or sympatry, can be driven by selection or unselected, and can be phenotypically manifested immediately or remain latent until manifested in a newly encountered environment. Diversification of host-parasite interactions is frequently studied in the context of intrinsically selective coevolution, but the potential for host-parasite interaction phenotypes to diversify latently during parasite-blind host evolution is rarely considered. Here, we use a social bacterium experimentally adapted to several environments in the absence of phage to analyse allopatric diversification of host quality-the degree to which a host population supports a viral epidemic. Phage-blind evolution reduced host quality overall, with some bacteria becoming completely resistant to growth suppression by phage. Selective-environment differences generated only mild divergence in host quality. However, selective environments nonetheless played a major role in shaping evolution by determining the degree of stochastic diversification among replicate populations within treatments. Ancestral motility genotype was also found to strongly shape patterns of latent host-quality evolution and diversification. These outcomes show that (i) adaptive landscapes can differ in how they constrain stochastic diversification of a latent phenotype and (ii) major effects of selection on biological diversification can be missed by focusing on trait means. Collectively, our findings suggest that latent-phenotype evolution should inform host-parasite evolution theory and that diversification should be conceived broadly to include latent phenotypes.
Collapse
Affiliation(s)
- Lisa Freund
- Institute for Integrative Biology, ETH Zürich 8092, Zürich, Switzerland
| | - Marie Vasse
- Institute for Integrative Biology, ETH Zürich 8092, Zürich, Switzerland
| | | |
Collapse
|
7
|
Evolutionary constraints in fitness landscapes. Heredity (Edinb) 2018; 121:466-481. [PMID: 29993041 DOI: 10.1038/s41437-018-0110-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/29/2022] Open
Abstract
In the last years, several genotypic fitness landscapes-combinations of a small number of mutations-have been experimentally resolved. To learn about the general properties of "real" fitness landscapes, it is key to characterize these experimental landscapes via simple measures of their structure, related to evolutionary features. Some of the most relevant measures are based on the selectively acessible paths and their properties. In this paper, we present some measures of evolutionary constraints based on (i) the similarity between accessible paths and (ii) the abundance and characteristics of "chains" of obligatory mutations, that are paths going through genotypes with a single fitter neighbor. These measures have a clear evolutionary interpretation. Furthermore, we show that chains are only weakly correlated to classical measures of epistasis. In fact, some of these measures of constraint are non-monotonic in the amount of epistatic interactions, but have instead a maximum for intermediate values. Finally, we show how these measures shed light on evolutionary constraints and predictability in experimentally resolved landscapes.
Collapse
|
8
|
Cervera H, Lalić J, Elena SF. Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations. Proc Biol Sci 2017; 283:rspb.2016.0984. [PMID: 27534955 DOI: 10.1098/rspb.2016.0984] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/26/2016] [Indexed: 12/25/2022] Open
Abstract
Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability. Here, we show that populations of an RNA virus move efficiently on a rugged landscape and scape from the basin of attraction of a local optimum. We have evolved a set of Tobacco etch virus genotypes located at increasing distances from a local adaptive optimum in a highly rugged fitness landscape, and we observed that few evolved lineages remained trapped in the local optimum, while many others explored distant regions of the landscape. Most of the diversification in fitness among the evolved lineages was explained by adaptation, while historical contingency and chance events contribution was less important. Our results demonstrate that the ruggedness of adaptive landscapes is not an impediment for RNA viruses to efficiently explore remote parts of it.
Collapse
Affiliation(s)
- Héctor Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Jasna Lalić
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| |
Collapse
|
9
|
Harmand N, Gallet R, Jabbour-Zahab R, Martin G, Lenormand T. Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradients. Evolution 2016; 71:23-37. [PMID: 27805262 DOI: 10.1111/evo.13111] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 12/15/2022]
Abstract
Fisher's geometrical model (FGM) has been widely used to depict the fitness effects of mutations. It is a general model with few underlying assumptions that gives a large and comprehensive view of adaptive processes. It is thus attractive in several situations, for example adaptation to antibiotics, but comes with limitations, so that more mechanistic approaches are often preferred to interpret experimental data. It might be possible however to extend FGM assumptions to better account for mutational data. This is theoretically challenging in the context of antibiotic resistance because resistance mutations are assumed to be rare. In this article, we show with Escherichia coli how the fitness effects of resistance mutations screened at different doses of nalidixic acid vary across a dose-gradient. We found experimental patterns qualitatively consistent with the basic FGM (rate of resistance across doses, gamma distributed costs) but also unexpected patterns such as a decreasing mean cost of resistance with increasing screen dose. We show how different extensions involving mutational modules and variations in trait covariance across environments, can be discriminated based on these data. Overall, simple extensions of the FGM accounted well for complex mutational effects of resistance mutations across antibiotic doses.
Collapse
Affiliation(s)
- Noémie Harmand
- UMR 5175 CEFE, CNRS-Université Montpellier-Université P. Valéry-EPHE, Montpellier Cedex 5, France
| | - Romain Gallet
- INRA-UMR BGPI, Cirad TA A-54/K Campus International de Baillarguet 34398 Montpellier Cedex 5, France
| | - Roula Jabbour-Zahab
- UMR 5175 CEFE, CNRS-Université Montpellier-Université P. Valéry-EPHE, Montpellier Cedex 5, France
| | - Guillaume Martin
- Institut des Sciences de l'Evolution de Montpellier, UMR CNRS-UM II 5554, Université Montpellier II, 34 095 Montpellier cedex 5, France
| | - Thomas Lenormand
- UMR 5175 CEFE, CNRS-Université Montpellier-Université P. Valéry-EPHE, Montpellier Cedex 5, France
| |
Collapse
|
10
|
Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes. Nat Commun 2016; 7:12860. [PMID: 27653556 PMCID: PMC5036157 DOI: 10.1038/ncomms12860] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/09/2016] [Indexed: 11/17/2022] Open
Abstract
Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes. Adaptive radiations are well-known for animals and plants, but not for microbes. Here, Hehemann et al. show that there has been a recent adaptive radiation of bacteria in the Vibrionaceae to use different forms of alginate and that this radiation has been mediated by horizontal gene transfer.
Collapse
|
11
|
Measuring epistasis in fitness landscapes: The correlation of fitness effects of mutations. J Theor Biol 2016; 396:132-43. [DOI: 10.1016/j.jtbi.2016.01.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/25/2016] [Accepted: 01/30/2016] [Indexed: 01/06/2023]
|
12
|
Vagne C, David J, Tavaud M, Fontez B. Reciprocal sign epistasis and truncation selection: When is recombination favorable in a pre-breeding program with a selfing species? J Theor Biol 2015; 386:44-54. [PMID: 26334476 DOI: 10.1016/j.jtbi.2015.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/29/2015] [Accepted: 08/17/2015] [Indexed: 11/29/2022]
Abstract
Since the dawn of agriculture, humans have applied artificial selection on traits of interest, regardless of their genetic architecture. Yet, still today, most models used to study and streamline this process overlook genetic interactions. In this study, we determined the conditions in which a target genotype can be fixed when truncation selection is applied on an epistatic trait. Previous studies have shown that reciprocal sign epistasis with two fitness peaks of unequal height involves multiple equilibrium states, i.e. below one critical parameter value, such as a critical recombination rate, one genotype may be fixed, and above it, another one may be fixed. Using a haploid bi-locus model, we identified which genotype would be fixed, and how quickly, in an infinite population selected for a phenotypic trait subject to reciprocal sign epistasis with unequal peak heights, depending on two criteria: the recombination rate and percentage of selected individuals. The critical parameter values at which bistability sets in, were also calculated. These results were complemented by stochastic simulations in finite populations. Our results confirmed that, in the case of fitness under reciprocal sign epistasis, high recombination rates induce blockage at the local optimum or attainment of an equilibrium state between the two peaks. However, if linkage disequilibrium is negative in the initial population, recombination is necessary to create the most favorable genotype. Therefore, in this case, reciprocal sign epistasis favors non-null recombination rates, particularly if selection is intense.
Collapse
Affiliation(s)
| | - Jacques David
- Montpellier SupAgro, UMR AGAP, F-34060 Montpellier, France.
| | - Muriel Tavaud
- Montpellier SupAgro, UMR AGAP, F-34060 Montpellier, France.
| | | |
Collapse
|
13
|
Kun Á, Szathmáry E. Fitness Landscapes of Functional RNAs. Life (Basel) 2015; 5:1497-517. [PMID: 26308059 PMCID: PMC4598650 DOI: 10.3390/life5031497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/26/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022] Open
Abstract
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.
Collapse
Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- MTA-ELTE-MTMT Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| |
Collapse
|
14
|
Blanquart F, Achaz G, Bataillon T, Tenaillon O. Properties of selected mutations and genotypic landscapes under Fisher's geometric model. Evolution 2014; 68:3537-54. [PMID: 25311558 DOI: 10.1111/evo.12545] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/05/2014] [Indexed: 02/06/2023]
Abstract
The fitness landscape-the mapping between genotypes and fitness-determines properties of the process of adaptation. Several small genotypic fitness landscapes have recently been built by selecting a handful of beneficial mutations and measuring fitness of all combinations of these mutations. Here, we generate several testable predictions for the properties of these small genotypic landscapes under Fisher's geometric model of adaptation. When the ancestral strain is far from the fitness optimum, we analytically compute the fitness effect of selected mutations and their epistatic interactions. Epistasis may be negative or positive on average depending on the distance of the ancestral genotype to the optimum and whether mutations were independently selected, or coselected in an adaptive walk. Simulations show that genotypic landscapes built from Fisher's model are very close to an additive landscape when the ancestral strain is far from the optimum. However, when it is close to the optimum, a large diversity of landscape with substantial roughness and sign epistasis emerged. Strikingly, small genotypic landscapes built from several replicate adaptive walks on the same underlying landscape were highly variable, suggesting that several realizations of small genotypic landscapes are needed to gain information about the underlying architecture of the fitness landscape.
Collapse
Affiliation(s)
- François Blanquart
- Bioinformatics Research Centre, University of Aarhus, 8000C, Aarhus, Denmark.
| | | | | | | |
Collapse
|
15
|
de Visser JAGM, Krug J. Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet 2014; 15:480-90. [PMID: 24913663 DOI: 10.1038/nrg3744] [Citation(s) in RCA: 402] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The genotype-fitness map (that is, the fitness landscape) is a key determinant of evolution, yet it has mostly been used as a superficial metaphor because we know little about its structure. This is now changing, as real fitness landscapes are being analysed by constructing genotypes with all possible combinations of small sets of mutations observed in phylogenies or in evolution experiments. In turn, these first glimpses of empirical fitness landscapes inspire theoretical analyses of the predictability of evolution. Here, we review these recent empirical and theoretical developments, identify methodological issues and organizing principles, and discuss possibilities to develop more realistic fitness landscape models.
Collapse
Affiliation(s)
- J Arjan G M de Visser
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Joachim Krug
- Institute for Theoretical Physics, University of Cologne, Zülpicher Str. 77, 50937 Köln, Germany
| |
Collapse
|
16
|
Fragata I, Simões P, Lopes-Cunha M, Lima M, Kellen B, Bárbaro M, Santos J, Rose MR, Santos M, Matos M. Laboratory selection quickly erases historical differentiation. PLoS One 2014; 9:e96227. [PMID: 24788553 PMCID: PMC4008540 DOI: 10.1371/journal.pone.0096227] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/04/2014] [Indexed: 11/19/2022] Open
Abstract
The roles of history, chance and selection have long been debated in evolutionary biology. Though uniform selection is expected to lead to convergent evolution between populations, contrasting histories and chance events might prevent them from attaining the same adaptive state, rendering evolution somewhat unpredictable. The predictability of evolution has been supported by several studies documenting repeatable adaptive radiations and convergence in both nature and laboratory. However, other studies suggest divergence among populations adapting to the same environment. Despite the relevance of this issue, empirical data is lacking for real-time adaptation of sexual populations with deeply divergent histories and ample standing genetic variation across fitness-related traits. Here we analyse the real-time evolutionary dynamics of Drosophila subobscura populations, previously differentiated along the European cline, when colonizing a new common environment. By analysing several life-history, physiological and morphological traits, we show that populations quickly converge to the same adaptive state through different evolutionary paths. In contrast with other studies, all analysed traits fully converged regardless of their association with fitness. Selection was able to erase the signature of history in highly differentiated populations after just a short number of generations, leading to consistent patterns of convergent evolution.
Collapse
Affiliation(s)
- Inês Fragata
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail: (IF); (PS)
| | - Pedro Simões
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail: (IF); (PS)
| | - Miguel Lopes-Cunha
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Margarida Lima
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Bárbara Kellen
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Margarida Bárbaro
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Josiane Santos
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Michael R. Rose
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Mauro Santos
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Margarida Matos
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
17
|
Soto W, Rivera FM, Nishiguchi MK. Ecological diversification of Vibrio fischeri serially passaged for 500 generations in novel squid host Euprymna tasmanica. MICROBIAL ECOLOGY 2014; 67:700-721. [PMID: 24402368 PMCID: PMC3965629 DOI: 10.1007/s00248-013-0356-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 12/16/2013] [Indexed: 06/03/2023]
Abstract
Vibrio fischeri isolated from Euprymna scolopes (Cephalopoda: Sepiolidae) was used to create 24 lines that were serially passaged through the non-native host Euprymna tasmanica for 500 generations. These derived lines were characterized for biofilm formation, swarming motility, carbon source utilization, and in vitro bioluminescence. Phenotypic assays were compared between "ES" (E. scolopes) and "ET" (E. tasmanica) V. fischeri wild isolates to determine if convergent evolution was apparent between E. tasmanica evolved lines and ET V. fischeri. Ecological diversification was observed in utilization of most carbon sources examined. Convergent evolution was evident in motility, biofilm formation, and select carbon sources displaying hyperpolymorphic usage in V. fischeri. Convergence in bioluminescence (a 2.5-fold increase in brightness) was collectively evident in the derived lines relative to the ancestor. However, dramatic changes in other properties--time points and cell densities of first light emission and maximal light output and emergence of a lag phase in growth curves of derived lines--suggest that increased light intensity per se was not the only important factor. Convergent evolution implies that gnotobiotic squid light organs subject colonizing V. fischeri to similar selection pressures. Adaptation to novel hosts appears to involve flexible microbial metabolism, establishment of biofilm and swarmer V. fischeri ecotypes, and complex changes in bioluminescence. Our data demonstrate that numerous alternate fitness optima or peaks are available to V. fischeri in host adaptive landscapes, where novel host squids serve as habitat islands. Thus, V. fischeri founder flushes occur during the initiation of light organ colonization that ultimately trigger founder effect diversification.
Collapse
Affiliation(s)
- William Soto
- University of Minnesota-Twin Cities, Department of Ecology, Evolution, & Behavior, 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, MN 55108, (612) 626-6200
| | - Ferdinand M. Rivera
- New Mexico State University, Department of Biology, Box 30001, MSC 3AF, Las Cruces, NM 88003, (575) 646-3721 FAX (575) 646-5665
| | - Michele K. Nishiguchi
- New Mexico State University, Department of Biology, Box 30001, MSC 3AF, Las Cruces, NM 88003, (575) 646-3721 FAX (575) 646-5665
| |
Collapse
|
18
|
Bedhomme S, Lafforgue G, Elena SF. Genotypic but not phenotypic historical contingency revealed by viral experimental evolution. BMC Evol Biol 2013; 13:46. [PMID: 23421472 PMCID: PMC3598485 DOI: 10.1186/1471-2148-13-46] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 02/15/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The importance of historical contingency in determining the potential of viral populations to evolve has been largely unappreciated. Identifying the constraints imposed by past adaptations is, however, of importance for understanding many questions in evolutionary biology, such as the evolution of host usage dynamics by multi-host viruses or the emergence of escape mutants that persist in the absence of antiviral treatments. To address this issue, we undertook an experimental approach in which sixty lineages of Tobacco etch potyvirus that differ in their past evolutionary history and degree of adaptation to Nicotiana tabacum were allowed to adapt to this host for 15 rounds of within host multiplication and transfer. We thereafter evaluated the degree of adaptation to the new host as well as to the original ones and characterized the consensus sequence of each lineage. RESULTS We found that past evolutionary history did not determine the phenotypic outcome of this common host evolution phase, and that the signal of local adaptation to past hosts had largely disappeared. By contrast, evolutionary history left footprints at the genotypic level, since the majority of host-specific mutations present at the beginning of this experiment were retained in the end-point populations and may have affected which new mutations were consequently fixed. This resulted in further divergence between the sequences despite a shared selective environment. CONCLUSIONS The present experiment reinforces the idea that the answer to the question "How important is historical contingency in evolution?" strongly depends on the level of integration of the traits studied. A strong historical contingency was found for TEV genotype, whereas a weak effect of on phenotypic evolution was revealed. In an applied context, our results imply that viruses are not easily trapped into suboptimal phenotypes and that (re)emergence is not evolutionarily constrained.
Collapse
Affiliation(s)
- Stéphanie Bedhomme
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022, València, Spain
- Present address: Infections and Cancer, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Guillaume Lafforgue
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022, València, Spain
- The Santa Fe Institute, Santa Fe, 87501, New Mexico
| |
Collapse
|
19
|
Sanad YM, Closs G, Kumar A, LeJeune JT, Rajashekara G. Molecular epidemiology and public health relevance of Campylobacter isolated from dairy cattle and European starlings in Ohio, USA. Foodborne Pathog Dis 2012; 10:229-36. [PMID: 23259503 DOI: 10.1089/fpd.2012.1293] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dairy cattle serve as a potential source for Campylobacter infection in humans. Outbreaks associated with consumption of either Campylobacter contaminated raw milk or contaminated milk after treatment were previously recorded in the United States. Further, starlings have been implicated in the spread of bacterial pathogens among livestock. Here, we determined the prevalence, genotypic, and phenotypic properties of Campylobacter isolated from fecal samples of dairy cattle and starlings found on the same establishment in northeastern Ohio. Campylobacter were detected in 83 (36.6%) and 57 (50.4%) out of 227 dairy and 113 starling fecal samples, respectively. Specifically, 79 C. jejuni, five C. coli, and two other Campylobacter spp. were isolated from dairy feces, while all isolates from starlings (n=57) were C. jejuni. Our results showed that the prevalence of C. jejuni in birds was significantly (p<0.01) higher than that in dairy cattle. The pulsed-field gel electrophoresis analysis showed that C. jejuni were genotypically diverse and host restricted; however, there were several shared genotypes between dairy cattle and starling isolates. Likewise, many shared clonal complexes (CC) between dairy cattle and starlings were observed by multilocus sequence typing (MLST) analysis. As in humans, both in cattle and starlings, the CC 45 and CC 21 were the most frequently represented CCs. As previously reported, CC 177 and CC 682 were restricted to the bird isolates, while CC 42 was restricted to dairy cattle isolates. Further, two new sequence types (STs) were detected in C. jejuni from dairy cattle. Interestingly, cattle and starling C. jejuni showed high resistance to multiple antimicrobials, including ciprofloxacin, erythromycin, and gentamicin. In conclusion, our results highlight starlings as potential reservoirs for C. jejuni, and they may play an important role in the epidemiology of clinically important C. jejuni in dairy population.
Collapse
Affiliation(s)
- Yasser M Sanad
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, Ohio State University, Wooster, Ohio 44691, USA
| | | | | | | | | |
Collapse
|
20
|
Flores-Moya A, Rouco M, García-Sánchez MJ, García-Balboa C, González R, Costas E, López-Rodas V. Effects of adaptation, chance, and history on the evolution of the toxic dinoflagellate Alexandrium minutum under selection of increased temperature and acidification. Ecol Evol 2012; 2:1251-9. [PMID: 22833798 PMCID: PMC3402198 DOI: 10.1002/ece3.198] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 11/21/2022] Open
Abstract
The roles of adaptation, chance, and history on evolution of the toxic dinoflagellate Alexandrium minutum Halim, under selective conditions simulating global change, have been addressed. Two toxic strains (AL1V and AL2V), previously acclimated for two years at pH 8.0 and 20°C, were transferred to selective conditions: pH 7.5 to simulate acidification and 25°C. Cultures under selective conditions were propagated until growth rate and toxin cell quota achieved an invariant mean value at 720 days (ca. 250 and ca. 180 generations for strains AL1V and AL2V, respectively). Historical contingencies strongly constrained the evolution of growth rate and toxin cell quota, but the forces involved in the evolution were not the same for both traits. Growth rate was 1.5–1.6 times higher than the one measured in ancestral conditions. Genetic adaptation explained two-thirds of total adaptation while one-third was a consequence of physiological adaptation. On the other hand, the evolution of toxin cell quota showed a pattern attributable to neutral mutations because the final variances were significantly higher than those measured at the start of the experiment. It has been hypothesized that harmful algal blooms will increase under the future scenario of global change. Although this study might be considered an oversimplification of the reality, it can be hypothesized that toxic blooms will increase but no predictions can be advanced about toxicity.
Collapse
|
21
|
Feng X, Pechen A, Jha A, Wu R, Rabitz H. Global optimality of fitness landscapes in evolution. Chem Sci 2012. [DOI: 10.1039/c1sc00648g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
22
|
Abstract
The repeatability of adaptive evolution depends on the ruggedness of the underlying adaptive landscape. We contrasted the relative ruggedness of two adaptive landscapes by measuring the variance in fitness and metabolic phenotype within and among genetically distinct strains of Pseudomonas fluorescens in two environments differing only in the carbon source provided (glucose vs. xylose). Fitness increased in all lines, plateauing in one environment but not the other. The pattern of variance in fitness among replicate lines was unique to the selection environment; it increased over the course of the experiment in xylose but not in glucose. Metabolic phenotypes displayed two results: (1) populations adapted via changes that were distinctive to their selection environment, and (2) endpoint phenotypes were less variable in glucose than in xylose. These results indicate that although the response to selection is highly repeatable at the level of fitness, the underlying genetic routes taken were different for each environment and more variable in xylose. We suggest that this reflects a more rugged adaptive landscape in xylose compared to glucose. Our study demonstrates the utility of using replicate selection lines with different evolutionary starting points to try and quantify the relative ruggedness of adaptive landscapes.
Collapse
Affiliation(s)
- Anita H Melnyk
- Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada.
| | | |
Collapse
|
23
|
Brockhurst MA, Colegrave N, Rozen DE. Next-generation sequencing as a tool to study microbial evolution. Mol Ecol 2010; 20:972-80. [PMID: 20874764 DOI: 10.1111/j.1365-294x.2010.04835.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Thanks to their short generation times and large population sizes, microbes evolve rapidly. Evolutionary biologists have exploited this to observe evolution in real time. The falling costs of whole-genome sequencing using next-generation technologies now mean that it is realistic to use this as a tool to study this rapid microbial evolution both in the laboratory and in the wild. Such experiments are being used to accurately estimate the rates of mutation, reveal the genetic targets and dynamics of natural selection, uncover the correlation (or lack thereof) between genetic and phenotypic change, and provide data to test long-standing evolutionary hypotheses. These advances have important implications for our understanding of the within- and between-host evolution of microbial pathogens.
Collapse
Affiliation(s)
- Michael A Brockhurst
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | | | | |
Collapse
|
24
|
Raymond B, Wright DJ, Bonsall MB. Effects of host plant and genetic background on the fitness costs of resistance to Bacillus thuringiensis. Heredity (Edinb) 2010; 106:281-8. [PMID: 20517345 DOI: 10.1038/hdy.2010.65] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Novel resistance to pathogens and pesticides is commonly associated with a fitness cost. However, measurements of the fitness costs of insecticide resistance have used diverse methods to control for genetic background and rarely assess the effects of environmental variation. Here, we explored how genetic background interacts with resource quality to affect the expression of the fitness costs associated with resistance. We used a serially backcrossed line of the diamondback moth, Plutella xylostella, resistant to the biopesticide Bacillus thuringiensis, to estimate the costs of resistance for insects feeding on two Brassica species. We found that fitness costs increased on the better-defended Brassica oleracea cultivars. These data were included in two meta-analyses of fitness cost experiments that used standardized protocols (and a common resistant insect stock) but which varied in the methodology used to control for the effects of genetic background. The meta-analysis confirmed that fitness costs were higher on the low-quality host (B. oleracea); and experimental methodology did not influence estimates of fitness costs on that plant species. In contrast, fitness costs were heterogeneous in the Brassica pekinensis studies: fitness costs in genetically homogenized lines were significantly higher than in studies using revertant insects. We hypothesize that fitness modifiers can moderate fitness costs on high-quality plants but may not affect fitness when resource quality is low.
Collapse
Affiliation(s)
- B Raymond
- Department of Zoology, University of Oxford, Oxford, UK.
| | | | | |
Collapse
|
25
|
Cooper TF, Lenski RE. Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations. BMC Evol Biol 2010; 10:11. [PMID: 20070898 PMCID: PMC2827396 DOI: 10.1186/1471-2148-10-11] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 01/13/2010] [Indexed: 12/11/2023] Open
Abstract
BACKGROUND Environmental conditions affect the topology of the adaptive landscape and thus the trajectories followed by evolving populations. For example, a heterogeneous environment might lead to a more rugged adaptive landscape, making it more likely that replicate populations would evolve toward distinct adaptive peaks, relative to a uniform environment. To date, the influence of environmental variability on evolutionary dynamics has received relatively little experimental study. RESULTS We report findings from an experiment designed to test the effects of environmental variability on the adaptation and divergence of replicate populations of E. coli. A total of 42 populations evolved for 2000 generations in 7 environmental regimes that differed in the number, identity, and presentation of the limiting resource. Regimes were organized in two sets, having the sugars glucose and maltose singly and in combination, or glucose and lactose singly and in combination. Combinations of sugars were presented either simultaneously or as temporally fluctuating resource regimes. This design allowed us to compare the effects of resource identity and presentation on the evolutionary trajectories followed by replicate populations. After 2000 generations, the fitness of all populations had increased relative to the common ancestor, but to different extents. Populations evolved in glucose improved the least, whereas populations evolving in maltose or lactose increased the most in their respective sets. Among-population divergence also differed across regimes, with variation higher in those groups that evolved in fluctuating environments than in those that faced constant resource regimens. This divergence under the fluctuating conditions increased between 1000 and 2000 generations, consistent with replicate populations evolving toward distinct adaptive peaks. CONCLUSIONS These results support the hypothesis that environmental heterogeneity can give rise to more rugged adaptive landscapes, which in turn promote evolutionary diversification. These results also demonstrate that this effect depends on the form of environmental heterogeneity, with greater divergence when the pairs of resources fluctuated temporally rather than being presented simultaneously.
Collapse
Affiliation(s)
- Tim F Cooper
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.
| | | |
Collapse
|
26
|
Hall AR, Griffiths VF, MacLean RC, Colegrave N. Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa. Proc Biol Sci 2009; 277:643-50. [PMID: 19889704 DOI: 10.1098/rspb.2009.1630] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding adaptation by natural selection requires understanding the genetic factors that determine which beneficial mutations are available for selection. Here, using experimental evolution of rifampicin-resistant Pseudomonas aeruginosa, we show that different genotypes vary in their capacity for adaptation to the cost of antibiotic resistance. We then use sequence data to show that the beneficial mutations associated with fitness recovery were specific to particular genetic backgrounds, suggesting that genotypes had access to different sets of beneficial mutations. When we manipulated the supply rate of beneficial mutations, by altering effective population size during evolution, we found that it constrained adaptation in some selection lines by restricting access to rare beneficial mutations, but that the effect varied among the genotypes in our experiment. These results suggest that mutational neighbourhood varies even among genotypes that differ by a single amino acid change, and this determines their capacity for adaptation as well as the influence of population biology processes that alter mutation supply rate.
Collapse
Affiliation(s)
- Alex R Hall
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| | | | | | | |
Collapse
|
27
|
Vos M. Why do bacteria engage in homologous recombination? Trends Microbiol 2009; 17:226-32. [PMID: 19464181 DOI: 10.1016/j.tim.2009.03.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 03/15/2009] [Accepted: 03/20/2009] [Indexed: 11/27/2022]
Abstract
Microbiologists have long recognized that the uptake and incorporation of homologous DNA from outside the cell is a common feature of bacteria, with important implications for their evolution. However, the exact reasons why bacteria engage in homologous recombination remain elusive. This Opinion article aims to reinvigorate the debate by examining the costs and benefits that homologous recombination could engender in natural populations of bacteria. It specifically focuses on the hypothesis that homologous recombination is selectively maintained because the genetic variation it generates improves the response of bacterial populations to natural selection, analogous to sex in eukaryotes.
Collapse
Affiliation(s)
- Michiel Vos
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| |
Collapse
|
28
|
Jalasvuori M, Bamford JKH. Did the ancient crenarchaeal viruses from the dawn of life survive exceptionally well the eons of meteorite bombardment? ASTROBIOLOGY 2009; 9:131-137. [PMID: 19317626 DOI: 10.1089/ast.2007.0189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The viruses of Crenarchaeota are unexpectedly diverse in their morphologies, and most have no, or few, genes related to bacterial, eukaryal, euryarchaeal, or other crenarchaeal viruses. Though several different virus morphotypes have been discovered in enrichment cultures of microbial communities collected from geothermally heated environments around the world, the origins of such differences are unknown. We present a model that combines consideration of Earth's geological history, the early emergence of hyperthermophiles, and the early formation of viruses from primordial genes with the intent to explain this vast diversity of crenarchaeal viruses. Several meteorite- or flood basalt-induced extinction events in the past resulted in a reduction in the numbers of cellular organisms. Acidophilic hyperthermophiles survived the global thermal rises and, therefore, still host a wide variety of ancient virus morphotypes. In contrast, other, more "recent" cellular lineages have lost the majority of their original viruses, as they have been separated geologically and genetically, and have gone through several near-extinction-level episodes of decimation. This view suggests that, among crenarchaeal viruses, the direct descendants of very early genetic elements are well preserved; thus, their examination would improve our understanding as to how life actually evolved from its origins to the complex cellular systems we see today. We also present a hypothesis that describes the role of viral armadas and extinctions during evolution, as extinctions may have episodically eliminated most of the abusive parasites.
Collapse
Affiliation(s)
- Matti Jalasvuori
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
| | | |
Collapse
|
29
|
Colles FM, McCarthy ND, Howe JC, Devereux CL, Gosler AG, Maiden MCJ. Dynamics of Campylobacter colonization of a natural host, Sturnus vulgaris (European starling). Environ Microbiol 2008; 11:258-67. [PMID: 18826435 PMCID: PMC2702492 DOI: 10.1111/j.1462-2920.2008.01773.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Wild European Starlings (Sturnus vulgaris) shed Campylobacter at high rates, suggesting that they may be a source of human and farm animal infection. A survey of Campylobacter shedding of 957 wild starlings was undertaken by culture of faecal specimens and genetic analysis of the campylobacters isolated: shedding rates were 30.6% for Campylobacter jejuni, 0.6% for C. coli and 6.3% for C. lari. Genotyping by multilocus sequence typing (MLST) and antigen sequence typing established that these bacteria were distinct from poultry or human disease isolates with the ST-177 and ST-682 clonal complexes possibly representing starling-adapted genotypes. There was seasonal variation in both shedding rate and genotypic diversity, both exhibiting a maximum during the late spring/early summer. Host age also affected Campylobacter shedding, which was higher in younger birds, and turnover was rapid with no evidence of cross-immunity among Campylobacter species or genotypes. In nestlings, C. jejuni shedding was evident from 9 days of age but siblings were not readily co-infected. The dynamics of Campylobacter infection of starlings differed from that observed in commercial poultry and consequently there was no evidence that wild starlings represent a major source of Campylobacter infections of food animals or humans.
Collapse
Affiliation(s)
- F M Colles
- The Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK.
| | | | | | | | | | | |
Collapse
|
30
|
Rozen DE, Habets MGJL, Handel A, de Visser JAGM. Heterogeneous adaptive trajectories of small populations on complex fitness landscapes. PLoS One 2008; 3:e1715. [PMID: 18320036 PMCID: PMC2248617 DOI: 10.1371/journal.pone.0001715] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 01/18/2008] [Indexed: 11/19/2022] Open
Abstract
Background Small populations are thought to be adaptively handicapped, not only because they suffer more from deleterious mutations but also because they have limited access to new beneficial mutations, particularly those conferring large benefits. Methodology/Principal Findings Here, we test this widely held conjecture using both simulations and experiments with small and large bacterial populations evolving in either a simple or a complex nutrient environment. Consistent with expectations, we find that small populations are adaptively constrained in the simple environment; however, in the complex environment small populations not only follow more heterogeneous adaptive trajectories, but can also attain higher fitness than the large populations. Large populations are constrained to near deterministic fixation of rare large-benefit mutations. While such determinism speeds adaptation on the smooth adaptive landscape represented by the simple environment, it can limit the ability of large populations from effectively exploring the underlying topography of rugged adaptive landscapes characterized by complex environments. Conclusions Our results show that adaptive constraints often faced by small populations can be circumvented during evolution on rugged adaptive landscapes.
Collapse
Affiliation(s)
- Daniel E Rozen
- Department of Genetics, Wageningen University, Wageningen, The Netherlands.
| | | | | | | |
Collapse
|
31
|
Abstract
The suggestion that there are characteristics of living organisms that have evolved because they increase the rate of evolution is controversial and difficult to study. In this review, we examine the role that experimental evolution might play in resolving this issue. We focus on three areas in which experimental evolution has been used previously to examine questions of evolvability; the evolution of mutational supply, the evolution of genetic exchange and the evolution of genetic architecture. In each case, we summarize what studies of experimental evolution have told us so far and speculate on where progress might be made in the future. We show that, while experimental evolution has helped us to begin to understand the evolutionary dynamics of traits that affect evolvability, many interesting questions remain to be answered.
Collapse
|
32
|
|
33
|
Perron GG, Gonzalez A, Buckling A. Source-sink dynamics shape the evolution of antibiotic resistance and its pleiotropic fitness cost. Proc Biol Sci 2007; 274:2351-6. [PMID: 17650474 PMCID: PMC2288555 DOI: 10.1098/rspb.2007.0640] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Understanding the conditions that favour the evolution and maintenance of antibiotic resistance is the central goal of epidemiology. A crucial feature explaining the adaptation to harsh, or 'sink', environments is the supply of beneficial mutations via migration from a 'source' population. Given that antibiotic resistance is frequently associated with antagonistic pleiotropic fitness costs, increased migration rate is predicted not only to increase the rate of resistance evolution but also to increase the probability of fixation of resistance mutations with minimal fitness costs. Here we report in vitro experiments using the nosocomial pathogenic bacterium Pseudomonas aeruginosa that support these predictions: increasing rate of migration into environments containing antibiotics increased the rate of resistance evolution and decreased the associated costs of resistance. Consistent with previous theoretical work, we found that resistance evolution arose more rapidly in the presence of a single antibiotic than two. Evolution of resistance was also more rapid when bacteria were subjected to sequential exposure with two antibiotics (cycling therapy) compared with simultaneous exposure (bi-therapy). Furthermore, pleiotropic fitness costs of resistance to two antibiotics were higher than for one antibiotic, and were also higher under bi-therapy than cycling therapy, although the cost of resistance depended on the order of the antibiotics through time. These results may be relevant to the clinical setting where immigration is known to be important between chemotherapeutically treated patients, and demonstrate the importance of ecological and evolutionary dynamics in the control of antibiotic resistance.
Collapse
Affiliation(s)
- Gabriel G Perron
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| | | | | |
Collapse
|
34
|
Brockhurst MA, Morgan AD, Fenton A, Buckling A. Experimental coevolution with bacteria and phage. The Pseudomonas fluorescens--Phi2 model system. INFECTION GENETICS AND EVOLUTION 2007; 7:547-52. [PMID: 17320489 DOI: 10.1016/j.meegid.2007.01.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 01/16/2007] [Accepted: 01/18/2007] [Indexed: 10/23/2022]
Abstract
Parasites are ubiquitous in biological systems and antagonistic coevolution between hosts and parasites is thought be a major ecological and evolutionary force. Recent experiments using laboratory populations of bacteria and their parasitic viruses, phage, have provided the first direct empirical evidence of antagonistic coevolution in action. In this article we describe this model system and synthesise recent findings that address the causes and consequences of antagonistic coevolution.
Collapse
Affiliation(s)
- Michael A Brockhurst
- School of Biological Sciences, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK.
| | | | | | | |
Collapse
|
35
|
Edwards AWF. Fisher, Demetrius and Wright: contending models. Bioessays 2006; 28:440; author reply 441-2. [PMID: 16547948 DOI: 10.1002/bies.20395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
36
|
Colegrave N, Buckling A. Reply to Edwards' response. Bioessays 2006. [DOI: 10.1002/bies.20397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|