1
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Toch K, Buczek M, Labocha MK. Genetic Interactions in Various Environmental Conditions in Caenorhabditis elegans. Genes (Basel) 2023; 14:2080. [PMID: 38003023 PMCID: PMC10671385 DOI: 10.3390/genes14112080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Although it is well known that epistasis plays an important role in many evolutionary processes (e.g., speciation, evolution of sex), our knowledge on the frequency and prevalent sign of epistatic interactions is mainly limited to unicellular organisms or cell cultures of multicellular organisms. This is even more pronounced in regard to how the environment can influence genetic interactions. To broaden our knowledge in that respect we studied gene-gene interactions in a whole multicellular organism, Caenorhabditis elegans. We screened over one thousand gene interactions, each one in standard laboratory conditions, and under three different stressors: heat shock, oxidative stress, and genotoxic stress. Depending on the condition, between 7% and 22% of gene pairs showed significant genetic interactions and an overall sign of epistasis changed depending on the condition. Sign epistasis was quite common, but reciprocal sign epistasis was extremally rare. One interaction was common to all conditions, whereas 78% of interactions were specific to only one environment. Although epistatic interactions are quite common, their impact on evolutionary processes will strongly depend on environmental factors.
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Affiliation(s)
| | | | - Marta K. Labocha
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Krakow, Poland; (K.T.); (M.B.)
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2
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Johnson MS, Desai MM. Mutational robustness changes during long-term adaptation in laboratory budding yeast populations. eLife 2022; 11:76491. [PMID: 35880743 PMCID: PMC9355567 DOI: 10.7554/elife.76491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
As an adapting population traverses the fitness landscape, its local neighborhood (i.e., the collection of fitness effects of single-step mutations) can change shape because of interactions with mutations acquired during evolution. These changes to the distribution of fitness effects can affect both the rate of adaptation and the accumulation of deleterious mutations. However, while numerous models of fitness landscapes have been proposed in the literature, empirical data on how this distribution changes during evolution remains limited. In this study, we directly measure how the fitness landscape neighborhood changes during laboratory adaptation. Using a barcode-based mutagenesis system, we measure the fitness effects of 91 specific gene disruption mutations in genetic backgrounds spanning 8000–10,000 generations of evolution in two constant environments. We find that the mean of the distribution of fitness effects decreases in one environment, indicating a reduction in mutational robustness, but does not change in the other. We show that these distribution-level patterns result from differences in the relative frequency of certain patterns of epistasis at the level of individual mutations, including fitness-correlated and idiosyncratic epistasis.
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Affiliation(s)
- Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
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3
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Samant N, Nachum G, Tsepal T, Bolon DNA. Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease. Protein Sci 2022; 31:e4366. [PMID: 35762719 DOI: 10.1002/pro.4366] [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: 03/03/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022]
Abstract
The infectivity of HIV-1 requires its protease (PR) cleave multiple cut-sites with low sequence similarity. The diversity of cleavage sites has made it challenging to investigate the underlying sequence properties that determine binding and turnover of substrates by PR. We engineered a mutational scanning approach utilizing yeast display, flow cytometry, and deep sequencing to systematically measure the impacts of all individual amino acid changes at 12 positions in three different cut-sites (MA/CA, NC/p1, and p1/p6). The resulting fitness landscapes revealed common physical features that underlie cutting of all three cut-sites at the amino acid positions closest to the scissile bond. In contrast, positions more than two amino acids away from the scissile bond exhibited a strong dependence on the sequence background of the rest of the cut-site. We observed multiple amino acid changes in cut-sites that led to faster cleavage rates, including a preference for negative charge five and six amino acids away from the scissile bond at locations where the surface of protease is positively charged. Analysis of individual cut sites using full-length matrix-capsid proteins indicate that long-distance sequence context can contribute to cutting efficiency such that analyses of peptides or shorter engineered constructs including those in this work should be considered carefully. This work provides a framework for understanding how diverse substrates interact with HIV-1 PR and can be extended to investigate other viral PRs with similar properties.
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Affiliation(s)
- Neha Samant
- Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Gily Nachum
- Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Tenzin Tsepal
- Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Daniel N A Bolon
- Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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4
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Barnes JE, Miller CR, Ytreberg FM. Searching for a mechanistic description of pairwise epistasis in protein systems. Proteins 2022; 90:1474-1485. [DOI: 10.1002/prot.26328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/05/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Jonathan E. Barnes
- Department of Physics University of Idaho Moscow Idaho USA
- Institute for Modeling Collaboration and Innovation, University of Idaho Moscow Idaho USA
| | - Craig R. Miller
- Institute for Modeling Collaboration and Innovation, University of Idaho Moscow Idaho USA
- Department of Biological Sciences University of Idaho Moscow Idaho USA
- Institute for Interdisciplinary Data Sciences, University of Idaho Moscow Idaho USA
| | - Frederick Marty Ytreberg
- Department of Physics University of Idaho Moscow Idaho USA
- Institute for Modeling Collaboration and Innovation, University of Idaho Moscow Idaho USA
- Institute for Interdisciplinary Data Sciences, University of Idaho Moscow Idaho USA
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5
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Ogbunugafor CB. The mutation effect reaction norm (mu-rn) highlights environmentally dependent mutation effects and epistatic interactions. Evolution 2022; 76:37-48. [PMID: 34989399 DOI: 10.1111/evo.14428] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/23/2021] [Indexed: 11/27/2022]
Abstract
Since the modern synthesis, the fitness effects of mutations and epistasis have been central yet provocative concepts in evolutionary and population genetics. Studies of how the interactions between parcels of genetic information can change as a function of environmental context have added a layer of complexity to these discussions. Here I introduce the "mutation effect reaction norm" (Mu-RN), a new instrument through which one can analyze the phenotypic consequences of mutations and interactions across environmental contexts. It embodies the fusion of measurements of genetic interactions with the reaction norm, a classic depiction of the performance of genotypes across environments. I demonstrate the utility of the Mu-RN through the signature of a "compensatory ratchet" mutation that undermines reverse evolution of antimicrobial resistance. More broadly, I argue that the mutation effect reaction norm may help us resolve the dynamism and unpredictability of evolution, with implications for theoretical biology, genetic modification technology, and public health. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
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6
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Lyons DM, Zou Z, Xu H, Zhang J. Idiosyncratic epistasis creates universals in mutational effects and evolutionary trajectories. Nat Ecol Evol 2020; 4:1685-1693. [PMID: 32895516 PMCID: PMC7710555 DOI: 10.1038/s41559-020-01286-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 07/23/2020] [Indexed: 01/06/2023]
Abstract
Patterns of epistasis and shapes of fitness landscapes are of wide interest because of their bearings on a number of evolutionary theories. The common phenomena of slowing fitness increases during adaptations and diminishing returns from beneficial mutations are believed to reflect a concave fitness landscape and a preponderance of negative epistasis. Paradoxically, fitness decreases tend to decelerate and harm from deleterious mutations shrinks during the accumulation of random mutations-patterns thought to indicate a convex fitness landscape and a predominance of positive epistasis. Current theories cannot resolve this apparent contradiction. Here, we show that the phenotypic effect of a mutation varies substantially depending on the specific genetic background and that this idiosyncrasy in epistasis creates all of the above trends without requiring a biased distribution of epistasis. The idiosyncratic epistasis theory explains the universalities in mutational effects and evolutionary trajectories as emerging from randomness due to biological complexity.
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Affiliation(s)
| | | | | | - Jianzhi Zhang
- Correspondence to Jianzhi Zhang, Department of Ecology and Evolutionary Biology, University of Michigan, 4018 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109, USA, Phone: 734-763-0527,
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7
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Wu Y, Lin F, Zhou Y, Wang J, Sun S, Wang B, Zhang Z, Li G, Lin X, Wang X, Sun Y, Dong Q, Xu C, Gong L, Wendel JF, Zhang Z, Liu B. Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids. Natl Sci Rev 2020; 8:nwaa277. [PMID: 34691642 PMCID: PMC8288387 DOI: 10.1093/nsr/nwaa277] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/01/2020] [Indexed: 01/03/2023] Open
Abstract
Allopolyploidy is an important process in plant speciation, yet newly formed allopolyploid species typically suffer from extreme genetic bottlenecks. One escape from this impasse might be homoeologous meiotic pairing, during which homoeologous exchanges (HEs) generate phenotypically variable progeny. However, the immediate genome-wide patterns and resulting phenotypic diversity generated by HEs remain largely unknown. Here, we analyzed the genome composition of 202 phenotyped euploid segmental allopolyploid individuals from the fourth selfed generation following chromosomal doubling of reciprocal F1 hybrids of crosses between rice subspecies, using whole-genome sequencing. We describe rampant occurrence of HEs that, by overcoming incompatibility or conferring superiority of hetero-cytonuclear interactions, generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration in tetraploids affects known-function genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level following a single initial hybridization. Our results illuminate the immediate genomic landscapes possible in a tetraploid genomic environment, and underscore HE as an important mechanism that fuels rapid phenotypic diversification accompanying the initial stages of allopolyploid evolution.
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Affiliation(s)
- Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
- Department of Crop & Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Fan Lin
- Brightseed Inc., San Francisco, CA 94107, USA
| | - Yao Zhou
- Department of Crop & Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Shuai Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Yue Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Qianli Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Zhiwu Zhang
- Department of Crop & Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
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8
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Villa TG, Abril AG, Sánchez S, de Miguel T, Sánchez-Pérez A. Animal and human RNA viruses: genetic variability and ability to overcome vaccines. Arch Microbiol 2020; 203:443-464. [PMID: 32989475 PMCID: PMC7521576 DOI: 10.1007/s00203-020-02040-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/29/2020] [Accepted: 09/12/2020] [Indexed: 02/06/2023]
Abstract
RNA viruses, in general, exhibit high mutation rates; this is mainly due to the low fidelity displayed by the RNA-dependent polymerases required for their replication that lack the proofreading machinery to correct misincorporated nucleotides and produce high mutation rates. This lack of replication fidelity, together with the fact that RNA viruses can undergo spontaneous mutations, results in genetic variants displaying different viral morphogenesis, as well as variation on their surface glycoproteins that affect viral antigenicity. This diverse viral population, routinely containing a variety of mutants, is known as a viral ‘quasispecies’. The mutability of their virions allows for fast evolution of RNA viruses that develop antiviral resistance and overcome vaccines much more rapidly than DNA viruses. This also translates into the fact that pathogenic RNA viruses, that cause many diseases and deaths in humans, represent the major viral group involved in zoonotic disease transmission, and are responsible for worldwide pandemics.
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Affiliation(s)
- T G Villa
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain.
| | - Ana G Abril
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - S Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - T de Miguel
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - A Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
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9
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Liard V, Parsons DP, Rouzaud-Cornabas J, Beslon G. The Complexity Ratchet: Stronger than Selection, Stronger than Evolvability, Weaker than Robustness. ARTIFICIAL LIFE 2020; 26:38-57. [PMID: 32027534 DOI: 10.1162/artl_a_00312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using the in silico experimental evolution platform Aevol, we have tested the existence of a complexity ratchet by evolving populations of digital organisms under environmental conditions in which simple organisms can very well thrive and reproduce. We observed that in most simulations, organisms become complex although such organisms are a lot less fit than simple ones and have no robustness or evolvability advantage. This excludes selection from the set of possible explanations for the evolution of complexity. However, complementary experiments showed that selection is nevertheless necessary for complexity to evolve, also excluding non-selective effects. Analyzing the long-term fate of complex organisms, we showed that complex organisms almost never switch back to simplicity despite the potential fitness benefit. On the contrary, they consistently accumulate complexity in the long term, meanwhile slowly increasing their fitness but never overtaking that of simple organisms. This suggests the existence of a complexity ratchet powered by negative epistasis: Mutations leading to simple solutions, which are favorable at the beginning of the simulation, become deleterious after other mutations-leading to complex solutions-have been fixed. This also suggests that this complexity ratchet cannot be beaten by selection, but that it can be overthrown by robustness because of the constraints it imposes on the coding capacity of the genome.
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Affiliation(s)
- Vincent Liard
- Inria Beagle Team
- Université de Lyon
- INSA-Lyon
- CNRS
- LIRIS
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10
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Abstract
Fitness interactions between mutations can influence a population's evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.
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Affiliation(s)
- Christelle Fraïsse
- 1 Institut des Sciences de l'Evolution, CNRS-UM-IRD , Montpellier , France.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK.,3 Institute of Science and Technology Austria , Am Campus 1, Klosterneuburg 3400 , Austria
| | - John J Welch
- 2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
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11
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12
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Domínguez-García S, García C, Quesada H, Caballero A. Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster. Heredity (Edinb) 2019; 123:709-722. [PMID: 31477803 PMCID: PMC6834575 DOI: 10.1038/s41437-019-0263-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 08/15/2019] [Accepted: 08/18/2019] [Indexed: 01/21/2023] Open
Abstract
Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.
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Affiliation(s)
- Sara Domínguez-García
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain
| | - Carlos García
- CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain. .,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain.
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13
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Levin-Reisman I, Brauner A, Ronin I, Balaban NQ. Epistasis between antibiotic tolerance, persistence, and resistance mutations. Proc Natl Acad Sci U S A 2019; 116:14734-14739. [PMID: 31262806 PMCID: PMC6642377 DOI: 10.1073/pnas.1906169116] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Understanding the evolution of microorganisms under antibiotic treatments is a burning issue. Typically, several resistance mutations can accumulate under antibiotic treatment, and the way in which resistance mutations interact, i.e., epistasis, has been extensively studied. We recently showed that the evolution of antibiotic resistance in Escherichia coli is facilitated by the early appearance of tolerance mutations. In contrast to resistance, which reduces the effectiveness of the drug concentration, tolerance increases resilience to antibiotic treatment duration in a nonspecific way, for example when bacteria transiently arrest their growth. Both result in increased survival under antibiotics, but the interaction between resistance and tolerance mutations has not been studied. Here, we extend our analysis to include the evolution of a different type of tolerance and a different antibiotic class and measure experimentally the epistasis between tolerance and resistance mutations. We derive the expected model for the effect of tolerance and resistance mutations on the dynamics of survival under antibiotic treatment. We find that the interaction between resistance and tolerance mutations is synergistic in strains evolved under intermittent antibiotic treatment. We extend our analysis to mutations that result in antibiotic persistence, i.e., to tolerance that is conferred only on a subpopulation of cells. We show that even when this population heterogeneity is included in our analysis, a synergistic interaction between antibiotic persistence and resistance mutations remains. We expect our general framework for the epistasis in killing conditions to be relevant for other systems as well, such as bacteria exposed to phages or cancer cells under treatment.
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Affiliation(s)
- Irit Levin-Reisman
- Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
- The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Asher Brauner
- Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
- The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Irine Ronin
- Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
- The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Nathalie Q Balaban
- Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel;
- The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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14
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Abstract
Many organisms disperse in groups, yet this process is understudied in viruses. Recent work, however, has uncovered different types of collective infectious units, all of which lead to the joint delivery of multiple viral genome copies to target cells, favoring co-infections. Collective spread of viruses can occur through widely different mechanisms, including virion aggregation driven by specific extracellular components, cloaking inside lipid vesicles, encasement in protein matrices, or binding to cell surfaces. Cell-to-cell viral spread, which allows the transmission of individual virions in a confined environment, is yet another mode of clustered virus dissemination. Nevertheless, the selective advantages of dispersing in groups remain poorly understood in most cases. Collective dispersal might have emerged as a means of sharing efficacious viral transmission vehicles. Alternatively, increasing the cellular multiplicity of infection may confer certain short-term benefits to viruses, such as overwhelming antiviral responses, avoiding early stochastic loss of viral components required for initiating infection, or complementing genetic defects present in different viral genomes. However, increasing infection multiplicity may also entail long-term costs, such as mutation accumulation and the evolution of defective particles or other types of cheater viruses. These costs and benefits, in turn, should depend on the genetic relatedness among collective infectious unit members. Establishing the genetic basis of collective viral dispersal and performing controlled experiments to pinpoint fitness effects at different spatial and temporal scales should help us clarify the implications of these spread modes for viral fitness, pathogenicity, and evolution.
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Affiliation(s)
- Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/Catedrático Agustín Escardino 9, Paterna, València, Spain
| | - María-Isabel Thoulouze
- Institut Pasteur, Structural Virology Unit, Biofilm & Viral Transmission Group, Paris, France
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15
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Costa CLN, Lemos-Costa P, Marquitti FMD, Fernandes LD, Ramos MF, Schneider DM, Martins AB, de Aguiar MAM. Signatures of Microevolutionary Processes in Phylogenetic Patterns. Syst Biol 2018; 68:131-144. [PMID: 29939352 DOI: 10.1093/sysbio/syy049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem, we analyzed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.
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Affiliation(s)
- Carolina L N Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Paula Lemos-Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Flavia M D Marquitti
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900 Piracicaba, SP, Brazil
| | - Marlon F Ramos
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Ayana B Martins
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Department of Fish Ecology & Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
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16
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Tekin E, Yeh PJ, Savage VM. General Form for Interaction Measures and Framework for Deriving Higher-Order Emergent Effects. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00166] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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17
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Tekin E, White C, Kang TM, Singh N, Cruz-Loya M, Damoiseaux R, Savage VM, Yeh PJ. Prevalence and patterns of higher-order drug interactions in Escherichia coli. NPJ Syst Biol Appl 2018; 4:31. [PMID: 30181902 PMCID: PMC6119685 DOI: 10.1038/s41540-018-0069-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 01/23/2023] Open
Abstract
Interactions and emergent processes are essential for research on complex systems involving many components. Most studies focus solely on pairwise interactions and ignore higher-order interactions among three or more components. To gain deeper insights into higher-order interactions and complex environments, we study antibiotic combinations applied to pathogenic Escherichia coli and obtain unprecedented amounts of detailed data (251 two-drug combinations, 1512 three-drug combinations, 5670 four-drug combinations, and 13608 five-drug combinations). Directly opposite to previous assumptions and reports, we find higher-order interactions increase in frequency with the number of drugs in the bacteria’s environment. Specifically, as more drugs are added, we observe an elevated frequency of net synergy (effect greater than expected based on independent individual effects) and also increased instances of emergent antagonism (effect less than expected based on lower-order interaction effects). These findings have implications for the potential efficacy of drug combinations and are crucial for better navigating problems associated with the combinatorial complexity of multi-component systems. Interactions play an important role in determining the dynamics of complex systems yet higher-order interactions that involve more than two components are poorly understood. A research team from University of California, Los Angeles led by Pamela Yeh, use a bacteria system to show that higher-order interactions among antibiotics are prevalent and also that there are systematic patterns in how they occur: the frequency of higher-order interactions increases with the number of components, net interactions tend to be more synergistic, and emergent interactions—arising at specific higher-order levels—tend toward antagonism. By detecting patterns in interactions as the number of drugs increases, they provide a method to handle the combinatorial complexity that results from higher-order interactions, yielding a solid foundation for exploring the patterns and consequences of emergent phenomena in other research areas.
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Affiliation(s)
- Elif Tekin
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA.,2Department of Biomathematics, University of California, David Geffen School of Medicine, Los Angeles, CA 90095 USA
| | - Cynthia White
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
| | - Tina Manzhu Kang
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
| | - Nina Singh
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
| | - Mauricio Cruz-Loya
- 2Department of Biomathematics, University of California, David Geffen School of Medicine, Los Angeles, CA 90095 USA
| | - Robert Damoiseaux
- 3California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA 90095 USA
| | - Van M Savage
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA.,2Department of Biomathematics, University of California, David Geffen School of Medicine, Los Angeles, CA 90095 USA.,4Santa Fe Institute, Santa Fe, NM 87501 USA
| | - Pamela J Yeh
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA.,4Santa Fe Institute, Santa Fe, NM 87501 USA
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18
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Lyons DM, Lauring AS. Mutation and Epistasis in Influenza Virus Evolution. Viruses 2018; 10:E407. [PMID: 30081492 PMCID: PMC6115771 DOI: 10.3390/v10080407] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/30/2018] [Accepted: 07/30/2018] [Indexed: 12/25/2022] Open
Abstract
Influenza remains a persistent public health challenge, because the rapid evolution of influenza viruses has led to marginal vaccine efficacy, antiviral resistance, and the annual emergence of novel strains. This evolvability is driven, in part, by the virus's capacity to generate diversity through mutation and reassortment. Because many new traits require multiple mutations and mutations are frequently combined by reassortment, epistatic interactions between mutations play an important role in influenza virus evolution. While mutation and epistasis are fundamental to the adaptability of influenza viruses, they also constrain the evolutionary process in important ways. Here, we review recent work on mutational effects and epistasis in influenza viruses.
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Affiliation(s)
- Daniel M Lyons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Adam S Lauring
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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19
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Leeks A, Segredo-Otero EA, Sanjuán R, West SA. Beneficial coinfection can promote within-host viral diversity. Virus Evol 2018; 4:vey028. [PMID: 30288300 PMCID: PMC6166523 DOI: 10.1093/ve/vey028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In many viral infections, a large number of different genetic variants can coexist within a host, leading to more virulent infections that are better able to evolve antiviral resistance and adapt to new hosts. But how is this diversity maintained? Why do faster-growing variants not outcompete slower-growing variants, and erode this diversity? One hypothesis is if there are mutually beneficial interactions between variants, with host cells infected by multiple different viral genomes producing more, or more effective, virions. We modelled this hypothesis with both mathematical models and simulations, and found that moderate levels of beneficial coinfection can maintain high levels of coexistence, even when coinfection is relatively rare, and when there are significant fitness differences between competing variants. Rare variants are more likely to be coinfecting with a different variant, and hence beneficial coinfection increases the relative fitness of rare variants through negative frequency dependence, and maintains diversity. We further find that coexisting variants sometimes reach unequal frequencies, depending on the extent to which different variants benefit from coinfection, and the ratio of variants which leads to the most productive infected cells. These factors could help drive the evolution of defective interfering particles, and help to explain why the different segments of multipartite viruses persist at different equilibrium frequencies.
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Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ernesto A Segredo-Otero
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, UK
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20
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Mauck KE, Chesnais Q, Shapiro LR. Evolutionary Determinants of Host and Vector Manipulation by Plant Viruses. Adv Virus Res 2018; 101:189-250. [PMID: 29908590 DOI: 10.1016/bs.aivir.2018.02.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Plant viruses possess adaptations for facilitating acquisition, retention, and inoculation by vectors. Until recently, it was hypothesized that these adaptations are limited to virus proteins that enable virions to bind to vector mouthparts or invade their internal tissues. However, increasing evidence suggests that viruses can also manipulate host plant phenotypes and vector behaviors in ways that enhance their own transmission. Manipulation of vector-host interactions occurs through virus effects on host cues that mediate vector orientation, feeding, and dispersal behaviors, and thereby, the probability of virus transmission. Effects on host phenotypes vary by pathosystem but show a remarkable degree of convergence among unrelated viruses whose transmission is favored by the same vector behaviors. Convergence based on transmission mechanism, rather than phylogeny, supports the hypothesis that virus effects are adaptive and not just by-products of infection. Based on this, it has been proposed that viruses manipulate hosts through multifunctional proteins that facilitate exploitation of host resources and elicitation of specific changes in host phenotypes. But this proposition is rarely discussed in the context of the numerous constraints on virus evolution imposed by molecular and environmental factors, which figure prominently in research on virus-host interactions not dealing with host manipulation. To explore the implications of this oversight, we synthesized available literature to identify patterns in virus effects among pathogens with shared transmission mechanisms and discussed the results of this synthesis in the context of molecular and environmental constraints on virus evolution, limitations of existing studies, and prospects for future research.
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Affiliation(s)
- Kerry E Mauck
- Department of Entomology, University of California, Riverside, Riverside, CA, United States.
| | - Quentin Chesnais
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Lori R Shapiro
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
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21
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Schoustra S, Hwang S, Krug J, de Visser JAGM. Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus. Proc Biol Sci 2017; 283:rspb.2016.1376. [PMID: 27559062 PMCID: PMC5013798 DOI: 10.1098/rspb.2016.1376] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/01/2016] [Indexed: 12/29/2022] Open
Abstract
Adaptive evolution ultimately is fuelled by mutations generating novel genetic variation. Non-additivity of fitness effects of mutations (called epistasis) may affect the dynamics and repeatability of adaptation. However, understanding the importance and implications of epistasis is hampered by the observation of substantial variation in patterns of epistasis across empirical studies. Interestingly, some recent studies report increasingly smaller benefits of beneficial mutations once genotypes become better adapted (called diminishing-returns epistasis) in unicellular microbes and single genes. Here, we use Fisher's geometric model (FGM) to generate analytical predictions about the relationship between the effect size of mutations and the extent of epistasis. We then test these predictions using the multicellular fungus Aspergillus nidulans by generating a collection of 108 strains in either a poor or a rich nutrient environment that each carry a beneficial mutation and constructing pairwise combinations using sexual crosses. Our results support the predictions from FGM and indicate negative epistasis among beneficial mutations in both environments, which scale with mutational effect size. Hence, our findings show the importance of diminishing-returns epistasis among beneficial mutations also for a multicellular organism, and suggest that this pattern reflects a generic constraint operating at diverse levels of biological organization.
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Affiliation(s)
- Sijmen Schoustra
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Sungmin Hwang
- Institute of Theoretical Physics, University of Cologne, Cologne, Germany
| | - Joachim Krug
- Institute of Theoretical Physics, University of Cologne, Cologne, Germany
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22
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Osmond MM, Klausmeier CA. An evolutionary tipping point in a changing environment. Evolution 2017; 71:2930-2941. [PMID: 28986985 DOI: 10.1111/evo.13374] [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: 03/13/2017] [Accepted: 09/18/2017] [Indexed: 01/18/2023]
Abstract
Populations can persist in directionally changing environments by evolving. Quantitative genetic theory aims to predict critical rates of environmental change beyond which populations go extinct. Here, we point out that all current predictions effectively assume the same specific fitness function. This function causes selection on the standing genetic variance of quantitative traits to become increasingly strong as mean trait values depart from their optima. Hence, there is no bound on the rate of evolution and persistence is determined by the critical rate of environmental change at which populations cease to grow. We then show that biologically reasonable changes to the underlying fitness function can impose a qualitatively different extinction threshold. In particular, inflection points caused by weakening selection create local extrema in the strength of selection and thus in the rate of evolution. These extrema can produce evolutionary tipping points, where long-run population growth rates drop from positive to negative values without ever crossing zero. Generic early-warning signs of tipping points are found to have little power to detect imminent extinction, and require hard-to-gather data. Furthermore, we show how evolutionary tipping points produce evolutionary hysteresis, creating extinction debts.
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Affiliation(s)
- Matthew M Osmond
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Christopher A Klausmeier
- Kellogg Biological Station, Department of Plant Biology, and Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, Hickory Corners, Michigan 49060
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23
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Beppler C, Tekin E, Mao Z, White C, McDiarmid C, Vargas E, Miller JH, Savage VM, Yeh PJ. Uncovering emergent interactions in three-way combinations of stressors. J R Soc Interface 2017; 13:rsif.2016.0800. [PMID: 27974577 DOI: 10.1098/rsif.2016.0800] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/23/2016] [Indexed: 11/12/2022] Open
Abstract
Understanding how multiple stressors interact is needed to predict the dynamical outcomes of diverse biological systems, ranging from drug-resistant pathogens that are combated and treated with combination drug therapies to ecosystems impacted by environmental toxicants or disturbances. Nevertheless, extensive studies of higher-order (more than two component) interactions have been lacking. Here, we conduct experiments using 20 three-drug combinations and their effects on the bacterial growth of Escherichia coli We report our measurements of growth rates in single, pairwise and triple-drug combinations. To uncover emergent interactions, we derive a simple framework to calculate expectations for three-way interactions based on the measured impact of each individual stressor and of each pairwise interaction. Using our framework, we find that (i) emergent antagonisms are more common than emergent synergies and (ii) emergent antagonisms are more common and emergent synergies are more rare than would be inferred from measures of net effects that do not disentangle pairwise interactions from three-way interactions.
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Affiliation(s)
- Casey Beppler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Elif Tekin
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Zhiyuan Mao
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Cynthia White
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Cassandra McDiarmid
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Emily Vargas
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Jeffrey H Miller
- Department of Microbiology, Immunology, and Molecular Genetics, The Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Van M Savage
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Pamela J Yeh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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24
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The road less traveled: from genotype to phenotype in flies and humans. Mamm Genome 2017; 29:5-23. [DOI: 10.1007/s00335-017-9722-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022]
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25
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Wu B, Arranz J, Du J, Zhou D, Traulsen A. Evolving synergetic interactions. J R Soc Interface 2017; 13:rsif.2016.0282. [PMID: 27466437 PMCID: PMC4971219 DOI: 10.1098/rsif.2016.0282] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 06/30/2016] [Indexed: 11/12/2022] Open
Abstract
Cooperators forgo their own interests to benefit others. This reduces their fitness and thus cooperators are not likely to spread based on natural selection. Nonetheless, cooperation is widespread on every level of biological organization ranging from bacterial communities to human society. Mathematical models can help to explain under which circumstances cooperation evolves. Evolutionary game theory is a powerful mathematical tool to depict the interactions between cooperators and defectors. Classical models typically involve either pairwise interactions between individuals or a linear superposition of these interactions. For interactions within groups, however, synergetic effects may arise: their outcome is not just the sum of its parts. This is because the payoffs via a single group interaction can be different from the sum of any collection of two-player interactions. Assuming that all interactions start from pairs, how can such synergetic multiplayer games emerge from simpler pairwise interactions? Here, we present a mathematical model that captures the transition from pairwise interactions to synergetic multiplayer ones. We assume that different social groups have different breaking rates. We show that non-uniform breaking rates do foster the emergence of synergy, even though individuals always interact in pairs. Our work sheds new light on the mechanisms underlying such synergetic interactions.
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Affiliation(s)
- Bin Wu
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany School of Sciences, Beijing University of Posts and Telecommunications, Beijing 100876, People's Republic of China
| | - Jordi Arranz
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Jinming Du
- Liaoning Key Laboratory of Manufacturing Systems and Logistics, Institute of Industrial Engineering and Logistics Optimization, Northeastern University, Shenyang 110819, People's Republic of China Center for Systems and Control, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Da Zhou
- School of Mathematical Sciences, Xiamen University, Xiamen 361005, People's Republic of China
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
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26
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Tekin E, Beppler C, White C, Mao Z, Savage VM, Yeh PJ. Enhanced identification of synergistic and antagonistic emergent interactions among three or more drugs. J R Soc Interface 2017; 13:rsif.2016.0332. [PMID: 27278366 DOI: 10.1098/rsif.2016.0332] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/17/2016] [Indexed: 02/02/2023] Open
Abstract
Interactions among drugs play a critical role in the killing efficacy of multi-drug treatments. Recent advances in theory and experiment for three-drug interactions enable the search for emergent interactions-ones not predictable from pairwise interactions. Previous work has shown it is easier to detect synergies and antagonisms among pairwise interactions when a rescaling method is applied to the interaction metric. However, no study has carefully examined whether new types of normalization might be needed for emergence. Here, we propose several rescaling methods for enhancing the classification of the higher order drug interactions based on our conceptual framework. To choose the rescaling that best separates synergism, antagonism and additivity, we conducted bacterial growth experiments in the presence of single, pairwise and triple-drug combinations among 14 antibiotics. We found one of our rescaling methods is far better at distinguishing synergistic and antagonistic emergent interactions than any of the other methods. Using our new method, we find around 50% of emergent interactions are additive, much less than previous reports of greater than 90% additivity. We conclude that higher order emergent interactions are much more common than previously believed, and we argue these findings for drugs suggest that appropriate rescaling is crucial to infer higher order interactions.
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Affiliation(s)
- Elif Tekin
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Casey Beppler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Cynthia White
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Zhiyuan Mao
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Van M Savage
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Pamela J Yeh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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27
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van Dijk T, Hwang S, Krug J, de Visser JAGM, Zwart MP. Mutation supply and the repeatability of selection for antibiotic resistance. Phys Biol 2017; 14:055005. [PMID: 28699625 DOI: 10.1088/1478-3975/aa7f36] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of antibiotic resistance gene TEM-1 β-lactamase in Escherichia coli, generated by error-prone PCR, were subjected to different antibiotic concentrations. We determined whether populations went extinct or survived, and sequenced the TEM gene of the surviving populations. The distribution of mutations per allele in our mutant libraries followed a Poisson distribution. Extinction patterns could be explained by a simple stochastic model that assumed the sampling of beneficial mutations was key for survival. In most surviving populations, alleles containing at least one known large-effect beneficial mutation were present. These genotype data also support a model which only invokes sampling effects to describe the occurrence of alleles containing large-effect driver mutations. Hence, evolution is largely predictable given cursory knowledge of mutational fitness effects, the mutation rate and population size. There were no clear trends in the repeatability of selected mutants when we considered all mutations present. However, when only known large-effect mutations were considered, the outcome of selection is less repeatable for large libraries, in contrast to expectations. We show experimentally that alleles carrying multiple mutations selected from large libraries confer higher resistance levels relative to alleles with only a known large-effect mutation, suggesting that the scarcity of high-resistance alleles carrying multiple mutations may contribute to the decrease in repeatability at large library sizes.
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Affiliation(s)
- Thomas van Dijk
- Laboratory of Genetics, Wageningen University, Wageningen, Netherlands. These authors contributed equally
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28
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Beppler C, Tekin E, White C, Mao Z, Miller JH, Damoiseaux R, Savage VM, Yeh PJ. When more is less: Emergent suppressive interactions in three-drug combinations. BMC Microbiol 2017; 17:107. [PMID: 28477626 PMCID: PMC5420147 DOI: 10.1186/s12866-017-1017-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 04/26/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND In drug-drug interactions, there are surprising cases in which the growth inhibition of bacteria by a single antibiotic decreases when a second antibiotic is added. These interactions are termed suppressive and have been argued to have the potential to limit the evolution of resistance. Nevertheless, little attention has been given to suppressive interactions because clinical studies typically search for increases in killing efficiency and because suppressive interactions are believed to be rare based on pairwise studies. RESULTS Here, we quantify the effects of single-, double-, and triple-drug combinations from a set of 14 antibiotics and 3 bacteria strains, totaling 364 unique three-drug combinations per bacteria strain. We find that increasing the number of drugs can increase the prevalence of suppressive interactions: 17% of three-drug combinations are suppressive compared to 5% of two-drug combinations in this study. Most cases of suppression we find (97%) are "hidden" cases for which the triple-drug bacterial growth is less than the single-drug treatments but exceeds that of a pairwise combination. CONCLUSIONS We find a surprising number of suppressive interactions in higher-order drug combinations. Without examining lower-order (pairwise) bacterial growth, emergent suppressive effects would be missed, potentially affecting our understanding of evolution of resistance and treatment strategies for resistant pathogens. These findings suggest that careful examination of the full factorial of drug combinations is needed to uncover suppressive interactions in higher-order combinations.
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Affiliation(s)
- Casey Beppler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Elif Tekin
- Department of Biomathematics, University of California, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Cynthia White
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Zhiyuan Mao
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Jeffrey H Miller
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Robert Damoiseaux
- Department of Medical and Molecular Pharmacology, University of California, Los Angeles, CA, USA
| | - Van M Savage
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Department of Biomathematics, University of California, David Geffen School of Medicine, Los Angeles, CA, USA.,Santa Fe Institute, Santa Fe, NM, USA
| | - Pamela J Yeh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
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29
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Nshogozabahizi JC, Dench J, Aris-Brosou S. Widespread Historical Contingency in Influenza Viruses. Genetics 2017; 205:409-420. [PMID: 28049709 PMCID: PMC5223518 DOI: 10.1534/genetics.116.193979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/04/2016] [Indexed: 11/18/2022] Open
Abstract
In systems biology and genomics, epistasis characterizes the impact that a substitution at a particular location in a genome can have on a substitution at another location. This phenomenon is often implicated in the evolution of drug resistance or to explain why particular "disease-causing" mutations do not have the same outcome in all individuals. Hence, uncovering these mutations and their locations in a genome is a central question in biology. However, epistasis is notoriously difficult to uncover, especially in fast-evolving organisms. Here, we present a novel statistical approach that replies on a model developed in ecology and that we adapt to analyze genetic data in fast-evolving systems such as the influenza A virus. We validate the approach using a two-pronged strategy: extensive simulations demonstrate a low-to-moderate sensitivity with excellent specificity and precision, while analyses of experimentally validated data recover known interactions, including in a eukaryotic system. We further evaluate the ability of our approach to detect correlated evolution during antigenic shifts or at the emergence of drug resistance. We show that in all cases, correlated evolution is prevalent in influenza A viruses, involving many pairs of sites linked together in chains; a hallmark of historical contingency. Strikingly, interacting sites are separated by large physical distances, which entails either long-range conformational changes or functional tradeoffs, for which we find support with the emergence of drug resistance. Our work paves a new way for the unbiased detection of epistasis in a wide range of organisms by performing whole-genome scans.
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Affiliation(s)
| | - Jonathan Dench
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ontario K1N 6N5, Canada
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30
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Hayden EJ. Empirical analysis of RNA robustness and evolution using high-throughput sequencing of ribozyme reactions. Methods 2016; 106:97-104. [PMID: 27215494 DOI: 10.1016/j.ymeth.2016.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 10/21/2022] Open
Abstract
RNA molecules provide a realistic but tractable model of a genotype to phenotype relationship. This relationship has been extensively investigated computationally using secondary structure prediction algorithms. Enzymatic RNA molecules, or ribozymes, offer access to genotypic and phenotypic information in the laboratory. Advancements in high-throughput sequencing technologies have enabled the analysis of sequences in the lab that now rivals what can be accomplished computationally. This has motivated a resurgence of in vitro selection experiments and opened new doors for the analysis of the distribution of RNA functions in genotype space. A body of computational experiments has investigated the persistence of specific RNA structures despite changes in the primary sequence, and how this mutational robustness can promote adaptations. This article summarizes recent approaches that were designed to investigate the role of mutational robustness during the evolution of RNA molecules in the laboratory, and presents theoretical motivations, experimental methods and approaches to data analysis.
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Affiliation(s)
- Eric J Hayden
- Department of Biological Sciences, Biomolecular Sciences PhD Program, Boise State University, Boise, ID 83725, United States.
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Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. PLoS Genet 2015; 11:e1005392. [PMID: 26177190 PMCID: PMC4503671 DOI: 10.1371/journal.pgen.1005392] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/25/2015] [Indexed: 11/21/2022] Open
Abstract
The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution. Mutations that have little influence on biological function are referred to as neutral mutations and frequently appear in molecular phylogenetic analyses. The fixation of neutral mutations in populations has been attributed to genetic drift in fitness-steady evolutionary processes or hitchhiking in adaptive evolution. We examined the fitness-increasing evolution of Escherichia coli for thermal adaptation to observe the fixation dynamics of genome-wide mutations. In the adaptive evolution, all genomes in the population equally accumulated neutral mutations by replication errors. The infrequent occurrence of an adaptive mutation on one of the genomes by chance resulted in the fixation of the neutral mutations that had pre-accumulated in the same genome by hitchhiking. Via successive hitchhiking events, the neutral mutations were fixed in the population linearly over generations at the same rate as the spontaneous mutation accumulation rate in the genome. The molecular clock of neutral mutations thus functions even in adaptive evolution. The evolutionary period characterized by the accumulation of numerous neutral mutations observed in molecular phylogenetic trees may not be specific to neutral evolution but may occur in adaptive evolution as well.
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Abiotic stress does not magnify the deleterious effects of spontaneous mutations. Heredity (Edinb) 2015; 115:503-8. [PMID: 26103946 DOI: 10.1038/hdy.2015.51] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 04/30/2015] [Accepted: 05/06/2015] [Indexed: 01/10/2023] Open
Abstract
Although the effects of deleterious alleles often are predicted to be greater in stressful environments, there is no theoretical basis for this prediction and the empirical evidence is mixed. Here we characterized the effects of three types of abiotic stress (thermal, oxidative and hyperosmotic) on two sets of nematode (Caenorhabditis elegans) mutation accumulation (MA) lines that differ by threefold in fitness. We compared the survival and egg-to-adult viability between environments (benign and stressful) and between fitness categories (high-fitness MA, low-fitness MA). If the environment and mutation load have synergistic effects on trait means, then the difference between the high and low-fitness MA lines should be larger in stressful environments. Although the stress treatments consistently decreased survival and/or viability, we did not detect significant interactions between fitness categories and environment types. In contrast, we did find consistent evidence for synergistic effects on (micro)environmental variation. The lack of signal in trait means likely reflects the very low starting fitness of some low-fitness MA lines, the potential for cross-stress responses and the context dependence of mutational effects. In addition, the large increases in the environmental variance in the stressful environments may have masked small changes in trait means. These results do not provide evidence for synergism between mutation and stress.
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Cuevas JM, Willemsen A, Hillung J, Zwart MP, Elena SF. Temporal dynamics of intrahost molecular evolution for a plant RNA virus. Mol Biol Evol 2015; 32:1132-47. [PMID: 25660377 DOI: 10.1093/molbev/msv028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution.
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Affiliation(s)
- José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Anouk Willemsen
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain The Santa Fe Institute, Santa Fe, NM
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Botha AM, Burger NFV, Van Eck L. Hypervirulent Diuraphis noxia (Hemiptera: Aphididae) biotype SAM avoids triggering defenses in its host (Triticum aestivum) (Poales: Poaceae) during feeding. ENVIRONMENTAL ENTOMOLOGY 2014; 43:672-81. [PMID: 24874154 DOI: 10.1603/en13331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the molecular arms race between aphids and plants, both organisms rely on adaptive strategies to outcompete their evolutionary rival. In the current study, we investigated the difference in elicited defense responses of wheat (Triticum aestivum L.) near-isogenic lines with different Dn resistance genes, upon feeding by an avirulent and hypervirulent Diuraphis noxia Kurdjumov biotype. After measuring the activity of a suite of enzymes associated with plant defense, it became apparent that the host does not recognize the invasion by the hypervirulent aphid because none of these were induced, while feeding by the avirulent biotype did result in induction of enzyme activity. Genomic plasticity in D. noxia may be a likely explanation for the observed differences in virulence between D. noxia biotype SA1 and SAM, as demonstrated in the current study.
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Affiliation(s)
- Anna-Maria Botha
- Genetics Department, Stellenbosch University, Private Bag X1, Matieland, 7601, South Africa
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Abstract
A central question in protein molecular evolution is whether an amino acid that occurs at a given site makes an independent contribution to fitness or whether its contribution depends on other amino acid sites in the protein sequence, a phenomenon known as intragenic epistasis. In the absence of intragenic epistasis, natural selection acts on a protein mutation independent of its genetic background, and the experimentally determined fitness for a mutation should be the same across all genetic backgrounds. We tested this hypothesis by using site-directed mutagenesis to introduce a well-characterized deleterious single amino acid substitution in 56 different hepatitis C virus NS3 protease variants. The catalytic efficiency of the mutated proteases was determined and compared with the corresponding wild-type protein. Fitness effects ranged from lethality to significantly beneficial. Although primarily deleterious and lethal effects were observed (41 and 5 out of 56 tested variants, respectively), deleterious effects ranged from near neutral (-26.7% reduction of fitness) to near lethal (-98.5%). Our findings demonstrate that the introduced amino acid substitution has different fitness effects in different protein variants and provide independent support for the relevant role of intragenic epistasis in protein evolution.
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Affiliation(s)
- Mariona Parera
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Miguel Angel Martinez
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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Morton ER, Platt TG, Fuqua C, Bever JD. Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids. Proc Biol Sci 2014; 281:20132173. [PMID: 24500159 PMCID: PMC3924060 DOI: 10.1098/rspb.2013.2173] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/07/2014] [Indexed: 11/12/2022] Open
Abstract
Plasmids play an important role in shaping bacterial evolution and adaptation to heterogeneous environments. As modular genetic elements that are often conjugative, the selective pressures that act on plasmid-borne genes are distinct from those that act on the chromosome. Many bacteria are co-infected by multiple plasmids that impart niche-specific phenotypes. Thus, in addition to host-plasmid dynamics, interactions between co-infecting plasmids are likely to be important drivers of plasmid population dynamics, evolution and ecology. Agrobacterium tumefaciens is a facultative plant pathogen that commonly harbours two distinct megaplasmids. Virulence depends on the presence of the tumour-inducing (Ti) plasmid, with benefits that are primarily restricted to the disease environment. Here, we demonstrate that a second megaplasmid, the At plasmid, confers a competitive advantage in the rhizosphere. To assess the individual and interactive costs of these plasmids, we generated four isogenic derivatives: plasmidless, pAt only, pTi only and pAtpTi, and performed pairwise competitions under carbon-limiting conditions. These studies reveal a low cost to the virulence plasmid when outside of the disease environment, and a strikingly high cost to the At plasmid. In addition, the costs of pAt and pTi in the same host were significantly lower than predicted based on single plasmid costs, signifying the first demonstration of non-additivity between naturally occurring co-resident plasmids. Based on these empirically demonstrated costs and benefits, we developed a resource-consumer model to generate predictions about the frequencies of these genotypes in relevant environments, showing that non-additivity between co-residing plasmids allows for their stable coexistence across environments.
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Affiliation(s)
- Elise R. Morton
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Kaltenbach M, Tokuriki N. Dynamics and constraints of enzyme evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:468-87. [DOI: 10.1002/jez.b.22562] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
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Boucher B, Jenna S. Genetic interaction networks: better understand to better predict. Front Genet 2013; 4:290. [PMID: 24381582 PMCID: PMC3865423 DOI: 10.3389/fgene.2013.00290] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/28/2013] [Indexed: 12/21/2022] Open
Abstract
A genetic interaction (GI) between two genes generally indicates that the phenotype of a double mutant differs from what is expected from each individual mutant. In the last decade, genome scale studies of quantitative GIs were completed using mainly synthetic genetic array technology and RNA interference in yeast and Caenorhabditis elegans. These studies raised questions regarding the functional interpretation of GIs, the relationship of genetic and molecular interaction networks, the usefulness of GI networks to infer gene function and co-functionality, the evolutionary conservation of GI, etc. While GIs have been used for decades to dissect signaling pathways in genetic models, their functional interpretations are still not trivial. The existence of a GI between two genes does not necessarily imply that these two genes code for interacting proteins or that the two genes are even expressed in the same cell. In fact, a GI only implies that the two genes share a functional relationship. These two genes may be involved in the same biological process or pathway; or they may also be involved in compensatory pathways with unrelated apparent function. Considering the powerful opportunity to better understand gene function, genetic relationship, robustness and evolution, provided by a genome-wide mapping of GIs, several in silico approaches have been employed to predict GIs in unicellular and multicellular organisms. Most of these methods used weighted data integration. In this article, we will review the later knowledge acquired on GI networks in metazoans by looking more closely into their relationship with pathways, biological processes and molecular complexes but also into their modularity and organization. We will also review the different in silico methods developed to predict GIs and will discuss how the knowledge acquired on GI networks can be used to design predictive tools with higher performances.
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Affiliation(s)
- Benjamin Boucher
- Laboratory of Integrative Genomics and Cell Signalling, Pharmaqam, Biomed, Department of Chemistry, Université du Québec à Montréal Montréal, QC, Canada
| | - Sarah Jenna
- Laboratory of Integrative Genomics and Cell Signalling, Pharmaqam, Biomed, Department of Chemistry, Université du Québec à Montréal Montréal, QC, Canada
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SENSITIVITY OF THE DISTRIBUTION OF MUTATIONAL FITNESS EFFECTS TO ENVIRONMENT, GENETIC BACKGROUND, AND ADAPTEDNESS: A CASE STUDY WITHDROSOPHILA. Evolution 2013; 68:840-53. [DOI: 10.1111/evo.12309] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 10/22/2013] [Indexed: 12/22/2022]
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Perfeito L, Sousa A, Bataillon T, Gordo I. Rates of fitness decline and rebound suggest pervasive epistasis. Evolution 2013; 68:150-62. [PMID: 24372601 PMCID: PMC3912910 DOI: 10.1111/evo.12234] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 07/19/2013] [Indexed: 11/30/2022]
Abstract
Unraveling the factors that determine the rate of adaptation is a major question in evolutionary biology. One key parameter is the effect of a new mutation on fitness, which invariably depends on the environment and genetic background. The fate of a mutation also depends on population size, which determines the amount of drift it will experience. Here, we manipulate both population size and genotype composition and follow adaptation of 23 distinct Escherichia coli genotypes. These have previously accumulated mutations under intense genetic drift and encompass a substantial fitness variation. A simple rule is uncovered: the net fitness change is negatively correlated with the fitness of the genotype in which new mutations appear—a signature of epistasis. We find that Fisher's geometrical model can account for the observed patterns of fitness change and infer the parameters of this model that best fit the data, using Approximate Bayesian Computation. We estimate a genomic mutation rate of 0.01 per generation for fitness altering mutations, albeit with a large confidence interval, a mean fitness effect of mutations of −0.01, and an effective number of traits nine in mutS−E. coli. This framework can be extended to confront a broader range of models with data and test different classes of fitness landscape models.
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Affiliation(s)
- L Perfeito
- Instituto Gulbenkian de Ciência, Oeiras, Portugal; The authors contributed equally to this work
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Dikicioglu D, Pir P, Oliver SG. Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. Biotechnol J 2013; 8:1017-34. [PMID: 24031036 PMCID: PMC3910164 DOI: 10.1002/biot.201300138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 07/15/2013] [Accepted: 08/07/2013] [Indexed: 11/08/2022]
Abstract
There is an increasing use of systems biology approaches in both "red" and "white" biotechnology in order to enable medical, medicinal, and industrial applications. The intricate links between genotype and phenotype may be explained through the use of the tools developed in systems biology, synthetic biology, and evolutionary engineering. Biomedical and biotechnological research are among the fields that could benefit most from the elucidation of this complex relationship. Researchers have studied fitness extensively to explain the phenotypic impacts of genetic variations. This elaborate network of dependencies and relationships so revealed are further complicated by the influence of environmental effects that present major challenges to our achieving an understanding of the cellular mechanisms leading to healthy or diseased phenotypes or optimized production yields. An improved comprehension of complex genotype-phenotype interactions and their accurate prediction should enable us to more effectively engineer yeast as a cell factory and to use it as a living model of human or pathogen cells in intelligent screens for new drugs. This review presents different methods and approaches undertaken toward improving our understanding and prediction of the growth phenotype of the yeast Saccharomyces cerevisiae as both a model and a production organism.
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Affiliation(s)
- Duygu Dikicioglu
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
| | - Pınar Pir
- Babraham Institute, Babraham Research Campus, CB22 3AT, Cambridge, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
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Velenich A, Gore J. The strength of genetic interactions scales weakly with mutational effects. Genome Biol 2013; 14:R76. [PMID: 23889884 PMCID: PMC4053755 DOI: 10.1186/gb-2013-14-7-r76] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 07/26/2013] [Indexed: 11/18/2022] Open
Abstract
Background Genetic interactions pervade every aspect of biology, from evolutionary theory, where they determine the accessibility of evolutionary paths, to medicine, where they can contribute to complex genetic diseases. Until very recently, studies on epistatic interactions have been based on a handful of mutations, providing at best anecdotal evidence about the frequency and the typical strength of genetic interactions. In this study, we analyze a publicly available dataset that contains the growth rates of over five million double knockout mutants of the yeast Saccharomyces cerevisiae. Results We discuss a geometric definition of epistasis that reveals a simple and surprisingly weak scaling law for the characteristic strength of genetic interactions as a function of the effects of the mutations being combined. We then utilized this scaling to quantify the roughness of naturally occurring fitness landscapes. Finally, we show how the observed roughness differs from what is predicted by Fisher's geometric model of epistasis, and discuss the consequences for evolutionary dynamics. Conclusions Although epistatic interactions between specific genes remain largely unpredictable, the statistical properties of an ensemble of interactions can display conspicuous regularities and be described by simple mathematical laws. By exploiting the amount of data produced by modern high-throughput techniques, it is now possible to thoroughly test the predictions of theoretical models of genetic interactions and to build informed computational models of evolution on realistic fitness landscapes.
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Schenk MF, Szendro IG, Salverda ML, Krug J, de Visser JAG. Patterns of Epistasis between beneficial mutations in an antibiotic resistance gene. Mol Biol Evol 2013; 30:1779-87. [PMID: 23676768 PMCID: PMC3708503 DOI: 10.1093/molbev/mst096] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding epistasis is central to biology. For instance, epistatic interactions determine the topography of the fitness landscape and affect the dynamics and determinism of adaptation. However, few empirical data are available, and comparing results is complicated by confounding variation in the system and the type of mutations used. Here, we take a systematic approach by quantifying epistasis in two sets of four beneficial mutations in the antibiotic resistance enzyme TEM-1 β-lactamase. Mutations in these sets have either large or small effects on cefotaxime resistance when present as single mutations. By quantifying the epistasis and ruggedness in both landscapes, we find two general patterns. First, resistance is maximal for combinations of two mutations in both fitness landscapes and declines when more mutations are added due to abundant sign epistasis and a pattern of diminishing returns with genotype resistance. Second, large-effect mutations interact more strongly than small-effect mutations, suggesting that the effect size of mutations may be an organizing principle in understanding patterns of epistasis. By fitting the data to simple phenotype resistance models, we show that this pattern may be explained by the nonlinear dependence of resistance on enzyme stability and an unknown phenotype when mutations have antagonistically pleiotropic effects. The comparison to a previously published set of mutations in the same gene with a joint benefit further shows that the enzyme's fitness landscape is locally rugged but does contain adaptive pathways that lead to high resistance.
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Affiliation(s)
| | - Ivan G. Szendro
- Institute for Theoretical Physics, University of Cologne, Köln, Germany
| | | | - Joachim Krug
- Institute for Theoretical Physics, University of Cologne, Köln, Germany
- Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Köln, Germany
| | - J. Arjan G.M. de Visser
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
- *Corresponding author: E-mail:
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Ying BW, Seno S, Kaneko F, Matsuda H, Yomo T. Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome. BMC Genomics 2013; 14:25. [PMID: 23324527 PMCID: PMC3553035 DOI: 10.1186/1471-2164-14-25] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 12/29/2012] [Indexed: 12/24/2022] Open
Abstract
Background Both large deletions in genome and heat shock stress would lead to alterations in the gene expression profile; however, whether there is any potential linkage between these disturbances to the transcriptome have not been discovered. Here, the relationship between the genomic and environmental contributions to the transcriptome was analyzed by comparing the transcriptomes of the bacterium Escherichia coli (strain MG1655 and its extensive genomic deletion derivative, MDS42) grown in regular and transient heat shock conditions. Results The transcriptome analysis showed the following: (i) there was a reorganization of the transcriptome in accordance with preferred chromosomal periodicity upon genomic or heat shock perturbation; (ii) there was a considerable overlap between the perturbed regulatory networks and the categories enriched for differentially expressed genes (DEGs) following genome reduction and heat shock; (iii) the genes sensitive to genome reduction tended to be located close to genomic scars, and some were also highly responsive to heat shock; and (iv) the genomic and environmental contributions to the transcriptome displayed not only a positive correlation but also a negatively compensated relationship (i.e., antagonistic epistasis). Conclusion The contributions of genome reduction and heat shock to the Escherichia coli transcriptome were evaluated at multiple levels. The observations of overlapping perturbed networks, directional similarity in transcriptional changes, positive correlation and epistatic nature linked the two contributions and suggest somehow a crosstalk guiding transcriptional reorganization in response to both genetic and environmental disturbances in bacterium E. coli.
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Affiliation(s)
- Bei-Wen Ying
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, Japan
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Cabanillas L, Arribas M, Lázaro E. Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus. BMC Evol Biol 2013; 13:11. [PMID: 23323937 PMCID: PMC3556134 DOI: 10.1186/1471-2148-13-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 01/11/2013] [Indexed: 11/30/2022] Open
Abstract
Background When beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them. This interference among mutations is mainly determined by the rate of beneficial mutations, which in turn depends on the population size, the total error rate, and the degree of adaptation of the population. RNA viruses, with their large population sizes and high error rates, are good candidates to present a great extent of interference. To test this hypothesis, in the current study we have investigated whether competition among beneficial mutations was responsible for the prolonged presence of polymorphisms in the mutant spectrum of an RNA virus, the bacteriophage Qβ, evolved during a large number of generations in the presence of the mutagenic nucleoside analogue 5-azacytidine. Results The analysis of the mutant spectra of bacteriophage Qβ populations evolved at artificially increased error rate shows a large number of polymorphic mutations, some of them with demonstrated selective value. Polymorphisms distributed into several evolutionary lines that can compete among them, making it difficult the emergence of a defined consensus sequence. The presence of accompanying deleterious mutations, the high degree of recurrence of the polymorphic mutations, and the occurrence of epistatic interactions generate a highly complex interference dynamics. Conclusions Interference among beneficial mutations in bacteriophage Qβ evolved at increased error rate permits the coexistence of multiple adaptive pathways that can provide selective advantages by different molecular mechanisms. In this way, interference can be seen as a positive factor that allows the exploration of the different local maxima that exist in rugged fitness landscapes.
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Affiliation(s)
- Laura Cabanillas
- Centro de Astrobiología (CSIC-INTA) Ctra de Ajalvir Km 4, Torrejón de Ardoz, Madrid, 28850, Spain
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Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections. Proc Natl Acad Sci U S A 2012; 110:E250-9. [PMID: 23271804 DOI: 10.1073/pnas.1207025110] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
How diversity evolves and persists in biofilms is essential for understanding much of microbial life, including the uncertain dynamics of chronic infections. We developed a biofilm model enabling long-term selection for daily adherence to and dispersal from a plastic bead in a test tube. Focusing on a pathogen of the cystic fibrosis lung, Burkholderia cenocepacia, we sequenced clones and metagenomes to unravel the mutations and evolutionary forces responsible for adaptation and diversification of a single biofilm community during 1,050 generations of selection. The mutational patterns revealed recurrent evolution of biofilm specialists from generalist types and multiple adaptive alleles at relatively few loci. Fitness assays also demonstrated strong interference competition among contending mutants that preserved genetic diversity. Metagenomes from five other independently evolved biofilm lineages revealed extraordinary mutational parallelism that outlined common routes of adaptation, a subset of which was found, surprisingly, in a planktonic population. These mutations in turn were surprisingly well represented among mutations that evolved in cystic fibrosis isolates of both Burkholderia and Pseudomonas. These convergent pathways included altered metabolism of cyclic diguanosine monophosphate, polysaccharide production, tricarboxylic acid cycle enzymes, global transcription, and iron scavenging. Evolution in chronic infections therefore may be driven by mutations in relatively few pathways also favored during laboratory selection, creating hope that experimental evolution may illuminate the ecology and selective dynamics of chronic infections and improve treatment strategies.
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Steiner CF. Environmental noise, genetic diversity and the evolution of evolvability and robustness in model gene networks. PLoS One 2012; 7:e52204. [PMID: 23284934 PMCID: PMC3527431 DOI: 10.1371/journal.pone.0052204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 11/16/2012] [Indexed: 12/02/2022] Open
Abstract
The ability of organisms to adapt and persist in the face of environmental change is accepted as a fundamental feature of natural systems. More contentious is whether the capacity of organisms to adapt (or “evolvability”) can itself evolve and the mechanisms underlying such responses. Using model gene networks, I provide evidence that evolvability emerges more readily when populations experience positively autocorrelated environmental noise (red noise) compared to populations in stable or randomly varying (white noise) environments. Evolvability was correlated with increasing genetic robustness to effects on network viability and decreasing robustness to effects on phenotypic expression; populations whose networks displayed greater viability robustness and lower phenotypic robustness produced more additive genetic variation and adapted more rapidly in novel environments. Patterns of selection for robustness varied antagonistically with epistatic effects of mutations on viability and phenotypic expression, suggesting that trade-offs between these properties may constrain their evolutionary responses. Evolution of evolvability and robustness was stronger in sexual populations compared to asexual populations indicating that enhanced genetic variation under fluctuating selection combined with recombination load is a primary driver of the emergence of evolvability. These results provide insight into the mechanisms potentially underlying rapid adaptation as well as the environmental conditions that drive the evolution of genetic interactions.
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Agrawal AF, Whitlock MC. Mutation Load: The Fitness of Individuals in Populations Where Deleterious Alleles Are Abundant. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-110411-160257] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many multicellular eukaryotes have reasonably high per-generation mutation rates. Consequently, most populations harbor an abundance of segregating deleterious alleles. These alleles, most of which are of small effect individually, collectively can reduce substantially the fitness of individuals relative to what it would be otherwise; this is mutation load. Mutation load can be lessened by any factor that causes more mutations to be removed per selective death, such as inbreeding, synergistic epistasis, population structure, or harsh environments. The ecological effects of load are not clear-cut because some conditions (such as selection early in life, sexual selection, reproductive compensation, and intraspecific competition) reduce the effects of load on population size and persistence, but other conditions (such as interspecific competition and load on resource use efficiency) can cause small amounts of load to have strong effects on the population, even extinction. We suggest a series of studies to improve our understanding of the effects of mutation load.
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Affiliation(s)
- Aneil F. Agrawal
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Michael C. Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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Abstract
Deleterious mutations can have a strong influence on the outcome of evolution. The nature of this influence depends on how mutations combine together to affect fitness. “Negative epistasis” occurs when a new deleterious mutation causes the greatest loss in fitness in a genome that already contains many deleterious mutations. Negative epistasis is a key ingredient for some of the leading hypotheses regarding the evolution of recombination, the evolution of sex, and a variety of other phenomena. In general, laboratory studies have not supported the idea that negative epistasis is ubiquitous, and this has led to doubts about its importance in biological evolution. Here, we show that these experimental results may be misleading, because negative epistasis can produce evolutionary advantages for sex and recombination while simultaneously being almost impossible to detect using current experimental methods. Under asexual reproduction, such hidden epistasis influences evolutionary outcomes only if the fittest individuals are present in substantial numbers, while also forming a very small proportion of the population as a whole. This implies that our results for asexuals will apply only for very large populations, and also limits the extent of the fitness benefits that hidden epistasis can provide. Despite these caveats, our results show that the fitness consequences of sex and recombination cannot always be inferred from observable epistasis alone.
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Lalić J, Elena SF. Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus. Heredity (Edinb) 2012; 109:71-7. [PMID: 22491062 PMCID: PMC3400743 DOI: 10.1038/hdy.2012.15] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 02/21/2012] [Accepted: 02/28/2012] [Indexed: 11/09/2022] Open
Abstract
How epistatic interactions between mutations determine the genetic architecture of fitness is of central importance in evolution. The study of epistasis is particularly interesting for RNA viruses because of their genomic compactness, lack of genetic redundancy, and apparent low complexity. Moreover, interactions between mutations in viral genomes determine traits such as resistance to antiviral drugs, virulence and host range. In this study we generated 53 Tobacco etch potyvirus genotypes carrying pairs of single-nucleotide substitutions and measured their separated and combined deleterious fitness effects. We found that up to 38% of pairs had significant epistasis for fitness, including both positive and negative deviations from the null hypothesis of multiplicative effects. Interestingly, the sign of epistasis was correlated with viral protein-protein interactions in a model network, being predominantly positive between linked pairs of proteins and negative between unlinked ones. Furthermore, 55% of significant interactions were cases of reciprocal sign epistasis (RSE), indicating that adaptive landscapes for RNA viruses maybe highly rugged. Finally, we found that the magnitude of epistasis correlated negatively with the average effect of mutations. Overall, our results are in good agreement to those previously reported for other viruses and further consolidate the view that positive epistasis is the norm for small and compact genomes that lack genetic robustness.
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Affiliation(s)
- J Lalić
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain and
| | - S F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València, Spain and
- Santa Fe Institute, Santa Fe NM, USA
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