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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
- Cluster of Excellence Physics of Life TU Dresden Dresden Germany
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2
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Palazzo AF, Kejiou NS. Non-Darwinian Molecular Biology. Front Genet 2022; 13:831068. [PMID: 35251134 PMCID: PMC8888898 DOI: 10.3389/fgene.2022.831068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.
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Jouffrey V, Leonard AS, Ahnert SE. Gene duplication and subsequent diversification strongly affect phenotypic evolvability and robustness. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201636. [PMID: 34168886 PMCID: PMC8220273 DOI: 10.1098/rsos.201636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 03/17/2021] [Indexed: 06/13/2023]
Abstract
We study the effects of non-determinism and gene duplication on the structure of genotype-phenotype (GP) maps by introducing a non-deterministic version of the Polyomino self-assembly model. This model has previously been used in a variety of contexts to model the assembly and evolution of protein quaternary structure. Firstly, we show the limit of the current deterministic paradigm which leads to built-in anti-correlation between evolvability and robustness at the genotypic level. We develop a set of metrics to measure structural properties of GP maps in a non-deterministic setting and use them to evaluate the effects of gene duplication and subsequent diversification. Our generalized versions of evolvability and robustness exhibit positive correlation for a subset of genotypes. This positive correlation is only possible because non-deterministic phenotypes can contribute to both robustness and evolvability. Secondly, we show that duplication increases robustness and reduces evolvability initially, but that the subsequent diversification that duplication enables has a stronger, inverse effect, greatly increasing evolvability and reducing robustness relative to their original values.
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Affiliation(s)
- V. Jouffrey
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - A. S. Leonard
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - S. E. Ahnert
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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4
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Evolution in the weak-mutation limit: Stasis periods punctuated by fast transitions between saddle points on the fitness landscape. Proc Natl Acad Sci U S A 2021; 118:2015665118. [PMID: 33472973 PMCID: PMC7848522 DOI: 10.1073/pnas.2015665118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gradual character of evolution is a key feature of the Darwinian worldview. However, macroevolutionary events are often thought to occur in a nongradualist manner, in a regime known as punctuated equilibrium, whereby extended periods of evolutionary stasis are punctuated by rapid transitions between states. Here we analyze a simple mathematical model of population evolution on fitness landscapes and show that, for a large population in the weak-mutation limit, the process of adaptive evolution consists of extended periods of stasis, which the population spends around saddle points on the landscape, interrupted by rapid transitions to new saddle points when a beneficial mutation is fixed. Thus, phenomenologically, the default regime of biological evolution seems to closely resemble punctuated equilibrium. A mathematical analysis of the evolution of a large population under the weak-mutation limit shows that such a population would spend most of the time in stasis in the vicinity of saddle points on the fitness landscape. The periods of stasis are punctuated by fast transitions, in lnNe/s time (Ne, effective population size; s, selection coefficient of a mutation), when a new beneficial mutation is fixed in the evolving population, which accordingly moves to a different saddle, or on much rarer occasions from a saddle to a local peak. Phenomenologically, this mode of evolution of a large population resembles punctuated equilibrium (PE) whereby phenotypic changes occur in rapid bursts that are separated by much longer intervals of stasis during which mutations accumulate but the phenotype does not change substantially. Theoretically, PE has been linked to self-organized criticality (SOC), a model in which the size of “avalanches” in an evolving system is power-law-distributed, resulting in increasing rarity of major events. Here we show, however, that a PE-like evolutionary regime is the default for a very simple model of an evolving population that does not rely on SOC or any other special conditions.
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5
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Trubenová B, Krejca MS, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution 2019; 73:1356-1374. [PMID: 31206653 PMCID: PMC6771940 DOI: 10.1111/evo.13784] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 04/15/2019] [Indexed: 12/11/2022]
Abstract
The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.
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Affiliation(s)
- Barbora Trubenová
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Martin S Krejca
- Hasso Plattner Institute, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany
| | - Per Kristian Lehre
- School of Computer Science, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Timo Kötzing
- Hasso Plattner Institute, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam, Germany
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6
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Kusumi J, Ichinose M, Iizuka M. Effects of gene duplication, epistasis, recombination and gene conversion on the fixation time of compensatory mutations. J Theor Biol 2019; 467:134-141. [PMID: 30738048 DOI: 10.1016/j.jtbi.2019.02.001] [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: 07/28/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 11/16/2022]
Abstract
Gene duplication is one of the major mechanisms of molecular evolution. Gene duplication enables copies of a gene to accumulate mutations through functional redundancy. If a gene encodes a specific protein that interacts with other proteins, RNA, or DNA, the relaxation of selective constraints caused by gene duplication might contribute to the fixation of compensatory mutations that occur at the interacting sites. In this study, we investigate the effect of gene duplication, epistasis among the duplicated copies and gene conversion on the fixation time of compensatory mutations by extending the original model of compensatory evolution proposed by Kimura in 1985. Our simulation results reveal that the time to fixation of compensatory mutations can be decreased remarkably by gene duplication if one of the duplicated loci can completely mask the deleterious effects of a mutation that occurs at the other locus. Conversely, the fixation time can be increased by gene duplication if such functional compensation is weak. We also show that the combination of the degree of functional compensation and the rate of gene conversion between duplicate loci have contrasting effects on the time to fixation of compensatory mutations.
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Affiliation(s)
- Junko Kusumi
- Department of Environmental Changes, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Motoshi Ichinose
- Department of Contemporary Social Studies, Chikushi Jogakuen University, Dazaifu, Japan
| | - Masaru Iizuka
- Professor Emeritus, Kyushu Dental University, Kitakyushu, Japan
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7
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Bourg S, Jacob L, Menu F, Rajon E. Hormonal pleiotropy and the evolution of allocation trade-offs. Evolution 2019; 73:661-674. [PMID: 30734273 DOI: 10.1111/evo.13693] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 01/09/2019] [Indexed: 12/15/2022]
Abstract
Recent empirical evidence suggests that trade-off relationships can evolve, challenging the classical image of their high entrenchment. For energy reliant traits, this relationship should depend on the endocrine system that regulates resource allocation. Here, we model changes in this system by mutating the expression and conformation of its constitutive hormones and receptors. We show that the shape of trade-offs can indeed evolve in this model through the combined action of genetic drift and selection, such that their evolutionarily expected curvature and length depend on context. In particular, the shape of a trade-off should depend on the cost associated with resource storage, itself depending on the traded resource and on the ecological context. Despite this convergence at the phenotypic level, we show that a variety of physiological mechanisms may evolve in similar simulations, suggesting redundancy at the genetic level. This model should provide a useful framework to interpret and unify the overly complex observations of evolutionary endocrinology and evolutionary ecology.
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Affiliation(s)
- Salomé Bourg
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
| | - Laurent Jacob
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
| | - Frédéric Menu
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
| | - Etienne Rajon
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
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8
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Hawkins NJ, Bass C, Dixon A, Neve P. The evolutionary origins of pesticide resistance. Biol Rev Camb Philos Soc 2019; 94:135-155. [PMID: 29971903 PMCID: PMC6378405 DOI: 10.1111/brv.12440] [Citation(s) in RCA: 248] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 06/01/2018] [Accepted: 06/06/2018] [Indexed: 01/24/2023]
Abstract
Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre-existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target-site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non-chemical pest-control methods.
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Affiliation(s)
- Nichola J. Hawkins
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenAL5 4SEU.K.
| | - Chris Bass
- Department of BiosciencesUniversity of Exeter, Penryn CampusCornwallTR10 9FEU.K.
| | - Andrea Dixon
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenAL5 4SEU.K.
- Department of Plant BiologyUniversity of GeorgiaAthensGA 30602U.S.A.
| | - Paul Neve
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenAL5 4SEU.K.
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9
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Koubkova-Yu TCT, Chao JC, Leu JY. Heterologous Hsp90 promotes phenotypic diversity through network evolution. PLoS Biol 2018; 16:e2006450. [PMID: 30439936 PMCID: PMC6264905 DOI: 10.1371/journal.pbio.2006450] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/29/2018] [Accepted: 10/30/2018] [Indexed: 12/24/2022] Open
Abstract
Biological processes in living cells are often carried out by gene networks in which signals and reactions are integrated through network hubs. Despite their functional importance, it remains unclear to what extent network hubs are evolvable and how alterations impact long-term evolution. We investigated these issues using heat shock protein 90 (Hsp90), a central hub of proteostasis networks. When native Hsp90 in Saccharomyces cerevisiae cells was replaced by the ortholog from hypersaline-tolerant Yarrowia lipolytica that diverged from S. cerevisiae about 270 million years ago, the cells exhibited improved growth in hypersaline environments but compromised growth in others, indicating functional divergence in Hsp90 between the two yeasts. Laboratory evolution shows that evolved Y. lipolytica-HSP90–carrying S. cerevisiae cells exhibit a wider range of phenotypic variation than cells carrying native Hsp90. Identified beneficial mutations are involved in multiple pathways and are often pleiotropic. Our results show that cells adapt to a heterologous Hsp90 by modifying different subnetworks, facilitating the evolution of phenotypic diversity inaccessible to wild-type cells. Biological processes in living cells are often carried out by gene networks. Hubs are highly connected network components important for integrating signal inputs and generating responsive functional outputs. Heat shock protein 90 (Hsp90), a versatile hub in the protein homeostasis network, is a molecular chaperone essential for cell viability in all tested eukaryotic cells. In yeast, about a quarter of the expressed proteins are profoundly influenced when Hsp90 activity is reduced. Despite its pivotal role, we found that the function of Hsp90 has diverged between two yeast species, Yarrowia lipolytica and Saccharomyces cerevisiae, which split about 270 million years ago. To understand the impacts and adaptive strategies in cells with an altered network hub, we conducted laboratory evolution experiments using a S. cerevisiae strain in which native Hsp90 is replaced by its counterpart in Y. lipolytica. We observed different fitness gain or loss under various stress conditions in individual evolved clones, suggesting that cells adapted via different evolutionary paths. Genome sequencing and mutation reconstitution experiments show that beneficial mutations occurred in multiple Hsp90-related pathways that interact with each other. Our results show that a perturbed network allows cells to evolve a broader range of phenotypic diversity unavailable to wild-type cells.
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Affiliation(s)
- Tracy Chih-Ting Koubkova-Yu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Jung-Chi Chao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
- * E-mail:
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10
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Nelson P, Masel J. Evolutionary Capacitance Emerges Spontaneously during Adaptation to Environmental Changes. Cell Rep 2018; 25:249-258. [DOI: 10.1016/j.celrep.2018.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/26/2018] [Accepted: 09/04/2018] [Indexed: 11/28/2022] Open
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11
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Drift Barriers to Quality Control When Genes Are Expressed at Different Levels. Genetics 2016; 205:397-407. [PMID: 27838629 DOI: 10.1534/genetics.116.192567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/02/2016] [Indexed: 11/18/2022] Open
Abstract
Gene expression is imperfect, sometimes leading to toxic products. Solutions take two forms: globally reducing error rates, or ensuring that the consequences of erroneous expression are relatively harmless. The latter is optimal, but because it must evolve independently at so many loci, it is subject to a stringent "drift barrier"-a limit to how weak the effects of a deleterious mutation s can be, while still being effectively purged by selection, expressed in terms of the population size N of an idealized population such that purging requires s < -1/N In previous work, only large populations evolved the optimal local solution, small populations instead evolved globally low error rates, and intermediate populations were bistable, with either solution possible. Here, we take into consideration the fact that the effectiveness of purging varies among loci, because of variation in gene expression level, and variation in the intrinsic vulnerabilities of different gene products to error. The previously found dichotomy between the two kinds of solution breaks down, replaced by a gradual transition as a function of population size. In the extreme case of a small enough population, selection fails to maintain even the global solution against deleterious mutations, explaining the nonmonotonic relationship between effective population size and transcriptional error rate that was recently observed in experiments on Escherichia coli, Caenorhabditis elegans, and Buchnera aphidicola.
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12
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Hubert JN, Allal F, Hervet C, Ravakarivelo M, Jeney Z, Vergnet A, Guyomard R, Vandeputte M. How could fully scaled carps appear in natural waters in Madagascar? Proc Biol Sci 2016; 283:rspb.2016.0945. [PMID: 27559059 DOI: 10.1098/rspb.2016.0945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/01/2016] [Indexed: 01/02/2023] Open
Abstract
The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the 'mirror' reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to natural selection could evolve a wild-type-like scale cover in less than 40 generations from standing polygenic genetic variation, confirming similar findings mainly retrieved from model organisms.
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Affiliation(s)
- Jean-Noël Hubert
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - François Allal
- Ifremer, UMR 9190 MARBEC, 34250 Palavas-les-Flots, France
| | - Caroline Hervet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | | | - René Guyomard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France Ifremer, 34250 Palavas-les-Flots, France
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13
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Wilson BA, Garud NR, Feder AF, Assaf ZJ, Pennings PS. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens. Mol Ecol 2015; 25:42-66. [PMID: 26578204 PMCID: PMC4943078 DOI: 10.1111/mec.13474] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/28/2015] [Accepted: 10/08/2015] [Indexed: 01/09/2023]
Abstract
Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.
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Affiliation(s)
- Benjamin A Wilson
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Nandita R Garud
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Alison F Feder
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Zoe J Assaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Pleuni S Pennings
- Department of Biology, San Francisco State University, Room 520, Hensill Hall, 1600 Holloway Ave, San Francisco, CA, 94132, USA
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14
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Pavličev M, Cheverud JM. Constraints Evolve: Context Dependency of Gene Effects Allows Evolution of Pleiotropy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-120213-091721] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mihaela Pavličev
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229;
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15
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Tuğrul M, Paixão T, Barton NH, Tkačik G. Dynamics of Transcription Factor Binding Site Evolution. PLoS Genet 2015; 11:e1005639. [PMID: 26545200 PMCID: PMC4636380 DOI: 10.1371/journal.pgen.1005639] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/09/2015] [Indexed: 11/19/2022] Open
Abstract
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics. Evolution has produced a remarkable diversity of living forms that manifests in qualitative differences as well as quantitative traits. An essential factor that underlies this variability is transcription factor binding sites, short pieces of DNA that control gene expression levels. Nevertheless, we lack a thorough theoretical understanding of the evolutionary times required for the appearance and disappearance of these sites. By combining a biophysically realistic model for how cells read out information in transcription factor binding sites with model for DNA sequence evolution, we explore these timescales and ask what factors crucially affect them. We find that the emergence of binding sites from a random sequence is generically slow under point and insertion/deletion mutational mechanisms. Strong selection, sufficient genomic sequence in which the sites can evolve, the existence of partially decayed old binding sites in the sequence, as well as certain biophysical mechanisms such as cooperativity, can accelerate the binding site gain times and make them consistent with the timescales suggested by comparative analyses of genomic data.
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Affiliation(s)
- Murat Tuğrul
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- * E-mail:
| | - Tiago Paixão
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Gašper Tkačik
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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Santos M, Szathmáry E, Fontanari JF. Phenotypic plasticity, the Baldwin effect, and the speeding up of evolution: The computational roots of an illusion. J Theor Biol 2015; 371:127-36. [DOI: 10.1016/j.jtbi.2015.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
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DeHaan LR, Van Tassel DL. Useful insights from evolutionary biology for developing perennial grain crops. AMERICAN JOURNAL OF BOTANY 2014; 101:1801-1819. [PMID: 25326622 DOI: 10.3732/ajb.1400084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Annual grain crops dominate agricultural landscapes and provide the majority of calories consumed by humanity. Perennial grain crops could potentially ameliorate the land degradation and off-site impacts associated with annual grain cropping. However, herbaceous perennial plants with constitutively high allocation to harvestable seeds are rare to absent in nature. Recent trade-off theory models suggest that rugged fitness landscapes may explain the absence of this form better than sink competition models. Artificial selection for both grain production and multiyear lifespan can lead to more rapid progress in the face of fitness and genetic trade-offs than natural selection but is likely to result in plant types that differ substantially from all current domestic crops. Perennial grain domestication is also likely to require the development of selection strategies that differ from published crop breeding methods, despite their success in improving long-domesticated crops; for this purpose, we have reviewed literature in the areas of population and evolutionary genetics, domestication, and molecular biology. Rapid domestication will likely require genes with large effect that are expected to exhibit strong pleiotropy and epistasis. Cryptic genetic variation will need to be deliberately exposed both to purge mildly deleterious alleles and to generate novel agronomic phenotypes. We predict that perennial grain domestication programs will benefit from population subdivision followed by selection for simple traits in each subpopulation, the evaluation of very large populations, high selection intensity, rapid cycling through generations, and heterosis. The latter may be particularly beneficial in the development of varieties with stable yield and tolerance to crowding.
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Affiliation(s)
- Lee R DeHaan
- The Land Institute, 2440 E. Water Well Rd., Salina, Kansas 67401 USA
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Jones AG, Bürger R, Arnold SJ. Epistasis and natural selection shape the mutational architecture of complex traits. Nat Commun 2014; 5:3709. [PMID: 24828461 PMCID: PMC4024485 DOI: 10.1038/ncomms4709] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 03/24/2014] [Indexed: 01/24/2023] Open
Abstract
The evolutionary trajectories of complex traits are constrained by levels of genetic variation as well as genetic correlations among traits. As the ultimate source of all genetic variation is mutation, the distribution of mutations entering populations profoundly affects standing variation and genetic correlations. Here we use an individual-based simulation model to investigate how natural selection and gene interactions (that is, epistasis) shape the evolution of mutational processes affecting complex traits. We find that the presence of epistasis allows natural selection to mould the distribution of mutations, such that mutational effects align with the selection surface. Consequently, novel mutations tend to be more compatible with the current forces of selection acting on the population. These results suggest that in many cases mutational effects should be seen as an outcome of natural selection rather than as an unbiased source of genetic variation that is independent of other evolutionary processes.
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Affiliation(s)
- Adam G Jones
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, Texas 77843, USA
| | - Reinhard Bürger
- Institut für Mathematik, Universität Wien, Wien 1090, Austria
| | - Stevan J Arnold
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331, USA
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Abstract
Cryptic genetic variation (CGV) is invisible under normal conditions, but it can fuel evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles that are in need of constant suppression. CGV emerges from both neutral and selective processes, and it may inform about how human populations respond to change. CGV facilitates adaptation in experimental settings, but does it have an important role in the real world? Here, we review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution.
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Affiliation(s)
- Annalise B Paaby
- Department of Biology, and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York 10003, USA
| | - Matthew V Rockman
- Department of Biology, and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York 10003, USA
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Calvete JJ. Next-generation snake venomics: protein-locus resolution through venom proteome decomplexation. Expert Rev Proteomics 2014; 11:315-29. [PMID: 24678852 DOI: 10.1586/14789450.2014.900447] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Venom research has been continuously enhanced by technological advances. High-throughput technologies are changing the classical paradigm of hypothesis-driven research to technology-driven approaches. However, the thesis advocated in this paper is that full proteome coverage at locus-specific resolution requires integrating the best of both worlds into a protocol that includes decomplexation of the venom proteome prior to liquid chromatography-tandem mass spectrometry matching against a species-specific transcriptome. This approach offers the possibility of proof-checking the species-specific contig database using proteomics data. Immunoaffinity chromatography constitutes the basis of an antivenomics workflow designed to quantify the extent of cross-reactivity of antivenoms against homologous and heterologous venom toxins. In the author's view, snake venomics and antivenomics form part of a biology-driven conceptual framework to unveil the genesis and natural history of venoms, and their within- and between-species toxicological and immunological divergences and similarities. Understanding evolutionary trends across venoms represents the Rosetta Stone for generating broad-ranging polyspecific antivenoms.
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Affiliation(s)
- Juan J Calvete
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain +34 963 391 778 +34 963 690 800
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