1
|
Hu G, Wang Y, Liu X, Strube ML, Wang B, Kovács ÁT. Species and condition shape the mutational spectrum in experimentally evolved biofilms. mSystems 2023; 8:e0054823. [PMID: 37768063 PMCID: PMC10654089 DOI: 10.1128/msystems.00548-23] [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: 05/27/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Biofilm formation is a vital factor for the survival and adaptation of bacteria in diverse environmental niches. Experimental evolution combined with the advancement of whole-population genome sequencing provides us a powerful tool to understand the genomic dynamic of evolutionary adaptation to different environments, such as during biofilm development. Previous studies described the genetic and phenotypic changes of selected clones from experimentally evolved Bacillus thuringiensis and Bacillus subtilis that were adapted under abiotic and biotic biofilm conditions. However, the full understanding of the dynamic evolutionary landscapes was lacking. Furthermore, the differences and similarities of adaptive mechanisms in B. thuringiensis and B. subtilis were not identified. To overcome these limitations, we performed longitudinal whole-population genome sequencing to study the underlying genetic dynamics at high resolution. Our study provides the first comprehensive mutational landscape of two bacterial species' biofilms that is adapted to an abiotic and biotic surface.
Collapse
Affiliation(s)
- Guohai Hu
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Yue Wang
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- BGI Research, Beijing, China
| | - Xin Liu
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- BGI Research, Beijing, China
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Bo Wang
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI Research, Shenzhen, China
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
- Institute of Biology, Leiden University, Leiden, The Netherlands
| |
Collapse
|
2
|
Venkataram S, Kryazhimskiy S. Evolutionary repeatability of emergent properties of ecological communities. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220047. [PMID: 37004728 PMCID: PMC10067272 DOI: 10.1098/rstb.2022.0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 04/04/2023] Open
Abstract
Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
Collapse
Affiliation(s)
- Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, UC San Diego, La Jolla, CA 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, UC San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
3
|
Bafort Q, Prost L, Aydogdu E, Van de Vloet A, Casteleyn G, Van de Peer Y, De Clerck O. Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas. Methods Mol Biol 2023; 2545:351-372. [PMID: 36720822 DOI: 10.1007/978-1-0716-2561-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related Chlamydomonas experiment. These steps include strain selection, ploidy determination, different methods of making diplo- and polyploid Chlamydomonas cells, replication, culturing conditions, preservation, and the ways to quantify phenotypic and genotypic change.
Collapse
Affiliation(s)
- Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Lucas Prost
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Eylem Aydogdu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Antoine Van de Vloet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Griet Casteleyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | |
Collapse
|
4
|
Bisschop K, Blankers T, Mariën J, Wortel MT, Egas M, Groot AT, Visser ME, Ellers J. Population bottleneck has only marginal effect on fitness evolution and its repeatability in dioecious Caenorhabditis elegans. Evolution 2022; 76:1896-1904. [PMID: 35795889 PMCID: PMC9545033 DOI: 10.1111/evo.14556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
The predictability of evolution is expected to depend on the relative contribution of deterministic and stochastic processes. This ratio is modulated by effective population size. Smaller effective populations harbor less genetic diversity and stochastic processes are generally expected to play a larger role, leading to less repeatable evolutionary trajectories. Empirical insight into the relationship between effective population size and repeatability is limited and focused mostly on asexual organisms. Here, we tested whether fitness evolution was less repeatable after a population bottleneck in obligately outcrossing populations of Caenorhabditis elegans. Replicated populations founded by 500, 50, or five individuals (no/moderate/strong bottleneck) were exposed to a novel environment with a different bacterial prey. As a proxy for fitness, population size was measured after one week of growth before and after 15 weeks of evolution. Surprisingly, we found no significant differences among treatments in their fitness evolution. Even though the strong bottleneck reduced the relative contribution of selection to fitness variation, this did not translate to a significant reduction in the repeatability of fitness evolution. Thus, although a bottleneck reduced the contribution of deterministic processes, we conclude that the predictability of evolution may not universally depend on effective population size, especially in sexual organisms.
Collapse
Affiliation(s)
- Karen Bisschop
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdam1090 GEThe Netherlands,Origins CenterGroningenThe Netherlands,Terrestrial Ecology UnitGhent UniversityGhent9000Belgium,Laboratory of Aquatic BiologyKU Leuven KulakKortrijk8500Belgium
| | - Thomas Blankers
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdam1090 GEThe Netherlands,Origins CenterGroningenThe Netherlands
| | - Janine Mariën
- Animal EcologyVU AmsterdamAmsterdam1081 HVThe Netherlands
| | - Meike T. Wortel
- Swammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdam1090 GEThe Netherlands
| | - Martijn Egas
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdam1090 GEThe Netherlands
| | - Astrid T. Groot
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdam1090 GEThe Netherlands
| | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABThe Netherlands
| | | |
Collapse
|
5
|
Mitchell N, Luu H, Owens GL, Rieseberg LH, Whitney KD. Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus). Evolution 2022; 76:1512-1528. [PMID: 35665925 PMCID: PMC9544064 DOI: 10.1111/evo.14536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 01/22/2023]
Abstract
To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than that of nonhybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to nonhybrid controls. We created hybrids between Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both hybrids and nonhybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus nonrepeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time, while controls did not, although trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus nonhybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.
Collapse
Affiliation(s)
- Nora Mitchell
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA,Department of BiologyUniversity of Wisconsin – Eau ClaireEau ClaireWisconsinUSA
| | - Hoang Luu
- Department of Environmental and Plant BiologyOhio UniversityAthensOhioUSA
| | - Gregory L. Owens
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaBritish ColumbiaCanada
| | | |
Collapse
|
6
|
Melero-Jiménez IJ, Bañares-España E, García-Sánchez MJ, Flores-Moya A. Changes in the growth rate of Chlamydomonas reinhardtii under long-term selection by temperature and salinity: Acclimation vs. evolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153467. [PMID: 35093356 DOI: 10.1016/j.scitotenv.2022.153467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
We investigated the roles of acclimation and different components involved in evolution (adaptation, chance and history) on the changes in the growth rate of the model freshwater microalga Chlamydomonas reinhardtii P. A. Dang. exposed to selective temperature and salinity. Three C. reinhardtii strains previously grown during one year in freshwater medium and 20 °C were exposed to 5 °C temperature increase and a salinity of 5 g L-1 NaCl. Cultures under each selective scenario and in combination (increase of salinity and temperature), were propagated until growth rate achieved an invariant mean value for 6 months (100-350 generations, varying as a function of scenario and strain). The changes of the growth rate under increased temperature were due to both adaptation and acclimation, as well as history. However, acclimation was the only mechanism detected under salinity increase as well as in the selective scenario of both temperature and salinity, suggesting that genetic variability would not allow survival at salinity higher than that to which experimental populations were exposed. Therefore, it could be hypothesized that under a global change scenario an increase in salinity would be a greater challenge than warming for some freshwater phytoplankton.
Collapse
Affiliation(s)
- Ignacio J Melero-Jiménez
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain.
| | - Elena Bañares-España
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - María J García-Sánchez
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Antonio Flores-Moya
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| |
Collapse
|
7
|
Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution. Nat Ecol Evol 2022; 6:439-447. [PMID: 35241808 DOI: 10.1038/s41559-022-01669-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022]
Abstract
Mutations with large fitness benefits and mutations occurring at high rates may both cause parallel evolution, but their contribution is predicted to depend on population size. Moreover, high-rate and large-benefit mutations may have different long-term adaptive consequences. We show that small and 100-fold larger bacterial populations evolve resistance to a β-lactam antibiotic by using similar numbers, but different types of mutations. Small populations frequently substitute similar high-rate structural variants and loss-of-function point mutations, including the deletion of a low-activity β-lactamase, and evolve modest resistance levels. Large populations more often use low-rate, large-benefit point mutations affecting the same targets, including mutations activating the β-lactamase and other gain-of-function mutations, leading to much higher resistance levels. Our results demonstrate the separation by clonal interference of mutation classes with divergent adaptive consequences, causing a shift from high-rate to large-benefit mutations with increases in population size.
Collapse
|
8
|
Soares ADA, Wardil L, Klaczko LB, Dickman R. Hidden role of mutations in the evolutionary process. Phys Rev E 2021; 104:044413. [PMID: 34781575 DOI: 10.1103/physreve.104.044413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 10/05/2021] [Indexed: 11/07/2022]
Abstract
Mutations not only alter allele frequencies in a genetic pool but may also determine the fate of an evolutionary process. Here we study which allele fixes in a one-step, one-way model including the wild type and two adaptive mutations. We study the effect of the four basic evolutionary mechanisms-genetic drift, natural selection, mutation, and gene flow-on mutant fixation and its kinetics. Determining which allele is more likely to fix is not simply a question of comparing fitnesses and mutation rates. For instance, if the allele of interest is less fit than the other, then not only must it have a greater mutation rate, but also its mutation rate must exceed a specific threshold for it to prevail. We find exact expressions for such conditions. Our conclusions are based on the mathematical description of two extreme but important regimes, as well as on simulations.
Collapse
Affiliation(s)
- Alexandre de Aquino Soares
- Departamento de Física, Instituto de Ciências Exatas (ICEx), Universidade Federal de Minas Gerais (UFMG), 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Lucas Wardil
- Departamento de Física, Instituto de Ciências Exatas (ICEx), Universidade Federal de Minas Gerais (UFMG), 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Louis Bernard Klaczko
- Departmento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (Unicamp), C. P. 6109, 13083-970 Campinas, São Paulo, Brazil
| | - Ronald Dickman
- Departamento de Física and National Institute of Science and Technology for Complex Systems, Instituto de Ciências Exatas (ICEx), Universidade Federal de Minas Gerais (UFMG), C. P. 702, 30123-970 Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
9
|
Sierocinski P, Soria Pascual J, Padfield D, Salter M, Buckling A. The impact of propagule pressure on whole community invasions in biomethane-producing communities. iScience 2021; 24:102659. [PMID: 34151242 PMCID: PMC8192723 DOI: 10.1016/j.isci.2021.102659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/29/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
Microbes can invade as whole communities, but the ecology of whole community invasions is poorly understood. Here, we investigate how invader propagule pressure (the number of invading organisms) affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of propagule pressure, which varied between 0.01 and 10% of the size resident community. Invasion resulted in enhanced biogas production (to the level of the pure invading community) but only when propagule pressure was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower richness of invading taxa at lower propagule pressures, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings. Complex communities can successfully invade other communities Invasions change the community composition independently of propagule pressure Number of taxa invading increases with increased propagule pressure Larger propagule pressure impacts both the community structure and function
Collapse
Affiliation(s)
- Pawel Sierocinski
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | - Jesica Soria Pascual
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | - Daniel Padfield
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | | | - Angus Buckling
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| |
Collapse
|
10
|
Ruelens P, de Visser JAGM. Clonal Interference and Mutation Bias in Small Bacterial Populations in Droplets. Genes (Basel) 2021; 12:223. [PMID: 33557200 PMCID: PMC7913962 DOI: 10.3390/genes12020223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 01/19/2023] Open
Abstract
Experimental evolution studies have provided key insights into the fundamental mechanisms of evolution. One striking observation is that parallel and convergent evolution during laboratory evolution can be surprisingly common. However, these experiments are typically performed with well-mixed cultures and large effective population sizes, while pathogenic microbes typically experience strong bottlenecks during infection or drug treatment. Yet, our knowledge about adaptation in very small populations, where selection strength and mutation supplies are limited, is scant. In this study, wild-type and mutator strains of the bacterium Escherichia coli were evolved for about 100 generations towards increased resistance to the β-lactam antibiotic cefotaxime in millifluidic droplets of 0.5 µL and effective population size of approximately 27,000 cells. The small effective population size limited the adaptive potential of wild-type populations, where adaptation was limited to inactivating mutations, which caused the increased production of outer-membrane vesicles, leading to modest fitness increases. In contrast, mutator clones with an average of ~30-fold higher mutation rate adapted much faster by acquiring both inactivating mutations of an outer-membrane porin and particularly inactivating and gain-of-function mutations, causing the upregulation or activation of a common efflux pump, respectively. Our results demonstrate how in very small populations, clonal interference and mutation bias together affect the choice of adaptive trajectories by mediating the balance between high-rate and large-benefit mutations.
Collapse
|
11
|
Wein T, Dagan T. The Effect of Population Bottleneck Size and Selective Regime on Genetic Diversity and Evolvability in Bacteria. Genome Biol Evol 2019; 11:3283-3290. [PMID: 31688900 PMCID: PMC7145630 DOI: 10.1093/gbe/evz243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2019] [Indexed: 12/20/2022] Open
Abstract
Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity, and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. In this study, we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (small, medium, and large) in two temperature regimes (37 °C and 20 °C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity regardless the bottleneck size; hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.
Collapse
Affiliation(s)
- Tanita Wein
- Institute of Microbiology, Kiel University, Germany
| | - Tal Dagan
- Institute of Microbiology, Kiel University, Germany
| |
Collapse
|
12
|
Simões P, Fragata I, Santos J, Santos MA, Santos M, Rose MR, Matos M. How phenotypic convergence arises in experimental evolution. Evolution 2019; 73:1839-1849. [DOI: 10.1111/evo.13806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/12/2019] [Accepted: 06/15/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Pedro Simões
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de Lisboa Campo Grande 1749‐016 Lisboa Portugal
| | - Inês Fragata
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de Lisboa Campo Grande 1749‐016 Lisboa Portugal
| | - Josiane Santos
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de Lisboa Campo Grande 1749‐016 Lisboa Portugal
| | - Marta A. Santos
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de Lisboa Campo Grande 1749‐016 Lisboa Portugal
| | - Mauro Santos
- Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE)Universitat Autonòma de Barcelona 08193 Barcelona Spain
| | - Michael R. Rose
- Department of Ecology and Evolutionary BiologyUniversity of California, Irvine Irvine California 92697
| | - Margarida Matos
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de Lisboa Campo Grande 1749‐016 Lisboa Portugal
| |
Collapse
|
13
|
Chavhan YD, Ali SI, Dey S. Larger Numbers Can Impede Adaptation in Asexual Populations despite Entailing Greater Genetic Variation. Evol Biol 2019. [DOI: 10.1007/s11692-018-9467-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
14
|
Fragata I, Blanckaert A, Dias Louro MA, Liberles DA, Bank C. Evolution in the light of fitness landscape theory. Trends Ecol Evol 2019; 34:69-82. [DOI: 10.1016/j.tree.2018.10.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 01/28/2023]
|
15
|
Effects of Transmission Bottlenecks on the Diversity of Influenza A Virus. Genetics 2018; 210:1075-1088. [PMID: 30181193 DOI: 10.1534/genetics.118.301510] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/27/2018] [Indexed: 11/18/2022] Open
Abstract
We investigate the fate of de novo mutations that occur during the in-host replication of a pathogenic virus, predicting the probability that such mutations are passed on during disease transmission to a new host. Using influenza A virus as a model organism, we develop a life-history model of the within-host dynamics of the infection, deriving a multitype branching process with a coupled deterministic model to capture the population of available target cells. We quantify the fate of neutral mutations and mutations affecting five life-history traits: clearance, attachment, budding, cell death, and eclipse phase timing. Despite the severity of disease transmission bottlenecks, our results suggest that in a single transmission event, several mutations that appeared de novo in the donor are likely to be transmitted to the recipient. Even in the absence of a selective advantage for these mutations, the sustained growth phase inherent in each disease transmission cycle generates genetic diversity that is not eliminated during the transmission bottleneck.
Collapse
|
16
|
Vogwill T, Phillips RL, Gifford DR, MacLean RC. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution. Proc Biol Sci 2017; 283:rspb.2016.0749. [PMID: 27466449 PMCID: PMC4971204 DOI: 10.1098/rspb.2016.0749] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/04/2016] [Indexed: 12/30/2022] Open
Abstract
There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale. However, bottlenecking had a profound impact on the genes involved in antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions.
Collapse
Affiliation(s)
- Tom Vogwill
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Robyn L Phillips
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Danna R Gifford
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - R Craig MacLean
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| |
Collapse
|
17
|
Vahdati AR, Wagner A. Population Size Affects Adaptation in Complex Ways: Simulations on Empirical Adaptive Landscapes. Evol Biol 2017. [DOI: 10.1007/s11692-017-9440-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
18
|
Kraemer SA, Böndel KB, Ness RW, Keightley PD, Colegrave N. Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii. Evolution 2017; 71:2918-2929. [PMID: 28884790 PMCID: PMC5765464 DOI: 10.1111/evo.13360] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 01/08/2023]
Abstract
Although all genetic variation ultimately stems from mutations, their properties are difficult to study directly. Here, we used multiple mutation accumulation (MA) lines derived from five genetic backgrounds of the green algae Chlamydomonas reinhardtii that have been previously subjected to whole genome sequencing to investigate the relationship between the number of spontaneous mutations and change in fitness from a nonevolved ancestor. MA lines were on average less fit than their ancestors and we detected a significantly negative correlation between the change in fitness and the total number of accumulated mutations in the genome. Likewise, the number of mutations located within coding regions significantly and negatively impacted MA line fitness. We used the fitness data to parameterize a maximum likelihood model to estimate discrete categories of mutational effects, and found that models containing one to two mutational effect categories (one neutral and one deleterious category) fitted the data best. However, the best‐fitting mutational effects models were highly dependent on the genetic background of the ancestral strain.
Collapse
Affiliation(s)
- Susanne A Kraemer
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH93FL, United Kingdom
| | - Katharina B Böndel
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH93FL, United Kingdom
| | - Robert W Ness
- Department of Biology, William G. Davis Building, University of Toronto, Mississuaga L5L1C6, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH93FL, United Kingdom
| | - Nick Colegrave
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH93FL, United Kingdom
| |
Collapse
|
19
|
Vahdati AR, Sprouffske K, Wagner A. Effect of Population Size and Mutation Rate on the Evolution of RNA Sequences on an Adaptive Landscape Determined by RNA Folding. Int J Biol Sci 2017; 13:1138-1151. [PMID: 29104505 PMCID: PMC5666329 DOI: 10.7150/ijbs.19436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/05/2017] [Indexed: 02/04/2023] Open
Abstract
The dynamics of populations evolving on an adaptive landscape depends on multiple factors, including the structure of the landscape, the rate of mutations, and effective population size. Existing theoretical work often makes ad hoc and simplifying assumptions about landscape structure, whereas experimental work can vary important parameters only to a limited extent. We here overcome some of these limitations by simulating the adaptive evolution of RNA molecules, whose fitness is determined by the thermodynamics of RNA secondary structure folding. We study the influence of mutation rates and population sizes on final mean population fitness, on the substitution rates of mutations, and on population diversity. We show that evolutionary dynamics cannot be understood as a function of mutation rate µ, population size N, or population mutation rate Nµ alone. For example, at a given mutation rate, clonal interference prevents the fixation of beneficial mutations as population size increases, but larger populations still arrive at a higher mean fitness. In addition, at the highest population mutation rates we study, mean final fitness increases with population size, because small populations are driven to low fitness by the relatively higher incidence of mutations they experience. Our observations show that mutation rate and population size can interact in complex ways to influence the adaptive dynamics of a population on a biophysically motivated fitness landscape.
Collapse
Affiliation(s)
- Ali R Vahdati
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kathleen Sprouffske
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, USA
| |
Collapse
|
20
|
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.
Collapse
Affiliation(s)
- Thomas van Dijk
- Laboratory of Genetics, Wageningen University, Wageningen, Netherlands. These authors contributed equally
| | | | | | | | | |
Collapse
|
21
|
Jablonski D. Approaches to Macroevolution: 1. General Concepts and Origin of Variation. Evol Biol 2017; 44:427-450. [PMID: 29142333 PMCID: PMC5661017 DOI: 10.1007/s11692-017-9420-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022]
Abstract
Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities-i.e., an uneven density distribution-of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, "punctuated equilibrium" and "phyletic gradualism" simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.
Collapse
Affiliation(s)
- David Jablonski
- Department of Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637 USA
| |
Collapse
|
22
|
Predictable phenotypic, but not karyotypic, evolution of populations with contrasting initial history. Sci Rep 2017; 7:913. [PMID: 28424494 PMCID: PMC5430419 DOI: 10.1038/s41598-017-00968-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/21/2017] [Indexed: 02/07/2023] Open
Abstract
The relative impact of selection, chance and history will determine the predictability of evolution. There is a lack of empirical research on this subject, particularly in sexual organisms. Here we use experimental evolution to test the predictability of evolution. We analyse the real-time evolution of Drosophila subobscura populations derived from contrasting European latitudes placed in a novel laboratory environment. Each natural population was sampled twice within a three-year interval. We study evolutionary responses at both phenotypic (life-history, morphological and physiological traits) and karyotypic levels for around 30 generations of laboratory culture. Our results show (1) repeatable historical effects between years in the initial state, at both phenotypic and karyotypic levels; (2) predictable phenotypic evolution with general convergence except for body size; and (3) unpredictable karyotypic evolution. We conclude that the predictability of evolution is contingent on the trait and level of organization, highlighting the importance of studying multiple biological levels with respect to evolutionary patterns.
Collapse
|
23
|
Lachapelle J, Colegrave N. The effect of sex on the repeatability of evolution in different environments. Evolution 2017; 71:1075-1087. [PMID: 28181234 DOI: 10.1111/evo.13198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/25/2017] [Indexed: 12/28/2022]
Abstract
The adaptive function of sex has been extensively studied, while less consideration has been given to the potential downstream consequences of sex on evolution. Here, we investigate one such potential consequence, the effect of sex on the repeatability of evolution. By affecting the repeatability of evolution, sex could have important implications for biodiversity, and for our ability to make predictions about the outcome of environmental change. We allowed asexual and sexual populations of Chlamydomonas reinhardtii to evolve in novel environments and monitored both their change in fitness and variance in fitness after evolution. Sex affected the repeatability of evolution by changing the importance of the effect of selection, chance, and ancestral constraints on the outcome of the evolutionary process. In particular, the effects of sex were highly dependent on the initial genetic composition of the population and on the environment. Given the lack of a consistent effect of sex on repeatability across the environments used here, further studies to dissect in more detail the underlying reasons for these differences as well as studies in additional environments are required if we are to have a general understanding of the effects of sex on the repeatability of evolution.
Collapse
Affiliation(s)
- Josianne Lachapelle
- Department of Biology, University of Toronto Mississauga, William G. Davis Building, 3359 Mississauga Road, Mississauga, ON, Canada, L5L 1C6.,School of Biological Sciences, University of Edinburgh, King's Buildings, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, UK, EH9 3FL
| | - Nick Colegrave
- School of Biological Sciences, University of Edinburgh, King's Buildings, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, UK, EH9 3FL
| |
Collapse
|
24
|
LaBar T, Adami C. Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms. PLoS Comput Biol 2016; 12:e1005066. [PMID: 27923053 PMCID: PMC5140054 DOI: 10.1371/journal.pcbi.1005066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/18/2016] [Indexed: 12/02/2022] Open
Abstract
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population size decreases, selection weakens and genetic drift grows in importance. Because of this relationship, many theories invoke a role for population size in the evolution of complexity. Such theories are difficult to test empirically because of the time required for the evolution of complexity in biological populations. Here, we used digital experimental evolution to test whether large or small asexual populations tend to evolve greater complexity. We find that both small and large-but not intermediate-sized-populations are favored to evolve larger genomes, which provides the opportunity for subsequent increases in phenotypic complexity. However, small and large populations followed different evolutionary paths towards these novel traits. Small populations evolved larger genomes by fixing slightly deleterious insertions, while large populations fixed rare beneficial insertions that increased genome size. These results demonstrate that genetic drift can lead to the evolution of complexity in small populations and that purifying selection is not powerful enough to prevent the evolution of complexity in large populations.
Collapse
Affiliation(s)
- Thomas LaBar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Ecology, Evolutionary Biology, and Behavior Program, East Lansing, Michigan, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| | - Christoph Adami
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Ecology, Evolutionary Biology, and Behavior Program, East Lansing, Michigan, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of America
| |
Collapse
|