1
|
Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
Collapse
Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| |
Collapse
|
2
|
Hernández L, Aisenberg A, Molina J. Mating plugs and sexual cannibalism in the Colombian orb-web spiderLeucauge mariana. Ethology 2017. [DOI: 10.1111/eth.12697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Linda Hernández
- Centro de Investigaciones en Microbiología y Parasitología Tropical - CIMPAT; Bogotá Universidad de los Andes; Bogotá Colombia
| | - Anita Aisenberg
- Laboratorio de Etología, Ecología y Evolución; Instituto de Investigaciones Biológicas Clemente Estable; Montevideo Uruguay
| | - Jorge Molina
- Centro de Investigaciones en Microbiología y Parasitología Tropical - CIMPAT; Bogotá Universidad de los Andes; Bogotá Colombia
| |
Collapse
|
3
|
Santos M, Sapage M, Matos M, Varela SAM. Mate-choice copying: A fitness-enhancing behavior that evolves by indirect selection. Evolution 2017; 71:1456-1464. [DOI: 10.1111/evo.13235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/27/2017] [Accepted: 03/09/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Mauro Santos
- Departament de Genètica i de Microbiologia; Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Manuel Sapage
- cE3c-Centre for Ecology; Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa; Campo Grande 1749-016 Lisboa Portugal
| | - Margarida Matos
- cE3c-Centre for Ecology; Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa; Campo Grande 1749-016 Lisboa Portugal
| | - Susana A. M. Varela
- cE3c-Centre for Ecology; Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa; Campo Grande 1749-016 Lisboa Portugal
| |
Collapse
|
4
|
Porcelli D, Westram AM, Pascual M, Gaston KJ, Butlin RK, Snook RR. Gene expression clines reveal local adaptation and associated trade-offs at a continental scale. Sci Rep 2016; 6:32975. [PMID: 27599812 PMCID: PMC5013434 DOI: 10.1038/srep32975] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/18/2016] [Indexed: 01/03/2023] Open
Abstract
Local adaptation, where fitness in one environment comes at a cost in another, should lead to spatial variation in trade-offs between life history traits and may be critical for population persistence. Recent studies have sought genomic signals of local adaptation, but often have been limited to laboratory populations representing two environmentally different locations of a species’ distribution. We measured gene expression, as a proxy for fitness, in males of Drosophila subobscura, occupying a 20° latitudinal and 11 °C thermal range. Uniquely, we sampled six populations and studied both common garden and semi-natural responses to identify signals of local adaptation. We found contrasting patterns of investment: transcripts with expression positively correlated to latitude were enriched for metabolic processes, expressed across all tissues whereas negatively correlated transcripts were enriched for reproductive processes, expressed primarily in testes. When using only the end populations, to compare our results to previous studies, we found that locally adaptive patterns were obscured. While phenotypic trade-offs between metabolic and reproductive functions across widespread species are well-known, our results identify underlying genetic and tissue responses at a continental scale that may be responsible for this. This may contribute to understanding population persistence under environmental change.
Collapse
Affiliation(s)
- Damiano Porcelli
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Anja M Westram
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Marta Pascual
- Departament de Genètica, Microbiologia I Estabdistica and IrBio, Universitat de Barcelona, Barcelona 08028, ES
| | - Kevin J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Rhonda R Snook
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| |
Collapse
|
5
|
Xue HJ, Wei JN, Magalhães S, Zhang B, Song KQ, Liu J, Li WZ, Yang XK. Contact pheromones of 2 sympatric beetles are modified by the host plant and affect mate choice. Behav Ecol 2016. [DOI: 10.1093/beheco/arv238] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
6
|
Fragata I, Lopes-Cunha M, Bárbaro M, Kellen B, Lima M, Faria GS, Seabra SG, Santos M, Simões P, Matos M. Keeping your options open: Maintenance of thermal plasticity during adaptation to a stable environment. Evolution 2015; 70:195-206. [PMID: 26626438 DOI: 10.1111/evo.12828] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/19/2015] [Indexed: 12/14/2022]
Abstract
Phenotypic plasticity may allow species to cope with environmental variation. The study of thermal plasticity and its evolution helps understanding how populations respond to variation in temperature. In the context of climate change, it is essential to realize the impact of historical differences in the ability of populations to exhibit a plastic response to thermal variation and how it evolves during colonization of new environments. We have analyzed the real-time evolution of thermal reaction norms of adult and juvenile traits in Drosophila subobscura populations from three locations of Europe in the laboratory. These populations were kept at a constant temperature of 18ºC, and were periodically assayed at three experimental temperatures (13ºC, 18ºC, and 23ºC). We found initial differentiation between populations in thermal plasticity as well as evolutionary convergence in the shape of reaction norms for some adult traits, but not for any of the juvenile traits. Contrary to theoretical expectations, an overall better performance of high latitude populations across temperatures in early generations was observed. Our study shows that the evolution of thermal plasticity is trait specific, and that a new stable environment did not limit the ability of populations to cope with environmental challenges.
Collapse
Affiliation(s)
- Inês Fragata
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Miguel Lopes-Cunha
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Margarida Bárbaro
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Bárbara Kellen
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Margarida Lima
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Gonçalo S Faria
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Sofia G Seabra
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade 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, Bellaterra, Barcelona, Spain
| | - Pedro Simões
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Margarida Matos
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| |
Collapse
|