1
|
McLean DJ, Herberstein ME, Kokko H. Asymmetric arms races between predators and prey: a tug of war between the life-dinner principle and the rare-enemy principle. Proc Biol Sci 2024; 291:20241052. [PMID: 39378992 PMCID: PMC11461046 DOI: 10.1098/rspb.2024.1052] [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: 09/12/2023] [Revised: 07/15/2024] [Accepted: 09/05/2024] [Indexed: 10/10/2024] Open
Abstract
Antagonistic co-evolution can be asymmetric, where one species lags behind another. Asymmetry in a predator-prey context is expressed by the 'life-dinner principle', a classic informal model predicting that prey should be in some sense ahead in this arms race, since prey are running for their lives, while predators lag as they only run for their dinner. The model has undergone surprisingly little theoretical scrutiny. We derive analytical models that show coevolutionary outcomes do not always align with the life-dinner principle. Our results show that other important asymmetries can easily reverse the outcome, especially the rare-enemy principle: predators are usually outnumbered by their prey, sometimes substantially (trophic asymmetry), which can make selection on prey relatively weak. We additionally show that the antagonists typically exhibit different evolutionary responses to a situation where both predator and prey start out as equally fast runners. Although predators sometimes become so efficient that attacks always succeed, attack success often reaches a stable intermediate value. We conclude that the life-dinner principle has some validity as a metaphor, but its effect is of an 'all else being equal' type, which is surprisingly easily overridden by other features of the evolutionary dynamics.
Collapse
Affiliation(s)
- Donald James McLean
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Marie E. Herberstein
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
- Leibniz Institute of the Analysis of Biodiversity Change, Hamburg20146, Germany
- Institute of Animal Cell and Systems Biology, University of Hamburg, Hamburg20148, Germany
| | - Hanna Kokko
- Department of Evolutionary and Environmental Studies, University of Zurich, Zurich8057, Switzerland
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Mainz55128, Germany
- Institute for Quantitative and Computational Biosciences, Mainz55128, Germany
| |
Collapse
|
2
|
Peters MAE, Mideo N, MacPherson A. The maintenance of genetic diversity under host-parasite coevolution in finite, structured populations. J Evol Biol 2023; 36:1328-1341. [PMID: 37610056 DOI: 10.1111/jeb.14207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 08/24/2023]
Abstract
As a corollary to the Red Queen hypothesis, host-parasite coevolution has been hypothesized to maintain genetic variation in both species. Recent theoretical work, however, suggests that reciprocal natural selection alone is insufficient to maintain variation at individual loci. As highlighted by our brief review of the theoretical literature, models of host-parasite coevolution often vary along multiple axes (e.g. inclusion of ecological feedbacks or abiotic selection mosaics), complicating a comprehensive understanding of the effects of interacting evolutionary processes on diversity. Here we develop a series of comparable models to explore the effect of interactions between spatial structures and antagonistic coevolution on genetic diversity. Using a matching alleles model in finite populations connected by migration, we find that, in contrast to panmictic populations, coevolution in a spatially structured environment can maintain genetic variation relative to neutral expectations with migration alone. These results demonstrate that geographic structure is essential for understanding the effect of coevolution on biological diversity.
Collapse
Affiliation(s)
- Madeline A E Peters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ailene MacPherson
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| |
Collapse
|
3
|
Oyejobi GK, Zhang X, Xiong D, Ogolla F, Xue H, Wei H. Phage-bacterial evolutionary interactions: experimental models and complications. Crit Rev Microbiol 2023; 49:283-296. [PMID: 35358006 DOI: 10.1080/1040841x.2022.2052793] [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: 11/03/2022]
Abstract
Phage treatment of bacterial infections has offered some hope even as the crisis of antimicrobial resistance continues to be on the rise. However, bacterial resistance to phage is another looming challenge capable of undermining the effectiveness of phage therapy. Moreover, the consideration of including phage therapy in modern medicine calls for more careful research around every aspect of phage study. In an attempt to adequately prepare for the events of phage resistance, many studies have attempted to experimentally evolve phage resistance in different bacterial strains, as well as train phages to evolve counter-infectivity of resistant bacterial mutants, in view of answering such questions as coevolutionary dynamics between phage and bacteria, mechanisms of phage resistance, fitness costs of phage resistance on bacteria, etc. In this review, we summarised many such studies and by careful examination, highlighted critical issues to the outcome of phage therapy. We also discuss the insufficiency of many of these in vitro studies to represent actual disease conditions during phage application, alongside other complications that exist in phage-bacterial evolutionary interactions. Conclusively, we present the exploitation of phage-bacterial interactions for successful infection managements, as well as some future perspectives to direct phage research.
Collapse
Affiliation(s)
- Greater Kayode Oyejobi
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China.,Department of Microbiology, Osun State University, Osogbo, Nigeria.,Organization of African Academic Doctors, Nairobi, Kenya
| | - Xiaoxu Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Dongyan Xiong
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Faith Ogolla
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China.,Organization of African Academic Doctors, Nairobi, Kenya.,Sino-Africa Joint Research Center, Nairobi, Kenya
| | - Heng Xue
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Nairobi, Kenya
| |
Collapse
|
4
|
Gómez P, Hall AR, Paterson S, Buckling A. Rapid decline of adaptation of Pseudomonas fluorescens to soil biotic environment. Biol Lett 2022; 18:20210593. [PMID: 35259940 PMCID: PMC8905175 DOI: 10.1098/rsbl.2021.0593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Interactions between microbes can both constrain and enhance their adaptation to the environment. However, most studies to date have employed simplified microbial communities and environmental conditions. We determined how the presence of a commercial potting compost microbial community affected adaptation of the soil bacterium Pseudomonas fluorescens SBW25 in potting compost. Pseudomonas fluorescens clones isolated from populations evolved in both the presence and absence of the community showed similar fitness increases when measured in the absence of the community. This suggests the presence of the community did not constrain adaptation. By contrast, fitness measured in the presence of the community increased for community-evolved populations, but decreased below the ancestral state for populations evolved in the absence of the community. This suggests some, but not all, mutations that were beneficial with respect to the abiotic environment were costly in the presence of the community, with the former selected against in the presence of the community. Whole-genome sequencing supports this interpretation: most mutations underpinning fitness changes were clone-specific, suggesting multiple genetic pathways to adaptation. Such extreme mutational effects have not been observed in comparable in vitro studies, suggesting that caution is needed when extrapolating results from simplified in vitro systems to natural contexts.
Collapse
Affiliation(s)
- Pedro Gómez
- Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
| | - Alex R Hall
- Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
| | - Steve Paterson
- Department of Ecology, Evolution and Behaviour, University of Liverpool, Liverpool, UK
| | - Angus Buckling
- Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
| |
Collapse
|
5
|
Eyck HJF, Brown GP, Rollins LA, Shine R. In an arms race between host and parasite, a lungworm's ability to infect a toad is determined by host susceptibility not parasite preference. Biol Lett 2022; 18:20210552. [PMID: 35259944 PMCID: PMC8905180 DOI: 10.1098/rsbl.2021.0552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolutionary arms races can alter both parasite infectivity and host resistance, and it is difficult to separate the effects of these twin determinants of infection outcomes. We used a co-introduced, invasive host-parasite system (the lungworm Rhabdias pseudosphaerocephala and cane toads Rhinella marina), where rapid adaptation and dispersal have led to population differences in infection resistance. We quantified behavioural responses of parasite larvae to skin-chemical cues of toads from different invasive populations, and rates at which juvenile hosts became infected following standardized exposure to lungworms. Chemical cues from toad skin altered host-seeking behaviour by parasites, similarly among populations. The number of infection attempts (parasite larvae entering the host's body) also did not differ between populations, but rates of successful infection (establishment of adult worm in host lungs) were higher for range-edge toads than for range-core conspecifics. Thus, lower resistance to parasite infection in range-edge juvenile toads appears to be due to less effective immune defences of the host rather than differential behavioural responses of the parasite. In this ongoing host-parasite arms race, changing outcomes appear to be driven by shifts in host immunocompetence.
Collapse
Affiliation(s)
- Harrison J F Eyck
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Gregory P Brown
- Department of Biological Sciences, Macquarie University, New South Wales, Australia
| | - Lee A Rollins
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, New South Wales, Australia
| |
Collapse
|
6
|
Buckingham LJ, Ashby B. Coevolutionary theory of hosts and parasites. J Evol Biol 2022; 35:205-224. [PMID: 35030276 PMCID: PMC9305583 DOI: 10.1111/jeb.13981] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/14/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Host and parasite evolution are closely intertwined, with selection for adaptations and counter-adaptations forming a coevolutionary feedback loop. Coevolutionary dynamics are often difficult to intuit due to these feedbacks and are hard to demonstrate empirically in most systems. Theoretical models have therefore played a crucial role in shaping our understanding of host-parasite coevolution. Theoretical models vary widely in their assumptions, approaches and aims, and such variety makes it difficult, especially for non-theoreticians and those new to the field, to: (1) understand how model approaches relate to one another; (2) identify key modelling assumptions; (3) determine how model assumptions relate to biological systems; and (4) reconcile the results of different models with contrasting assumptions. In this review, we identify important model features, highlight key results and predictions and describe how these pertain to model assumptions. We carry out a literature survey of theoretical studies published since the 1950s (n = 219 papers) to support our analysis. We identify two particularly important features of models that tend to have a significant qualitative impact on the outcome of host-parasite coevolution: population dynamics and the genetic basis of infection. We also highlight the importance of other modelling features, such as stochasticity and whether time proceeds continuously or in discrete steps, that have received less attention but can drastically alter coevolutionary dynamics. We finish by summarizing recent developments in the field, specifically the trend towards greater model complexity, and discuss likely future directions for research.
Collapse
Affiliation(s)
- Lydia J. Buckingham
- Department of Mathematical SciencesUniversity of BathBathUK
- Milner Centre for EvolutionUniversity of BathBathUK
| | - Ben Ashby
- Department of Mathematical SciencesUniversity of BathBathUK
- Milner Centre for EvolutionUniversity of BathBathUK
| |
Collapse
|
7
|
Dewald-Wang EA, Parr N, Tiley K, Lee A, Koskella B. Multiyear Time-Shift Study of Bacteria and Phage Dynamics in the Phyllosphere. Am Nat 2022; 199:126-140. [DOI: 10.1086/717181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
8
|
Pérez-González J, Carranza J, Martínez R, Benítez-Medina JM. Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis. Animals (Basel) 2021; 11:1630. [PMID: 34072907 PMCID: PMC8229303 DOI: 10.3390/ani11061630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.
Collapse
Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Córdoba, Spain;
| | - Remigio Martínez
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
| | - José Manuel Benítez-Medina
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
| |
Collapse
|
9
|
The Maze Pathway of Coevolution: A Critical Review over the Leishmania and Its Endosymbiotic History. Genes (Basel) 2021; 12:genes12050657. [PMID: 33925663 PMCID: PMC8146029 DOI: 10.3390/genes12050657] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 01/10/2023] Open
Abstract
The description of the genus Leishmania as the causative agent of leishmaniasis occurred in the modern age. However, evolutionary studies suggest that the origin of Leishmania can be traced back to the Mesozoic era. Subsequently, during its evolutionary process, it achieved worldwide dispersion predating the breakup of the Gondwana supercontinent. It is assumed that this parasite evolved from monoxenic Trypanosomatidae. Phylogenetic studies locate dixenous Leishmania in a well-supported clade, in the recently named subfamily Leishmaniinae, which also includes monoxenous trypanosomatids. Virus-like particles have been reported in many species of this family. To date, several Leishmania species have been reported to be infected by Leishmania RNA virus (LRV) and Leishbunyavirus (LBV). Since the first descriptions of LRVs decades ago, differences in their genomic structures have been highlighted, leading to the designation of LRV1 in L. (Viannia) species and LRV2 in L. (Leishmania) species. There are strong indications that viruses that infect Leishmania spp. have the ability to enhance parasitic survival in humans as well as in experimental infections, through highly complex and specialized mechanisms. Phylogenetic analyses of these viruses have shown that their genomic differences correlate with the parasite species infected, suggesting a coevolutionary process. Herein, we will explore what has been described in the literature regarding the relationship between Leishmania and endosymbiotic Leishmania viruses and what is known about this association that could contribute to discussions about the worldwide dispersion of Leishmania.
Collapse
|
10
|
van Houte S, Padfield D, Gómez P, Luján AM, Brockhurst MA, Paterson S, Buckling A. Compost spatial heterogeneity promotes evolutionary diversification of a bacterium. J Evol Biol 2020; 34:246-255. [PMID: 33111439 PMCID: PMC7984246 DOI: 10.1111/jeb.13722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/20/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
Spatial resource heterogeneity is expected to be a key driver for the evolution of diversity. However, direct empirical support for this prediction is limited to studies carried out in simplified laboratory environments. Here, we investigate how altering spatial heterogeneity of potting compost-by the addition of water and mixing-affects the evolutionary diversification of a bacterial species, Pseudomonas fluorescens, that is naturally found in the environment. There was a greater propensity of resource specialists to evolve in the unmanipulated compost, while more generalist phenotypes dominated the compost-water mix. Genomic data were consistent with these phenotypic findings. Competition experiments strongly suggest these results are due to diversifying selection as a result of resource heterogeneity, as opposed to other covariables. Overall, our findings corroborate theoretical and in vitro findings, but in semi-natural, more realistic conditions.
Collapse
Affiliation(s)
| | | | - Pedro Gómez
- ESI and CEC, Biosciences, University of Exeter, Penryn, UK
| | - Adela M Luján
- ESI and CEC, Biosciences, University of Exeter, Penryn, UK
| | | | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Angus Buckling
- ESI and CEC, Biosciences, University of Exeter, Penryn, UK
| |
Collapse
|
11
|
Measuring Coevolutionary Dynamics in Species-Rich Communities. Trends Ecol Evol 2020; 35:539-550. [DOI: 10.1016/j.tree.2020.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 12/18/2022]
|
12
|
How long do Red Queen dynamics survive under genetic drift? A comparative analysis of evolutionary and eco-evolutionary models. BMC Evol Biol 2020; 20:8. [PMID: 31931696 PMCID: PMC6958710 DOI: 10.1186/s12862-019-1562-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/12/2019] [Indexed: 11/26/2022] Open
Abstract
Background Red Queen dynamics are defined as long term co-evolutionary dynamics, often with oscillations of genotype abundances driven by fluctuating selection in host-parasite systems. Much of our current understanding of these dynamics is based on theoretical concepts explored in mathematical models that are mostly (i) deterministic, inferring an infinite population size and (ii) evolutionary, thus ecological interactions that change population sizes are excluded. Here, we recall the different mathematical approaches used in the current literature on Red Queen dynamics. We then compare models from game theory (evo) and classical theoretical ecology models (eco-evo), that are all derived from individual interactions and are thus intrinsically stochastic. We assess the influence of this stochasticity through the time to the first loss of a genotype within a host or parasite population. Results The time until the first genotype is lost (“extinction time”), is shorter when ecological dynamics, in the form of a changing population size, is considered. Furthermore, when individuals compete only locally with other individuals extinction is even faster. On the other hand, evolutionary models with a fixed population size and competition on the scale of the whole population prolong extinction and therefore stabilise the oscillations. The stabilising properties of intra-specific competitions become stronger when population size is increased and the deterministic part of the dynamics gain influence. In general, the loss of genotype diversity can be counteracted with mutations (or recombination), which then allow the populations to recurrently undergo negative frequency-dependent selection dynamics and selective sweeps. Conclusion Although the models we investigated are equal in their biological motivation and interpretation, they have diverging mathematical properties both in the derived deterministic dynamics and the derived stochastic dynamics. We find that models that do not consider intraspecific competition and that include ecological dynamics by letting the population size vary, lose genotypes – and thus Red Queen oscillations – faster than models with competition and a fixed population size.
Collapse
|
13
|
Abstract
Viral population numbers are extremely large compared with those of their host species. Population bottlenecks are frequent during the life cycle of viruses and can reduce viral populations transiently to very few individuals. Viruses have to confront several types of constraints that can be divided into basal, cell-dependent, and organism-dependent constraints. Viruses overcome them exploiting a number of molecular mechanisms, with an important contribution of population numbers and genome variation. The adaptive potential of viruses is reflected in modifications of cell tropism and host range, escape to components of the host immune response, and capacity to alternate among different host species, among other phenotypic changes. Despite a fitness cost of most mutations required to overcome a selective constraint, viruses can find evolutionary pathways that ensure their survival in equilibrium with their hosts.
Collapse
|
14
|
Scanlan JG, Hall AR, Scanlan PD. Impact of bile salts on coevolutionary dynamics between the gut bacterium Escherichia coli and its lytic phage PP01. INFECTION GENETICS AND EVOLUTION 2019; 73:425-432. [DOI: 10.1016/j.meegid.2019.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/21/2019] [Accepted: 05/29/2019] [Indexed: 01/21/2023]
|
15
|
Approximate Bayesian estimation of coevolutionary arms races. PLoS Comput Biol 2019; 15:e1006988. [PMID: 30986245 PMCID: PMC6483265 DOI: 10.1371/journal.pcbi.1006988] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 04/25/2019] [Accepted: 03/29/2019] [Indexed: 11/19/2022] Open
Abstract
Exaggerated traits involved in species interactions have long captivated the imagination of evolutionary biologists and inspired the durable metaphor of the coevolutionary arms race. Despite decades of research, however, we have only a handful of examples where reciprocal coevolutionary change has been rigorously established as the cause of trait exaggeration. Support for a coevolutionary mechanism remains elusive because we lack generally applicable tools for quantifying the intensity of coevolutionary selection. Here we develop an approximate Bayesian computation (ABC) approach for estimating the intensity of coevolutionary selection using population mean phenotypes of traits mediating interspecific interactions. Our approach relaxes important assumptions of a previous maximum likelihood approach by allowing gene flow among populations, variable abiotic environments, and strong coevolutionary selection. Using simulated data, we show that our ABC method accurately infers the strength of coevolutionary selection if reliable estimates are available for key background parameters and ten or more populations are sampled. Applying our approach to the putative arms race between the plant Camellia japonica and its seed predatory weevil, Curculio camelliae, provides support for a coevolutionary hypothesis but fails to preclude the possibility of unilateral evolution. Comparing independently estimated selection gradients acting on Camellia pericarp thickness with values simulated by our model reveals a correlation between predicted and observed selection gradients of 0.941. The strong agreement between predicted and observed selection gradients validates our method.
Collapse
|
16
|
Ecological and Evolutionary Processes Shaping Viral Genetic Diversity. Viruses 2019; 11:v11030220. [PMID: 30841497 PMCID: PMC6466605 DOI: 10.3390/v11030220] [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: 01/24/2019] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023] Open
Abstract
The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.
Collapse
|
17
|
Sousa JAMD, Rocha EPC. Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation. Sci Rep 2019; 9:3149. [PMID: 30816246 PMCID: PMC6395636 DOI: 10.1038/s41598-019-39773-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/07/2019] [Indexed: 01/21/2023] Open
Abstract
Microbial communities are shaped by bacteriophages through predation and lysogeny. A better understanding of the interactions between these processes across different types of environments is key to elucidate how phages mediate microbial competition and to design efficient phage therapies. We introduce an individual-based model (eVIVALDI) to investigate the role of environmental structure in the elimination of a population with a combined treatment of antibiotics and virulent phages, and in the invasion of a population of phage-sensitive bacteria by lysogens. We show that structured environments facilitate the emergence of double resistance, to antibiotics and phages, due to limited diffusion of phage particles and increased nutrient availability from dead cells. They also hinder phage amplification, thus decreasing the generation of phage genetic diversity and increasing the unpredictability of phage-bacteria arms-races. We used a machine learning approach to determine the variables most important for the invasion of sensitive populations by lysogens. They revealed that phage-associated traits and environmental structure are the key drivers of the process. Structured environments hinder invasions, and accounting for their existence improves the fit of the model to published in vivo experimental data. Our results underline environmental structure as key to understand in vivo phage-bacteria interactions.
Collapse
Affiliation(s)
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, 75015, France
| |
Collapse
|
18
|
Yuan Y, Peng Q, Zhang S, Liu T, Yang S, Yu Q, Wu Y, Gao M. Phage Reduce Stability for Regaining Infectivity during Antagonistic Coevolution with Host Bacterium. Viruses 2019; 11:v11020118. [PMID: 30699954 PMCID: PMC6410104 DOI: 10.3390/v11020118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/15/2019] [Accepted: 01/28/2019] [Indexed: 12/19/2022] Open
Abstract
The coevolution between phage and host bacterium is an important force that drives the evolution of the microbial community, yet the coevolution mechanisms have still not been well analyzed. Here, by analyzing the interaction between a Bacillus phage vB_BthS_BMBphi and its host bacterium, the coevolution mechanisms of the first-generation phage-resistant bacterial mutants and regained-infectivity phage mutants were studied. The phage-resistant bacterial mutants showed several conserved mutations as a potential reason for acquiring phage resistance, including the mutation in flagellum synthesis protein FlhA and cell wall polysaccharide synthesis protein DltC. All the phage-resistant bacterial mutants showed a deleted first transmembrane domain of the flagellum synthesis protein FlhA. Meanwhile, the regain-infectivity phage mutants all contained mutations in three baseplate-associated phage tail proteins by one nucleotide, respectively. A polymorphism analysis of the three mutant nucleotides in the wild-type phage revealed that the mutations existed before the interaction of the phage and the bacterium, while the wild-type phage could not infect the phage-resistant bacterial mutants, which might be because the synchronized mutations of the three nucleotides were essential for regaining infectivity. This study for the first time revealed that the synergism mutation of three phage baseplate-associated proteins were essential for the phages’ regained infectivity. Although the phage mutants regained infectivity, their storage stability was decreased and the infectivity against the phage-resistant bacterial mutants was reduced, suggesting the phage realized the continuation of the species by way of “dying to survive”.
Collapse
Affiliation(s)
- Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Qin Peng
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Shaowen Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Tingting Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Shuo Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Qiuhan Yu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| |
Collapse
|
19
|
Theodosiou L, Hiltunen T, Becks L. The role of stressors in altering eco‐evolutionary dynamics. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Loukas Theodosiou
- Community Dynamics GroupMax Planck Institute for Evolutionary Biology Plön Germany
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary Biology Plön Germany
| | - Teppo Hiltunen
- Department of MicrobiologyUniversity of Helsinki Helsinki Finland
- Department of BiologyUniversity of Turku Turku Finland
| | - Lutz Becks
- Community Dynamics GroupMax Planck Institute for Evolutionary Biology Plön Germany
- Limnology ‐ Aquatic Ecology and Evolution, Limnological InstituteUniversity of Konstanz Konstanz Germany
| |
Collapse
|
20
|
Oechslin F. Resistance Development to Bacteriophages Occurring during Bacteriophage Therapy. Viruses 2018; 10:E351. [PMID: 29966329 PMCID: PMC6070868 DOI: 10.3390/v10070351] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 12/29/2022] Open
Abstract
Bacteriophage (phage) therapy, i.e., the use of viruses that infect bacteria as antimicrobial agents, is a promising alternative to conventional antibiotics. Indeed, resistance to antibiotics has become a major public health problem after decades of extensive usage. However, one of the main questions regarding phage therapy is the possible rapid emergence of phage-resistant bacterial variants, which could impede favourable treatment outcomes. Experimental data has shown that phage-resistant variants occurred in up to 80% of studies targeting the intestinal milieu and 50% of studies using sepsis models. Phage-resistant variants have also been observed in human studies, as described in three out of four clinical trials that recorded the emergence of phage resistance. On the other hand, recent animal studies suggest that bacterial mutations that confer phage-resistance may result in fitness costs in the resistant bacterium, which, in turn, could benefit the host. Thus, phage resistance should not be underestimated and efforts should be made to develop methodologies for monitoring and preventing it. Moreover, understanding and taking advantage of the resistance-induced fitness costs in bacterial pathogens is a potentially promising avenue.
Collapse
Affiliation(s)
- Frank Oechslin
- Department of Fundamental Microbiology (DMF), University of Lausanne, CH-1015 Lausanne, Switzerland.
| |
Collapse
|
21
|
Cantanhêde LM, Fernandes FG, Ferreira GEM, Porrozzi R, Ferreira RDGM, Cupolillo E. New insights into the genetic diversity of Leishmania RNA Virus 1 and its species-specific relationship with Leishmania parasites. PLoS One 2018; 13:e0198727. [PMID: 29912912 PMCID: PMC6005476 DOI: 10.1371/journal.pone.0198727] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/23/2018] [Indexed: 12/16/2022] Open
Abstract
Cutaneous leishmaniasis is a neglected parasitic disease that manifests in infected individuals under different phenotypes, with a range of factors contributing to its broad clinical spectrum. One factor, Leishmania RNA Virus 1 (LRV1), has been described as an endosymbiont present in different species of Leishmania. LRV1 significantly worsens the lesion, exacerbating the immune response in both experimentally infected animals and infected individuals. Little is known about the composition and genetic diversity of these viruses. Here, we investigated the relationship between the genetic composition of LRV1 detected in strains of Leishmania (Viannia) braziliensis and L. (V.) guyanensis and the interaction between the endosymbiont and the parasitic species, analyzing an approximately 850 base pair region of the viral genome. We also included one LRV1 sequence detected in L. (V.) shawi, representing the first report of LRV1 in a species other than L. braziliensis and L. guyanensis. The results illustrate the genetic diversity of the LRV1 strains analyzed here, with smaller divergences detected among viral sequences from the same parasite species. Phylogenetic analyses showed that the LRV1 sequences are grouped according to the parasite species and possibly according to the population of the parasite in which the virus was detected, corroborating the hypothesis of joint evolution of the viruses with the speciation of Leishmania parasites.
Collapse
Affiliation(s)
- Lilian Motta Cantanhêde
- Laboratório de Epidemiologia Genética, Fundação Oswaldo Cruz, Unidade Rondônia, Porto Velho, Rondônia, Brazil
| | - Flavia Gonçalves Fernandes
- Laboratório de Epidemiologia Genética, Fundação Oswaldo Cruz, Unidade Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Renato Porrozzi
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Elisa Cupolillo
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
22
|
Best A, Ashby B, White A, Bowers R, Buckling A, Koskella B, Boots M. Host-parasite fluctuating selection in the absence of specificity. Proc Biol Sci 2018; 284:rspb.2017.1615. [PMID: 29093222 PMCID: PMC5698645 DOI: 10.1098/rspb.2017.1615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022] Open
Abstract
Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific ‘matching-allele’ frameworks more likely to generate fluctuating selection dynamics (FSD) than ‘gene-for-gene’ (generalist–specialist) frameworks. However, the environment, ecological feedbacks and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco-evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD. Our key result is to demonstrate for the first time, to our knowledge, that specificity between hosts and parasites is not required to generate FSD. Furthermore, highly specific host–parasite interactions produce unstable, less robust stochastic fluctuations in contrast to interactions that lack specificity altogether or those that vary from generalist to specialist, which produce predictable limit cycles. Given the ubiquity of ecological feedbacks and the variation in the nature of specificity in host–parasite interactions, our work emphasizes the underestimated potential for host–parasite coevolution to generate fluctuating selection.
Collapse
Affiliation(s)
- Alex Best
- School of Mathematics and Statistics, University of Sheffield, Sheffield S3 7RH, UK
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.,Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Andy White
- Department of Mathematics and the Maxwell Institute for Mathematical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Roger Bowers
- Department of Mathematical Sciences, Division of Applied Mathematics, The University of Liverpool, Mathematical Sciences Building, Liverpool L69 7ZL, UK
| | - Angus Buckling
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Treliever Road, Penryn, Cornwall TR10 9EZ, UK
| | - Britt Koskella
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Mike Boots
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.,Biosciences, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Treliever Road, Penryn, Cornwall TR10 9EZ, UK
| |
Collapse
|
23
|
Cortez MH. Genetic variation determines which feedbacks drive and alter predator-prey eco-evolutionary cycles. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1304] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Michael H. Cortez
- Department of Mathematics and Statistics; Utah State University; Logan Utah 84322 USA
| |
Collapse
|
24
|
Gibson AK, Stoy KS, Lively CM. Bloody-minded parasites and sex: the effects of fluctuating virulence. J Evol Biol 2018; 31:611-620. [PMID: 29460507 PMCID: PMC5882519 DOI: 10.1111/jeb.13252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 12/18/2022]
Abstract
Asexual lineages can grow at a faster rate than sexual lineages. Why then is sexual reproduction so widespread? Much empirical evidence supports the Red Queen hypothesis. Under this hypothesis, coevolving parasites favour sexual reproduction by adapting to infect common asexual clones and driving them down in frequency. One limitation, however, seems to challenge the generality of the Red Queen: in theoretical models, parasites must be very virulent to maintain sex. Moreover, experiments show virulence to be unstable, readily shifting in response to environmental conditions. Does variation in virulence further limit the ability of coevolving parasites to maintain sex? To address this question, we simulated temporal variation in virulence and evaluated the outcome of competition between sexual and asexual females. We found that variation in virulence did not limit the ability of coevolving parasites to maintain sex. In fact, relatively high variation in virulence promoted parasite-mediated maintenance of sex. With sufficient variation, sexual females persisted even when mean virulence fell well below the threshold virulence required to maintain sex under constant conditions. We conclude that natural variation in virulence does not limit the relevance of the Red Queen hypothesis for natural populations; on the contrary, it could expand the range of conditions over which coevolving parasites can maintain sex.
Collapse
Affiliation(s)
- Amanda K Gibson
- Department of Biology, Indiana University, Bloomington, IN, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Kayla S Stoy
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Curtis M Lively
- Department of Biology, Indiana University, Bloomington, IN, USA
| |
Collapse
|
25
|
Blanquart F, Valero M, Alves-de-Souza C, Dia A, Lepelletier F, Bigeard E, Jeanthon C, Destombe C, Guillou L. Evidence for parasite-mediated selection during short-lasting toxic algal blooms. Proc Biol Sci 2017; 283:rspb.2016.1870. [PMID: 27798309 PMCID: PMC5095388 DOI: 10.1098/rspb.2016.1870] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022] Open
Abstract
Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relative A. minutum abundances, demonstrating strong parasite-mediated selection. There was genetic variability in infectivity in both parasite species, and in resistance in the host. We found no evidence for coevolution in one estuary; however, in the other estuary, we found high genetic diversity in the two parasite species, fluctuations in infectivity and suggestion that the two parasites are well adapted to their host, as in ‘Red Queen’ dynamics. Thus, coevolution is possible over the short time span of a bloom, but geographically variable, and may feedback on community dynamics.
Collapse
Affiliation(s)
- François Blanquart
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Myriam Valero
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,CNRS, UMI 3614, Pontifica Universidad Catolica de Chile, Universidad Austral de Chile, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Catharina Alves-de-Souza
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristovão, Rio de Janeiro, RJ, Brazil
| | - Aliou Dia
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Frédéric Lepelletier
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Estelle Bigeard
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Christian Jeanthon
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Christophe Destombe
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France.,CNRS, UMI 3614, Pontifica Universidad Catolica de Chile, Universidad Austral de Chile, Place Georges Teissier, CS90074, 29688 Roscoff, France
| | - Laure Guillou
- Station Biologique de Roscoff, Sorbonne Universités, Université Pierre et Marie Curie (Paris VI), Place Georges Teissier, CS90074, 29688 Roscoff, France .,Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, CS90074, 29688 Roscoff, France
| |
Collapse
|
26
|
Auld SKJR, Brand J. Environmental variation causes different (co) evolutionary routes to the same adaptive destination across parasite populations. Evol Lett 2017; 1:245-254. [PMID: 30283653 PMCID: PMC6121849 DOI: 10.1002/evl3.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/15/2017] [Indexed: 11/13/2022] Open
Abstract
Epidemics are engines for host-parasite coevolution, where parasite adaptation to hosts drives reciprocal adaptation in host populations. A key challenge is to understand whether parasite adaptation and any underlying evolution and coevolution is repeatable across ecologically realistic populations that experience different environmental conditions, or if each population follows a completely unique evolutionary path. We established twenty replicate pond populations comprising an identical suite of genotypes of crustacean host, Daphnia magna, and inoculum of their parasite, Pasteuria ramosa. Using a time-shift experiment, we compared parasite infection traits before and after epidemics and linked patterns of parasite evolution with shifts in host genotype frequencies. Parasite adaptation to the sympatric suite of host genotypes came at a cost of poorer performance on foreign genotypes across populations and environments. However, this consistent pattern of parasite adaptation was driven by different types of frequency-dependent selection that was contingent on an ecologically relevant environmental treatment (whether or not there was physical mixing of water within ponds). In unmixed ponds, large epidemics drove rapid and strong host-parasite coevolution. In mixed ponds, epidemics were smaller and host evolution was driven mainly by the mixing treatment itself; here, host evolution and parasite evolution were clear, but coevolution was absent. Population mixing breaks an otherwise robust coevolutionary cycle. These findings advance our understanding of the repeatability of (co)evolution across noisy, ecologically realistic populations.
Collapse
Affiliation(s)
- Stuart K. J. R. Auld
- Biological and Environmental SciencesUniversity of StirlingStirlingUnited Kingdom
| | - June Brand
- Biological and Environmental SciencesUniversity of StirlingStirlingUnited Kingdom
| |
Collapse
|
27
|
Abstract
AbstractCompetition between parasite species or genotypes can play an important role in the establishment of parasites in new host populations. Here, we investigate a mechanism by which a rare parasite is unable to establish itself in a host population if a common resident parasite is already present (a ‘priority effect’). We develop a simple epidemiological model and show that a rare parasite genotype is unable to invade if coinfecting parasite genotypes inhibit each other's transmission more than expected from simple resource partitioning. This is because a rare parasite is more likely to be in multiply-infected hosts than the common genotype, and hence more likely to pay the cost of reduced transmission. Experiments competing interfering clones of bacteriophage infecting a bacterium support the model prediction that the clones are unable to invade each other from rare. We briefly discuss the implications of these results for host-parasite ecology and (co)evolution.
Collapse
|
28
|
Gurney J, Aldakak L, Betts A, Gougat-Barbera C, Poisot T, Kaltz O, Hochberg ME. Network structure and local adaptation in co-evolving bacteria-phage interactions. Mol Ecol 2017; 26:1764-1777. [PMID: 28092408 DOI: 10.1111/mec.14008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023]
Abstract
Numerous theoretical and experimental studies have investigated antagonistic co-evolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individual molecular and phenotypic changes) may result in the emergence of structures at larger scales, such as co-evolutionary dynamics and local adaptation. We capitalized on methods commonly employed in community ecology to quantify how the structure of community interaction matrices, so-called bipartite networks, reflected observed co-evolutionary dynamics, and how phages from these communities may or may not have adapted locally to their bacterial hosts. We found a consistent nested network structure for two phage types, one previously demonstrated to exhibit arms race co-evolutionary dynamics and the other fluctuating co-evolutionary dynamics. Both phages increased their host ranges through evolutionary time, but we found no evidence for a trade-off with impact on bacteria. Finally, only bacteria from the arms race phage showed local adaptation, and we provide preliminary evidence that these bacteria underwent (sometimes different) molecular changes in the wzy gene associated with the LPS receptor, while bacteria co-evolving with the fluctuating selection phage did not show local adaptation and had partial deletions of the pilF gene associated with type IV pili. We conclude that the structure of phage-bacteria interaction networks is not necessarily specific to co-evolutionary dynamics, and discuss hypotheses for why only one of the two phages was, nevertheless, locally adapted.
Collapse
Affiliation(s)
- James Gurney
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université de Montpellier, CC065, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Lafi Aldakak
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université de Montpellier, CC065, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Alex Betts
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Claire Gougat-Barbera
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université de Montpellier, CC065, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, Pavillon Marie-Victorin, 90, avenue Vincent-d'Indy, Montréal, H2V 2S9, Canada
| | - Oliver Kaltz
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université de Montpellier, CC065, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Michael E Hochberg
- Institut des Sciences de l'Evolution de Montpellier, UMR5554, Université de Montpellier, CC065, Place E. Bataillon, 34095, Montpellier Cedex 5, France.,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA
| |
Collapse
|
29
|
Friedman J, Gore J. Ecological systems biology: The dynamics of interacting populations. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2016.12.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
30
|
Ashby B, Boots M. Multi-mode fluctuating selection in host-parasite coevolution. Ecol Lett 2017; 20:357-365. [DOI: 10.1111/ele.12734] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/30/2016] [Accepted: 12/19/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Ben Ashby
- Department of Mathematical Sciences; University of Bath; Bath BA2 7AY UK
- Integrative Biology; University of California Berkeley; Berkeley CA USA
| | - Mike Boots
- Integrative Biology; University of California Berkeley; Berkeley CA USA
- Department of Biosciences, College of Life and Environmental Sciences; University of Exeter; Penryn TR10 9EZ UK
| |
Collapse
|
31
|
Morley D, Broniewski JM, Westra ER, Buckling A, van Houte S. Host diversity limits the evolution of parasite local adaptation. Mol Ecol 2016; 26:1756-1763. [DOI: 10.1111/mec.13917] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/26/2016] [Accepted: 11/01/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Daniel Morley
- Environment and Sustainability Institute; Centre for Ecology and Conservation; University of Exeter; Biosciences; Penryn Cornwall UK
| | - Jenny M. Broniewski
- Environment and Sustainability Institute; Centre for Ecology and Conservation; University of Exeter; Biosciences; Penryn Cornwall UK
| | - Edze R. Westra
- Environment and Sustainability Institute; Centre for Ecology and Conservation; University of Exeter; Biosciences; Penryn Cornwall UK
| | - Angus Buckling
- Environment and Sustainability Institute; Centre for Ecology and Conservation; University of Exeter; Biosciences; Penryn Cornwall UK
| | - Stineke van Houte
- Environment and Sustainability Institute; Centre for Ecology and Conservation; University of Exeter; Biosciences; Penryn Cornwall UK
| |
Collapse
|
32
|
Parratt SR, Numminen E, Laine AL. Infectious Disease Dynamics in Heterogeneous Landscapes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032321] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Infectious diseases dynamics are affected by both spatial and temporal heterogeneity in their environments. Our ability to quantify and predict how this heterogeneity impacts risks of infection and disease emergence is the key to successful disease prevention efforts. Here, we review the literature on infectious diseases from human, agricultural, and wildlife ecosystems to describe the rapid ecological and evolutionary responses in pathogens to environmental heterogeneity, with expected impacts on their epidemiology. To date, the underlying network structures through which disease transmission proceeds have been notoriously difficult to quantify because of this variation. We show that with recent advances in statistical methods and genomic approaches, it is now more feasible than ever to trace disease transmission networks, the molecular underpinning of infection, and the environmental variation relevant to disease dynamics. We end by identifying major new opportunities and challenges in understanding disease dynamics in an ever-changing world.
Collapse
Affiliation(s)
- Steven R. Parratt
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland;, ,
| | - Elina Numminen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland;, ,
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland;, ,
| |
Collapse
|
33
|
van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
Collapse
Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
34
|
Gómez P, Paterson S, De Meester L, Liu X, Lenzi L, Sharma MD, McElroy K, Buckling A. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community. Nat Commun 2016; 7:12453. [PMID: 27501868 PMCID: PMC4980492 DOI: 10.1038/ncomms12453] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 07/04/2016] [Indexed: 01/26/2023] Open
Abstract
Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting. Though both the presence and traits of a species can influence the dynamics of its ecological community, the effects of these factors are difficult to disentangle. Here, Gómez et al. demonstrate in a microbial mesocosm that local adaptation of a focal species can influence the community as much as the presence of the focal species per se.
Collapse
Affiliation(s)
- Pedro Gómez
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK.,CEBAS-CSIC, Campus Espinardo, 30100 Murcia, Spain
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, 3000 Leuven, Belgium
| | - Xuan Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Luca Lenzi
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - M D Sharma
- CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Kerensa McElroy
- Common wealth Scientific and Industrial Research Organisation (CSIRO), Canberra GPO Box 1700, Australia
| | - Angus Buckling
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| |
Collapse
|
35
|
Abstract
The classical, ecological, paradox of enrichment describes a phenomenon that resource enrichment destabilizes predator-prey systems by exacerbating population oscillations. Here we suggest a new, evolutionary, paradox of enrichment. Resource enrichment can lead to more asymmetrical predator-prey coevolution (i.e., extremely high levels of prey defenses against predators) that decreases predator abundances and increases predator extinction risk. A major reason for this is that high resource availability can reduce fitness costs associated with prey defenses. In our experiments with a bacterium and its lytic phage, nutrient-balanced resource enrichment led to patterns in population demography and coevolutionary dynamics consistent with this coevolution-based paradox of enrichment; in particular, phage population extinction events were observed under nutrient-rich, not nutrient-poor, conditions. Consistent with ecological studies, carbon-biased resource enrichment (with carbon availability disproportionately increased relative to other nutrients) did not destabilize dynamics, and the asymmetry of coevolution was not altered in this context. Our work highlights the importance of integrating ecological and evolutionary thinking for studies of the consequences of nutrient pollution and other types of environmental changes.
Collapse
|
36
|
Koskella B, Parr N. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0297. [PMID: 26150663 PMCID: PMC4528495 DOI: 10.1098/rstb.2014.0297] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host-parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.
Collapse
Affiliation(s)
- Britt Koskella
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall, UK
| | - Nicole Parr
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall, UK
| |
Collapse
|
37
|
Harrison E, Truman J, Wright R, Spiers AJ, Paterson S, Brockhurst MA. Plasmid carriage can limit bacteria-phage coevolution. Biol Lett 2016; 11:rsbl.2015.0361. [PMID: 26268992 PMCID: PMC4571675 DOI: 10.1098/rsbl.2015.0361] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Coevolution with bacteriophages is a major selective force shaping bacterial populations and communities. A variety of both environmental and genetic factors has been shown to influence the mode and tempo of bacteria–phage coevolution. Here, we test the effects that carriage of a large conjugative plasmid, pQBR103, had on antagonistic coevolution between the bacterium Pseudomonas fluorescens and its phage, SBW25ϕ2. Plasmid carriage limited bacteria–phage coevolution; bacteria evolved lower phage-resistance and phages evolved lower infectivity in plasmid-carrying compared with plasmid-free populations. These differences were not explained by effects of plasmid carriage on the costs of phage resistance mutations. Surprisingly, in the presence of phages, plasmid carriage resulted in the evolution of high frequencies of mucoid bacterial colonies. Mucoidy can provide weak partial resistance against SBW25ϕ2, which may have limited selection for qualitative resistance mutations in our experiments. Taken together, our results suggest that plasmids can have evolutionary consequences for bacteria that go beyond the direct phenotypic effects of their accessory gene cargo.
Collapse
Affiliation(s)
- Ellie Harrison
- Department of Biology, University of York, York YO10 5DD, UK
| | - Julie Truman
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rosanna Wright
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | |
Collapse
|
38
|
Papkou A, Gokhale CS, Traulsen A, Schulenburg H. Host-parasite coevolution: why changing population size matters. ZOOLOGY 2016; 119:330-8. [PMID: 27161157 DOI: 10.1016/j.zool.2016.02.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/30/2016] [Accepted: 02/10/2016] [Indexed: 01/08/2023]
Abstract
Host-parasite coevolution is widely assumed to have a major influence on biological evolution, especially as these interactions impose high selective pressure on the reciprocally interacting antagonists. The exact nature of the underlying dynamics is yet under debate and may be determined by recurrent selective sweeps (i.e., arms race dynamics), negative frequency-dependent selection (i.e., Red Queen dynamics), or a combination thereof. These interactions are often associated with reciprocally induced changes in population size, which, in turn, should have a strong impact on co-adaptation processes, yet are neglected in most current work on the topic. Here, we discuss potential consequences of temporal variations in population size on host-parasite coevolution. The limited empirical data available and the current theoretical literature in this field highlight that the consideration of such interaction-dependent population size changes is likely key for the full understanding of the coevolutionary dynamics, and, thus, a more realistic view on the complex nature of species interactions.
Collapse
Affiliation(s)
- Andrei Papkou
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-University of Kiel, 24098, Kiel, Germany
| | - Chaitanya S Gokhale
- New Zealand Institute for Advanced Study, Massey University, Private Bag 102904, Auckland 0745, New Zealand
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-University of Kiel, 24098, Kiel, Germany.
| |
Collapse
|
39
|
Klimenko AI, Matushkin YG, Kolchanov NA, Lashin SA. Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study. BMC Microbiol 2016; 16 Suppl 1:10. [PMID: 26823184 PMCID: PMC4895265 DOI: 10.1186/s12866-015-0620-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Bacteriophages are known to be one of the driving forces of bacterial evolution. Besides promoting horizontal transfer of genes between cells, they may induce directional selection of cells (for instance, according to more or less resistance to phage infection). Switching between lysogenic and lytic pathways results in various types of (co)evolution in host-phage systems. Spatial (more generally, ecological) organization of the living environment is another factor affecting evolution. In this study, we have simulated and analyzed a series of computer models of microbial communities evolving in spatially distributed environments under the pressure of phage infection. Results We modeled evolving microbial communities living in spatially distributed flowing environments. Non-specific nutrient supplied in the only spatial direction, resulting in its non-uniform distribution in environment. We varied the time and the location of initial phage infestation of cells as well as switched chemotaxis on and off. Simulations were performed with the Haploid evolutionary constructor software (http://evol-constructor.bionet.nsc.ru/). Conclusion Simulations have shown that the spatial location of initial phage invasion may lead to different evolutionary scenarios. Phage infection decreases the speciation rate by more than one order as far as intensified selection blocks the origin of novel viable populations/species, which could carve out potential ecological niches. The dependence of speciation rate on the invasion node location varied on the time of invasion. Speciation rate was found to be lower when the phage invaded fully formed community of sedentary cells (at middle and late times) at the species-rich regions. This is especially noticeable in the case of late-time invasion. Our simulation study has shown that phage infection affects evolution of microbial community slowing down speciation and stabilizing the system as a whole. This influencing varied in its efficiency depending on spatially-ecological factors as well as community state at the moment of phage invasion. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0620-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alexandra Igorevna Klimenko
- Institute of Cytology and Genetics SB RAS, Lavrentiev Avenue 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090, Russia.
| | | | - Nikolay Alexandrovich Kolchanov
- Institute of Cytology and Genetics SB RAS, Lavrentiev Avenue 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090, Russia.
| | - Sergey Alexandrovich Lashin
- Institute of Cytology and Genetics SB RAS, Lavrentiev Avenue 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090, Russia.
| |
Collapse
|
40
|
Domingo E. Interaction of Virus Populations with Their Hosts. VIRUS AS POPULATIONS 2016. [PMCID: PMC7150142 DOI: 10.1016/b978-0-12-800837-9.00004-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Viral population numbers are extremely large compared with those of their host species. Population bottlenecks are frequent during the life cycle of viruses and can reduce viral populations transiently to very few individuals. Viruses have to confront several types of constraints that can be divided in basal, cell-dependent, and organism-dependent constraints. Viruses overcome them exploiting a number of molecular mechanisms, with an important contribution of population numbers and genome variation. The adaptive potential of viruses is reflected in modifications of cell tropism and host range, escape to components of the host immune response, and capacity to alternate among different host species, among other phenotypic changes. Despite a fitness cost of most mutations required to overcome a selective constraint, viruses can find evolutionary pathways that ensure their survival in equilibrium with their hosts.
Collapse
|
41
|
Frígols B, Quiles-Puchalt N, Mir-Sanchis I, Donderis J, Elena SF, Buckling A, Novick RP, Marina A, Penadés JR. Virus Satellites Drive Viral Evolution and Ecology. PLoS Genet 2015; 11:e1005609. [PMID: 26495848 PMCID: PMC4619825 DOI: 10.1371/journal.pgen.1005609] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 09/25/2015] [Indexed: 12/18/2022] Open
Abstract
Virus satellites are widespread subcellular entities, present both in eukaryotic and in prokaryotic cells. Their modus vivendi involves parasitism of the life cycle of their inducing helper viruses, which assures their transmission to a new host. However, the evolutionary and ecological implications of satellites on helper viruses remain unclear. Here, using staphylococcal pathogenicity islands (SaPIs) as a model of virus satellites, we experimentally show that helper viruses rapidly evolve resistance to their virus satellites, preventing SaPI proliferation, and SaPIs in turn can readily evolve to overcome phage resistance. Genomic analyses of both these experimentally evolved strains as well as naturally occurring bacteriophages suggest that the SaPIs drive the coexistence of multiple alleles of the phage-coded SaPI inducing genes, as well as sometimes selecting for the absence of the SaPI depressing genes. We report similar (accidental) evolution of resistance to SaPIs in laboratory phages used for Staphylococcus aureus typing and also obtain the same qualitative results in both experimental evolution and phylogenetic studies of Enterococcus faecalis phages and their satellites viruses. In summary, our results suggest that helper and satellite viruses undergo rapid coevolution, which is likely to play a key role in the evolution and ecology of the viruses as well as their prokaryotic hosts. Satellites are defined as viruses that have a life cycle dependent on a helper virus. Thus, they can be considered as parasites of parasites. In addition to their fascinating life cycle, these widespread infectious elements, present both in eukaryotic and prokaryotic cells, have a dramatic role in virulence by controlling the symptoms induced by their eukaryotic helper viruses or by encoding key bacterial virulence genes. While satellites can play an important role in the ecology of the viruses they parasitise, the evolutionary impact on their helper viruses is unclear. Here we show that staphylococcal pathogenicity islands (SaPIs), an example of a virus satellite, are a major selective force on the viruses (bacteriophages) they parasitise. Using both bioinformatic and experimental evolution data we have been able to confirm that pathogenicity islands are a major selective pressure enhancing the diversity of both genes and gene content in Staphylococcus aureus phages. Since SaPIs exploit the life cycle of their helper phages to enable their rapid replication and promiscuous spread, these strategies are mechanisms that reduce SaPI interference, thus facilitating the infectivity and dissemination of the helper phages in nature.
Collapse
Affiliation(s)
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Jorge Donderis
- Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Angus Buckling
- Department of Biosciences, Center for Ecology and Conservation, School of Biosciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Richard P. Novick
- Skirball Institute Program in Molecular Pathogenesis and Departments of Microbiology and Medicine, New York University Medical Center, New York, New York, United States of America
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| |
Collapse
|
42
|
Gómez P, Bennie J, Gaston KJ, Buckling A. The impact of resource availability on bacterial resistance to phages in soil. PLoS One 2015; 10:e0123752. [PMID: 25856079 PMCID: PMC4391944 DOI: 10.1371/journal.pone.0123752] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/03/2015] [Indexed: 11/19/2022] Open
Abstract
Resource availability can affect the coevolutionary dynamics between host and parasites, shaping communities and hence ecosystem function. A key finding from theoretical and in vitro studies is that host resistance evolves to greater levels with increased resources, but the relevance to natural communities is less clear. We took two complementary approaches to investigate the effect of resource availability on the evolution of bacterial resistance to phages in soil. First, we measured the resistance and infectivity of natural communities of soil bacteria and phage in the presence and absence of nutrient-providing plants. Second, we followed the real-time coevolution between defined bacteria and phage populations with resource availability manipulated by the addition or not of an artificial plant root exudate. Increased resource availability resulted in increases in bacterial resistance to phages, but without a concomitant increase in phage infectivity. These results suggest that phages may have a reduced impact on the control of bacterial densities and community composition in stable, high resource environments.
Collapse
Affiliation(s)
- Pedro Gómez
- Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
- * E-mail:
| | - Jonathan Bennie
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
| | - Kevin J. Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
| |
Collapse
|
43
|
Ashby B, King KC. Diversity and the maintenance of sex by parasites. J Evol Biol 2015; 28:511-20. [PMID: 25676723 DOI: 10.1111/jeb.12590] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/12/2015] [Indexed: 01/21/2023]
Abstract
The Red Queen hypothesis (RQH) predicts that parasite-mediated selection will maintain sexual individuals in the face of competition from asexual lineages. The prediction is that sexual individuals will be difficult targets for coevolving parasites if they give rise to more genetically diverse offspring than asexual lineages. However, increasing host genetic diversity is known to suppress parasite spread, which could provide a short-term advantage to clonal lineages and lead to the extinction of sex. We test these ideas using a stochastic individual-based model. We find that if parasites are readily transmissible, then sex is most likely to be maintained when host diversity is high, in agreement with the RQH. If transmission rates are lower, however, we find that sexual populations are most likely to persist for intermediate levels of diversity. Our findings thus highlight the importance of genetic diversity and its impact on epidemiological dynamics for the maintenance of sex by parasites.
Collapse
Affiliation(s)
- B Ashby
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | | |
Collapse
|