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Holmes IA, Durso AM, Myers CR, Hendry TA. Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters. PeerJ 2024; 12:e16910. [PMID: 38436008 PMCID: PMC10909344 DOI: 10.7717/peerj.16910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024] Open
Abstract
Correctly identifying the strength of selection that parasites impose on hosts is key to predicting epidemiological and evolutionary outcomes of host-parasite interactions. However, behavioral changes due to infection can alter the capture probability of infected hosts and thereby make selection difficult to estimate by standard sampling techniques. Mark-recapture approaches, which allow researchers to determine if some groups in a population are less likely to be captured than others, can be used to identify infection-driven capture biases. If a metric of interest directly compares infected and uninfected populations, calculated detection probabilities for both groups may be useful in identifying bias. Here, we use an individual-based simulation to test whether changes in capture rate due to infection can alter estimates of three key metrics: 1) reduction in the reproductive success of infected parents relative to uninfected parents, 2) the relative risk of infection for susceptible genotypes compared to resistant genotypes, and 3) changes in allele frequencies between generations. We explore the direction and underlying causes of the biases that emerge from these simulations. Finally, we argue that short series of mark-recapture sampling bouts, potentially implemented in under a week, can yield key data on detection bias due to infection while not adding a significantly higher burden to disease ecology studies.
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Affiliation(s)
- Iris A. Holmes
- Department of Microbiology, Cornell University, Ithaca, NY, United States
- Cornell Institute of Host Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States
| | - Andrew M. Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL, USA
| | - Christopher R. Myers
- Center for Advanced Computing & Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, United States
| | - Tory A. Hendry
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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2
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Zaffaroni M, Rimbaud L, Rey J, Papaïx J, Fabre F. Effects of pathogen reproduction system on the evolutionary and epidemiological control provided by deployment strategies for two major resistance genes in agricultural landscapes. Evol Appl 2024; 17:e13627. [PMID: 38283600 PMCID: PMC10810173 DOI: 10.1111/eva.13627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 01/30/2024] Open
Abstract
Resistant cultivars are of value for protecting crops from disease, but can be rapidly overcome by pathogens. Several strategies have been proposed to delay pathogen adaptation (evolutionary control), while maintaining effective protection (epidemiological control). Resistance genes can be (i) combined in the same cultivar (pyramiding), (ii) deployed in different cultivars sown in the same field (mixtures) or in different fields (mosaics), or (iii) alternated over time (rotations). The outcomes of these strategies have been investigated principally in pathogens displaying pure clonal reproduction, but many pathogens have at least one sexual event in their annual life cycles. Sexual reproduction may promote the emergence of superpathogens adapted to all the resistance genes deployed. Here, we improved the spatially explicit stochastic model landsepi to include pathogen sexual reproduction, and we used the improved model to investigate the effect of sexual reproduction on evolutionary and epidemiological outcomes across deployment strategies for two major resistance genes. Sexual reproduction favours the establishment of a superpathogen when single mutant pathogens are present together at a sufficiently high frequency, as in mosaic and mixture strategies. However, sexual reproduction did not affect the strategy recommendations for a wide range of mutation probabilities, associated fitness costs, and landscape organisations.
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Affiliation(s)
- Marta Zaffaroni
- INRAE, Bordeaux Sciences Agro, SAVEVillenave d'OrnonFrance
- INRAE, BioSPAvignonFrance
| | | | | | | | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVEVillenave d'OrnonFrance
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3
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Dundore-Arias JP, Michalska-Smith M, Millican M, Kinkel LL. More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:403-423. [PMID: 37217203 DOI: 10.1146/annurev-phyto-021021-041457] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.
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Affiliation(s)
- J P Dundore-Arias
- Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, California, USA
| | - M Michalska-Smith
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA;
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | | | - L L Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA;
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4
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Hulse SV, Antonovics J, Hood ME, Bruns EL. Host-pathogen coevolution promotes the evolution of general, broad-spectrum resistance and reduces foreign pathogen spillover risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.548430. [PMID: 37577528 PMCID: PMC10418218 DOI: 10.1101/2023.08.04.548430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Genetic variation for disease resistance within host populations can strongly impact the spread of endemic pathogens. In plants, recent work has shown that within-population variation in resistance can also affect the transmission of foreign spillover pathogens if that resistance is general. However, most hosts also possess specific resistance mechanisms that provide strong defenses against coevolved endemic pathogens. Here we use a modeling approach to ask how antagonistic coevolution between hosts and their endemic pathogen at the specific resistance locus can affect the frequency of general resistance, and therefore a host's vulnerability to foreign pathogens. We develop a two-locus model with variable recombination that incorporates both general (resistance to all pathogens) and specific (resistance to endemic pathogens only). We find that introducing coevolution into our model greatly expands the regions where general resistance can evolve, decreasing the risk of foreign pathogen invasion. Furthermore, coevolution greatly expands which conditions maintain polymorphisms at both resistance loci, thereby driving greater genetic diversity within host populations. This genetic diversity often leads to positive correlations between host resistance to foreign and endemic pathogens, similar to those observed in natural populations. However, if resistance loci become linked, the resistance correlations can shift to negative. If we include a third, linkage modifying locus into our model, we find that selection often favors complete linkage. Our model demonstrates how coevolutionary dynamics with an endemic pathogen can mold the resistance structure of host populations in ways that affect its susceptibility to foreign pathogen spillovers, and that the nature of these outcomes depends on resistance costs, as well as the degree of linkage between resistance genes.
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5
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Clin P, Grognard F, Andrivon D, Mailleret L, Hamelin FM. The proportion of resistant hosts in mixtures should be biased towards the resistance with the lowest breaking cost. PLoS Comput Biol 2023; 19:e1011146. [PMID: 37228168 DOI: 10.1371/journal.pcbi.1011146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Current agricultural practices facilitate emergence and spread of plant diseases through the wide use of monocultures. Host mixtures are a promising alternative for sustainable plant disease control. Their effectiveness can be partly explained by priming-induced cross-protection among plants. Priming occurs when plants are challenged with non-infective pathogen genotypes, resulting in increased resistance to subsequent infections by infective pathogen genotypes. We developed an epidemiological model to explore how mixing two distinct resistant varieties can reduce disease prevalence. We considered a pathogen population composed of three genotypes infecting either one or both varieties. We found that host mixtures should not contain an equal proportion of resistant plants, but a biased ratio (e.g. 80 : 20) to minimize disease prevalence. Counter-intuitively, the optimal ratio of resistant varieties should contain a lower proportion of the costliest resistance for the pathogen to break. This benefit is amplified by priming. This strategy also prevents the invasion of pathogens breaking all resistances.
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Affiliation(s)
- Pauline Clin
- Institut Agro, Univ Rennes, INRAE, IGEPP, Rennes, France
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia-Antipolis, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, Sophia-Antipolis, France
| | | | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia-Antipolis, France
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, Sophia-Antipolis, France
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6
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Jiranek J, Miller IF, An R, Bruns E, Metcalf CJE. Mechanistic models to meet the challenge of climate change in plant-pathogen systems. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220017. [PMID: 36744564 PMCID: PMC9900714 DOI: 10.1098/rstb.2022.0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/11/2022] [Indexed: 02/07/2023] Open
Abstract
Evidence that climate change will impact the ecology and evolution of individual plant species is growing. However, little, as yet, is known about how climate change will affect interactions between plants and their pathogens. Climate drivers could affect the physiology, and thus demography, and ultimately evolutionary processes affecting both plant hosts and their pathogens. Because the impacts of climate drivers may operate in different directions at different scales of infection, and, furthermore, may be nonlinear, abstracting across these processes may mis-specify outcomes. Here, we use mechanistic models of plant-pathogen interactions to illustrate how counterintuitive outcomes are possible, and we introduce how such framing may contribute to understanding climate effects on plant-pathogen systems. We discuss the evidence-base derived from wild and agricultural plant-pathogen systems that could inform such models, specifically in the direction of estimates of physiological, demographic and evolutionary responses to climate change. We conclude by providing an overview of knowledge gaps and directions for future research in this important area. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
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Affiliation(s)
- Juliana Jiranek
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO 81244, USA
| | - Ian F. Miller
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08450, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO 81244, USA
| | - Ruby An
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08450, USA
| | - Emme Bruns
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08450, USA
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7
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Lebeda A, Burdon JJ. Studying Wild Plant Pathosystems to Understand Crop Plant Pathosystems: Status, Gaps, Challenges, and Perspectives. PHYTOPATHOLOGY 2023; 113:365-380. [PMID: 36256745 DOI: 10.1094/phyto-01-22-0018-per] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phytopathology is a highly complex scientific discipline. Initially, its focus was on the study of plant-pathogen interactions in agricultural and forestry production systems. Host-pathogen interactions in natural plant communities were generally overlooked until the 1970s when plant pathologists and evolutionary biologists started to take an interest in these interactions, and their dynamics in natural plant populations, communities, and ecosystems. This article introduces the general principles of plant pathosystems, provides a basic critical overview of current knowledge of host-pathogen interactions in natural plant pathosystems, and shows how this knowledge is important for future developments in plant pathology especially as it applies in cropping systems, ecology, and evolutionary biology. Plant pathosystems can be further divided according to the structure and origin of control, as autonomous (wild plant pathosystems, WPPs) or deterministic (crop plant pathosystems, CPPs). WPPs are characterized by the disease triangle and closed-loop (feedback) controls, and CPPs are characterized by the disease tetrahedron and open-loop (non-feedback) controls. Basic general, ecological, genetic, and population structural and functional differences between WPPs and CPPs are described. It is evident that we lack a focus on long-term observations and research of diseases and their dynamics in natural plant populations, metapopulations, communities, ecosystems, and biomes, as well as their direct or indirect relationships to CPPs. Differences and connections between WPPs and CPPs, and why, and how, these are important for agriculture varies. WPP and CPP may be linked by strong biological interactions, especially where the pathogen is in common. This is demonstrated through a case study of lettuce (Lactuca spp., L. serriola and L. sativa) and lettuce downy mildew (Bremia lactucae). In other cases where there is no such direct biological linkage, the study of WPPs can provide a deeper understanding of how ecology and genetics interacts to drive disease through time. These studies provide insights into ways in which farming practices may be changed to limit disease development. Research on interactions between pathosystems, the "cross-talk" of WPPs and CPPs, is still very limited and, as shown in interactions between wild and cultivated Lactuca spp.-B. lactucae associations, can be highly complex. The implications and applications of this knowledge in plant breeding, crop management, and disease control measures are considered. This review concludes with a discussion of theoretical, general and specific aspects, challenges and limits of future WPP research, and application of their results in agriculture.
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Affiliation(s)
- Aleš Lebeda
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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8
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Predicting the effects of climate change on the cross-scale epidemiological dynamics of a fungal plant pathogen. Sci Rep 2022; 12:14823. [PMID: 36050344 PMCID: PMC9437057 DOI: 10.1038/s41598-022-18851-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
The potential for climate change to exacerbate the burden of human infectious diseases is increasingly recognized, but its effects on infectious diseases of plants have received less attention. Understanding the impacts of climate on the epidemiological dynamics of plant pathogens is imperative, as these organisms play central roles in natural ecosystems and also pose a serious threat to agricultural production and food security. We use the fungal ‘flax rust’ pathogen (Melampsora lini) and its subalpine wildflower host Lewis flax (Linum lewisii) to investigate how climate change might affect the dynamics of fungal plant pathogen epidemics using a combination of empirical and modeling approaches. Our results suggest that climate change will initially slow transmission at both the within- and between-host scales. However, moderate resurgences in disease spread are predicted as warming progresses, especially if the rate of greenhouse gas emissions continues to increase at its current pace. These findings represent an important step towards building a holistic understanding of climate effects on plant infectious disease that encompasses demographic, epidemiological, and evolutionary processes. A core result is that neglecting processes at any one scale of plant pathogen transmission may bias projections of climate effects, as climate drivers have variable and cascading impacts on processes underlying transmission that occur at different scales.
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9
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Genetic Characterization of Puccinia striiformis f. sp. tritici Populations from Different Wheat Cultivars Using Simple Sequence Repeats. J Fungi (Basel) 2022; 8:jof8070705. [PMID: 35887461 PMCID: PMC9319641 DOI: 10.3390/jof8070705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/12/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important fungal diseases affecting wheat (Triticum aestivum L.) worldwide. In this study, the genetic diversity and population structure of Pst isolates were analyzed using 15 microsatellite markers. Isolates were collected from five wheat cultivars with different levels of resistance from Yanting county and Fucheng district, Mianyang city, Sichuan province, China. The aim of this study was to investigate whether Pst populations are differentiated by wheat genotype or geographic origin. Seventy-six multilocus genotypes (MLGs) were identified from all 289 single uredinial isolates. In general, the genotypic diversity of Pst populations from five wheat cultivars in Fucheng was higher than that in Yanting. In addition, the genetic diversity was highest in the Pst populations from Mianmai 367, a cultivar considered to be highly resistant. The unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree, Bayesian clustering analysis, and minimum spanning network for the MLGs revealed two major genetic clusters based on geographical location. Greater differentiation was observed between the populations from the two sampling locations than between the populations from different hosts in the same location. The results suggest that geographic and environmental differences could partially explain the genetic differentiation of Pst more than wheat genotype. This study provides novel insight into the interactions between Pst populations and their hosts. The results could be helpful in designing more effective management strategies for stripe rust in wheat production.
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10
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Clin P, Grognard F, Andrivon D, Mailleret L, Hamelin FM. Host mixtures for plant disease control: Benefits from pathogen selection and immune priming. Evol Appl 2022; 15:967-975. [PMID: 35782013 PMCID: PMC9234633 DOI: 10.1111/eva.13386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/28/2022] [Accepted: 04/05/2022] [Indexed: 11/29/2022] Open
Abstract
Multiline and cultivar mixtures are highly effective methods for agroecological plant disease control. Priming-induced cross protection, occurring when plants are challenged by avirulent pathogen genotypes and resulting in increased resistance to subsequent infection by virulent ones, is one critical key to their lasting performance against polymorphic pathogen populations. Strikingly, this mechanism was until recently absent from mathematical models aiming at designing optimal host mixtures. We developed an epidemiological model to explore the effect of host mixtures composed of variable numbers of single-resistance cultivars on the equilibrium prevalence of the disease caused by pathogen populations polymorphic for virulence complexity. This model shows that a relatively large amount of resistance genes must be deployed to achieve low disease prevalence, as pathogen competition in mixtures tends to select for intermediate virulence complexity. By contrast, priming significantly reduces the number of plant genotypes needed to drop disease prevalence below an acceptable threshold. Given the limited availability of resistance genes in cultivars, this mechanism of plant immunity should be assessed when designing host mixtures.
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Affiliation(s)
- Pauline Clin
- Institut Agro, INRAE, IGEPPUniv RennesRennesFrance
- INRAE, CNRS, ISAUniversité Côte d’AzurNiceFrance
| | - Frédéric Grognard
- Inria, INRAE, CNRS, Sorbonne Université, BiocoreUniversité Côte d’AzurNiceFrance
| | | | - Ludovic Mailleret
- INRAE, CNRS, ISAUniversité Côte d’AzurNiceFrance
- Inria, INRAE, CNRS, Sorbonne Université, BiocoreUniversité Côte d’AzurNiceFrance
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11
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Host Diversification May Split Epidemic Spread into Two Successive Fronts Advancing at Different Speeds. Bull Math Biol 2022; 84:68. [DOI: 10.1007/s11538-022-01023-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/13/2022] [Indexed: 11/02/2022]
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12
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Ahlawat N, Maggu K, Jigisha, Arun MG, Meena A, Agarwala A, Prasad NG. No major cost of evolved survivorship in Drosophila melanogaster populations coevolving with Pseudomonas entomophila. Proc Biol Sci 2022; 289:20220532. [PMID: 35506222 PMCID: PMC9065972 DOI: 10.1098/rspb.2022.0532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Rapid exaggeration of host and pathogen traits via arms race dynamics is one possible outcome of host-pathogen coevolution. However, the exaggerated traits are expected to incur costs in terms of resource investment in other life-history traits. The current study investigated the costs associated with evolved traits in a host-pathogen coevolution system. We used the Drosophila melanogaster (host)-Pseudomonas entomophila (pathogen) system to experimentally derive two selection regimes, one where the host and pathogen both coevolved, and the other, where only the host evolved against a non-evolving pathogen. After 17 generations of selection, we found that hosts from both selected populations had better post-infection survivorship than controls. Even though the coevolving populations tended to have better survivorship post-infection, we found no clear evidence that the two selection regimes were significantly different from each other. There was weak evidence for the coevolving pathogens being more virulent than the ancestral pathogen. We found no major cost of increased post-infection survivorship. The costs were not different between the coevolving hosts and the hosts evolving against a non-evolving pathogen. We found no evolved costs in the coevolving pathogens. Thus, our results suggest that increased host immunity and pathogen virulence may not be costly.
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Affiliation(s)
- Neetika Ahlawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Mohali 140306, India
| | - Komal Maggu
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Mohali 140306, India,Department of Evolutionary and Environmental Studies, University of Zürich, Zürich 8057, Switzerland
| | - Jigisha
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Mohali 140306, India,Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland
| | - Manas Geeta Arun
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Mohali 140306, India
| | - Abhishek Meena
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Mohali 140306, India,Department of Evolutionary and Environmental Studies, University of Zürich, Zürich 8057, Switzerland
| | - Amisha Agarwala
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Mohali 140306, India,Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Nagaraj Guru Prasad
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Mohali 140306, India
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13
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McTaggart AR, James TY, Idnurm A, Park RF, Shuey LS, Demers MNK, Aime MC. Sexual reproduction is the null hypothesis for life cycles of rust fungi. PLoS Pathog 2022; 18:e1010439. [PMID: 35617196 PMCID: PMC9135232 DOI: 10.1371/journal.ppat.1010439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sexual reproduction, mutation, and reassortment of nuclei increase genotypic diversity in rust fungi. Sexual reproduction is inherent to rust fungi, coupled with their coevolved plant hosts in native pathosystems. Rust fungi are hypothesised to exchange nuclei by somatic hybridisation with an outcome of increased genotypic diversity, independent of sexual reproduction. We provide criteria to demonstrate whether somatic exchange has occurred, including knowledge of parental haplotypes and rejection of fertilisation in normal rust life cycles.
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Affiliation(s)
- Alistair R. McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Robert F. Park
- Plant Breeding Institute, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Louise S. Shuey
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Michelle N. K. Demers
- Plant Breeding Institute, The University of Sydney, Cobbitty, New South Wales, Australia
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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14
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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: 28] [Impact Index Per Article: 14.0] [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.
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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
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15
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Eck JL, Barrès B, Soubeyrand S, Sirén J, Numminen E, Laine AL. Strain Diversity and Spatial Distribution Are Linked to Epidemic Dynamics in Host Populations. Am Nat 2022; 199:59-74. [DOI: 10.1086/717179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Virulence management: Closing the feedback loop between healthcare interventions and virulence evolution. J Theor Biol 2021; 531:110900. [PMID: 34530031 DOI: 10.1016/j.jtbi.2021.110900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 11/22/2022]
Abstract
We study the evolution of virulence of an endemic pathogen in response to healthcare interventions which affect host recovery and pathogen transmission. By anticipating the evolutionary response of the pathogen we may develop effective long-term management strategies for controlling the impact of the endemic on the society. To that end, we use standard Adaptive Dynamics techniques in an SIS model. The recovery rate and the transmission rate, both of which can be affected by healthcare interventions, are used as evolutionary control variables. The effect of interventions may be density-independent (self-help based on healthcare instructions) or density-dependent (when assistance of a healthcare worker is required). We consider the evolutionary response of the pathogen both to abrupt changes and to gradual changes in the level of healthcare intervention. Healthcare intervention is optimised for three alternative objectives: minimisation of virulence, minimisation of the probability that an infected individual dies of the disease, and total eradication of the endemic. We find that the optimal strategy may depend on the objective. High levels of healthcare intervention may eradicate the pathogen, but this option may not be available for budgetary reasons or otherwise. Counterintuitively, to minimise virulence, one should keep healthcare interventions at a minimum, while to minimise the probability for an infected individual to die of the disease, both low and high levels of healthcare intervention suffice. Changes in the level of healthcare intervention should be implemented fast (not gradually) in order to avoid sudden changes in pathogen evolution and the possible emergence of multiple simultaneously coexisting pathogen strains.
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Singh NK, Karisto P, Croll D. Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici. Microb Genom 2021; 7:000678. [PMID: 34617882 PMCID: PMC8627204 DOI: 10.1099/mgen.0.000678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/29/2021] [Indexed: 11/18/2022] Open
Abstract
Pathogens cause significant challenges to global food security. On annual crops, pathogens must re-infect from environmental sources in every growing season. Fungal pathogens have evolved mixed reproductive strategies to cope with the distinct challenges of colonizing growing plants. However, how pathogen diversity evolves during growing seasons remains largely unknown. Here, we performed a deep hierarchical sampling in a single experimental wheat field infected by the major fungal pathogen Zymoseptoria tritici. We analysed whole genome sequences of 177 isolates collected from 12 distinct cultivars replicated in space at three time points of the growing season to maximize capture of genetic diversity. The field population was highly diverse with 37 SNPs per kilobase, a linkage disequilibrium decay within 200-700 bp and a high effective population size. Using experimental infections, we tested a subset of the collected isolates on the dominant cultivar planted in the field. However, we found no significant difference in virulence of isolates collected from the same cultivar compared to isolates collected on other cultivars. About 20 % of the isolate genotypes were grouped into 15 clonal groups. Pairs of clones were disproportionally found at short distances (<5 m), consistent with experimental estimates for per-generation dispersal distances performed in the same field. This confirms predominant leaf-to-leaf transmission during the growing season. Surprisingly, levels of clonality did not increase over time in the field although reproduction is thought to be exclusively asexual during the growing season. Our study shows that the pathogen establishes vast and stable gene pools in single fields. Monitoring short-term evolutionary changes in crop pathogens will inform more durable strategies to contain diseases.
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Affiliation(s)
- Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Petteri Karisto
- Plant Health, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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Rimbaud L, Fabre F, Papaïx J, Moury B, Lannou C, Barrett LG, Thrall PH. Models of Plant Resistance Deployment. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:125-152. [PMID: 33929880 DOI: 10.1146/annurev-phyto-020620-122134] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Owing to their evolutionary potential, plant pathogens are able to rapidly adapt to genetically controlled plant resistance, often resulting in resistance breakdown and major epidemics in agricultural crops. Various deployment strategies have been proposed to improve resistance management. Globally, these rely on careful selection of resistance sources and their combination at various spatiotemporal scales (e.g., via gene pyramiding, crop rotations and mixtures, landscape mosaics). However, testing and optimizing these strategies using controlled experiments at large spatiotemporal scales are logistically challenging. Mathematical models provide an alternative investigative tool, and many have been developed to explore resistance deployment strategies under various contexts. This review analyzes 69 modeling studies in light of specific model structures (e.g., demographic or demogenetic, spatial or not), underlying assumptions (e.g., whether preadapted pathogens are present before resistance deployment), and evaluation criteria (e.g., resistance durability, disease control, cost-effectiveness). It highlights major research findings and discusses challenges for future modeling efforts.
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Affiliation(s)
- Loup Rimbaud
- INRAE, Pathologie Végétale, 84140 Montfavet, France; ,
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, 33882 Villenave d'Ornon, France;
| | | | - Benoît Moury
- INRAE, Pathologie Végétale, 84140 Montfavet, France; ,
| | | | - Luke G Barrett
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
| | - Peter H Thrall
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia; ,
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Clin P, Grognard F, Mailleret L, Val F, Andrivon D, Hamelin FM. Taking Advantage of Pathogen Diversity and Immune Priming to Minimize Disease Prevalence in Host Mixtures: A Model. PHYTOPATHOLOGY 2021; 111:1219-1227. [PMID: 33297731 DOI: 10.1094/phyto-09-20-0429-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Host mixtures are a promising method for agroecological plant disease control. Plant immunity is key to the success of host mixtures against polymorphic pathogen populations. This immunity results from priming-induced cross-protection, whereby plants able to resist infection by specific pathogen genotypes become more resistant to other pathogen genotypes. Strikingly, this phenomenon was absent from mathematical models aiming at designing host mixtures. We developed a model to specifically explore how priming affects the coexistence of two pathogen genotypes in host mixtures composed of two host genotypes and how it affects disease prevalence. The main effect of priming is to reduce the coexistence region in the parameter space (due to the cross-protection) and to generate a singular mixture of resistant and susceptible hosts corresponding to the maximal reduction disease prevalence (in absence of priming, a resistant pure stand is optimal). The epidemiological advantage of host mixtures over a resistant pure stand thus appears as a direct consequence of immune priming. We also showed that there is indirect cross-protection between host genotypes in a mixture. Moreover, the optimal mix prevents the emergence of a resistance-breaking pathogen genotype. Our results highlight the importance of considering immune priming to design optimal and sustainable host mixtures.
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Affiliation(s)
- Pauline Clin
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
- Université Côte d'Azur, INRAE, CNRS, ISA, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, France
| | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISA, France
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, France
| | - Florence Val
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
| | - Didier Andrivon
- IGEPP, INRAE, Institut Agro, Université Rennes, 35000 Rennes, France
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20
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Host genotype and genetic diversity shape the evolution of a novel bacterial infection. THE ISME JOURNAL 2021; 15:2146-2157. [PMID: 33603148 PMCID: PMC8245636 DOI: 10.1038/s41396-021-00911-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 01/31/2023]
Abstract
Pathogens continue to emerge from increased contact with novel host species. Whilst these hosts can represent distinct environments for pathogens, the impacts of host genetic background on how a pathogen evolves post-emergence are unclear. In a novel interaction, we experimentally evolved a pathogen (Staphylococcus aureus) in populations of wild nematodes (Caenorhabditis elegans) to test whether host genotype and genetic diversity affect pathogen evolution. After ten rounds of selection, we found that pathogen virulence evolved to vary across host genotypes, with differences in host metal ion acquisition detected as a possible driver of increased host exploitation. Diverse host populations selected for the highest levels of pathogen virulence, but infectivity was constrained, unlike in host monocultures. We hypothesise that population heterogeneity might pool together individuals that contribute disproportionately to the spread of infection or to enhanced virulence. The genomes of evolved populations were sequenced, and it was revealed that pathogens selected in distantly-related host genotypes diverged more than those in closely-related host genotypes. S. aureus nevertheless maintained a broad host range. Our study provides unique empirical insight into the evolutionary dynamics that could occur in other novel infections of wildlife and humans.
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21
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Yin R, Luo Z, Zhuang P, Lin Z, Kwoh CK. VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments. Bioinformatics 2021; 37:737-743. [PMID: 33241321 DOI: 10.1093/bioinformatics/btaa901] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 01/16/2023] Open
Abstract
MOTIVATION Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics. The evolution of influenza viruses remains to be the main obstacle in the effectiveness of antiviral treatments due to rapid mutations. Previous work has been investigated to reveal the determinants of virulence of the influenza A virus. To further facilitate flu surveillance, explicit detection of influenza virulence is crucial to protect public health from potential future pandemics. RESULTS In this article, we propose a weighted ensemble convolutional neural network (CNN) for the virulence prediction of influenza A viruses named VirPreNet that uses all eight segments. Firstly, mouse lethal dose 50 is exerted to label the virulence of infections into two classes, namely avirulent and virulent. A numerical representation of amino acids named ProtVec is applied to the eight-segments in a distributed manner to encode the biological sequences. After splittings and embeddings of influenza strains, the ensemble CNN is constructed as the base model on the influenza dataset of each segment, which serves as the VirPreNet's main part. Followed by a linear layer, the initial predictive outcomes are integrated and assigned with different weights for the final prediction. The experimental results on the collected influenza dataset indicate that VirPreNet achieves state-of-the-art performance combining ProtVec with our proposed architecture. It outperforms baseline methods on the independent testing data. Moreover, our proposed model reveals the importance of PB2 and HA segments on the virulence prediction. We believe that our model may provide new insights into the investigation of influenza virulence. AVAILABILITY AND IMPLEMENTATION Codes and data to generate the VirPreNet are publicly available at https://github.com/Rayin-saber/VirPreNet. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rui Yin
- School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Zihan Luo
- School of Electronic Information and Communication, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Pei Zhuang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Zhuoyi Lin
- School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
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Kahlon PS, Verin M, Hückelhoven R, Stam R. Quantitative resistance differences between and within natural populations of Solanum chilense against the oomycete pathogen Phytophthora infestans. Ecol Evol 2021; 11:7768-7778. [PMID: 34188850 PMCID: PMC8216925 DOI: 10.1002/ece3.7610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 01/01/2023] Open
Abstract
The wild tomato species Solanum chilense is divided into geographically and genetically distinct populations that show signs of defense gene selection and differential phenotypes when challenged with several phytopathogens, including the oomycete causal agent of late blight Phytophthora infestans. To better understand the phenotypic diversity of this disease resistance in S. chilense and to assess the effect of plant genotype versus pathogen isolate, respectively, we evaluated infection frequency in a systematic approach and with large sample sizes. We studied 85 genetically distinct individuals representing nine geographically separated populations of S. chilense. This showed that differences in quantitative resistance can be observed between but also within populations at the level of individual plants. Our data also did not reveal complete immunity in any of the genotypes. We further evaluated the resistance of a subset of the plants against P. infestans isolates with diverse virulence properties. This confirmed that the relative differences in resistance phenotypes between individuals were mainly determined by the plant genotype under consideration with modest effects of pathogen isolate used in the study. Thus, our report suggests that the observed quantitative resistance against P. infestans in natural populations of a wild tomato species S. chilense is the result of basal defense responses that depend on the host genotype and are pathogen isolate-unspecific.
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Affiliation(s)
| | - Melissa Verin
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Ralph Hückelhoven
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Remco Stam
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
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23
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Wale N, Duffy MA. The Use and Underuse of Model Systems in Infectious Disease Ecology and Evolutionary Biology. Am Nat 2021; 198:69-92. [PMID: 34143716 DOI: 10.1086/714595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractEver since biologists began studying the ecology and evolution of infectious diseases (EEID), laboratory-based model systems have been important for developing and testing theory. Yet what EEID researchers mean by the term "model systems" and what they want from them is unclear. This uncertainty hinders our ability to maximally exploit these systems, identify knowledge gaps, and establish effective new model systems. Here, we borrow a definition of model systems from the biomolecular sciences to assess how EEID researchers are (and are not) using 10 key model systems. According to this definition, model systems in EEID are not being used to their fullest and, in fact, cannot even be considered model systems. Research using these systems consistently addresses only two of the three fundamental processes that underlie disease dynamics-transmission and disease, but not recovery. Furthermore, studies tend to focus on only a few scales of biological organization that matter for disease ecology and evolution. Moreover, the field lacks an infrastructure to perform comparative analyses. We aim to begin a discussion of what we want from model systems, which would further progress toward a thorough, holistic understanding of EEID.
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24
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O'Hara NB, Franks SJ, Kane NC, Tittes S, Rest JS. Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population. BMC Ecol Evol 2021; 21:61. [PMID: 33882815 PMCID: PMC8060997 DOI: 10.1186/s12862-021-01789-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/08/2021] [Indexed: 11/27/2022] Open
Abstract
Background Pathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa population, which we previously demonstrated evolved an increase in disease susceptibility to a necrotrophic fungal pathogen following a drought. Results Previously, we combined a resurrection experiment with genome-wide sequencing of 124 pooled ancestral and descendant plants. Here, using these previously generated sequence data (Franks et al. in Mol Ecol 25(15):3622–3631, 2016), we show that well-characterized necrotrophic fungal pathogen response (NFPR) genes have evolved, as indicated by changes in allele frequency, between ancestors and descendants, with several of them identified as extreme FST outliers. The jasmonic acid (JA) signaling pathway in particular seems to underlie the evolution of disease susceptibility, in addition to its well characterized role in plastic disease response. We identify a list of 260 genes that are both NFPR genes and are differentially expressed in response to drought, based on publicly available data. We present evidence that five of these genes evolved between ancestors and descendants, suggesting that the drought acted as the evolutionary driver, and that the accompanying increase in disease susceptibility may have been a consequence of genetic pleiotropy. Conclusions Our study provides evidence that for this population, standing variation in NFPR genes is affected by natural selection related to climate change. Our results reveal potentially important candidates that may underlie trait evolution in both crops and natural systems. Additionally, this trade-off between adaptation to biotic and abiotic stresses is an example of how climate change can have diverse and unexpected consequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01789-7.
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Affiliation(s)
- Niamh B O'Hara
- Jacobs Technion-Cornell Institute, Cornell Tech, New York, NY, 10011, USA. .,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA. .,Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Steven J Franks
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Nolan C Kane
- Department of Ecology and Evolution, The University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Silas Tittes
- Department of Ecology and Evolution, The University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
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25
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Dutt A, Anthony R, Andrivon D, Jumel S, Le Roy G, Baranger A, Leclerc M, Le May C. Competition and facilitation among fungal plant parasites affect their life‐history traits. OIKOS 2021. [DOI: 10.1111/oik.07747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Agathe Dutt
- INRAE UMR 1349 Inst. de Génétique Environnement et Protection des Plantes (IGEPP), Domaine de la Motte Le Rheu France
- Inst. Agro, centre de Rennes Rennes France
| | - Rault Anthony
- INRAE UMR 1349 Inst. de Génétique Environnement et Protection des Plantes (IGEPP), Domaine de la Motte Le Rheu France
| | - Didier Andrivon
- INRAE UMR 1349 Inst. de Génétique Environnement et Protection des Plantes (IGEPP), Domaine de la Motte Le Rheu France
| | - Stéphane Jumel
- INRAE UMR 1349 Inst. de Génétique Environnement et Protection des Plantes (IGEPP), Domaine de la Motte Le Rheu France
- UMT PISOM INRA/Terres Inovia Le Rheu France
| | - Gwenola Le Roy
- INRAE UMR 1349 Inst. de Génétique Environnement et Protection des Plantes (IGEPP), Domaine de la Motte Le Rheu France
- UMT PISOM INRA/Terres Inovia Le Rheu France
| | - Alain Baranger
- INRAE UMR 1349 Inst. de Génétique Environnement et Protection des Plantes (IGEPP), Domaine de la Motte Le Rheu France
- UMT PISOM INRA/Terres Inovia Le Rheu France
| | - Melen Leclerc
- INRAE UMR 1349 Inst. de Génétique Environnement et Protection des Plantes (IGEPP), Domaine de la Motte Le Rheu France
| | - Christophe Le May
- INRAE UMR 1349 Inst. de Génétique Environnement et Protection des Plantes (IGEPP), Domaine de la Motte Le Rheu France
- UMT PISOM INRA/Terres Inovia Le Rheu France
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Abstract
The COVID-19 pandemic imposed new norms on human interactions, perhaps best reflected in the widespread application of social distancing. But social distancing is not a human invention and has evolved independently in species as dissimilar as apes and lobsters. Epidemics are common in the wild, where their spread is enhanced by animal movement and sociality while curtailed by population fragmentation, host behavior, and the immune systems of hosts. In the present article, we explore the phenomenon of behavioral immunity in wild animals as compared with humans and its relevance to the control of disease in nature. We start by explaining the evolutionary benefits and risks of sociality, look at how pathogens have shaped animal evolution, and provide examples of pandemics in wild animal populations. Then we review the known occurrences of social distancing in wild animals, the cues used to enforce it, and its efficacy in controlling the spread of diseases in nature.
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Affiliation(s)
- Mark J Butler
- Institute of Environment and Department of Biological Sciences, Florida International University, Miami, Florida, United States
| | - Donald C Behringer
- Emerging Pathogens Institute and Fisheries and Aquatic Sciences Program, University of Florida, Gainesville, Florida, United States
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27
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Dutta A, Croll D, McDonald BA, Barrett LG. Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen. Evol Appl 2021; 14:335-347. [PMID: 33664780 PMCID: PMC7896723 DOI: 10.1111/eva.13117] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/04/2020] [Accepted: 08/13/2020] [Indexed: 11/27/2022] Open
Abstract
Genetic diversity within pathogen populations is critically important for predicting pathogen evolution, disease outcomes and prevalence. However, we lack a good understanding of the processes maintaining genetic variation and constraints on pathogen life-history evolution. Here, we analysed interactions between 12 wheat host genotypes and 145 strains of Zymoseptoria tritici from five global populations to investigate the evolution and maintenance of variation in pathogen virulence and reproduction. We found a strong positive correlation between virulence (amount of leaf necrosis) and reproduction (pycnidia density within lesions), with substantial variation in both traits maintained within populations. On average, highly virulent isolates exhibited higher reproduction, which might increase transmission potential in agricultural fields planted to homogeneous hosts at a high density. We further showed that pathogen strains with a narrow host range (i.e. specialists) for reproduction were on average less virulent, and those with a broader host range (i.e. generalists) were on average less fecund on a given specific host. These costs associated with adaptation to different host genotypes might constrain the emergence of generalists by disrupting the directional evolution of virulence and fecundity. We conclude that selection favouring pathogen strains that are virulent across diverse hosts, coupled with selection that maximizes fecundity on specific hosts, may explain the maintenance of these pathogenicity traits within and among populations.
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Affiliation(s)
- Anik Dutta
- Plant PathologyInstitute of Integrative BiologyETH ZurichZurichSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary GeneticsInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Bruce A. McDonald
- Plant PathologyInstitute of Integrative BiologyETH ZurichZurichSwitzerland
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28
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Kahlon PS, Seta SM, Zander G, Scheikl D, Hückelhoven R, Joosten MHAJ, Stam R. Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance. Proc Biol Sci 2020; 287:20202723. [PMID: 33352079 DOI: 10.1098/rspb.2020.2723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Natural plant populations encounter strong pathogen pressure and defence-associated genes are known to be under selection dependent on the pressure by the pathogens. Here, we use populations of the wild tomato Solanum chilense to investigate natural resistance against Cladosporium fulvum, a well-known ascomycete pathogen of domesticated tomatoes. Host populations used are from distinct geographical origins and share a defined evolutionary history. We show that distinct populations of S. chilense differ in resistance against the pathogen. Screening for major resistance gene-mediated pathogen recognition throughout the whole species showed clear geographical differences between populations and complete loss of pathogen recognition in the south of the species range. In addition, we observed high complexity in a homologues of Cladosporium resistance (Hcr) locus, underlying the recognition of C. fulvum, in central and northern populations. Our findings show that major gene-mediated recognition specificity is diverse in a natural plant-pathosystem. We place major gene resistance in a geographical context that also defined the evolutionary history of that species. Data suggest that the underlying loci are more complex than previously anticipated, with small-scale gene recombination being possibly responsible for maintaining balanced polymorphisms in the populations that experience pathogen pressure.
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Affiliation(s)
- Parvinderdeep S Kahlon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Shallet Mindih Seta
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Gesche Zander
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Daniela Scheikl
- Section of Population Genetics, TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann Str. 2, 85354 Freising, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
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29
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Watkinson-Powell B, Gilligan CA, Cunniffe NJ. When Does Spatial Diversification Usefully Maximize the Durability of Crop Disease Resistance? PHYTOPATHOLOGY 2020; 110:1808-1820. [PMID: 32500812 DOI: 10.1094/phyto-07-19-0261-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Maximizing the durability of crop disease resistance genes in the face of pathogen evolution is a major challenge in modern agricultural epidemiology. Spatial diversification in the deployment of resistance genes, where susceptible and resistant fields are more closely intermixed, is predicted to drive lower epidemic intensities over evolutionary timescales. This is due to an increase in the strength of dilution effects, caused by pathogen inoculum challenging host tissue to which it is not well-specialized. The factors that interact with and determine the magnitude of this spatial suppressive effect are not currently well understood, however, leading to uncertainty over the pathosystems where such a strategy is most likely to be cost-effective. We model the effect on landscape scale disease dynamics of spatial heterogeneity in the arrangement of fields planted with either susceptible or resistant cultivars, and the way in which this effect depends on the parameters governing the pathosystem of interest. Our multiseason semidiscrete epidemiological model tracks spatial spread of wild-type and resistance-breaking pathogen strains, and incorporates a localized reservoir of inoculum, as well as the effects of within and between field transmission. The pathogen dispersal characteristics, any fitness cost(s) of the resistance-breaking trait, the efficacy of host resistance, and the length of the timeframe of interest all influence the strength of the spatial diversification effect. A key result is that spatial diversification has the strongest beneficial effect at intermediate fitness costs of the resistance-breaking trait, an effect driven by a complex set of nonlinear interactions. On the other hand, however, if the resistance-breaking strain is not fit enough to invade the landscape, then a partially effective resistance gene can result in spatial diversification actually worsening the epidemic. These results allow us to make general predictions of the types of system for which spatial diversification is most likely to be cost-effective, paving the way for potential economic modeling and pathosystem specific evaluation. These results highlight the importance of studying the effect of genetics on landscape scale spatial dynamics within host-pathogen disease systems.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Benjamin Watkinson-Powell
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
| | - Christopher A Gilligan
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
| | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, United Kingdom
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30
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Elrashdy F, Redwan EM, Uversky VN. Why COVID-19 Transmission Is More Efficient and Aggressive Than Viral Transmission in Previous Coronavirus Epidemics? Biomolecules 2020; 10:E1312. [PMID: 32933047 PMCID: PMC7565143 DOI: 10.3390/biom10091312] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a pandemic of coronavirus disease 2019 (COVID-19). The worldwide transmission of COVID-19 from human to human is spreading like wildfire, affecting almost every country in the world. In the past 100 years, the globe did not face a microbial pandemic similar in scale to COVID-19. Taken together, both previous outbreaks of other members of the coronavirus family (severe acute respiratory syndrome (SARS-CoV) and middle east respiratory syndrome (MERS-CoV)) did not produce even 1% of the global harm already inflicted by COVID-19. There are also four other CoVs capable of infecting humans (HCoVs), which circulate continuously in the human population, but their phenotypes are generally mild, and these HCoVs received relatively little attention. These dramatic differences between infection with HCoVs, SARS-CoV, MERS-CoV, and SARS-CoV-2 raise many questions, such as: Why is COVID-19 transmitted so quickly? Is it due to some specific features of the viral structure? Are there some specific human (host) factors? Are there some environmental factors? The aim of this review is to collect and concisely summarize the possible and logical answers to these questions.
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Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy School of Medicine, Cairo University, Cairo 11562, Egypt;
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290 Moscow, Russia
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Jiao J, Gilchrist MA, Fefferman NH. The impact of host metapopulation structure on short-term evolutionary rescue in the face of a novel pathogenic threat. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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32
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Goss EM, Kendig AE, Adhikari A, Lane B, Kortessis N, Holt RD, Clay K, Harmon PF, Flory SL. Disease in Invasive Plant Populations. ANNUAL REVIEW OF PHYTOPATHOLOGY 2020; 58:97-117. [PMID: 32516034 DOI: 10.1146/annurev-phyto-010820-012757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Non-native invasive plants can establish in natural areas, where they can be ecologically damaging and costly to manage. Like cultivated plants, invasive plants can experience a relatively disease-free period upon introduction and accumulate pathogens over time. Diseases of invasive plant populations are infrequently studied compared to diseases of agriculture, forestry, and even native plant populations. We evaluated similarities and differences in the processes that are likely to affect pathogen accumulation and disease in invasive plants compared to cultivated plants, which are the dominant focus of the field of plant pathology. Invasive plants experience more genetic, biotic, and abiotic variation across space and over time than cultivated plants, which is expected to stabilize the ecological and evolutionary dynamics of interactions with pathogens and possibly weaken the efficacy of infectious disease in their control. Although disease is expected to be context dependent, the widespread distribution of invasive plants makes them important pathogen reservoirs. Research on invasive plant diseases can both protect crops and help manage invasive plant populations.
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Affiliation(s)
- Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA;
| | - Amy E Kendig
- Agronomy Department, University of Florida, Gainesville, Florida 32611, USA
| | - Ashish Adhikari
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA
| | - Brett Lane
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA
| | - Nicholas Kortessis
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Robert D Holt
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Keith Clay
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana 70118, USA
| | - Philip F Harmon
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA
| | - S Luke Flory
- Agronomy Department, University of Florida, Gainesville, Florida 32611, USA
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33
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Gibson AK, Baffoe-Bonnie H, Penley MJ, Lin J, Owens R, Khalid A, Morran LT. The evolution of parasite host range in heterogeneous host populations. J Evol Biol 2020; 33:773-782. [PMID: 32086852 PMCID: PMC7275899 DOI: 10.1111/jeb.13608] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/24/2020] [Accepted: 02/11/2020] [Indexed: 01/07/2023]
Abstract
Theory on the evolution of niche width argues that resource heterogeneity selects for niche breadth. For parasites, this theory predicts that parasite populations will evolve, or maintain, broader host ranges when selected in genetically diverse host populations relative to homogeneous host populations. To test this prediction, we selected the bacterial parasite Serratia marcescens to kill Caenorhabditis elegans in populations that were genetically heterogeneous (50% mix of two experimental genotypes) or homogeneous (100% of either genotype). After 20 rounds of selection, we compared the host range of selected parasites by measuring parasite fitness (i.e. virulence, the selected fitness trait) on the two focal host genotypes and on a novel host genotype. As predicted, heterogeneous host populations selected for parasites with a broader host range: these parasite populations gained or maintained virulence on all host genotypes. This result contrasted with selection in homogeneous populations of one host genotype. Here, host range contracted, with parasite populations gaining virulence on the focal host genotype and losing virulence on the novel host genotype. This pattern was not, however, repeated with selection in homogeneous populations of the second host genotype: these parasite populations did not gain virulence on the focal host genotype, nor did they lose virulence on the novel host genotype. Our results indicate that host heterogeneity can maintain broader host ranges in parasite populations. Individual host genotypes, however, vary in the degree to which they select for specialization in parasite populations.
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Affiliation(s)
- Amanda K Gibson
- Department of Biology, Emory University, Atlanta, GA 30322
- Department of Biology, University of Virginia, Virginia 22902, USA
| | | | | | - Julie Lin
- Department of Biology, Emory University, Atlanta, GA 30322
| | - Raythe Owens
- Department of Biology, Emory University, Atlanta, GA 30322
| | - Arooj Khalid
- Department of Biology, Emory University, Atlanta, GA 30322
| | - Levi T. Morran
- Department of Biology, Emory University, Atlanta, GA 30322
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34
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Genus-level change in aggressiveness with continuous invasions: a phylogenetically-informed Bayesian quantile regression. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02229-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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Cappelli SL, Pichon NA, Kempel A, Allan E. Sick plants in grassland communities: a growth-defense trade-off is the main driver of fungal pathogen abundance. Ecol Lett 2020; 23:1349-1359. [PMID: 32455502 DOI: 10.1111/ele.13537] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/29/2020] [Accepted: 04/30/2020] [Indexed: 01/21/2023]
Abstract
Aboveground fungal pathogens can substantially reduce biomass production in grasslands. However, we lack a mechanistic understanding of the drivers of fungal pathogen infection and impact. Using a grassland global change and biodiversity experiment we show that the trade-off between plant growth and defense is the main determinant of infection incidence. In contrast, nitrogen addition only indirectly increased incidence via shifting plant communities towards faster growing species. Plant diversity did not decrease incidence, likely because spillover of generalist pathogens or dominance of susceptible plants counteracted negative diversity effects. A fungicide treatment increased plant biomass production and high levels of infection incidence were associated with reduced biomass. However, pathogen impact was context dependent and infection incidence reduced biomass more strongly in diverse communities. Our results show that a growth-defense trade-off is the key driver of pathogen incidence, but pathogen impact is determined by several mechanisms and may depend on pathogen community composition.
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Affiliation(s)
- Seraina L Cappelli
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Noémie A Pichon
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Anne Kempel
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Eric Allan
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
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36
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Märkle H, Tellier A. Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments. PLoS Comput Biol 2020; 16:e1007668. [PMID: 32203545 PMCID: PMC7156111 DOI: 10.1371/journal.pcbi.1007668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 04/14/2020] [Accepted: 01/19/2020] [Indexed: 01/27/2023] Open
Abstract
There is a long-standing interest in understanding host-parasite coevolutionary dynamics and associated fitness effects. Increasing amounts of genomic data for both interacting species offer a promising source to identify candidate loci and to infer the main parameters of the past coevolutionary history. However, so far no method exists to perform the latter. By coupling a gene-for-gene model with coalescent simulations, we first show that three types of biological costs, namely, resistance, infectivity and infection, define the allele frequencies at the internal equilibrium point of the coevolution model. These in return determine the strength of selective signatures at the coevolving host and parasite loci. We apply an Approximate Bayesian Computation (ABC) approach on simulated datasets to infer these costs by jointly integrating host and parasite polymorphism data at the coevolving loci. To control for the effect of genetic drift on coevolutionary dynamics, we assume that 10 or 30 repetitions are available from controlled experiments or several natural populations. We study two scenarios: 1) the cost of infection and population sizes (host and parasite) are unknown while costs of infectivity and resistance are known, and 2) all three costs are unknown while populations sizes are known. Using the ABC model choice procedure, we show that for both scenarios, we can distinguish with high accuracy pairs of coevolving host and parasite loci from pairs of neutrally evolving loci, though the statistical power decreases with higher cost of infection. The accuracy of parameter inference is high under both scenarios especially when using both host and parasite data because parasite polymorphism data do inform on costs applying to the host and vice-versa. As the false positive rate to detect pairs of genes under coevolution is small, we suggest that our method complements recently developed methods to identify host and parasite candidate loci for functional studies.
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Affiliation(s)
- Hanna Märkle
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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37
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Understanding the Evolutionary Ecology of host--pathogen Interactions Provides Insights into the Outcomes of Insect Pest Biocontrol. Viruses 2020; 12:v12020141. [PMID: 31991772 PMCID: PMC7077243 DOI: 10.3390/v12020141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 01/07/2023] Open
Abstract
The use of viral pathogens to control thepopulation size of pest insects has produced both successful and unsuccessful outcomes. Here, we investigate whether those biocontrol successes and failures can be explained by key ecological and evolutionary processes between hosts and pathogens. Specifically, we examine how heterogeneity inpathogen transmission, ecological and evolutionary tradeoffs, andpathogen diversity affect insect population density and thus successful control. Wefirst review theexisting literature and then use numerical simulations of mathematical models to further explore these processes. Our results show that thecontrol of insect densities using viruses depends strongly on theheterogeneity of virus transmission among insects. Overall, increased heterogeneity of transmission reduces theeffect of viruses on insect densities and increases thelong-term stability of insect populations. Lower equilibrium insect densities occur when transmission is heritable and when there is atradeoff between mean transmission and insect fecundity compared to when theheterogeneity of transmission arises from non-genetic sources. Thus, theheterogeneity of transmission is akey parameter that regulates thelong-term population dynamics of insects and their pathogens. Wealso show that both heterogeneity of transmission and life-history tradeoffs modulate characteristics of population dynamics such as thefrequency and intensity of ``boom--bust" population cycles. Furthermore, we show that because of life-history tradeoffs affecting thetransmission rate, theuse of multiple pathogen strains is more effective than theuse of asingle strain to control insect densities only when thepathogen strains differ considerably intheir transmission characteristics. By quantifying theeffects of ecology and evolution on population densities, we are able to offer recommendations to assess thelong-term effects of classical biocontrol.
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38
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Živković D, John S, Verin M, Stephan W, Tellier A. Neutral genomic signatures of host-parasite coevolution. BMC Evol Biol 2019; 19:230. [PMID: 31856710 PMCID: PMC6924072 DOI: 10.1186/s12862-019-1556-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations. Results We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time. Conclusions Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species.
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Affiliation(s)
- Daniel Živković
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
| | - Sona John
- Section of Population Genetics, Technical University of Munich, Freising, Germany
| | - Mélissa Verin
- Section of Population Genetics, Technical University of Munich, Freising, Germany.,Department of Mathematics and Statistics, Queen's University, Kingston, Ontario, Canada
| | - Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Aurélien Tellier
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
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39
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Mestre A, Poulin R, Hortal J. A niche perspective on the range expansion of symbionts. Biol Rev Camb Philos Soc 2019; 95:491-516. [DOI: 10.1111/brv.12574] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Alexandre Mestre
- Cavanilles Institute of Biodiversity and Evolutionary BiologyUniversity of Valencia Av. Dr. Moliner 50, 46100 Burjassot Spain
- Department of BiologyUniversity of Concordia Richard J. Renaud Science Complex, 7141 Sherbrooke W., H4B 1R6 Montreal Canada
| | - Robert Poulin
- Department of ZoologyUniversity of Otago 340 Great King Street, 9054 Dunedin New Zealand
| | - Joaquín Hortal
- Department of Biogeography and Global ChangeMuseo Nacional de Ciencias Naturales (MNCN‐CSIC) C/José Gutiérrez Abascal 2, 28006 Madrid Spain
- Departamento de EcologiaICB, Universidade Federal de Goiás (UFG), Rodovia Goiânia‐Nerópolis Km 5, Campus II, Setor Itatiaia, Goiânia GO 74001‐970 Brazil
- cE3c–Centre for EcologyEvolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2 Piso 5, 1749‐016 Lisboa Portugal
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40
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Drenth A, McTaggart AR, Wingfield BD. Fungal clones win the battle, but recombination wins the war. IMA Fungus 2019; 10:18. [PMID: 32647622 PMCID: PMC7325676 DOI: 10.1186/s43008-019-0020-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
Clonal reproduction is common in fungi and fungal-like organisms during epidemics and invasion events. The success of clonal fungi shaped systems for their classification and some pathogens are tacitly treated as asexual. We argue that genetic recombination driven by sexual reproduction must be a starting hypothesis when dealing with fungi for two reasons: (1) Clones eventually crash because they lack adaptability; and (2) fungi find a way to exchange genetic material through recombination, whether sexual, parasexual, or hybridisation. Successful clones may prevail over space and time, but they are the product of recombination and the next successful clone will inevitably appear. Fungal pathogen populations are dynamic rather than static, and they need genetic recombination to adapt to a changing environment.
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Affiliation(s)
- André Drenth
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD 4102 Australia
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD 4102 Australia.,Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, Gauteng South Africa
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, Gauteng South Africa
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41
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One Small RNA of Fusarium graminearum Targets and Silences CEBiP Gene in Common Wheat. Microorganisms 2019; 7:microorganisms7100425. [PMID: 31600909 PMCID: PMC6843203 DOI: 10.3390/microorganisms7100425] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/04/2019] [Accepted: 10/06/2019] [Indexed: 12/24/2022] Open
Abstract
The pathogenic fungus Fusarium graminearum (F. graminearum), causing Fusarium head blight (FHB) or scab, is one of the most important cereal killers worldwide, exerting great economic and agronomic losses on global grain production. To repress pathogen invasion, plants have evolved a sophisticated innate immunity system for pathogen recognition and defense activation. Simultaneously, pathogens continue to evolve more effective means of invasion to conquer plant resistance systems. In the process of co-evolution of plants and pathogens, several small RNAs (sRNAs) have been proved in regulating plant immune response and plant-microbial interaction. In this study, we report that a F. graminearum sRNA (Fg-sRNA1) can suppress wheat defense response by targeting and silencing a resistance-related gene, which codes a Chitin Elicitor Binding Protein (TaCEBiP). Transcriptional level evidence indicates that Fg-sRNA1 can target TaCEBiP mRNA and trigger silencing of TaCEBiP in vivo, and in Nicotiana benthamiana (N. benthamiana) plants, Western blotting experiments and YFP Fluorescence observation proofs show that Fg-sRNA1 can suppress the accumulation of protein coding by TaCEBiP gene in vitro. F. graminearum PH-1 strain displays a weakening ability to invasion when Barley stripe mosaic virus (BSMV) vector induces effective silencing Fg-sRNA1 in PH-1 infected wheat plants. Taken together, our results suggest that a small RNA from F. graminearum can target and silence the wheat TaCEBiP gene to enhance invasion of F. graminearum.
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42
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Stam R, Silva-Arias GA, Tellier A. Subsets of NLR genes show differential signatures of adaptation during colonization of new habitats. THE NEW PHYTOLOGIST 2019; 224:367-379. [PMID: 31230368 DOI: 10.1111/nph.16017] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
Nucleotide binding site, leucine-rich repeat receptors (NLRs) are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonization of novel habitats in a model tomato species, Solanum chilense. We used R-gene enrichment sequencing to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonization by resequencing whole genomes from three S. chilense plants from three key populations and performing approximate Bayesian computation using data from the 14 populations. Using these parameters, we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution and identified small subsets of outlier NLRs exhibiting signatures of selection across populations. NLRs under selection between habitats are more often helper genes, whereas those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R-gene adaptation during colonization of different habitats.
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Affiliation(s)
- Remco Stam
- Phytopathology, Technical University Munich, 85354, Freising, Germany
- Population Genetics, Technical University Munich, 85354, Freising, Germany
| | | | - Aurelien Tellier
- Population Genetics, Technical University Munich, 85354, Freising, Germany
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43
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Abstract
Strategies to manage plant disease-from use of resistant varieties to crop rotation, elimination of reservoirs, landscape planning, surveillance, quarantine, risk modeling, and anticipation of disease emergences-all rely on knowledge of pathogen host range. However, awareness of the multitude of factors that influence the outcome of plant-microorganism interactions, the spatial and temporal dynamics of these factors, and the diversity of any given pathogen makes it increasingly challenging to define simple, all-purpose rules to circumscribe the host range of a pathogen. For bacteria, fungi, oomycetes, and viruses, we illustrate that host range is often an overlapping continuum-more so than the separation of discrete pathotypes-and that host jumps are common. By setting the mechanisms of plant-pathogen interactions into the scales of contemporary land use and Earth history, we propose a framework to assess the frontiers of host range for practical applications and research on pathogen evolution.
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Affiliation(s)
| | - Benoît Moury
- Pathologie Végétale, INRA, 84140, Montfavet, France;
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44
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Burdon JJ. Lessons from a Life in Time and Space. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:1-13. [PMID: 31082308 DOI: 10.1146/annurev-phyto-082718-095938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A research career investigating epidemiological and evolutionary patterns in both natural and crop host-pathogen systems emphasizes the need for flexibility in thinking and a willingness to adopt ideas from a wide diversity of subdisciplines. Here, I reflect on the pivotal issues, research areas, and interactions, including the role of science management, that shaped my career in the hope of demonstrating that career paths and collaborations in science can be as diverse and unpredictable as the natural world in which we study our organisms of choice.
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45
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González R, Butković A, Elena SF. Role of host genetic diversity for susceptibility-to-infection in the evolution of virulence of a plant virus. Virus Evol 2019; 5:vez024. [PMID: 31768264 PMCID: PMC6863064 DOI: 10.1093/ve/vez024] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Predicting viral emergence is difficult due to the stochastic nature of the underlying processes and the many factors that govern pathogen evolution. Environmental factors affecting the host, the pathogen and the interaction between both are key in emergence. In particular, infectious disease dynamics are affected by spatiotemporal heterogeneity in their environments. A broad knowledge of these factors will allow better estimating where and when viral emergence is more likely to occur. Here, we investigate how the population structure for susceptibility-to-infection genes of the plant Arabidopsis thaliana shapes the evolution of Turnip mosaic virus (TuMV). For doing so we have evolved TuMV lineages in two radically different host population structures: (1) a metapopulation subdivided into six demes (subpopulations); each one being composed of individuals from only one of six possible A. thaliana ecotypes and (2) a well-mixed population constituted by equal number of plants from the same six A. thaliana ecotypes. These two populations were evolved for twelve serial passages. At the end of the experimental evolution, we found faster adaptation of TuMV to each ecotype in the metapopulation than in the well-mixed heterogeneous host populations. However, viruses evolved in well-mixed populations were more pathogenic and infectious than viruses evolved in the metapopulation. Furthermore, the viruses evolved in the demes showed stronger signatures of local specialization than viruses evolved in the well-mixed populations. These results illustrate how the genetic diversity of hosts in an experimental ecosystem favors the evolution of virulence of a pathogen.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, València 46980, Spain
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, València 46980, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, València 46980, Spain.,The Santa Fe Institute, Santa Fe, 1399 Hyde Park Road, NM 87501, USA
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46
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Numminen E, Vaumourin E, Parratt SR, Poulin L, Laine AL. Variation and correlations between sexual, asexual and natural enemy resistance life-history traits in a natural plant pathogen population. BMC Evol Biol 2019; 19:142. [PMID: 31299905 PMCID: PMC6624897 DOI: 10.1186/s12862-019-1468-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/26/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Understanding the mechanisms by which diversity is maintained in pathogen populations is critical for epidemiological predictions. Life-history trade-offs have been proposed as a hypothesis for explaining long-term maintenance of variation in pathogen populations, yet the empirical evidence supporting trade-offs has remained mixed. This is in part due to the challenges of documenting successive pathogen life-history stages in many pathosystems. Moreover, little is understood of the role of natural enemies of pathogens on their life-history evolution. RESULTS We characterize life-history-trait variation and possible trade-offs in fungal pathogen Podosphaera plantaginis infecting the host plant Plantago lanceolata. We measured the timing of both asexual and sexual stages, as well as resistance to a hyperparasite of seven pathogen strains that vary in their prevalence in nature. We find significant variation among the strains in their life-history traits that constitute the infection cycle, but no evidence for trade-offs among pathogen development stages, apart from fast pathogen growth coninciding with fast hyperparasite growth. Also, the seemingly least fit pathogen strain was the most prevalent in the nature. CONCLUSIONS We conclude that in the nature environmental variation, and interactions with the antagonists of pathogens themselves may maintain variation in pathogen populations.
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Affiliation(s)
- Elina Numminen
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland.
| | - Elise Vaumourin
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland
| | - Steven R Parratt
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland.,University of Liverpool, Institute of Integrative Biology, Liverpool, L69 3BX, UK
| | - Lucie Poulin
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland.,Université de Nantes, Faculté des Sciences et des Techniques, Laboratoire de Biologie et de Pathologie Végétales (LBPV), EA 1157, SFR 4207 QUASAV, 2, rue de la Houssinière, BP 92 208, F-44322, Nantes Cedex 3, France
| | - Anna-Liisa Laine
- Department of Biosciences, University of Helsinki, Viikinkaari 1, PO Box 65, FI-00014, Helsinki, Finland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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Affiliation(s)
- Ian F Miller
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 05844, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 05844, USA. .,Woodrow Wilson School of Public and International Affairs. Princeton University, Princeton, NJ 08544, USA
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Peyraud R, Mbengue M, Barbacci A, Raffaele S. Intercellular cooperation in a fungal plant pathogen facilitates host colonization. Proc Natl Acad Sci U S A 2019; 116:3193-3201. [PMID: 30728304 PMCID: PMC6386666 DOI: 10.1073/pnas.1811267116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains, however, largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram toward division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during Arabidopsis thaliana colonization compared with in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta Using a multicell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.
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Affiliation(s)
- Rémi Peyraud
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de la Recherche Agronomique (INRA), CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Malick Mbengue
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de la Recherche Agronomique (INRA), CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Adelin Barbacci
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de la Recherche Agronomique (INRA), CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de la Recherche Agronomique (INRA), CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
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Mwangi JM, Niere B, Finckh MR, Krüssel S, Kiewnick S. Reproduction and life history traits of a resistance breaking Globodera pallida population. J Nematol 2019. [DOI: 10.21307/jofnem-2019-079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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50
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Mariette N, Kröner A, Mabon R, Montarry J, Marquer B, Corbière R, Androdias A, Andrivon D. A Trade-Off Between Sporangia Size and Number Exists in the Potato Late Blight Pathogen Phytophthora infestans, and Is Not Altered by Biotic and Abiotic Factors. FRONTIERS IN PLANT SCIENCE 2018; 9:1841. [PMID: 30619410 PMCID: PMC6305756 DOI: 10.3389/fpls.2018.01841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The negative relationship between offspring size and number is a classic example of trade-off between life-history traits, reported many times in animal and plant species. Here, we wanted to ascertain whether such a trade-off occurred in the oomycete Phytophthora infestans, and whether it was impacted by biotic and abiotic factors. We thus conducted three infection experiments under controlled conditions and measured the number and the size of sporangia (asexual propagules) produced on potato by different P. infestans isolates. In all experiments, we observed a negative relationship between sporangia size and number, demonstrating the existence of a trade-off. Moreover, although the potato host cultivar, temperature and host of origin (tomato or potato) all affected sporangia number, sporangia size or both, none of these biotic and abiotic factors did change the trade-off. Therefore, the trade-off between sporangia size and number could maintain the polyphenism for these traits in P. infestans populations, and favors the coexistence of distinct reproductive strategies within this species. Our results emphasize the relevance to focus on the relationship between offspring size and number in other fungal plant pathogens, as well as to study the impact of offspring size on fitness-linked traits (virulence and disease lesion development) in these organisms.
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Affiliation(s)
| | | | | | | | | | | | | | - Didier Andrivon
- INRA, UMR1349 Institute for Genetics, Environment and Plant Protection, Le Rheu, France
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