1
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Ameline C, Voegtli F, Andras J, Dexter E, Engelstädter J, Ebert D. Genetic slippage after sex maintains diversity for parasite resistance in a natural host population. SCIENCE ADVANCES 2022; 8:eabn0051. [PMID: 36399570 PMCID: PMC9674289 DOI: 10.1126/sciadv.abn0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Although parasite-mediated selection is a major driver of host evolution, its influence on genetic variation for parasite resistance is not yet well understood. We monitored resistance in a large population of the planktonic crustacean Daphnia magna over 8 years, as it underwent yearly epidemics of the bacterial pathogen Pasteuria ramosa. We observed cyclic dynamics of resistance: Resistance increased throughout the epidemics, but susceptibility was restored each spring when hosts hatched from sexual resting stages. Host resting stages collected across the year showed that largely resistant host populations can produce susceptible sexual offspring. A genetic model of resistance developed for this host-parasite system, based on multiple loci and strong epistasis, is in partial agreement with our findings. Our results reveal that, despite strong selection for resistance in a natural host population, genetic slippage after sexual reproduction can be a strong factor for the maintenance of genetic diversity of host resistance.
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Affiliation(s)
- Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Felix Voegtli
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Jason Andras
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Eric Dexter
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
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2
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Ebert D. Daphnia as a versatile model system in ecology and evolution. EvoDevo 2022; 13:16. [PMID: 35941607 PMCID: PMC9360664 DOI: 10.1186/s13227-022-00199-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
Water fleas of the genus Daphnia have been a model system for hundreds of years and is among the best studied ecological model organisms to date. Daphnia are planktonic crustaceans with a cyclic parthenogenetic life-cycle. They have a nearly worldwide distribution, inhabiting standing fresh- and brackish water bodies, from small temporary pools to large lakes. Their predominantly asexual reproduction allows for the study of phenotypes excluding genetic variation, enabling us to separate genetic from non-genetic effects. Daphnia are often used in studies related to ecotoxicology, predator-induced defence, host–parasite interactions, phenotypic plasticity and, increasingly, in evolutionary genomics. The most commonly studied species are Daphnia magna and D. pulex, for which a rapidly increasing number of genetic and genomic tools are available. Here, I review current research topics, where the Daphnia model system plays a critical role.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
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3
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Leigh DM, Peranić K, Prospero S, Cornejo C, Ćurković-Perica M, Kupper Q, Nuskern L, Rigling D, Ježić M. Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections. Virus Evol 2021; 7:veab101. [PMID: 35299787 PMCID: PMC8923234 DOI: 10.1093/ve/veab101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023] Open
Abstract
Intra-host dynamics are a core component of virus evolution but most intra-host data come from a narrow range of hosts or experimental infections. Gaining broader information on the intra-host diversity and dynamics of naturally occurring virus infections is essential to our understanding of evolution across the virosphere. Here we used PacBio long-read HiFi sequencing to characterize the intra-host populations of natural infections of the RNA mycovirus Cryphonectria hypovirus 1 (CHV1). CHV1 is a biocontrol agent for the chestnut blight fungus (Cryphonectria parasitica), which co-invaded Europe alongside the fungus. We characterized the mutational and haplotypic intra-host virus diversity of thirty-eight natural CHV1 infections spread across four locations in Croatia and Switzerland. Intra-host CHV1 diversity values were shaped by purifying selection and accumulation of mutations over time as well as epistatic interactions within the host genome at defense loci. Geographical landscape features impacted CHV1 inter-host relationships through restricting dispersal and causing founder effects. Interestingly, a small number of intra-host viral haplotypes showed high sequence similarity across large geographical distances unlikely to be linked by dispersal.
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Affiliation(s)
- Deborah M Leigh
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Karla Peranić
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
| | - Simone Prospero
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Carolina Cornejo
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | | | | | - Lucija Nuskern
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
| | - Daniel Rigling
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Marin Ježić
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
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4
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Matoo OB, Neiman M. Bringing Disciplines and People Together to Characterize the Plastic and Genetic Responses of Molluscs to Environmental Change. Integr Comp Biol 2021; 61:1689-1698. [PMID: 34435639 PMCID: PMC8699093 DOI: 10.1093/icb/icab186] [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] [Indexed: 11/12/2022] Open
Abstract
Molluscs are remarkably diverse and are found across nearly all ecosystems, meaning that members of this ancient animal phylum provide a powerful means to study genomic-phenotype connections in a climate change framework. Recent advances in genomic sequencing technologies and genome assembly approaches finally allow the relatively cheap and tractable assembly of high-quality mollusc genome resources. After a brief review of these issues and advances, we use a case-study approach to provide some concrete examples of phenotypic plasticity and genomic adaptation in molluscs in response to environmental factors expected to be influenced by climate change. Our goal is to use molluscs as a "common currency" to demonstrate how organismal and evolutionary biologists can use natural systems to make phenotype-genotype connections in the context of changing environments. In parallel, we emphasize the critical need to collaborate and integrate findings across taxa and disciplines in order to use new data and information to advance our understanding of mollusc biology in the context of global environmental change. We end with a brief synthetic summary of the papers inspired by the 2021 SICB Symposium "Genomic Perspectives in Comparative Physiology of Molluscs: Integration across Disciplines".
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Affiliation(s)
- Omera B Matoo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City 52242, IA, USA.,Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City 52242, IA, USA
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5
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Fredericksen M, Ameline C, Krebs M, Hüssy B, Fields PD, Andras JP, Ebert D. Infection phenotypes of a coevolving parasite are highly diverse, structured, and specific. Evolution 2021; 75:2540-2554. [PMID: 34431523 PMCID: PMC9290032 DOI: 10.1111/evo.14323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022]
Abstract
Understanding how diversity is maintained in natural populations is a major goal of evolutionary biology. In coevolving hosts and parasites, negative frequency-dependent selection is one mechanism predicted to maintain genetic variation. While much is known about host diversity, parasite diversity remains understudied in coevolutionary research. Here, we survey natural diversity in a bacterial parasite by characterizing infection phenotypes for over 50 isolates in relation to 12 genotypes of their host, Daphnia magna. We find striking phenotypic variation among parasite isolates, and we discover the parasite can infect its host through at least five different attachment sites. Variation in attachment success at each site is explained to varying degrees by host and parasite genotypes. A spatial correlation analysis showed that infectivity of different isolates does not correlate with geographic distance, meaning isolates from widespread populations are equally able to infect the host. Overall, our results reveal that infection phenotypes of this parasite are highly diverse. Our results are consistent with the prediction that under Red Queen coevolutionary dynamics both the host and the parasite should show high genetic diversity for traits of functional importance in their interactions.
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Affiliation(s)
- Maridel Fredericksen
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Michelle Krebs
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Benjamin Hüssy
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Jason P Andras
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland.,Department of Biological Sciences, Clapp Laboratory, Mount Holyoke College, South Hadley, Massachusetts
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
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6
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Bourgeois Y, Fields P, Bento G, Ebert D. Balancing selection for pathogen resistance reveals an intercontinental signature of Red Queen coevolution. Mol Biol Evol 2021; 38:4918-4933. [PMID: 34289047 PMCID: PMC8557431 DOI: 10.1093/molbev/msab217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The link between long-term host–parasite coevolution and genetic diversity is key to understanding genetic epidemiology and the evolution of resistance. The model of Red Queen host–parasite coevolution posits that high genetic diversity is maintained when rare host resistance variants have a selective advantage, which is believed to be the mechanistic basis for the extraordinarily high levels of diversity at disease-related genes such as the major histocompatibility complex in jawed vertebrates and R-genes in plants. The parasites that drive long-term coevolution are, however, often elusive. Here we present evidence for long-term balancing selection at the phenotypic (variation in resistance) and genomic (resistance locus) level in a particular host–parasite system: the planktonic crustacean Daphnia magna and the bacterium Pasteuria ramosa. The host shows widespread polymorphisms for pathogen resistance regardless of geographic distance, even though there is a clear genome-wide pattern of isolation by distance at other sites. In the genomic region of a previously identified resistance supergene, we observed consistent molecular signals of balancing selection, including higher genetic diversity, older coalescence times, and lower differentiation between populations, which set this region apart from the rest of the genome. We propose that specific long-term coevolution by negative-frequency-dependent selection drives this elevated diversity at the host's resistance loci on an intercontinental scale and provide an example of a direct link between the host’s resistance to a virulent pathogen and the large-scale diversity of its underlying genes.
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Affiliation(s)
- Yann Bourgeois
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Gilberto Bento
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
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7
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Ameline C, Bourgeois Y, Vögtli F, Savola E, Andras J, Engelstädter J, Ebert D. A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance. Mol Biol Evol 2021; 38:1512-1528. [PMID: 33258959 PMCID: PMC8042741 DOI: 10.1093/molbev/msaa311] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Parasites are a major evolutionary force, driving adaptive responses in host populations. Although the link between phenotypic response to parasite-mediated natural selection and the underlying genetic architecture often remains obscure, this link is crucial for understanding the evolution of resistance and predicting associated allele frequency changes in the population. To close this gap, we monitored the response to selection during epidemics of a virulent bacterial pathogen, Pasteuria ramosa, in a natural host population of Daphnia magna. Across two epidemics, we observed a strong increase in the proportion of resistant phenotypes as the epidemics progressed. Field and laboratory experiments confirmed that this increase in resistance was caused by selection from the local parasite. Using a genome-wide association study, we built a genetic model in which two genomic regions with dominance and epistasis control resistance polymorphism in the host. We verified this model by selfing host genotypes with different resistance phenotypes and scoring their F1 for segregation of resistance and associated genetic markers. Such epistatic effects with strong fitness consequences in host–parasite coevolution are believed to be crucial in the Red Queen model for the evolution of genetic recombination.
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Affiliation(s)
- Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Yann Bourgeois
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Felix Vögtli
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Eevi Savola
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Jason Andras
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Department of Biological Sciences, Clapp Laboratory, Mount Holyoke College, South Hadley, MA, USA
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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8
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Andras JP, Fields PD, Du Pasquier L, Fredericksen M, Ebert D. Genome-Wide Association Analysis Identifies a Genetic Basis of Infectivity in a Model Bacterial Pathogen. Mol Biol Evol 2021; 37:3439-3452. [PMID: 32658956 PMCID: PMC7743900 DOI: 10.1093/molbev/msaa173] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022] Open
Abstract
Knowledge of the genetic architecture of pathogen infectivity and host resistance is essential for a mechanistic understanding of coevolutionary processes, yet the genetic basis of these interacting traits remains unknown for most host-pathogen systems. We used a comparative genomic approach to explore the genetic basis of infectivity in Pasteuria ramosa, a Gram-positive bacterial pathogen of planktonic crustaceans that has been established as a model for studies of Red Queen host-pathogen coevolution. We sequenced the genomes of a geographically, phenotypically, and genetically diverse collection of P. ramosa strains and performed a genome-wide association study to identify genetic correlates of infection phenotype. We found multiple polymorphisms within a single gene, Pcl7, that correlate perfectly with one common and widespread infection phenotype. We then confirmed this perfect association via Sanger sequencing in a large and diverse sample set of P. ramosa clones. Pcl7 codes for a collagen-like protein, a class of adhesion proteins known or suspected to be involved in the infection mechanisms of a number of important bacterial pathogens. Consistent with expectations under Red Queen coevolution, sequence variation of Pcl7 shows evidence of balancing selection, including extraordinarily high diversity and absence of geographic structure. Based on structural homology with a collagen-like protein of Bacillus anthracis, we propose a hypothesis for the structure of Pcl7 and the physical location of the phenotype-associated polymorphisms. Our results offer strong evidence for a gene governing infectivity and provide a molecular basis for further study of Red Queen dynamics in this model host-pathogen system.
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Affiliation(s)
- Jason P Andras
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA
| | - Peter D Fields
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Louis Du Pasquier
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Maridel Fredericksen
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Dieter Ebert
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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9
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An alternative route of bacterial infection associated with a novel resistance locus in the Daphnia-Pasteuria host-parasite system. Heredity (Edinb) 2020; 125:173-183. [PMID: 32561843 PMCID: PMC7490384 DOI: 10.1038/s41437-020-0332-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 06/07/2020] [Accepted: 06/07/2020] [Indexed: 11/23/2022] Open
Abstract
To understand the mechanisms of antagonistic coevolution, it is crucial to identify the genetics of parasite resistance. In the Daphnia magna–Pasteuria ramosa host–parasite system, the most important step of the infection process is the one in which P. ramosa spores attach to the host’s foregut. A matching-allele model (MAM) describes the host–parasite genetic interactions underlying attachment success. Here we describe a new P. ramosa genotype, P15, which, unlike previously studied genotypes, attaches to the host’s hindgut, not to its foregut. Host resistance to P15 attachment shows great diversity across natural populations. In contrast to P. ramosa genotypes that use foregut attachment, P15 shows some quantitative variation in attachment success and does not always lead to successful infections, suggesting that hindgut attachment represents a less-efficient infection mechanism than foregut attachment. Using a Quantitative Trait Locus (QTL) approach, we detect two significant QTLs in the host genome: one that co-localizes with the previously described D. magna PR locus of resistance to foregut attachment, and a second, major QTL located in an unlinked genomic region. We find no evidence of epistasis. Fine mapping reveals a genomic region, the D locus, of ~13 kb. The discovery of a second P. ramosa attachment site and of a novel host-resistance locus increases the complexity of this system, with implications for both for the coevolutionary dynamics (e.g., Red Queen and the role of recombination), and for the evolution and epidemiology of the infection process.
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10
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Hall MD, Routtu J, Ebert D. Dissecting the genetic architecture of a stepwise infection process. Mol Ecol 2019; 28:3942-3957. [PMID: 31283079 DOI: 10.1111/mec.15166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023]
Abstract
How a host fights infection depends on an ordered sequence of steps, beginning with attempts to prevent a pathogen from establishing an infection, through to steps that mitigate a pathogen's control of host resources or minimize the damage caused during infection. Yet empirically characterizing the genetic basis of these steps remains challenging. Although each step is likely to have a unique genetic and environmental signature, and may therefore respond to selection in different ways, events that occur earlier in the infection process can mask or overwhelm the contributions of subsequent steps. In this study, we dissect the genetic architecture of a stepwise infection process using a quantitative trait locus (QTL) mapping approach. We control for variation at the first line of defence against a bacterial pathogen and expose downstream genetic variability related to the host's ability to mitigate the damage pathogens cause. In our model, the water-flea Daphnia magna, we found a single major effect QTL, explaining 64% of the variance, that is linked to the host's ability to completely block pathogen entry by preventing their attachment to the host oesophagus; this is consistent with the detection of this locus in previous studies. In susceptible hosts allowing attachment, however, a further 23 QTLs, explaining between 5% and 16% of the variance, were mapped to traits related to the expression of disease. The general lack of pleiotropy and epistasis for traits related to the different stages of the infection process, together with the wide distribution of QTLs across the genome, highlights the modular nature of a host's defence portfolio, and the potential for each different step to evolve independently. We discuss how isolating the genetic basis of individual steps can help to resolve discussion over the genetic architecture of host resistance.
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Affiliation(s)
- Matthew D Hall
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jarkko Routtu
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Molecular Ecology, Martin-Luther-Universität, Halle-Wittenberg, Germany
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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11
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Liu C, Gibson AK, Timper P, Morran LT, Tubbs RS. Rapid change in host specificity in a field population of the biological control organism Pasteuria penetrans. Evol Appl 2019; 12:744-756. [PMID: 30976307 PMCID: PMC6439493 DOI: 10.1111/eva.12750] [Citation(s) in RCA: 5] [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: 05/30/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/29/2022] Open
Abstract
In biological control, populations of both the biological control agent and the pest have the potential to evolve and even to coevolve. This feature marks the most powerful and unpredictable aspect of biological control strategies. In particular, evolutionary change in host specificity of the biological control agent could increase or decrease its efficacy. Here, we tested for change in host specificity in a field population of the biological control organism Pasteuria penetrans. Pasteuria penetrans is an obligate parasite of the plant parasitic nematodes Meloidogyne spp., which are major agricultural pests. From 2013 through 2016, we collected yearly samples of P. penetrans from eight plots in a field infested with M. arenaria. Plots were planted either with peanut (Arachis hypogaea) or with a rotation of peanut and soybean (Glycine max). To detect temporal change in host specificity, we tested P. penetrans samples annually for their ability to attach to (and thereby infect) four clonal lines of M. arenaria. After controlling for temporal variation in parasite abundance, we found that P. penetrans from each of the eight plots showed temporal variation in their attachment specificity to the clonal host lines. The trajectories of change in host specificity were largely unique to each plot. This result suggests that local forces, at the level of individual plots, drive change in specificity. We hypothesize that coevolution with local M. arenaria hosts may be one such force. Lastly, we observed an overall reduction in attachment rate with samples from rotation plots relative to samples from peanut plots. This result may reflect lower abundance of P. penetrans under crop rotation, potentially due to suppressed density of host nematodes. As a whole, the results show local change in specificity on a yearly basis, consistent with evolution of a biological control organism in its ability to infect and suppress its target pest.
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Affiliation(s)
- Chang Liu
- Department of Plant PathologyUniversity of GeorgiaTiftonGeorgia
| | | | | | | | - R. Scott Tubbs
- Crop and Soil Sciences, College of Agricultural and Environmental SciencesUniversity of GeorgiaTiftonGeorgia
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12
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Glander S, He F, Schmitz G, Witten A, Telschow A, de Meaux J. Assortment of Flowering Time and Immunity Alleles in Natural Arabidopsis thaliana Populations Suggests Immunity and Vegetative Lifespan Strategies Coevolve. Genome Biol Evol 2018; 10:2278-2291. [PMID: 30215800 PMCID: PMC6133262 DOI: 10.1093/gbe/evy124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/31/2022] Open
Abstract
The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host immunity, however, has seldom been documented. Optimal investment into immunity is expected to decrease with shortening lifespan, because a shorter life decreases the probability to encounter pathogens or enemies. Here, we document that in natural populations of Arabidopsis thaliana, the expression levels of immunity genes correlate positively with flowering time, which in annual species is a proxy for lifespan. Using a novel genetic strategy based on bulk-segregants, we partitioned flowering time-dependent from -independent immunity genes and could demonstrate that this positive covariation can be genetically separated. It is therefore not explained by the pleiotropic action of some major regulatory genes controlling both immunity and lifespan. Moreover, we find that immunity genes containing variants reported to impact fitness in natural field conditions are among the genes whose expression covaries most strongly with flowering time. Taken together, these analyses reveal that natural selection has likely assorted alleles promoting lower expression of immunity genes with alleles that decrease the duration of vegetative lifespan in A. thaliana and vice versa. This is the first study documenting a pattern of variation consistent with the impact that selection on flowering time is predicted to have on diversity in host immunity.
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Affiliation(s)
- Shirin Glander
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Germany
| | - Fei He
- Institute of Botany, University of Cologne, Germany
| | | | - Anika Witten
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Germany
| | - Arndt Telschow
- Institute for Evolution and Biodiversity, University of Münster, Germany
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13
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Andras JP, Fields PD, Ebert D. Spatial population genetic structure of a bacterial parasite in close coevolution with its host. Mol Ecol 2018; 27:1371-1384. [DOI: 10.1111/mec.14545] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Jason P. Andras
- Department of Biological Sciences; Clapp Laboratory; Mount Holyoke College; South Hadley MA USA
| | - Peter D. Fields
- Department of Environmental Sciences - Zoology; University of Basel; Basel Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences - Zoology; University of Basel; Basel Switzerland
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14
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Turko P, Tellenbach C, Keller E, Tardent N, Keller B, Spaak P, Wolinska J. Parasites driving host diversity: Incidence of disease correlated with Daphnia clonal turnover. Evolution 2018; 72:619-629. [PMID: 29238958 DOI: 10.1111/evo.13413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/16/2017] [Accepted: 12/05/2017] [Indexed: 11/30/2022]
Abstract
According to the Red Queen hypothesis, clonal diversity in asexual populations could be maintained by negative frequency-dependant selection by coevolving parasites. If common clones are selected against and rare clones gain a concomitant advantage, we expect that clonal turnover should be faster during parasite epidemics than between them. We tested this hypothesis exploring field data of the Daphnia-Caullerya host-parasite system. The clonal make-up and turnover of the Daphnia host population was tracked with high temporal resolution from 1998 until 2013, using first allozyme and later microsatellite markers. Significant differences in the clonal composition between random and infected subsamples of Daphnia populations were detected on six of seven tested occasions, confirming genetic specificity of the host-parasite interaction in this system. We used time series analysis to compare the rates of host clonal turnover to the incidence of parasitism, and found that Caullerya prevalence was significantly associated with microsatellite-based clonal turnover. As alternate hypotheses, we further tested whether turnover was related to a variety of biotic, abiotic, and host demographic parameters. Other significant correlates of turnover were cyanobacterial biomass and (weakly) temperature. Overall, parasitism seems to be a strong driver of host clonal turnover, in support of the Red Queen hypothesis.
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Affiliation(s)
- Patrick Turko
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Christoph Tellenbach
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Esther Keller
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Nadine Tardent
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Barbara Keller
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland.,Department of Systematic and Evolutionary Botany, University of Zurich, 8008 Zürich, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Justyna Wolinska
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany.,Department of Biology, Chemistry, and Pharmacy, Institute of Biology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany
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15
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Schenk H, Traulsen A, Gokhale CS. Chaotic provinces in the kingdom of the Red Queen. J Theor Biol 2017; 431:1-10. [PMID: 28757073 DOI: 10.1016/j.jtbi.2017.07.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 04/11/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Abstract
The interplay between parasites and their hosts is found in all kinds of species and plays an important role in understanding the principles of evolution and coevolution. Usually, the different genotypes of hosts and parasites oscillate in their abundances. The well-established theory of oscillatory Red Queen dynamics proposes an ongoing change in frequencies of the different types within each species. So far, it is unclear under what conditions Red Queen dynamics persists, especially when the number of types per species increases. Some models show that with many types of hosts and parasites or more species chaotic dynamics occur. In our analysis, an arbitrary number of types within two species are examined in a deterministic framework with constant or changing population size and very simple interactions. This general framework allows for analytical solutions for internal fixed points and their stability. The numerical analysis shows that for two species, once more than two types are considered per species, irregular dynamics in their frequencies can be observed in the long run. The nature of the dynamics depends strongly on the initial configuration of the system; the usual regular Red Queen oscillations are only observed when all types initially have similar abundance.
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Affiliation(s)
- Hanna Schenk
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann Str-2, Plön, 24306, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann Str-2, Plön, 24306, Germany
| | - Chaitanya S Gokhale
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann Str-2, Plön, 24306, Germany; New Zealand Institute for Advanced Study, Massey University, Albany, Private Bag 102904, North Shore Mail Centre, Auckland, 0745, New Zealand.
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16
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Abstract
Molecular and cellular studies reveal that the resistance of hosts to parasites and pathogens is a cascade-like process with multiple steps required to be passed for successful infection. By contrast, much of evolutionary reasoning is based on strongly simplified, one- or two-step infection processes with simple genetics or on resistance being a quantitative trait. Here we attempt a conceptual unification of these two perspectives with the aim of cross-fostering research and filling some of the gaps in our concepts of the ecology and evolution of disease. This conceptual unification has a profound impact on the way we understand the genetics and evolution of host resistance, ecological immunity, evolution of virulence, defence portfolios, and host-pathogen coevolution.
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Affiliation(s)
- Matthew D Hall
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Gilberto Bento
- Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Dieter Ebert
- Zoological Institute, University of Basel, Basel 4051, Switzerland; Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany.
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17
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da Silva J, Galbraith JD. Hill-Robertson interference maintained by Red Queen dynamics favours the evolution of sex. J Evol Biol 2017; 30:994-1010. [PMID: 28295769 DOI: 10.1111/jeb.13068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 02/17/2017] [Accepted: 03/06/2017] [Indexed: 12/21/2022]
Abstract
Although it is well established theoretically that selective interference among mutations (Hill-Robertson interference) favours meiotic recombination, genomewide mean rates of mutation and strengths of selection appear too low to support this as the mechanism favouring recombination in nature. A possible solution to this discrepancy between theory and observation is that selection is at least intermittently very strong due to the antagonistic coevolution between a host and its parasites. The Red Queen theory posits that such coevolution generates fitness epistasis among loci, which generates negative linkage disequilibrium among beneficial mutations, which in turn favours recombination. This theory has received only limited support. However, Red Queen dynamics without epistasis may provide the ecological conditions that maintain strong and frequent selective interference in finite populations that indirectly selects for recombination. This hypothesis is developed here through the simulation of Red Queen dynamics. This approach required the development of a method to calculate the exact frequencies of multilocus haplotypes after recombination. Simulations show that recombination is favoured by the moderately weak selection of many loci involved in the interaction between a host and its parasites, which results in substitution rates that are compatible with empirical estimates. The model also reproduces the previously reported rapid increase in the rate of outcrossing in Caenorhabditis elegans coevolving with a bacterial pathogen.
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Affiliation(s)
- J da Silva
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - J D Galbraith
- Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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18
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Bento G, Routtu J, Fields PD, Bourgeois Y, Du Pasquier L, Ebert D. The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model. PLoS Genet 2017; 13:e1006596. [PMID: 28222092 PMCID: PMC5340410 DOI: 10.1371/journal.pgen.1006596] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/07/2017] [Accepted: 01/20/2017] [Indexed: 11/18/2022] Open
Abstract
Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa. We fine-map one locus associated with D. magna resistance to P. ramosa and genetically characterize two haplotypes of the Pasteuria resistance (PR-) locus using de novo genome and transcriptome sequencing. Sequence comparison of PR-locus haplotypes finds dramatic structural polymorphisms between PR-locus haplotypes including a large portion of each haplotype being composed of non-homologous sequences resulting in haplotypes differing in size by 66 kb. The high divergence of PR-locus haplotypes suggest a history of multiple, diverse and repeated instances of structural mutation events and restricted recombination. Annotation of the haplotypes reveals striking differences in gene content. In particular, a group of glycosyltransferase genes that is present in the susceptible but absent in the resistant haplotype. Moreover, in natural populations, we find that the PR-locus polymorphism is associated with variation in resistance to different P. ramosa genotypes, pointing to the PR-locus polymorphism as being responsible for the matching-allele interactions that have been previously described for this system. Our results conclusively identify a genetic basis for the matching-allele interaction observed in a coevolving host-parasite system and provide a first insight into its molecular basis.
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Affiliation(s)
- Gilberto Bento
- Basel University, Zoological Institute, Vesalgasse 1, Basel, Switzerland
- * E-mail:
| | - Jarkko Routtu
- Basel University, Zoological Institute, Vesalgasse 1, Basel, Switzerland
| | - Peter D. Fields
- Basel University, Zoological Institute, Vesalgasse 1, Basel, Switzerland
| | - Yann Bourgeois
- Basel University, Zoological Institute, Vesalgasse 1, Basel, Switzerland
| | - Louis Du Pasquier
- Basel University, Zoological Institute, Vesalgasse 1, Basel, Switzerland
| | - Dieter Ebert
- Basel University, Zoological Institute, Vesalgasse 1, Basel, Switzerland
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19
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Higher rates of sex evolve during adaptation to more complex environments. Proc Natl Acad Sci U S A 2017; 114:534-539. [PMID: 28053226 DOI: 10.1073/pnas.1604072114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A leading hypothesis for the evolutionary maintenance of sexual reproduction proposes that sex is advantageous because it facilitates adaptation. Changes in the environment stimulate adaptation but not all changes are equivalent; a change may occur along one or multiple environmental dimensions. In two evolution experiments with the facultatively sexual rotifer Brachionus calyciflorus, we test how environmental complexity affects the evolution of sex by adapting replicate populations to various environments that differ from the original along one, two, or three environmental dimensions. Three different estimates of fitness (growth, lifetime reproduction, and population density) confirmed that populations adapted to their new environment. Growth measures revealed an intriguing cost of complex adaptations: populations that adapted to more complex environments lost greater amounts of fitness in the original environment. Furthermore, both experiments showed that B. calyciflorus became more sexual when adapting to a greater number of environmental dimensions. Common garden experiments confirmed that observed changes in sex were heritable. As environments in nature are inherently complex these findings help explain why sex is maintained in natural populations.
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