1
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Fredericksen M, Fields PD, Du Pasquier L, Ricci V, Ebert D. QTL study reveals candidate genes underlying host resistance in a Red Queen model system. PLoS Genet 2023; 19:e1010570. [PMID: 36730161 PMCID: PMC9894429 DOI: 10.1371/journal.pgen.1010570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/14/2022] [Indexed: 02/03/2023] Open
Abstract
Specific interactions of host and parasite genotypes can lead to balancing selection, maintaining genetic diversity within populations. In order to understand the drivers of such specific coevolution, it is necessary to identify the molecular underpinnings of these genotypic interactions. Here, we investigate the genetic basis of resistance in the crustacean host, Daphnia magna, to attachment and subsequent infection by the bacterial parasite, Pasteuria ramosa. We discover a single locus with Mendelian segregation (3:1 ratio) with resistance being dominant, which we call the F locus. We use QTL analysis and fine mapping to localize the F locus to a 28.8-kb region in the host genome, adjacent to a known resistance supergene. We compare the 28.8-kb region in the two QTL parents to identify differences between host genotypes that are resistant versus susceptible to attachment and infection by the parasite. We identify 13 genes in the region, from which we highlight eight biological candidates for the F locus, based on presence/absence polymorphisms and differential gene expression. The top candidates include a fucosyltransferase gene that is only present in one of the two QTL parents, as well as several Cladoceran-specific genes belonging to a large family that is represented in multiple locations of the host genome. Fucosyltransferases have been linked to resistance in previous studies of Daphnia-Pasteuria and other host-parasite systems, suggesting that P. ramosa spore attachment could be mediated by changes in glycan structures on D. magna cuticle proteins. The Cladoceran-specific candidate genes suggest a resistance strategy that relies on gene duplication. Our results add a new locus to a growing genetic model of resistance in the D. magna-P. ramosa system. The identified candidate genes will be used in future functional genetic studies, with the ultimate aim to test for cycles of allele frequencies in natural populations.
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Affiliation(s)
- Maridel Fredericksen
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
- * E-mail:
| | - Peter D. Fields
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Louis Du Pasquier
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Virginie Ricci
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
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2
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Henriques D, Lopes AR, Chejanovsky N, Dalmon A, Higes M, Jabal-Uriel C, Le Conte Y, Reyes-Carreño M, Soroker V, Martín-Hernández R, Pinto MA. A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.). Sci Rep 2021; 11:15317. [PMID: 34321557 PMCID: PMC8319136 DOI: 10.1038/s41598-021-94833-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
With a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3' and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.
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Affiliation(s)
- Dora Henriques
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Ana R Lopes
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Nor Chejanovsky
- Agricultural Research Organization, The Volcani Center, Rishon LeTsiyon, Israel
| | - Anne Dalmon
- INRAE, Unité Abeilles et Environnement, Avignon, France
| | - Mariano Higes
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
| | - Clara Jabal-Uriel
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
| | - Yves Le Conte
- INRAE, Unité Abeilles et Environnement, Avignon, France
| | | | - Victoria Soroker
- Agricultural Research Organization, The Volcani Center, Rishon LeTsiyon, Israel
| | - Raquel Martín-Hernández
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología (INCRECYT-FEDER), Fundación Parque Científico y Tecnológico de Castilla-La Mancha, 02006, Albacete, Spain
| | - M Alice Pinto
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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3
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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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4
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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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5
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Izhar R, Gilboa C, Ben‐Ami F. Disentangling the steps of the infection process responsible for juvenile disease susceptibility. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rony Izhar
- School of Zoology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv Israel
| | - Chen Gilboa
- School of Zoology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv Israel
| | - Frida Ben‐Ami
- School of Zoology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv Israel
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6
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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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7
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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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8
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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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9
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Auld SKJR, Tinkler SK, Tinsley MC. Sex as a strategy against rapidly evolving parasites. Proc Biol Sci 2017; 283:rspb.2016.2226. [PMID: 28003455 PMCID: PMC5204169 DOI: 10.1098/rspb.2016.2226] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/18/2016] [Indexed: 11/20/2022] Open
Abstract
Why is sex ubiquitous when asexual reproduction is much less costly? Sex disrupts coadapted gene complexes; it also causes costs associated with mate finding and the production of males who do not themselves bear offspring. Theory predicts parasites select for host sex, because genetically variable offspring can escape infection from parasites adapted to infect the previous generations. We examine this using a facultative sexual crustacean, Daphnia magna, and its sterilizing bacterial parasite, Pasteuria ramosa. We obtained sexually and asexually produced offspring from wild-caught hosts and exposed them to contemporary parasites or parasites isolated from the same population one year later. We found rapid parasite adaptation to replicate within asexual but not sexual offspring. Moreover, sexually produced offspring were twice as resistant to infection as asexuals when exposed to parasites that had coevolved alongside their parents (i.e. the year two parasite). This fulfils the requirement that the benefits of sex must be both large and rapid for sex to be favoured by selection.
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Affiliation(s)
- Stuart K J R Auld
- Division of Biological and Environmental Sciences, University of Stirling, Room 3B164, Cottrell Building, Stirling, Stirlingshire FK9 4LA, UK
| | - Shona K Tinkler
- Division of Biological and Environmental Sciences, University of Stirling, Room 3B164, Cottrell Building, Stirling, Stirlingshire FK9 4LA, UK
| | - Matthew C Tinsley
- Division of Biological and Environmental Sciences, University of Stirling, Room 3B164, Cottrell Building, Stirling, Stirlingshire FK9 4LA, UK
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10
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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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11
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Nuismer SL, Dybdahl MF. Quantifying the coevolutionary potential of multistep immune defenses. Evolution 2016; 70:282-95. [DOI: 10.1111/evo.12863] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 12/15/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Scott L. Nuismer
- Department of Biological Sciences; University of Idaho; Moscow Idaho 83844
| | - Mark F. Dybdahl
- School of Biological Sciences; Washington State University; Pullman Washington 99164
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12
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Metzger CMJA, Luijckx P, Bento G, Mariadassou M, Ebert D. The Red Queen lives: Epistasis between linked resistance loci. Evolution 2016; 70:480-7. [DOI: 10.1111/evo.12854] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 02/05/2023]
Affiliation(s)
| | - Pepijn Luijckx
- Zoological Institute; University of Basel; CH-4051 Basel Switzerland
- Department of Ecology & Evolutionary Biology; University of Toronto; M5S 3B2 Toronto Ontario Canada
| | - Gilberto Bento
- Zoological Institute; University of Basel; CH-4051 Basel Switzerland
| | - Mahendra Mariadassou
- Zoological Institute; University of Basel; CH-4051 Basel Switzerland
- INRA, UR1404 Unité Mathématique et Informatique Appliquées du Génome à l'Environnement; 78350 Jouy-en-Josas France
| | - Dieter Ebert
- Zoological Institute; University of Basel; CH-4051 Basel Switzerland
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13
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Mushegian AA, Burcklen E, Schär TMM, Ebert D. Temperature-dependent benefits of bacterial exposure in embryonic development of Daphnia magna resting eggs. J Exp Biol 2016; 219:897-904. [DOI: 10.1242/jeb.134759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/12/2016] [Indexed: 11/20/2022]
Abstract
The environments in which animals develop and evolve are profoundly shaped by bacteria, which affect animals both indirectly through their roles in biogeochemical processes and also through direct antagonistic or beneficial interactions. The outcomes of these activities can differ according to environmental context. In a series of laboratory experiments with diapausing eggs of the water flea Daphnia magna, we manipulated two environmental parameters, temperature and presence of bacteria, and examined their effect on development. At elevated temperatures (≥26 °C), resting eggs developing without live bacteria had reduced hatching success and correspondingly higher rates of severe morphological abnormalities compared to eggs with bacteria in their environment. The beneficial effect of bacteria was strongly reduced at 20 °C. Neither temperature nor presence of bacteria affected directly developing parthenogenetic eggs. The mechanistic basis of this effect of bacteria on development is unclear, but these results highlight the complex interplay of biotic and abiotic factors influencing animal development after diapause.
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Affiliation(s)
| | | | | | - Dieter Ebert
- Zoological Institute, Universität Basel, Basel, Switzerland
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14
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Ebert D, Duneau D, Hall MD, Luijckx P, Andras JP, Du Pasquier L, Ben-Ami F. A Population Biology Perspective on the Stepwise Infection Process of the Bacterial Pathogen Pasteuria ramosa in Daphnia. ADVANCES IN PARASITOLOGY 2015; 91:265-310. [PMID: 27015951 DOI: 10.1016/bs.apar.2015.10.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The infection process of many diseases can be divided into series of steps, each one required to successfully complete the parasite's life and transmission cycle. This approach often reveals that the complex phenomenon of infection is composed of a series of more simple mechanisms. Here we demonstrate that a population biology approach, which takes into consideration the natural genetic and environmental variation at each step, can greatly aid our understanding of the evolutionary processes shaping disease traits. We focus in this review on the biology of the bacterial parasite Pasteuria ramosa and its aquatic crustacean host Daphnia, a model system for the evolutionary ecology of infectious disease. Our analysis reveals tremendous differences in the degree to which the environment, host genetics, parasite genetics and their interactions contribute to the expression of disease traits at each of seven different steps. This allows us to predict which steps may respond most readily to selection and which steps are evolutionarily constrained by an absence of variation. We show that the ability of Pasteuria to attach to the host's cuticle (attachment step) stands out as being strongly influenced by the interaction of host and parasite genotypes, but not by environmental factors, making it the prime candidate for coevolutionary interactions. Furthermore, the stepwise approach helps us understanding the evolution of resistance, virulence and host ranges. The population biological approach introduced here is a versatile tool that can be easily transferred to other systems of infectious disease.
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Affiliation(s)
- Dieter Ebert
- Zoological Institute, University of Basel, Basel, Switzerland
| | - David Duneau
- Zoological Institute, University of Basel, Basel, Switzerland; Department Ecologie et Diversité Biologique, University Paul Sabatier-Toulouse III, Toulouse, France
| | - Matthew D Hall
- Zoological Institute, University of Basel, Basel, Switzerland; Monash University, School of Biological Sciences, Clayton Campus, Melbourne, VIC, Australia
| | - Pepijn Luijckx
- Zoological Institute, University of Basel, Basel, Switzerland; Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason P Andras
- Zoological Institute, University of Basel, Basel, Switzerland; Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | | | - Frida Ben-Ami
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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15
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Song Y, Gokhale CS, Papkou A, Schulenburg H, Traulsen A. Host-parasite coevolution in populations of constant and variable size. BMC Evol Biol 2015; 15:212. [PMID: 26419522 PMCID: PMC4589230 DOI: 10.1186/s12862-015-0462-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 08/21/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The matching-allele and gene-for-gene models are widely used in mathematical approaches that study the dynamics of host-parasite interactions. Agrawal and Lively (Evolutionary Ecology Research 4:79-90, 2002) captured these two models in a single framework and numerically explored the associated time discrete dynamics of allele frequencies. RESULTS Here, we present a detailed analytical investigation of this unifying framework in continuous time and provide a generalization. We extend the model to take into account changing population sizes, which result from the antagonistic nature of the interaction and follow the Lotka-Volterra equations. Under this extension, the population dynamics become most complex as the model moves away from pure matching-allele and becomes more gene-for-gene-like. While the population densities oscillate with a single oscillation frequency in the pure matching-allele model, a second oscillation frequency arises under gene-for-gene-like conditions. These observations hold for general interaction parameters and allow to infer generic patterns of the dynamics. CONCLUSION Our results suggest that experimentally inferred dynamical patterns of host-parasite coevolution should typically be much more complex than the popular illustrations of Red Queen dynamics. A single parasite that infects more than one host can substantially alter the cyclic dynamics.
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Affiliation(s)
- Yixian Song
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, 24306, Germany.
| | - Chaitanya S Gokhale
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.
| | - Andrei Papkou
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
| | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, 24306, Germany.
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Routtu J, Ebert D. Genetic architecture of resistance in Daphnia hosts against two species of host-specific parasites. Heredity (Edinb) 2014; 114:241-8. [PMID: 25335558 DOI: 10.1038/hdy.2014.97] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 08/21/2014] [Accepted: 08/27/2014] [Indexed: 02/04/2023] Open
Abstract
Understanding the genetic architecture of host resistance is key for understanding the evolution of host-parasite interactions. Evolutionary models often assume simple genetics based on few loci and strong epistasis. It is unknown, however, whether these assumptions apply to natural populations. Using a quantitative trait loci (QTL) approach, we explore the genetic architecture of resistance in the crustacean Daphnia magna to two of its natural parasites: the horizontally transmitted bacterium Pasteuria ramosa and the horizontally and vertically transmitted microsporidium Hamiltosporidium tvaerminnensis. These two systems have become models for studies on the evolution of host-parasite interactions. In the QTL panel used here, Daphnia's resistance to P. ramosa is controlled by a single major QTL (which explains 50% of the observed variation). Resistance to H. tvaerminnensis horizontal infections shows a signature of a quantitative trait based in multiple loci with weak epistatic interactions (together explaining 38% variation). Resistance to H. tvaerminnensis vertical infections, however, shows only one QTL (explaining 13.5% variance) that colocalizes with one of the QTLs for horizontal infections. QTLs for resistance to Pasteuria and Hamiltosporidium do not colocalize. We conclude that the genetics of resistance in D. magna are drastically different for these two parasites. Furthermore, we infer that based on these and earlier results, the mechanisms of coevolution differ strongly for the two host-parasite systems. Only the Pasteuria-Daphnia system is expected to follow the negative frequency-dependent selection (Red Queen) model. How coevolution works in the Hamiltosporidium-Daphnia system remains unclear.
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Affiliation(s)
- J Routtu
- Zoologisches Institut, Universität Basel, Basel, Switzerland
| | - D Ebert
- Zoologisches Institut, Universität Basel, Basel, Switzerland
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17
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Water fleas require microbiota for survival, growth and reproduction. ISME JOURNAL 2014; 9:59-67. [PMID: 25026374 DOI: 10.1038/ismej.2014.116] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 05/27/2014] [Accepted: 06/07/2014] [Indexed: 02/07/2023]
Abstract
Microbiota have diverse roles in the functioning of their hosts; experiments using model organisms have enabled investigations into these functions. In the model crustacean Daphnia, little knowledge exists about the effect of microbiota on host well being. We assessed the effect of microbiota on Daphnia magna by experimentally depriving animals of their microbiota and comparing their growth, survival and fecundity to that of their bacteria-bearing counterparts. We tested Daphnia coming from both lab-reared parthenogenetic eggs of a single genotype and from genetically diverse field-collected resting eggs. We showed that bacteria-free hosts are smaller, less fecund and have higher mortality than those with microbiota. We also manipulated the association by exposing bacteria-free Daphnia to a single bacterial strain of Aeromonas sp., and to laboratory environmental bacteria. These experiments further demonstrated that the Daphnia-microbiota system is amenable to manipulation under various experimental conditions. The results of this study have implications for studies of D. magna in ecotoxicology, ecology and environmental genomics.
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Dybdahl MF, Jenkins CE, Nuismer SL. Identifying the Molecular Basis of Host-Parasite Coevolution: Merging Models and Mechanisms. Am Nat 2014; 184:1-13. [DOI: 10.1086/676591] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Schlotz N, Ebert D, Martin-Creuzburg D. Dietary supply with polyunsaturated fatty acids and resulting maternal effects influence host--parasite interactions. BMC Ecol 2013; 13:41. [PMID: 24175981 PMCID: PMC3826666 DOI: 10.1186/1472-6785-13-41] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 10/29/2013] [Indexed: 01/16/2023] Open
Abstract
Background Interactions between hosts and parasites can be substantially modulated by host nutrition. Polyunsaturated fatty acids (PUFAs) are essential dietary nutrients; they are indispensable as structural components of cell membranes and as precursors for eicosanoids, signalling molecules which act on reproduction and immunity. Here, we explored the potential of dietary PUFAs to affect the course of parasitic infections using a well-established invertebrate host – parasite system, the freshwater herbivore Daphnia magna and its bacterial parasite Pasteuria ramosa. Results Using natural food sources differing in their PUFA composition and by experimentally modifying the availability of dietary arachidonic acid (ARA) and eicosapentaenoic acid (EPA) we examined PUFA-mediated effects resulting from direct consumption as well as maternal effects on offspring of treated mothers. We found that both host and parasite were affected by food quality. Feeding on C20 PUFA-containing food sources resulted in higher offspring production of hosts and these effects were conveyed to a great extent to the next generation. While feeding on a diet containing high PUFA concentrations significantly reduced the likelihood of becoming infected, the infection success in the next generation increased whenever the maternal diet contained PUFAs. We suggest that this opposing effect was caused by a trade-off between reproduction and immunity in the second generation. Conclusions Considering the direct and maternal effects of dietary PUFAs on host and parasite we propose that host – parasite interactions and thus disease dynamics under natural conditions are subject to the availability of dietary PUFAs.
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Affiliation(s)
- Nina Schlotz
- Limnological Institute, University of Konstanz, Konstanz 78464, Germany.
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20
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Auld SKJR, Wilson PJ, Little TJ. Rapid change in parasite infection traits over the course of an epidemic in a wild host-parasite population. OIKOS 2013. [DOI: 10.1111/j.1600-0706.2013.00720.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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A Matching-Allele Model Explains Host Resistance to Parasites. Curr Biol 2013; 23:1085-8. [DOI: 10.1016/j.cub.2013.04.064] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/02/2013] [Accepted: 04/24/2013] [Indexed: 11/20/2022]
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22
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Ben-Ami F, Routtu J. The expression and evolution of virulence in multiple infections: the role of specificity, relative virulence and relative dose. BMC Evol Biol 2013; 13:97. [PMID: 23641899 PMCID: PMC3659053 DOI: 10.1186/1471-2148-13-97] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/29/2013] [Indexed: 11/11/2022] Open
Abstract
Background Multiple infections of the same host by different strains of the same microparasite species are believed to play a crucial role during the evolution of parasite virulence. We investigated the role of specificity, relative virulence and relative dose in determining the competitive outcome of multiple infections in the Daphnia magna-Pasteuria ramosa host-parasite system. Results We found that infections by P. ramosa clones (single genotype) were less virulent and produced more spores than infections by P. ramosa isolates (possibly containing multiple genotypes). We also found that two similarly virulent isolates of P. ramosa differed considerably in their within-host competitiveness and their effects on host offspring production when faced with coinfecting P. ramosa isolates and clones. Although the relative virulence of a P. ramosa isolate/clone appears to be a good indicator of its competitiveness during multiple infections, the relative dose may alter the competitive outcome. Moreover, spore counts on day 20 post-infection indicate that the competitive outcome is largely decided early in the parasite’s growth phase, possibly mediated by direct interference or apparent competition. Conclusions Our results emphasize the importance of epidemiology as well as of various parasite traits in determining the outcome of within-host competition. Incorporating realistic epidemiological and ecological conditions when testing theoretical models of multiple infections, as well as using a wider range of host and parasite genotypes, will enable us to better understand the course of virulence evolution.
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Affiliation(s)
- Frida Ben-Ami
- Department of Zoology, George S, Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.
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23
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Andras JP, Ebert D. A novel approach to parasite population genetics: Experimental infection reveals geographic differentiation, recombination and host‐mediated population structure inPasteuria ramosa, a bacterial parasite ofDaphnia. Mol Ecol 2012; 22:972-86. [DOI: 10.1111/mec.12159] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 10/15/2012] [Accepted: 10/21/2012] [Indexed: 11/29/2022]
Affiliation(s)
- J. P. Andras
- Zoologisches Institut, Evolutionsbiologie Universität Basel Vesalgasse 1 CH‐4051 Basel Switzerland
| | - D. Ebert
- Zoologisches Institut, Evolutionsbiologie Universität Basel Vesalgasse 1 CH‐4051 Basel Switzerland
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24
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Magwire MM, Fabian DK, Schweyen H, Cao C, Longdon B, Bayer F, Jiggins FM. Genome-wide association studies reveal a simple genetic basis of resistance to naturally coevolving viruses in Drosophila melanogaster. PLoS Genet 2012; 8:e1003057. [PMID: 23166512 PMCID: PMC3499358 DOI: 10.1371/journal.pgen.1003057] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/14/2012] [Indexed: 12/04/2022] Open
Abstract
Variation in susceptibility to infectious disease often has a substantial genetic component in animal and plant populations. We have used genome-wide association studies (GWAS) in Drosophila melanogaster to identify the genetic basis of variation in susceptibility to viral infection. We found that there is substantially more genetic variation in susceptibility to two viruses that naturally infect D. melanogaster (DCV and DMelSV) than to two viruses isolated from other insects (FHV and DAffSV). Furthermore, this increased variation is caused by a small number of common polymorphisms that have a major effect on resistance and can individually explain up to 47% of the heritability in disease susceptibility. For two of these polymorphisms, it has previously been shown that they have been driven to a high frequency by natural selection. An advantage of GWAS in Drosophila is that the results can be confirmed experimentally. We verified that a gene called pastrel--which was previously not known to have an antiviral function--is associated with DCV-resistance by knocking down its expression by RNAi. Our data suggest that selection for resistance to infectious disease can increase genetic variation by increasing the frequency of major-effect alleles, and this has resulted in a simple genetic basis to variation in virus resistance.
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Affiliation(s)
| | | | | | | | | | | | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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25
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Tack AJM, Thrall PH, Barrett LG, Burdon JJ, Laine AL. Variation in infectivity and aggressiveness in space and time in wild host-pathogen systems: causes and consequences. J Evol Biol 2012; 25:1918-1936. [PMID: 22905782 DOI: 10.1111/j.1420-9101.2012.02588.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/02/2012] [Accepted: 07/05/2012] [Indexed: 12/18/2022]
Abstract
Variation in host resistance and in the ability of pathogens to infect and grow (i.e. pathogenicity) is important as it provides the raw material for antagonistic (co)evolution and therefore underlies risks of disease spread, disease evolution and host shifts. Moreover, the distribution of this variation in space and time may inform us about the mode of coevolutionary selection (arms race vs. fluctuating selection dynamics) and the relative roles of G × G interactions, gene flow, selection and genetic drift in shaping coevolutionary processes. Although variation in host resistance has recently been reviewed, little is known about overall patterns in the frequency and scale of variation in pathogenicity, particularly in natural systems. Using 48 studies from 30 distinct host-pathogen systems, this review demonstrates that variation in pathogenicity is ubiquitous across multiple spatial and temporal scales. Quantitative analysis of a subset of extensively studied plant-pathogen systems shows that the magnitude of within-population variation in pathogenicity is large relative to among-population variation and that the distribution of pathogenicity partly mirrors the distribution of host resistance. At least part of the variation in pathogenicity found at a given spatial scale is adaptive, as evidenced by studies that have examined local adaptation at scales ranging from single hosts through metapopulations to entire continents and - to a lesser extent - by comparisons of pathogenicity with neutral genetic variation. Together, these results support coevolutionary selection through fluctuating selection dynamics. We end by outlining several promising directions for future research.
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Affiliation(s)
- A J M Tack
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - P H Thrall
- CSIRO-Plant Industry, Canberra, ACT, Australia
| | - L G Barrett
- CSIRO-Plant Industry, Canberra, ACT, Australia
| | - J J Burdon
- CSIRO-Plant Industry, Canberra, ACT, Australia
| | - A-L Laine
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland
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