Can parasites drive population divergence in three-spined stickleback?
Author(s): El Nagar, A, MacColl, A
The role of parasites in driving the evolution of hosts is poorly understood. Adaptive evolution occurs with a change in adaptive allele frequencies derived either from standing genetic variation or from new mutations. Looking at population structure of adaptive genes together with neutral markers may reveal whether the adaptive traits that differ between populations are likely to have resulted from divergent selection or genetic drift.
Parasites can be potent agents of selection which act both directly on survival and have also been known to affect mate choice. The three-spined stickleback Gasterosteus aculeatus is a good model system to study mechanisms of adaptive evolution due to its propensity to radiate into young postglacial habitats. We have surveyed the composition and abundance of parasites in stickleback populations on the Island of North Uist, Scotland for four years, and conducted infection experiments on lab bred naïve progeny. Our previous results show that populations display adaptation to their parasites in that they are resistant to naturally occurring parasites. Furthermore this is genetically based; maternal effects were ruled out through breeding schemes and experiment replicates over generations.
An RNAseq experiment was conducted and used to identify genes that were differentially expressed when fish were experimentally infected with a parasite. Some of these genes were selected together with known candidate immune genes. Linked microsatellites were found and genotyped together with a set of neutral microsatellites (as controls). Stickleback samples were from populations with known parasite communities. Any detectable selection on these loci, together with adaptive (immune) and neutral structure will be presented in correlation with parasite composition.
Institute of Integrative Biology
Coevolution and life cycle specialization of plant cell wall degrading enzymes in a hemibiotrophic pathogen
Author(s): Brunner, PC, Torriani, SFF, Croll, D, Stukenbrock, EH, McDonald, BA
Zymoseptoria tritici is an important fungal pathogen on wheat that originated in the Fertile Crescent. Its closely related sister species Z. pseudotritici and Z. ardabiliae infect wild grasses in the same region. This recently emerged host-pathogen system provides a rare opportunity to investigate the evolutionary processes shaping the genome of an emerging pathogen. Here, we investigate genetic signatures in plant cell wall degrading enzymes (PCWDEs) that are likely affected by or driving coevolution in plant-pathogen systems. We hypothesize four main evolutionary scenarios and combine comparative genomics, transcriptomics and selection analyses to assign the majority of PCWDEs in Z. tritici to one of these scenarios. We found widespread differential transcription among different members of the same gene family, challenging the idea of functional redundancy and suggesting instead that specialized enzymatic activity occurs during different stages of the pathogen life-cycle. We also find that natural selection has significantly affected at least 19 of the 48 identified PCWDEs. The majority of genes showed signatures of purifying selection, typical for the scenario of conserved substrate optimization. However, six genes showed diversifying selection that could be attributed to either host adaptation or host evasion. This study provides a powerful framework to better understand the roles played by different members of multi-gene families and to determine which genes are the most appropriate targets for wet lab experimentation, for example to elucidate enzymatic function during relevant phases of a pathogen’s life-cycle.
Institute of Evolutionary Biology
Discovery, distribution and evolutionary genomics of viruses naturally infecting Drosophila melanogaster
Author(s): Obbard, DJ, Webster, CL
Drosophila melanogaster is an important model for innate immunity, and is arguably our primary model for antiviral resistance in arthropods. Several groups have used population-genetic and phylogenetic approaches to show that some antiviral immune genes in Drosophila (notably the antiviral RNAi pathway) display highly elevated rates of adaptive evolution. However, although this is consistent with a host-virus arms race, the evolutionary genetics of Drosophila viruses are almost unstudied - only a handful of viruses which naturally infect Drosophila melanogaster are known, and only Drosophila Sigma Virus (a Rhabdovirus) has been regularly isolated from wild populations.
In an attempt to understand the evolutionary genetics of Drosophila viruses, we have sequenced both RNAseq, and small-RNA, libraries from large pooled samples of wild-caught D. melanogaster. This has allowed us to identify several new viruses, including several RNA viruses (viruses with sequence similarity to Sacbrood Virus, Slow Bee Paralysis Virus, Chronic Bee paralysis virus, Acyrthosiphon Pisum Virus, Flaviviruses, and Cypoviruses) and a DNA virus (Nudivirus).
Following a geographic survey of D. melanogaster, we find that the previously known viruses of D. melanogaster (including DAV, Sigma and Nora) are widespread at low to intermediate prevalence. None of the viruses shows high rates of adaptive evolution, and in general (despite substantial synonymous divergence) protein sequences are very highly conserved. However, while this may indicate that these viruses are not engaged in ‘arms race'-like coevolution, we suspect that the short timescale of viral co-ancestry (tens to hundreds, rather than thousands, of years) makes this process extremely difficult to detect. This is in sharp contrast to viral evolution in response to vertebrate adaptive immunity, which adapts plastically on the same timescale as viral evolution.
Institute of Zoology
Evolution of Daphnia magna resistance to the pathogen Pasteuria ramosa
Author(s): Bento, G, Routtu, J, Hall, M, Ebert, D
Crustaceans of the genus Daphnia have long been used as models in studies of ecology and evolution and of host-pathogen coevolution in particular. However, little is known about the genetic and molecular basis of Daphnia resistance to pathogens. A well-known ecology combined with recent advances in genomic, genetic and molecular tools make Daphnia crustaceans, and in particular Daphnia magna and Daphnia pulex, remarkable models for modern evolution and ecology. D. magna is colonized by a wide range of parasites and pathogens, among them the bacterium Pasteuria ramosa. The study of inheritance patterns of resistance and susceptibility of D. magna clones to different P. ramosa genetic isolates reveals strong genotype-to-genotype interactions, suggesting coevolution between host and pathogen populations. Resistance and susceptibility of D. magna to different P. ramosa isolates follow mendelian patterns of inheritance and segregation, suggesting that a small number of loci underlie natural variation in D. magna resistance to P. ramosa infection. A F2 panel of D. magna was generated, with more than 200 genotypes that are kept by clonal reproduction. A QTL analysis revealed one genomic region of 150kb in linkage group 4 that explaining approximately 60% of the observed variation. However, further inheritance analysis showed that at least 3 loci underlie natural variation in D. magna resistance to P. ramosa infection. One of those loci corresponds to an indel of approximately 50kb. We are currently fine-mapping the QTL interval to identify genes and polymorphisms underlying Daphnia resistance to Pasteuria. We aim to identify which genes and networks and which polymorphisms underlie the natural variation and evolution of pathogen resistance in D. magna. We plan to use molecular tools recently developed for D. magna to achieve our objectives.
Experimental evolution for increased virus resistance in Drosophila melanogaster reveals no costs and a simple genetic basis
Author(s): Martins, NE, Faria, VG, Nolte, V, Schlötterer, C, Teixeira, L, Sucena, É, Magalhães, S
Because hosts and parasites exert strong selection pressure on each other, it is particularly relevant to study their interaction in an evolutionary context. Experimental Evolution permits the establishment of causality between evolutionary processes and adaptation patterns. Here we use experimental evolution of Drosophila melanogaster exposed to Drosophila C virus (DCV) to address the phenotypic and genotypic changes of hosts evolving in presence of parasites. Upon exposure to the virus, Drosophila survival increased from 33% to almost 90% after 35 generations of selection. This response carried no detectable costs in fitness in the absence of infection, and was not lost after 10 generations in the absence of selection. Cross-resistance was found for other viruses, such as CrPV and FHV, but not to bacterial pathogens. Whole genome sequencing of pooled samples of virus-selected populations and their matching controls at generation 20 uncovered two regions of significant differentiation between these groups of populations. The first corresponded to a region of 4 megabases(Mb) in the 3L chromosomal arm. This region’s peak of differentiation corresponded to a polymorphism in pastrel (pst), a gene recently associated with increased DCV resistance. The second was a pair of significantly differentiated SNPs in the X chromosome, in genes not previously associated with virus resistance. Results with a panel of deficiencies in the 3L chromosome confirmed that deficiencies which encompass pst are the ones with more influence on survival after DCV infection, in a region of approximately 2 Mb. There is ongoing work to confirm the involvement of other candidate genes in this region and of the genes in the X chromosome in resistance to DCV infection. Overall we show that selection for increased virus resistance I) is stable and bears little costs, II) is advantageous in the defense against other viral pathogens, and III) has a simple genetic basis.
Department of Biology
Footprints of directional selection in wild populations of Atlantic salmon: evidence for parasite-driven evolution?
Author(s): Zueva, KJ, Lumme, J, Veselov, AE, Kent, MP, Lien, S, Primmer, CR
European populations of Atlantic salmon (Salmo salar) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris, ranging from resistance to extreme susceptibility, and thus are a good model for studying the evolution of virulence and resistance. Advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of natural selection in wild populations. However, distinguishing the molecular signatures of genetic drift and environment-associated selection may challenge the search for specific pathogen driven selection. We used a novel genome-scan analysis approach aimed at i) identifying signals of selection in salmon populations affected by genetic drift at varying levels; and ii) separating the potentially selected loci identified into those affected by pathogen (G. salaris)-driven selection and salinity-driven selection. 4631 single nucleotide polymorphisms (SNPs) were screened in 472 salmon individuals from 12 different north European salmon populations. We identified several genomic regions potentially affected exclusively by parasite-driven selection, as well as several regions affected by salinity mediated directional selection. Functional annotation of candidate SNPs supported the participation of the detected genomic regions in immune defense and osmoregulation. These results provide new insights in genetic basis of pathogen susceptibility/resistance and adaptation to various salinity levels in Atlantic salmon, and open possibilities for specific candidate gene search.
EBI UMR CNRS 7267
Functional analysis of differentially expressed genes in the symbiotic association between the pill-bug Armadillidium vulgare and the feminising Wolbachia
Author(s): Didier, B, Yves, M, Marie-Christine, C, Fabrice, V, Christine, B, Pierre, G, Frédéric, C
Today, there is a wide consensus on the essential role of microbial associations to eukaryote evolution. In most cases, the relationship between host and symbiont is so close that the microorganisms cannot be cultured, making them difficult to study. However, high-throughput sequencing has offered new opportunities for symbiosis research. Due to their widespread association with the Wolbachia endosymbionts, terrestrial isopods represent a model system to understand intimate symbioses. Wolbachia are vertically transmitted facultative bacteria acting as reproductive parasites in isopods, inducing the feminisation of genetic males in the pill bug Armadillidium vulgare. Among the three feminising Wolbachia identified in this host, two strains (wVulC and wVulM) vary in their prevalence and extended phenotypes. wVulC, the most prevalent strain exhibiting the strongest feminising effect, is also the most virulent strain inducing various fitness costs. To decipher the conflicting associations between wVulC, wVulM and A. vulgare, we have constructed cDNA libraries from ovaries and from whole animals challenged by pathogenic intracellular bacteria according to their Wolbachia infection status. RNA from infected and uninfected animals was subjected to RNA-seq sequencing followed by de novo data assembly and annotation. This process generated a library of 33,120 annotated transcripts. Identification of differentially genes (DE) genes as well as overrepresented gene ontology (GO) terms was then carried out using the R packages DESeq and GOSeq. Interestingly the highest number of DE genes was recorded in the animals infected by the less virulent strain wVulM. In most treatments, these DE genes could be assigned to GO categories that are underrepresented when Wolbachia are on board. This study is part of the widest program ImmunSymbArt granted by the French National Research Agency which aims to determine the symbiotic syndrome in four model systems.
Institut de Recherches sur la Biologie de l’Insecte
Genomic adaptation in the bracovirus of Cotesia sesamiae identified by targeted resequencing
Author(s): Gauthier, J, Gayral, P, Le Ru, B, Dupas, S, Gaypay, G, Jancek, S, Kaiser, L, Herniou, EA
Cotesia sesamiae are small parasitoid wasps parasitizing over twenty lepidopteran African stem borer species. It is thought that local adaptation to these different host species is mediated by their symbiotic bracoviruses (BVs). BVs derive from large DNA viruses and have been stably integrated in the wasp genome. The wasp use BVs to introduce ~150 genes in parasitized caterpillars, inducing immunosuppression and allowing wasp larval development. In C. sesamiae, different alleles of the CrV1 BV gene explain parasitic success in a particular host species. Nonetheless, other BV genes could be involved in wasp local adaptation or specialization to their lepidopteran hosts. To investigate this, we focused on the BV genome of 25 samples representative of different African C. sesamiae populations. As we worked with tiny organisms, we used custom-made targeted sequence capture to enrich our sequence library in BV genomes (257 kb) prior to Illumina resequencing. This proved to be a very efficient technique as we obtained high target coverage (1100X) and high percentage of mapped reads (90%) for all C. sesamiae populations and for the more distant outgroups. First, we used population genetics tools to identify regions under strong divergent selection by comparing nucleotide diversity (π) and genetic differentiation (FST) along the BV genome and between populations. Secondly, we used a phylogenomic approach to establish the evolutionary relationships between these populations using BV sequence of three outgroup species. Third, comparative genomics helped to assess the effects of particular mutations and identify sites evolving under positive selection. Last, we compared the molecular evolution of all orthologous BV genes both between and within populations and measured the rate of non-synonymous versus synonymous substitutions under a branch-site evolutionary model. Overall our results indicate that different BV genes are at play depending on local host context.
Science & Technology, KULAK
Host allelic diversity drives long-term host-parasite coevolutionary dynamics
Author(s): Decaestecker, E, De Gersem, H, Michalakis, Y, Rayemaekers, JAM
Background: Hosts and parasites are involved in a coevolutionary interaction in which hosts do not evolve as fast as their parasites. Yet, fast adaptive genetic changes occur upon infection, especially if host-parasite interactions are characterized by Red Queen dynamics. Red Queen dynamics between both antagonists are caused by negative frequency-dependent selection and are assumed to have constant amplitudes. Here, a long-term time shift experiment, based on a unique historical reconstruction of a Daphnia-parasite coevolution, reveals that infectivity cycles with a smaller amplitude in experienced than in naive hosts. Experienced hosts were isolated from recent time periods, naive hosts from past time periods. A coevolution model, incorporating an increase in allelic diversity over time in the host confirmed the asymmetry in the infectivity cycles. In contrast, increased virulence over time did not confirm the observed experimental results. The accumulation of resistance alleles affects long-term Red Queen dynamics. Long-term effects in host-parasite coevolution have so far been neglected, but this reconstruction in combination with a theoretical study on long-term time shifts between a host and a parasite extends current insight into the dynamics of co-evolutionary antagonistic interactions.
Host-specificity in hybrids of two Schistocephalus species with different stickleback hosts
Author(s): Henrich, T, Kalbe, M
Schistocephalus solidus is a highly specific tapeworm that only infects the three spined stickleback Gasterosteus aculeatus as a second intermediate host. The closely related S. pungitii uses the nine-spined stickleback Pungitius pungitius as second intermediate host, showing the same host specificity at this level. Both parasites potentially share the same final hosts – piscivorous birds - and can occur in sympatry. It is therefore possible that natural hybridization takes place but they have not been detected. We used an in vitro breeding system to hybridize S. solidus and S. pungitii and quantified the hybridization rate using microsatellite markers. We measured several fitness relevant traits in pure lines of the parental parasite species as well as in their hybrids: hatching rates, infection rates in the copepod first host, and infection rates and growth in the two species of stickleback second hosts. We show that the parasites can hybridize in the in vitro system, although the proportion of self-fertilized offspring was higher in the heterospecific breeding pairs than in the control pure parental species. Hybrids have a lower hatching rate, but do not show any disadvantages in infection of copepods. In fish, hybrids were able to infect both stickleback species with equal frequency, whereas the pure lines were only able to infect their normal host species. This suggests that the hybrids have given up the host specificity and raises the question why natural hybrids have not been identified in the wild. We are currently investigating pre- and postzygotic mechanisms that might prevent natural hybridization. Our results furthermore indicate a co-dominance of the genes responsible for infection of different fish hosts. This system offers the unique possibility to investigate the genetic mechanisms underlying this host specificity using backcrosses and a QTL approach.