Institute of Environmental Sciences
Antler quality in red deer: a test of Hamilton and Zuk hypothesis
Author(s): Buczek, M, Radwan, J, Okarma, H
The evolution and maintenance of elaborate secondary sexual traits in males has been the subject of intense interest since Darwin. Hamilton and Zuk (1982) hypothesis of parasite-mediated sexual selection suggests that genetically resistant males can afford to invest more in costly ornaments. Therefore elaborated sexual traits can serve as honest indicators of male health and parasite load. We study the association between the MHC (Major Histocompatibility Complex) class II genes, gastro-intestinal and lung parasite burden and the development of antler (sexual ornament) in red deer (Cervus elaphus). We analyzed associations between antler elaboration (mass and 8 other measurements) and parasite burden (lung nematode larva, abomasum nematodes and fecal egg counts). We found a very complex pattern of relationships. The mass of antler was significantly affected by the lung nematode larva burden. We used 8 antler measurements to describe antler size using principal component analysis (PCA). PC1 (explaining 80% of variance in antler size) was significantly affected by lung nematodes burden and PC3 (explaining 5% of variance) by abomasum nematode burden. We will additionally present results of analyses investigating the effect of MHC genotype on parasite load.
Department Biology II
Bioinformatic analysis of amplicon sequencing data to study spatial and temporal variation in a Daphnia microparasite
Author(s): Gonzalez Tortuero, E, Rusek, J, Giessler, S, Petrusek, A, Wolinska, J
Caullerya mesnili (Opisthokonta, Ichthyosporea) is an endoparasite infecting Daphnia (Crustacea, Cladocera) gut. This protozoan has high virulence and a strong genetic specificity for the infection, thus it seems to be a good model to study host-parasite coevolution dynamics. However, little is known about population structure of this microparasite. Previous work based on cloned sequences has shown that variation of the ITS region (internal transcribed spacer of ribosomal DNA) can be used to analyse spatial and temporal variation in C. mesnili. However, high-throughput next generation sequencing (NGS) allows much larger scale analyses. In this work we will present a bioinformatic pipeline analysing 392 bp long ITS amplicons from Caullerya obtained from 454 pyrosequencing. With this approach, it is possible to study in detail aspects such as the spatio-temporal distribution of Caullerya in different host populations or clones. We will also demonstrate the comparison of patterns obtained by cloning with the NGS approach.
Can differential gene expression explain differential host resistance?
Author(s): Konijnendijk, N, Raeymaekers, J, Howes, T, Milan, M, Volckaert, F
Our ability to find signatures of selection in the genome is rapidly increasing. As a consequence we now know that strong selection leading to local adaptation can affect many regions in the genome. However, not all local adaptations result in structural gene changes. Changes in regulation of existing genes might be at least as important. To what extend this happens and whether selection only affects genes directly related to the focal trait, or also other gene classes is for many cases unknown. Host-parasite systems are very suitable for testing the importance of gene expression alterations in local adaptation. Selection is often strong due to the fact that parasites can have a big impact of fitness of the individual, making it probable we can pick up alterations in expression. Start and finish of changes in gene expression are much easier to predict than for many other (somatic) traits and temporal an spatial fluctuations in parasite abundance are common in nature, which may favor changes in gene expression rather than genetic changes as they are much easier to reverse. We used the F2 generation of two populations of stickleback fish that differ in host resistance, in order to identify which genes are involved in resistance and to understand whether heritable differences in resistance across populations are linked to differential gene expression. We infected naive fish with Gyrodactylus gasterostei, a parasitic flatworm and tracked the infection by counting parasites on the skin over time. Targeting the beginning and peak of the infection, we used microarrays to identify differential gene expression across the genome. We will present whether differences in host resistance result in differential expression patterns among populations and whether infection only affects immune related genes or a wider set of genes, thereby contributing to a better understanding of the role of gene expression alterations in host adaptation to parasites.
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.
Department Biologie II
Capturing the population structure of microparasites: using ITS-sequence data and a pooled DNA approach
Author(s): Giessler, S, Wolinska, J
The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a central target not only for molecular identification of different taxa and strains but also for analyses of population structure of wild microparasite communities. Importantly, the multi-copy nature of this region allows for successful amplification of low quantity samples of the target DNA, a common problem in studies on unicellular, unculturable microparasites. We analysed ITS-sequences from the protozoan parasite Caullerya mesnili (class Ichthyosporea) infecting waterflea (Daphnia) hosts, across several host population samples. We showed that analysing representative ITS-types (as identified by statistical parsimony networks) is a suitable method to address relevant polymorphism. The spatial patterns were consistent regardless of whether parasite DNA was extracted from individual hosts or pooled host samples. Remarkably, the efficiency to detect different sequence types was even higher after sample pooling. As shown by simulations, an easily manageable number of sequences from pooled DNA samples was already sufficient to resolve the spatial population structure in this system. In summary, the ITS-region analysed from pooled DNA samples can provide valuable insights into the spatial and temporal dynamics of microparasites. Moreover, for the analysis of sequence variation in multi-copy gene regions, the application of statistical parsimony network analysis is clearly advantageous.
Institute of Biology
Cell sacrifice in the gut: an adaptive response towards Nosema spp. infection in honey bees
Author(s): Kurze, C, Huang, Q, Moritz, RFA
The microsporidian Nosema ceranae is a natural parasite of the Asian honeybee Apis cerana but is now also a widespread cause of Nosemosis in the European honey bee A. mellifera. N. cerana infections can have severe effects on honey bee fitness at the individual and colony level. We found that the extensive breeding effort by Danish beekeepers against the native microsporidian parasite N. apis has produced a Nosema tolerant honey bee strain, which revealed a strongly up-regulated immune response when challenged by N. cerana infection compared to an unselected strain. After transmission via the fecal-oral route, spores normally germinate in the midgut, where they penetrate, replicate and destroy the cells of the gut epithelium. To understand the effect of the altered immune response on the level of infestation and destruction of the midgut epithelium, we compare sections between the selected and an unselected strain over the course of infection. We discuss these results in the context of an adaptive immune response and other underlying biological mechanisms of the selected strain against N. ceranae infection.
Characterization of candidate genes from a QTL analysis of the skin microbiota in house mice
Author(s): Belheouane, M, Ibrahim, S, Baines, JF
Meriem BELHEOUANE1,2, Saleh IBRAHIM3 and John F. BAINES1,2 1Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Germany 2Max Planck Institute for Evolutionary Biology, Plön, Germany 3Department of Dermatology, University of Lübeck, Lübeck, Germany
The skin is a complex ecosystem inhabited by diverse microbial communities, and various factors including host genetics, immune status and the environment influence community structure and diversity over space and time. Several skin diseases are postulated to have a microbial component, but little is known about the underlying mechanisms or origins of disease susceptibility. To measure the host genetic contribution to the structure and diversity of the skin microbiota and its potential contribution to disease, we performed quantitative trait locus (QTL) mapping of both autoimmune skin blistering and bacterial traits in an advanced intercross between house mouse strains derived from multiple subspecies. To understand the evolutionary origin of host genetic variability influencing both individual bacterial abundances and susceptibility to disease, we are subjecting candidate regions to more detailed molecular population genetic analysis in natural populations of house mice. In parallel, bacterial species with putative probiotic effects will be cultured and subject to genomic analysis to shed light on the role of host - commensal microbe coevolution in maintaining homeostasis of the skin community.
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.
Department of Biology
Contrasting evolutionary patterns in recent and deep time suggest old origins for East-African arenaviruses and strong specificity to their multimammate mouse hosts
Author(s): Gryseels, S, Baird, SJE, Makundi, R, Borremans, B, Bryjová, A, Leirs, H, Goüy de Bellocq, J
To understand the relationship between evolutionary histories of zoonotic RNA viruses and their hosts, we study patterns of viral divergence across a host geographic range structured by both recent and ancient events. We focus on East African arenaviruses closely related to the virus causing human Lassa fever in West Africa and which infect the same natural host, the multimammate mouse Mastomys natalensis. We sampled at regular intervals along a 200 km transect in Tanzania, capturing a total of 1284 multimammate mice, of which 57 harbored arenaviruses. Multilocus microsatellite, mitochondrial and Y chromosome markers reveal a cryptic host contact zone between two M. natalensis taxa along the transect, with one admixed central locality and the surrounding 11 localities dominated by one of either taxon. The host mitochondrial lineages split about 1 million years ago and the current zone is likely the outcome of secondary contact of M. natalensis geographic isolates some thousands of years ago, driven by Holocene climate oscillations. We show that each M. natalensis taxon hosts a very distinct arenavirus, yet both arenavirus species are present in the host-admixed locality. Both hosts and viruses show further genetic differentiation within each host-taxon’s ranges, but on this level the geographic patterns of host and virus structure are not correlated. These observations suggest that recent host evolutionary history has little effect on recent arenaviral divergence (despite similar differentiation time scales), yet host-virus associations at a deeper taxonomic level have likely persisted since their shared isolation during the last glacial cycle, predating current ancestry estimates for these RNA viruses. Furthermore, if arenavirus species are unable to cross between pairs of taxonomically cryptic host sister taxa in geographic contact, a rapid arenavirus spread across M. natalensis’ pan-African range, likely home to many such cryptic taxa, seems remote.
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.