Department of Invertebrate Zoology
A novel functional polymorphism in the Fatty Acid Desaturase 2 gene (FADS2): possible role in basal metabolic rate
Author(s): Czajkowska, M, Swislocka, M, Duda, N, Dobrzyn, P, Brzek, P, Konarzewski, M, Ratkiewicz, M
As membrane components, polyunsaturated fatty acids (PUFAs) play an important role in cellular processes and have been shown to be associated with basal metabolic rate (BMR). While the link between BMR and membrane lipid composition is clear on an interspecific level, the underlying mechanism linking them on an intraspecific level is not well understood. Probably one reason for this is that variation of a physiological trait like BMR is much narrower within a species than between organisms from two different species, and in turn the mechanisms explaining any observed variation could be subtler. In this circumstance, a much stronger methodology for studying BMR should be found in artificial selection experiments which manipulate the frequencies of genes directly related to the trait under study. Here we describe a new polymorphism in the fatty acid desaturase (Fads2) gene for Δ-6 desaturase (D6D), a key enzyme for PUFA synthesis, in 120 males from two genetic lines of outbred Swiss Webster laboratory mice (Mus musculus) selectively bred for 32 generations (F32) towards low and high BMR. For controlling the force of genetic drift, we also used 78 mice of generation 22 (F22). For the same reason, we analyzed 36 mice from three unselected lines of mice maintained in a separate, concurrent selection experiment in generation 16 (F16). The aim of this study was to verify a possible association between Fads2 genotypes and BMR. We found significant correlation between Fads2 variants and BMR within selected, as well as unselected lines of mice. We also used a FST outlier test to asses the effect of selection on the variation between L-BMR and H-BMR lines of mice at the Fads2 gene, using the Fads2 gene, together with data from the 11 microsatellite loci. Taken together, these results suggest that Fads2 is expected to become a major focus of membrane, metabolic rate and human metabolic syndrome research.
Génétique Animale et Biologie Intégrative
Detection of traces of selection with numerous SNP in small experimental populations undergoing directional selection
Author(s): Hospital, F, Bed’Hom, B, Gautier, M, Silveri, L, Bruneau, N, Coville, J, Gourichon, D, Pinard-van der Laan, M
Three lines of chickens (L1, L2, L3) have been selected for 12 generations for three different immune response traits. A fourth line (L4) was a contemporary random bred Control (Minozzi et al. 2008). Each generation, 200 chicks per line were hatched in a single batch. Selection for each trait was done by mass selection based on individual phenotype. Individuals from the three selected lines and the control line at generation G9, as well as individuals from the founding population (G0) were sampled (20 individuals/line) and genotyped with a 60K SNP chip. We present the use of this dataset to detect traces of selection in the three selected Chicken lines. An original method was designed to detect traces of selection by comparing the SNP allele frequencies between generations G0 and G9 for each line. The method was able to pinpoint a dwarfing gene known to have undergone strong selection hence, serving as a validation. In addition it highlights numerous SNPs that seem to behave non-neutrally, providing candidate regions for future search for selected genes. While classical approaches generally focus on traces of ‘historical’ (long term) selection, this work demonstrates that it is possible to detect short-term selection in experimental population using SNPs.
Minozzi, G, et al., BMC GENETICS, 9:5, 2008.
Institute of Integrative Biology
Edaphic adaptation in the 'omics' era: a genomic view of the calcicole-calcifuge problem
Author(s): Guggisberg, A, Fischer, MC, Zoller, S, Widmer, A
Since almost 200 years, plant ecologists are debating about the causal factors underlying the striking floristic differences observed between plant communities occupying calcareous versus siliceous substrates. Indeed, it remains unclear which chemical (e.g. aluminium and bicarbonate toxicity, nitrate or phosphate depletion) or physical factors (e.g. water or temperature stress) actually drive edaphic adaptation in natural plant populations, advocating for comparative genomic studies on calcicole-calcifuge vicariants, i.e. sister taxa that grow on either soil type. We herewith propose to fill this knowledge gap, by deciphering the genetic basis of local adaptation in two diploid species of Arabidopsis (A. lyrata and A. arenosa, Brassicaceae) that grow on both calcareous and siliceous bedrocks. Using whole-genome re-sequencing of pooled DNA libraries (totalling 240 individuals per species), along with outlier analyses based on allele frequency divergence, we have identified a hundred loci that are enriched for genes acting at the cell periphery in response to ion homeostasis and trans-membrane transporter activity. Among them, a dozen contain up to 130 outlier SNPs, and constitute excellent candidates for functional validation. Overall, our results suggest that chemical soil composition is the main cause of ecological differentiation in these species. Our work further highlights the potential of Arabidopsis as a new model system in experimental studies on edaphic adaptation in plants.
Evolutionary Biology Centre
Effects of experimental mating system variation on transcriptome evolution and mating response in female Drosophila pseudoobscura
Author(s): Immonen, E, Snook, RR, Ritchie, MG
Interactions between the sexes are believed to be a potent source of selection on sex-specific evolution, but the way in which sexual interactions influence females at the molecular level is poorly understood. We examined the effects of 100 generations of elevated polyandry and enforced monandry on gene expression evolution in female Drosophila pseudoobscura. We assessed differences in gene expression between females from the two selection regimes and how the expression response to mating depended on female sexual selection history, indirect genetic effects (IGEs) due to the genotype of the male and female-by-male genotype interactions. Our data show large-scale gene expression divergence between the experimentally evolved females, with selection mainly targeting female-biased genes expressed in the ovaries. Most of the expression differences were un-affected by mating, however we also observed substantial differences in the expression response to mating between the experimental females. The indirect genetic effects of the male selection history on the female gene expression response were surprisingly small. Our results provide critical experimental evidence for a role of female-specific selection arising from polyandry in promoting rapid evolution of the female transcriptome.
Department of Biology
Evolution of sperm competitive ability as a correlated response to selection on environmental stress resistance
Author(s): Singh, K, Prasad, NG
Sperm competitive ability in Drosophila melanogaster is a crucial component of male fitness. Few empirical studies have focused on the effects of environment on evolution of sperm competition. We evolved laboratory population of Drosophila melanogaster to resist cold shock. After 11 generation of selection we found that the selected population eggs had higher hatchability post cold shock. Interestingly, following a cold shock, males from the selected populations were able to induce previously mated females to mate again. They also sired more progeny indicating better ability of sperm competition. There results indicate that sperm competition can evolve rapidly under adaptation to environmental stresses.
Department of Ecology and Evolution
Evolution under monogamy feminizes gene expression
Author(s): Hollis, B, Kawecki, TJ, Keller, L, Yan, Z, Houle, D
Many genes have evolved sexually dimorphic expression as a consequence of divergent selection in males and females. However, the degree to which evolution can shape gene expression independently in each sex is controversial. It is possible to directly test whether genetic constraints have prevented sex-specific optima from being obtained by enforcing a monogamous mating system, which eliminates both female choice and male-male competition. This relaxed selection on males should result in evolution towards female-specific optima for any genes previously under antagonistic selection in males. Here we demonstrate broad constraints on the evolution of sexually dimorphic gene expression by maintaining populations of Drosophila melanogaster for 65 generations under strict monogamy. Compared to polygamous controls, monogamous populations evolved lower expression of male-biased transcripts and higher expression of female-biased transcripts. This pattern of feminization was present in both sexes, evident throughout the genome and across tissue types, and strongest for genes located on the X chromosome, a known hotspot for sexually antagonistic genetic variation. The breadth of the evolutionary response to monogamy indicates that sexually antagonistic selection is ubiquitous in the genome and likely to play a major role in maintaining genetic variation, driving the evolution of sex chromosomes, and reducing population-level fitness.
Centre for Ecological and Evolutionary Studies (CEES)
Experimental evolution and transcriptional plasticity in an insect-fungus interaction
Author(s): Trienens, M, Wertheim, B
Organisms rarely occur solitary; viewed in this light, interaction is forced upon them. The fruit fly Drosophila melanogaster, frequently used as a model organism in evolutionary studies, makes use of rotting fruits as breeding sites. Concurrently, filamentous fungi utilise rotting organic material to obtain their nutritional substances. One trait of many fungi is the production of toxic secondary metabolites. It is hypothesised that these toxins hold a function as a chemical defence against other microbes, e.g. antibiotics like Penicillin, but furthermore features also a defence against larger organisms like insects. Drosophila larvae are constrained in leaving a food patch, due to the risk of desiccation, and have evolved other traits to cope with noxious fungi and their toxins on infested substrates. In an experimental-evolution approach, we mimic the infestation of Drosophila habitats by the filamentous fungus Aspergillus nidulans. A wild-type and a toxin-production-impaired mutant strain, as well as the mycotoxin Sterigmatocystin are used as selection pressures. After multiple confrontations, over 25 generations, we will analyse changes in the transcriptional response of the fly larvae using RNAseq. Additionally, changes in the immune respons and in phenotypic traits will be recorded. Currently, we are analysing the transcriptional plasticity of the fly larvae by disentangling the response towards the fungus and the mycotoxin. For this purpose we have confronted fly larvae with the 3 treatments (WT, mutant, toxin) that are used in the selection experiment. Over a time series, samples were taken and sequenced through NGS. We will compare this, yet unknown, larval response to the transcriptional response after experimental evolution of increased tolerance and/or resistance against the noxious fungus. Here we will present our current results on the dynamics of the interaction between Drosophila larvae and the toxin-producing fungus A. nidulans.
Institute for Evolution and Biodiversity
Experimental evolution and transcriptomics of Tribolium castaneum infections with Bacillus thuringiensis
Author(s): Kurtz, J, Behrens, S, Peuß, R, Milutinovic, B, Eggert, H, Bornberg-Bauer, E, Esser, D, Rosenstiel, P
Experimental evolution of hosts and parasites can help to elucidate the genomic basis of fast evolutionary processes. We are therefore using experimental coevolution in the red flour beetle Tribolium castaneum and its microparasite Bacillus thuringiensis to address evolving genetic specificity, while experimental selection on the hosts' immune system addresses the evolution of immunological specificity. We use two different infection routes, the oral route of infection, and infection through septic prick injury, which brings the bacterium into direct contact with the host’s immune system. Through RNA sequencing we characterised the genomic responses of the host to these two infection routes. We found astonishingly distinct transcriptomic responses for oral versus septic infection. To test for genetic differences between host populations we compared the transcriptomic responses to infection between a commonly used laboratory strain and a newly collected, genetically diverse field population. Not only is the latter population more resistant upon oral infection, but we also found that a much higher number of genes were differentially expressed after oral infection. Studying the transcriptomes of the evolved hosts will thus shed further light on the genomic basis of host-parasite coevolution.
Experimental evolution of Escherichia coli under inefficient selection reveals the evolutionary trajectories of symbiotic bacteria
Author(s): Fares, MA, Toft, C, Ruiz-González, MX, Alvarez-Ponce, D
Many bacteria that establish mutualistic associations with insects are transmitted from mother to offspring under a vertical regime. This transmission mode imposes strong bottlenecks on the effective population sizes of bacteria, resulting in a high genetic drift effect and, consequently, increased genetic variability among populations and decreased polymorphism within populations. Inactivation and degradation of genes that are unnecessary in an intracellular environment is a common symptom of symbiotic lifestyle. Two main questions remain unanswered with regards to the evolution of these bacteria: (a) how do essential genes for symbiosis counteract the effect of mutations fixed under inefficient selection in the genome? And (b) what mechanisms increase the mutational robustness of symbiotic genes? Here we have conducted an evolution experiment using the bacterium Escherichia coli to simulate the mutation dynamics under inefficient natural selection occurring in symbiotic bacteria. Evolution of E. coli for more than 5000 generations reveals the network of interactions between mutations, the set of useful, although not essential, genes for symbiosis and the role of GroEL in mutational robustness. Our results unveil a more complex scenario for the evolution of symbiosis than anticipated by previous studies.
Department of Biological Sciences
Experimental evolution of female traits under different levels of inter sexual conflict
Author(s): Prasad, NG, Nandy, B
A number of studies have documented the evolution of female resistance to mate harm in response to the alteration of intersexual conflict in the populations. However, the life-history consequence of such evolution is still a subject of debate. In the present study, we subjected replicate populations of Drosophila melanogaster to different levels of sexual conflict (generated by altering the operational sex ratio) for over 45 generations. Our results suggest that females from populations experiencing higher level of intersexual conflict evolved increased resistance to mate harm, in terms of both longevity and progeny production. These females were also found to have increased locomotor activity, a possible correlated response to the selection on males in that regime. Females from the populations with low conflict were significantly heavier at eclosion and were more susceptible to mate harm in terms of progeny production under continuous exposure to the males. However, these females produced more progeny upon single mating and had significantly higher longevity in absence of any male exposure – a potential evidence of trade-offs between resistance-related traits and other life-history traits, such as fecundity and longevity. We also report tentative evidence, suggesting an increased male cost of interacting with more resistant females.