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.
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.
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.
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.
Experimental thermal evolution in D. melanogaster reveals temperature dependent population genomic signal of adaptation
Author(s): Tobler, RE, Orozco-terWengel, P, Nolte, V, Hermisson, J, Schlötterer, C
How adaptation effects segregating variation at the population genomic level in sexually reproducing diploids remains a poorly understood yet fundamental biological question. However, recent advances in sequencing technology in combination with experimental evolution have promised to reveal the temporal patterns of genomic adaptation down to individual SNP resolution. Here I discuss results from 15 generations of experimental evolution in replicated populations of D. melanogaster maintained in two separate thermal environments, which mimic either heat and cold stress. When taking the top candidate SNPs from each base-evolved population comparison, we find an enrichment of hot candidate SNPs in genes associated with heat tolerance, and likewise for cold candidate SNPs in cold tolerance genes, but not vice versa. Furthermore, we find that the rising allele (i.e. that most likely to be under selection) tends to start at either low or intermediate frequencies in the hot and cold treatments, respectively. Hence, it appears that thermal selection is involved in driving changes between the two treatments and is deferentially dependent on the starting allele frequency. The possible causes behind these intriguing patterns are discussed with respect to our emerging understanding of thermal adaption in D. melanogaster.
From artificial selection to transcriptomics: The cognitive benefits of, and the gene responsible for, a large brain in fish
Author(s): Kotrschal, A, Harrison, PW, Mank, J, Kolm, N
The evolutionary causes and consequences of the enormous phenotypic variation in brain size among vertebrates remain enigmatic. Positive selection for increased cognitive abilities is a likely driver of brain size evolution, but the genetic bases of vertebrate brain size variation is largely unexplored. An experiment linking brain size, cognition and gene expression differences is therefore lacking. We used artificial selection for large and small brain size relative to body size in the guppy (Poecilia reticulata) to experimentally investigate the link between brain size, cognitive ability, and its genetic background. We found that brain size evolved rapidly in response to divergent selection, and that large-brained females outperformed small-brained females in a numerical learning assay designed to test cognitive ability. Whole transcriptome sequencing (RNA-Seq) of the brain of large- and small-brained fish revealed a dramatic expression difference in a single gene, Angiopoietin-1, which is an endothelial growth factor highly conserved among vertebrates and known to promote both neural proliferation and neural differentiation. We therefore show that a large brain size indeed confers cognitive benefits and nominate Angiopoeitin-1 as the candidate gene mediating the evolution of brain size and cognitive ability in vertebrates.
Laboratory of Plant-Microbes interactions
Genomics of adaptation during experimental evolution of legume symbionts
Author(s): Clerissi, C, Capela, D, Remigi, P, Torchet, R, Cruveiller, S, Rocha, E, Masson-Boivin, C
Exchange of genetic material plays a major role in bacterium evolution. Among the best illustrations are nitrogen-fixing legume symbionts that evolved and spread in many unrelated phylogenetic branches through lateral transfer of essential symbiotic genes. The full phenotypic expression of the acquired traits may require readjustment of the new genetic background. However mechanisms allowing post-LGT adaptation are largely unknown. To address this question, we took advantage of the experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into legume symbionts (1). The chimeric Ralstonia was progressively adapted to nodule tissues by 9 parallel lineages of serial ex planta-in planta passages. Evolution was very fast, since the two first major symbiotic steps, nodulation and intracellular infection, have been acquired in less than 16 cycles (1,2). Genome resequencing revealed an overabundance of mutations in our evolution experiment. A total of ca. 500 point-mutations were detected in the 9 final clones as compared to the original ancestor. We will present a first analysis of the genomic changes that came along with the adaptation process, i. e. mutation spectra, evolution of the number and nature of mutations and molecular convergences between lineages at the gene, operon and pathways levels.