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Santiago Elena

Empirical fitness landscapes reveals a limited number of accessible adaptive pathways for an RNA virus


Author(s): Elena, SF, Lalic, J, Franke, J, DelaIglesia, F


RNA viruses are the main source of emerging infectious diseases owed to the evolutionary potential bestow by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important parameter, which is usually neglected, is the topography of the fitness landscape, that is, how many fitness maxima exist and how well connected they are, which determines the number of accessible evolutionary pathways. To address this question, we have reconstructed a fitness landscape describing the adaptation of Tobacco etch potyvirus to a new host, Arabidopsis thaliana. Two fitness traits were measured for most of the genotypes in the landscape, infectivity and virus accumulation. We found prevailing epistatic effects between mutations in the early steps of adaptation, while independent effects became more common at latter stages. Results suggest that the landscape was rather smooth, with a high number of potential neutral paths and a single fitness peak.

Ivo Chelo
Instituto Gulbenkian de Ciência

Evading genetic drift: an experimental test of the probability of fixation of new genetic variants


Author(s): Chelo, IM, Nédli, J, Gordo, I, Teotónio, H


Progression through an adaptive fitness landscape requires the appearance and fixation of beneficial mutations. But fixation of a beneficial variant is not a necessary outcome, as deduced by J.B.S. Haldane in 1927, instead its probability can be given by twice the fitness effect: Pfix= 2s. This is based in the reasoning that even beneficial variants are lost with high probability by genetic drift. In this work, we performed invasion experiments with inbred lines of Caenorhabditis elegans in well-defined demographic conditions to experimentally demonstrate the determinant role of drift in the initial dynamics of new beneficial alleles. We provide the evidence that extinction rates (Pext) decrease with the initial numbers of beneficial variants, as expected. We also show that the extinction of a deleterious variant, when at low frequency, is higher than that of a beneficial variant thus establishing that classical population genetics theory can accurately predict the fate of low frequency variants. Remarkably though we also find that, when at high frequency the fate of these variants is distinct from their low frequency dynamics, which results not in their ultimate fixation or loss, but on their maintenance. Our data confirm one of the key results of population genetics theory and highlights the complex nature of adaptation, where polymorphism can be maintained or lost depending on population structure.

Nadine Timmermeyer
University of Oregon
Institute of Ecology and Evolution
United States

Evolutionary consequences of female promiscuity


Author(s): Timmermeyer, N, Michiels, NK, Phillips, PC


To cope with stressful conditions like parasite attacks or temperature changes, females can increase their offspring diversity and fitness by mating multiply with several males. This can result in male harm but can be advantageous in fluctuating environments. Populations with promiscuous females therefore are supposed to be more stable than populations with monogamous females. We study the gonochoristic nematode Caenorhabditis remanei, which is mating multiply and affected by male harm. Using experimental evolution, we were able to show that females, in contrast to males, were able to adapt to sex ratio manipulations. Additionally, offspring of promiscuous females had a higher fitness than monogamous females under the influence of the microparasite Bacillus thuringiensis. Even though a powerful tool to investigate fitness effects, manipulating sex ratios in nematodes in scientifically meaningful numbers is very work intensive if done by hand. To increase the population size and replicate number and therefore decrease the effects of drift, we are using differently labeled males and females and an automated sorting device. Worms are loaded onto a polymeric silicon chip (PDMS) and screened for fluorescent makers, resulting in separated males and females, which can be combined in different sex ratios depending on the treatment. These populations will be tested under stressful conditions to investigate whether populations with promiscuous females are more resistant to stressful changes in their environment compared to the monogamous control. Additionally, individual females will be compared to analyze within and between population fitness.

Shraddha Karve
Indian Institute of Science Education and Research, Pune

Evolving in an unpredictable world - the E. coli story


Author(s): Karve, S, Daniel, S, Chavan, Y, Anand, A, Dey, S


Effects of temporally fluctuating environments on the fitness of populations are less explored compared to the effects of directional selection regimes. Existing studies on temporally fluctuating environments employ a narrow selection regime i.e. mostly one environmental parameter fluctuating predictably between two limit points and the fitness measurements happen in the environmental backgrounds similar to that of selection. Obviously such studies fail to predict the fitness outcomes in the complex and/or novel, unpredictable environments. We select replicate microbial populations under randomly fluctuating complex, stressful environmental regime. When fitness proxies of these selected lines are compared with the control populations grown in benign environments, under multiple novel environmental backgrounds, selected lines display ‘Generalist’ properties. We further characterize these Generalists by fitness proxy measurements at different time intervals during the growth in the novel environments. We see that acclimation is beneficial in both selected and control populations but consistently more advantageous in the populations with the history of randomly fluctuating environment. Characterization of the Generalists on the mechanistic level, shows that the commonly evoked explanations of evolution of hypermutators or modified permeability or carry over plasticity are not sufficient to explain observed Generalist phenomenon.

Monika Marxer
Institute of Integrative Biology ETH Zurich

Experimental evolution for growth rate and its implications for infection success, co-infection dynamics, and virulence in a trypanosome parasite of bumblebees


Author(s): Marxer, M


Host-parasite interactions and their outcomes are strongly affected by several factors such as host and parasite genotypes and environmental conditions. Selection on basic growth properties in parasites may have far reaching consequences for numerous parasite traits, infection outcome and importantly the consequences for host fitness. It is know that strains of the trypanosome parasite of bumblebees Crithidia bombi have widely varying growth rates when cultured in vitro. We aim to experimentally evolve this parasite in vitro selecting for fast and slow growing sub-lines. This will enable us to investigate the costs, benefits and fitness trade-offs related to parasite growth rate by subsequently measuring in vivo infection profiles, transmission, and competitive ability under co-infection. To our knowledge, it would be the first time ecological trypanosome isolates have been experimentally evolved in vitro. These results will help define the fitness consequences for the observed natural variation in C. bombi growth, and will also inform important aspects of host-parasite evolution including the evolution of virulence.

Valerie Morley
Yale University
Department of Ecology and Evolutionary Biology
United States

Experimental evolution of an RNA virus in mixed host environments


Author(s): Morley, VJ, Usme Ciro, J, Wasik, BR, Turner, PE


Spatially heterogeneous environments pose unique challenges for evolving asexual populations. One possibility is that selection will lead to high genetic variance, where multiple subpopulations adapt to specialize on a subset of the available habitats. In contrast, spatial heterogeneity may lead to evolution of generalism, where the population is dominated by a single genotype with a broad niche. However, the evolution of populations in spatially heterogeneous environments has been rarely examined outside of theory, and to date there have been no experiments that test how rapidly evolving RNA virus populations adapt in the face of this challenge. Here, we allowed vesicular stomatitis virus (VSV) to evolve in replicated environments containing different mixtures of two host types in laboratory tissue culture: cancer-derived HeLa cells and non-cancerous BHK cells. After 25 passages (100 generations), the fitness (growth) of evolved viruses was assayed on each host type, relative to the common ancestor. We observed a correlated response to selection when VSV was evolved on pure cultures of either host (100% BHK or 100% HeLa). However, in mixed environments this correlated response was broken; populations evolved in spatially heterogeneous environments consistently improved on HeLa cells, even when HeLa cells were rare, but were much more variable in their improvement on BHK cells. Current work examines whole-genomics of evolved populations, to determine how simple versus spatially-complex environments affect genetic variation in VSV populations, and to compare/contrast trajectories of phenotypic and genetic change within and among treatments. This study demonstrates that simple versus mixed environments can pose fundamentally different challenges for adapting populations, and the need for theory that addresses how environmental complexity may influence adaptive trajectories.

Florien Gorter
Wageningen University
Plant Sciences

Experimental evolution of heavy metal tolerance in changing environments


Author(s): Gorter, FA, Aarts, MMG, Zwaan, BJ, De Visser, JGM


In most long-term laboratory evolution experiments, organisms are exposed to a constant selection regime that initially causes a large reduction in fitness. However, the ecological relevance of this treatment may be questioned: under natural circumstances, environmental variables likely vary with time. We were interested in how the rate of directional environmental change affects the evolution of heavy metal tolerance in Saccharomyces cerevisiae. To this end, we grew replicate lines of yeast for 500 generations in the presence of (i) a constant high concentration of Cd, Ni or Zn or (ii) gradually increasing concentrations of these metals. We anticipated that these contrasting selection regimes would result in different adaptive dynamics and evolutionary endpoints, as the shape of the fitness landscape changes as a function of metal concentration. More specifically, we propose the following alternative scenarios: 1) the most resistant genotype is most fit at all metal concentrations, but strength of selection is proportional to concentration 2) the optimal genotype changes with concentration, such that the optimal genotype at intermediate concentrations will confer an intermediate level of tolerance. These scenarios predict that a gradual increase of metal concentration (as opposed to a constant high concentration) causes mutations of large effect to be fixed at later time points (scenario 1), only mutations of small or intermediate effect to be fixed (scenario 2) and, if the fitness landscape is rugged, evolutionary endpoints to be fitter and more diverse (both scenarios). Here, we present results from competition assays that were used to determine the relative fitness of evolved and ancestral isolates and thus differentiate between the alternative hypotheses. Although evolutionary dynamics differed between the treatments, evolutionary endpoints had a similar fitness, reflecting a smooth fitness landscape that changes as a function of metal concentration.

Elisabetta Versace
Vetmeduni Vienna
Institut für Populationsgenetik

Experimental evolution uncovers environment dependent fitness differences among Wolbachia strains in Drosophila melanogaster


Author(s): Versace, E, Schlötterer, C


Natural populations of Drosophila melanogaster carry different Wolbachia strains, but it is not clear whether these Wolbachia strains are functionally diverged. To address this question, we exposed a natural D. melanogaster population to two different environments (hot and cold) and traced the relative frequency of different Wolbachia haplotypes during the experiment. Our D. melanogaster population sample from Portugal contained a highly polymorphic Wolbachia population in which three of the six described clades were present. Using Pool-Seq, we found that in the hot environment the Wolbachia composition remained remarkably stable over 37 generations. In the cold environment, however, Wolbachia strains from two clades increased in frequency. To distinguish between host and Wolbachia mediated effects, we exposed flies that evolved for 37 generations in the hot environment to the cold environment. Interestingly, we observed a very similar pattern to the previous experiment, suggesting that Wolbachia from two clades have a fitness advantage in the cold environment.

Louis Du Plessis
ETH Zürich
Environmental Systems Sciences

Exploring the validity of representing high-dimensional fitness landscapes with a quadratic approximation


Author(s): Du Plessis, L, Bonhoeffer, S


A predictive model for in vitro replicative fitness of HIV, that estimates main fitness effects and epistatic interactions of mutations with a generalized kernel ridge regression, was presented in [1]. The predictive power of the resulting quadratic approximation was found to be high when testing on an independent dataset. A quantitative analysis of the resulting fitness landscape further showed that it was less rugged, less neutral and more correlated than expected [2]. However, due to the high-dimensionality of the sequence space it is intractable to assess its performance on all possible sequence variants.

We evaluate the regressor’s generalization performance by approximating quasi-empirical fitness landscapes based on RNA secondary structure. This is the only known system where a genotype-phenotype map can be easily and accurately computed [3]. Although fitness does not solely depend on RNA secondary structure, it is a good proxy. Unbiased datasets and datasets biased to contain sequences close to the target genotype or phenotype are simulated. Fitness is measured as a combination of thermodynamic stability and the distance to a target structure. The model is alternately trained and tested on each pair of datasets. In addition, the approximations are compared to the real quasi-empirical fitness landscapes with respect to ruggedness, neutrality and correlation length. Together, this provides an analysis of the validity of using a quadratic approximation to represent high-dimensional fitness landscapes.

[1] Hinkley, T., Martins, J., Chappey C. et al. A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat Genet, 43, 2011. [2] Kouyos, R.D., Leventhal, G.E., Hinkley, T. et al. Exploring the complexity of the HIV-1 fitness landscape. PLoS Genet, 8(3) 2012. [3] Schuster, P., Fontana, W., Stadler, P.F. and Hofacker, I.L., From sequences to shapes and back: A case study in RNA secondary structures. Proc R Soc B, 255(1344) 1994.

Ioannis Theologidis
Instituto Gulbenkian de Ciência

Reproductive assurance drives mating system transitions to selfing


Author(s): Theologidis, I, Chelo, IM, Teotónio, H


Evolutionary transitions from outcrossing to selfing are thought to occur because selfing reproductively assures the persistence of populations when mates or pollinators are unreliable. Direct evidence for reproductive assurance is however equivocal, in particular because outcrossing can easily overcome the adaptive benefits of selfing. To test for the impact of reproductive assurance by selfing, we performed invasion experiments of hermaphrodites into predominantly male-female populations of the nematode Caenorhabditis elegans. The invasion and fixation of selfing resulted in adaptation when populations evolved in a new environment that hindered mating. In contrast, when selfing failed to invade, adaptation to the novel environment was compromised because mating was possible. Using Monte Carlo simulations we further explored the factors that might have influenced the invasion dynamics of selfing. We confirm that reproductive assurance was responsible for the experimental transition from outcrossing to selfing.


Chairman: Octávio S. Paulo
Tel: 00 351 217500614 direct
Tel: 00 351 217500000 ext22359
Fax: 00 351 217500028


XIV Congress of the European Society for Evolutionary Biology

Organization Team
Department of Animal Biology (DBA)
Faculty of Sciences of the University of Lisbon
P-1749-016 Lisbon


Computational Biology & Population Genomics Group