Let’s move beyond costs of resistance!

International audienceA recommendation – based on reviews by Danna Gifford, Helen Alexander and 1 anonymous referee – of:Lenormand T, Harmand N, Gallet R. 2018. Cost of resistance: an unreasonably expensive concept. bioRxiv 276675, ver. 3 peer-reviewed by Peer Community In Evolutionary Biology doi: 10.1101/27667

Manteniment de la plasticitat fenotípica

La plasticitat fenotípica és la capacitat dels organismes per alterar el seu fenotip d'acord amb les condicions ambientals. Tot i que és important per fer front a les pertorbacions ambientals, el seu manteniment sol resultar costós per als organismes i es pot perdre durant l'evolució sota condicions constants i no estressants. En aquest estudi s'ha analitzat l'evolució de la plasticitat tèrmica en un ambient estable i s'ha observat que els individus mantenien la seva plasticitat fenotípica, malgrat que hi hagi algunes diferències entre les poblacions.La plasticidad fenotípica es la capacidad de los organismos para alterar su fenotipo de acuerdo con las condiciones ambientales. Aunque es importante para hacer frente a las perturbaciones ambientales, su mantenimiento suele resultar costoso para los organismos y puede perderse durante la evolución bajo condiciones constantes y no estresantes. En este estudio se ha analizado la evolución de la plasticidad térmica en un ambiente estable y se ha observado que los individuos mantenían su plasticidad fenotípica, a pesar de existir algunas diferencias entre las poblaciones.Phenotypic plasticity is the ability of organisms to change their phenotype according to the environment. While plasticity is important to cope with environmental changes, it may also be costly and be lost during evolution in a constant, non-challenging environment. In this study, we analyzed the evolution of thermal plasticity in an environment with a constant temperature. We observed that plasticity was not lost, though some differences between populations occurred during the evolution

Alterações evolutivas durante a adaptação ao cativeiro:análise de características morfológicas, comportamentais e da história da vida

Tese de mestrado, Biologia (Biologia Evolutiva e do Desenvolvimento), 2007, Universidade de Lisboa, Faculdade de CiênciasA dinâmica da adaptação ao cativeiro é um tema que tem gerado alguma controvérsia na área da Evolução Experimental. Nesta tese abordam-se diversos aspectos da dinâmica da adaptação ao laboratório, traçando trajectórias evolutivas para características da história da vida em populações de Drosophila subobscura. Os principais aspectos focados são 1) a importância de efeitos temporais e geográficos (diferentes anos e locais de fundação) na dinâmica evolutiva inicial na adaptação ao laboratório, 2) a comparação dessa dinâmica quando analisada quer pelo método da evolução em tempo real, quer quando inferida através do método comparativo, e 3) a existência de diferenças entre populações há mais e menos tempo em laboratório, em termos de fecundidade, resistência à inanição, comportamento e tamanho do corpo do adulto. Os resultados sugerem um padrão geral de adaptação nas populações fundadas até 2005, embora as respostas evolutivas de algumas características possam ser afectadas pelo ano e/ou local de fundação. Observou-se ainda uma falha na capacidade de previsão das dinâmicas evolutivas traçadas pelo método comparativo, quando introduzida a fundação CW. Os resultados da comparação da diferenciação de populações há mais e menos tempo em laboratório sugerem que, apesar de não haver diferenças no tamanho do adulto, fecundidade e resistência à inanição, existem diferenças no comportamento dos machos durante o acasalamento. No compto geral este trabalho mostra o papel preponderante da selecção natural durante a adaptação ao laboratório, apesar de existirem contingências, ilustradas na similaridade inesperada de populações recém-introduzidas e populações já estabilizadas no laboratório. Este problema apenas reforça o facto de ser necessário cuidado com as inferências a tirar a partir de estudos evolutivos, nomeadamente quando é utilizado o método comparativo, apelando a um estudo mais diversificado de características relacionadas com a fitness, de modo a obter uma caracterização mais fina e precisa das dinâmicas evolutivas subjacentes ao laboratórioThe dynamics of adaptation to captivity has raised some controversial issues in the area of Experimental Evolution. In this thesis I tackle different aspects of evolutionary dynamics of adaptation to the laboratory environment, by generating real time evolutionary trajectories of life history traits for Drosophila subobscura populations. The main issues are 1) the impact of temporal and geographical effects of foundation in the initial dynamics of laboratory evolution (i.e. repeatability of the adaptive process); 2) the comparison of evolutionary dynamics analysed either with comparative or with real time evolution, and 3) the existence of differences in traits like fecundity, starvation resistance, behaviour and adult body size between populations recently founded and longer established in the laboratory. The results point to a general adaptive response in populations founded until 2005, although evolutionary responses of some traits can be influenced by year and/or local of foundation. It was also observed a lack of consistence between the dynamics inferred through comparative method and evolutionary trajectories, suggesting a low predictive capacity of the first. The comparison of initial differentiation between recently founded and a longer established population suggests that, although there aren't differences in adult body size and life history traits, there are some differences between these populations in male mating ability. This work shows that natural selection plays a major role in adaptation to laboratorial environment, although there are some contingencies during the study of this process, as illustrated by the unexpected similarity of CW and NW populations in their initial performance. This issue strengthens the need for caution when making evolutionary inferences, especially if using the comparative method. It also enlightens the necessity to pursue a more diversified study of fitness related traits in different populations, so that there can be more precise characterization of evolutionary dynamics subjacent to laboratory adaptatio

Playing evolution in the laboratory: From the first major evolutionary transition to global warming

Experimental evolution allows testing hypotheses derived from theory or from observed patterns in nature. We have designed a droplet-based microfluidic "evolution machine" to test how transient compartmentalization ("trait-groups") of independent molecular replicators (likely a critical step in the origin of life) could have prevented the spread of parasitic mutants; that is, inactive RNAs that have been reported to spoil a system of free replicators. In remarkable agreement with the theory, we show that this simple population structure was sufficient to prevent takeover by inactive RNAs. A more complex scenario arises when we use experimental evolution to test field-derived hypotheses; for instance, the idea that temperature is driving genetic spatiotemporal patterns of climate change. In the fly Drosophila subobscura, latitudinal dines in gene arrangement frequencies occur worldwide, and more equatorial gene arrangements are becoming more frequent at higher latitudes as a correlated response to climate change. However, the evolution at different constant temperatures in the laboratory was not consistent with patterns in nature, suggesting some limitations of experimental evolution. Finally, also in D. subobscura, we show that repeatability in experimental evolution is staggeringly consistent for life history traits, making evolution quite predictable and suggesting that laboratory selection can quickly erase differences between populations. Yet, the genetic paths used to attain the same adaptive phenotypes are complex and unpredictable. Copyright (C) EPLA, 201

Editorial: Coping With Climate Change: A Genomic Perspective on Thermal Adaptation

info:eu-repo/semantics/publishedVersio

The adaptive potential of the M-domain of yeast Hsp90 [preprint]

Comparing the distribution of fitness effects (DFE) of new mutations across different environments quantifies the potential for adaptation in a given environment and its cost in other environments. So far, results regarding the cost of adaptation across environments have been mixed, and there were no sufficiently large data sets to map its variation along the genome. Here, we study the DFEs of ≈2500 amino-acid changing mutations obtained from deep mutational scanning of the 118 amino-acid-long middle domain of the heat-shock protein Hsp90 in five environments and at two expression levels. This region is known to be important for client binding, stabilization of the Hsp90 dimer, stabilization of the N-M and M-C interdomains and regulation of ATPase-chaperone activity. Despite the diverse and stressful environments, we find that fitness correlates well across environments, with the exception of one environment, diamide. Consistent with these results, we find very little cost of adaptation; on average only one in seven beneficial mutations is deleterious in another environment. We identify a hotspot of beneficial mutations in a region of the protein that is located within an allosteric center. The identified protein regions that are enriched in beneficial, deleterious, and costly mutations coincide with residues that are involved in the stabilization of Hsp90 interdomains and stabilization of client binding interfaces or residues that are involved in ATPase chaperone activity of Hsp90. Thus, our study yields information regarding the role and adaptive potential of a protein sequence that complements and extends known structural information

How phenotypic convergence arises in experimental evolution

Evolutionary convergence is a core issue in the study of adaptive evolution, as well as a highly debated topic at present. Few studies have analyzed this issue using a "real-time" or evolutionary trajectory approach. Do populations that are initially differentiated converge to a similar adaptive state when experiencing a common novel environment? Drosophila subobscura populations founded from different locations and years showed initial differences and variation in evolutionary rates in several traits during short-term (∼20 generations) laboratory adaptation. Here, we extend that analysis to 40 more generations to analyze (1) how differences in evolutionary dynamics among populations change between shorter and longer time spans, and (2) whether evolutionary convergence occurs after 60 generations of evolution in a common environment. We found substantial variation in longer term evolutionary trajectories and differences between short- and longer term evolutionary dynamics. Although we observed pervasive patterns of convergence toward the character values of long-established populations, populations still remain differentiated for several traits at the final generations analyzed. This pattern might involve transient divergence, as we report in some cases, indicating that more generations should lead to final convergence. These findings highlight the importance of longer term studies for understanding convergent evolution.info:eu-repo/semantics/publishedVersio

Predictable phenotypic, but not karyotypic, evolution of populations with contrasting initial history

This study was financed by Portuguese National Funds through FCT - ‘Fundação para a Ciência e Tecnologia’ within the projects PTDC/BIA-BEC/098213/2008, PTDC/BIA-BIC/2165/2012 and cE3c Unit FCT funding UID/BIA/00329/2013. I.F. had a PhD grant (SFRH/BD/60734/2009), P.S. has a Post Doc grant (SFRH/BPD/86186/2012) and S.G.S. has a Post Doc grant (SFRH/BPD/108413/2015) from FCT. M.S. is funded by grant CGL2013-42432-P from the Ministerio de Economía y Competitividad (Spain) and grant 2014 SGR 1346 from Generalitat de Catalunya. The datasets generated during and/or analysed during the current study are available in the figshare repository, at https://doi.org/10.6084/m9.figshare.4797550.The relative impact of selection, chance and history will determine the predictability of evolution. There is a lack of empirical research on this subject, particularly in sexual organisms. Here we use experimental evolution to test the predictability of evolution. We analyse the real-time evolution of Drosophila subobscura populations derived from contrasting European latitudes placed in a novel laboratory environment. Each natural population was sampled twice within a three-year interval. We study evolutionary responses at both phenotypic (life-history, morphological and physiological traits) and karyotypic levels for around 30 generations of laboratory culture. Our results show (1) repeatable historical effects between years in the initial state, at both phenotypic and karyotypic levels; (2) predictable phenotypic evolution with general convergence except for body size; and (3) unpredictable karyotypic evolution. We conclude that the predictability of evolution is contingent on the trait and level of organization, highlighting the importance of studying multiple biological levels with respect to evolutionary patterns.Publisher PDFPeer reviewe

Limited host availability disrupts the genetic correlation between virulence and transmission

Virulence is expected to be linked to parasite fitness via transmission. However, it is not clear whether this relationship is genetically determined, nor if it differs when transmission occurs continuously during, or only at the end of, the infection period. Here, we used inbred lines of the macroparasitic spider mite Tetranychus urticae to disentangle genetic vs. nongenetic correlations among traits, while varying parasite density and opportunities for transmission. A positive genetic correlation between virulence and the number of transmitting stages produced was found under continuous transmission. However, if transmission occurred only at the end of the infection period, this genetic correlation disappeared. Instead, we observed a negative relationship between virulence and the num ber of transmitting stages, driven by density dependence. Thus, within-host density dependence caused by reduced opportunities for transmission may hamper selection for higher virulence, providing a novel explanation as to why limited host availability leads to lower virulenceinfo:eu-repo/semantics/publishedVersio

Different genomic changes underlie adaptive evolution in populations of contrasting history

Funding Information: This work was supported by Portuguese National Funds through “Fundac¸ão para a Ciência e a Tecnologia” (projects PTDC/ BIA-BEC/098213/2008, PTDC/BIA-BIC/2165/2012 and cE3c Unit FCT funding UID/BIA/00329/2013, grants SFRH/BD/ 60734/2009 to I.F. and SFRH/BPD/86186/2012 to P.S.). We thank Miguel Lopes-Cunha for help in the laboratory, Francisco Pina-Martins for help with computing, Josiane Santos and Ana Sofia Quina for discussions, and Mauro Santos and Anthony Long for advice on the study and comments on the manuscript. We also thank the three anonymous reviewers for their constructive suggestions.Experimental evolution is a powerful tool to understand the adaptive potential of populations under environmental change. Here, we study the importance of the historical genetic background in the outcome of evolution at the genomewide level. Using the natural clinal variation of Drosophila subobscura, we sampled populations from two contrasting latitudes (Adraga, Portugal and Groningen, Netherlands) and introduced them in a new common environment in the laboratory. We characterized the genome-wide temporal changes underlying the evolutionary dynamics of these populations, which had previously shown fast convergence at the phenotypic level, but not at chromosomal inversion frequencies. We found that initially differentiated populations did not converge either at genome-wide level or at candidate SNPs with signs of selection. In contrast, populations from Portugal showed convergence to the control population that derived from the same geographical origin and had been long-established in the laboratory. Candidate SNPs showed a variety of different allele frequency change patterns across generations, indicative of an underlying polygenic basis. We did not detect strong linkage around candidate SNPs, but rather a small but long-ranging effect. In conclusion, we found that history played a major role in genomic variation and evolution, with initially differentiated populations reaching the same adaptive outcome through different genetic routes.publishersversionpublishe