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19 Feb 2018
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Genomic imprinting mediates dosage compensation in a young plant XY system

Dosage compensation by upregulation of maternal X alleles in both males and females in young plant sex chromosomes

Recommended by and based on reviews by 3 anonymous reviewers

Sex chromosomes evolve as recombination is suppressed between the X and Y chromosomes. The loss of recombination on the sex-limited chromosome (the Y in mammals) leads to degeneration of both gene expression and gene content for many genes [1]. Loss of gene expression or content from the Y chromosome leads to differences in gene dose between males and females for X-linked genes. Because expression levels are often correlated with gene dose [2], these hemizygous genes have a lower expression levels in the heterogametic sex. This in turn disrupts the stoichiometric balance among genes in protein complexes that have components on both the sex chromosomes and autosomes [3], which could have serious deleterious consequences for the heterogametic sex.
To overcome these deleterious effects of degeneration, the expression levels of dosage sensitive X-linked genes, and in some organisms, entire X chromosomes, are compensated, the expression of the single copy of in the heterogametic sex being increased. Dosage compensation for such genes has evolved in several species, restoring similar expression levels as in the ancestral state in males and/or equal gene expression in males and females [4-8]. The mechanisms for dosage compensation are variable among species and their evolutionary paths are not fully understood, as the few model sex chromosomes studied so far have old, and highly degenerate sex chromosomes [4-7].
Muyle et al. [9] studied the young sex chromosomes of the plant Silene latifolia, which has young sex chromosomes (4 MY) and highly variable dosage compensation [10, 11]. The authors used both an outgroup species without sex chromosomes for obtaining a proxy for ancestral expression levels before Y degeneration, and implemented methods to identify sex-linked genes and disentangle paternal versus maternal allele expression [12]. Using these elements, Muyle et al. [9] reveal upregulation of maternal X alleles in both males and females in the young S. latifolia sex chromosomes [9], possibly by genomic imprinting. The upregulation in both sexes of the maternal X alleles likely yields non-optimal gene expression in females, which is strikingly consistent with the theoretical first step of dosage compensation as postulated by Ohno [8], which predicts restoration of ancestral expression in males, over-expression in females, and unequal expression in the two sexes. These findings provide surprising insight into the earliest stages of dosage compensation, one of the most intriguing aspects of evolutionary biology.

References
[1] Bachtrog D. 2013. Y chromosome evolution: emerging insights into processes of Y-chromosome degeneration? Nature Reviews Genetics 14: 113–124. doi: 10.1038/nrg3366
[2] Malone JH, Cho D-Y, Mattiuzzo NR, Artieri CG, Jiang L, Dale RK, Smith HE, McDaniel J, Munro S, Salit M, Andrews J, Przytycka TM and Oliver B. 2012. Mediation of Drosophila autosomal dosage effects and compensation by network interactions. Genome Biology 13: R28. doi: 10.1186/gb-2012-13-4-r28
[3] Pessia E, Makino T, Bailly-Bechet M, McLysaght A and Marais GAB. 2012. Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. Proceedings of the National Academy of Sciences of the United States of America. 109: 5346–5351. doi: 10.1073/pnas.1116763109.
[4] Graves JAM. 2016. Evolution of vertebrate sex chromosomes and dosage compensation. Nature Reviews Genetics 17: 33–46. doi: 10.1038/nrg.2015.2
[5] Mank JE. 2013. Sex chromosome dosage compensation: definitely not for everyone. Trends in Genetics 12: 677–683. doi: 10.1016/j.tig.2013.07.005
[6] Pessia E and Engelstädter J. 2014. The evolution of X chromosome inactivation in mammals: the demise of Ohno’s hypothesis? Cellular and Molecular Life Sciences 71: 1383–1394. doi: 10.1007/s00018-013-1499-6
[7] Muyle A, Shearn R and Marais GAB. 2017. The evolution of sex chromosomes and dosage compensation in plants. Genome Biology and Evolution 9: 627–645. doi: 10.1093/gbe/evw282
[8] Ohno S. 1967. Sex chromosomes and sex linked genes. Springer, Berlin Heidelberg New York.
[9] Muyle A, Zemp N, Fruchard C, Cegan R, Vrana J, Deschamps C, Tavares R, Picard F, Hobza R, Widmer A and Marais GAB. 2018. Genomic imprinting mediates dosage compensation in a young plant XY system. bioRxiv 118695, ver. 6 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/179044
[10] Papadopulos AST, Chester M, Ridout K and Filatov DA. 2015. Rapid Y degeneration and dosage compensation in plant sex chromosomes. Proceedings of the National Academy of Sciences of the United States of America 112: 13021–13026. doi: 10.1073/pnas.1508454112
[11] Bergero R, Qiu S and Charlesworth D. 2015. Gene loss from a plant sex chromosome system. Current Biology 25: 1234–1240. doi: 10.1016/j.cub.2015.03.015
[12] Muyle A, Kafer J, Zemp N, Mousset S, Picard F and Marais GAB. 2016. SEX-DETector: a probabilistic approach to study sex chromosomes in non-model organisms. Genome Biology and Evolution 8: 2530–2543. doi: 10.1093/gbe/evw172

Genomic imprinting mediates dosage compensation in a young plant XY systemAline Muyle, Niklaus Zemp, Cecile Fruchard, Radim Cegan, Jan Vrana, Clothilde Deschamps, Raquel Tavares, Franck Picard, Roman Hobza, Alex Widmer, Gabriel Marais<p>During the evolution of sex chromosomes, the Y degenerates and its expression gets reduced relative to the X and autosomes. Various dosage compensation mechanisms that recover ancestral expression levels in males have been described in animals....Bioinformatics & Computational Biology, Expression Studies, Genome Evolution, Molecular Evolution, Reproduction and SexTatiana Giraud2017-09-20 20:39:46 View
24 Oct 2019
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Testing host-plant driven speciation in phytophagous insects : a phylogenetic perspective

Phylogenetic approaches for reconstructing macroevolutionary scenarios of phytophagous insect diversification

Recommended by based on reviews by Brian O'Meara and 1 anonymous reviewer

Plant-animal interactions have long been identified as a major driving force in evolution. However, only in the last two decades have rigorous macroevolutionary studies of the topic been made possible, thanks to the increasing availability of densely sampled molecular phylogenies and the substantial development of comparative methods. In this extensive and thoughtful perspective [1], Jousselin and Elias thoroughly review current hypotheses, data, and available macroevolutionary methods to understand how plant-insect interactions may have shaped the diversification of phytophagous insects. First, the authors review three main hypotheses that have been proposed to lead to host-plant driven speciation in phytophagous insects: the ‘escape and radiate’, ‘oscillation’, and ‘musical chairs’ scenarios, each with their own set of predictions. Jousselin and Elias then synthesize a vast core of recent studies on different clades of insects, where explicit phylogenetic approaches have been used. In doing so, they highlight heterogeneity in both the methods being used and predictions being tested across these studies and warn against the risk of subjective interpretation of the results. Lastly, they advocate for standardization of phylogenetic approaches and propose a series of simple tests for the predictions of host-driven speciation scenarios, including the characterization of host-plant range history and host breadth history, and diversification rate analyses. This helpful review will likely become a new point of reference in the field and undoubtedly help many researchers formalize and frame questions of plant-insect diversification in future studies of phytophagous insects.

References

[1] Jousselin, E., Elias, M. (2019). Testing Host-Plant Driven Speciation in Phytophagous Insects: A Phylogenetic Perspective. arXiv, 1910.09510, ver. 1 peer-reviewed and recommended by PCI Evol Biol. https://arxiv.org/abs/1910.09510v1

Testing host-plant driven speciation in phytophagous insects : a phylogenetic perspective Emmanuelle Jousselin, Marianne Elias <p>During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation. Phytophagous ...Macroevolution, Phylogenetics / Phylogenomics, Speciation, Species interactionsHervé Sauquet2019-02-25 17:31:33 View
21 Nov 2019
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Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity

Nutrition-dependent effects of gut bacteria on growth plasticity in Drosophila melanogaster

Recommended by based on reviews by Pedro Simões and 1 anonymous reviewer

It is well known that the rearing environment has strong effects on life history and fitness traits of organisms. Microbes are part of every environment and as such likely contribute to such environmental effects. Gut bacteria are a special type of microbe that most animals harbor, and as such they are part of most animals’ environment. Such microbial symbionts therefore likely contribute to local adaptation [1]. The main question underlying the laboratory study by Guilhot et al. [2] was: How much do particular gut bacteria affect the organismal phenotype, in terms of life history and larval foraging traits, of the fruit fly Drosophila melanogaster, a common laboratory model species in biology?
To investigate the above question, the authors isolated 4 taxa of bacteria from the gut of a (randomly picked) Drosophila melanogaster lab strain, and subsequently let Drosophila melanogaster eggs and larvae (stemming from their own, different lab strain) develop both in the typical artificial laboratory medium as well as in grapes, a natural “new” habitat for Drosophila larvae, inoculated with theses bacteria, singly and in combination, also including a bacteria-free control. By investigating various relevant developmental and size traits, the authors found that adding particularly Enterobacteria had some visible effects on several traits, both upward (indicting improvement) and downward (being detrimental) (with three other types of bacteria showing only minor or even no effects). In general, the grape medium reduced performance relative to the standard lab medium. Strongest interactive effects occurred for development time and body size, together making up growth plasticity [3], with lesser such effects on some related behavioral (feeding) traits (Figs. 2,3).
The study premise is interesting, its general objectives are clearly laid out, and the practical work was conducted correctly as far as I can evaluate. The study remains largely descriptive in that no particular a priori hypotheses or predictions in relation to the specific bacteria isolated were formulated, not least because the bacteria were necessarily somewhat arbitrarily chosen and there were apparently no prior studies from which to derive concrete predictions. Overall, the results of this study should be of interest to the community of evolutionary ecologists, especially those working on nutritional and microbiome effects on animal life histories. I consider this work to be primarily ecological, with limited evolutionary content (e.g. no genetics) though some evolutionary implications, as mentioned in the paper’s Conclusions. So this paper would best fit in a microbial or physiological ecology outlet/journal.
The inclusion of a natural medium (grapes) must be commended because this permits inferences and conclusions for at least one natural environment, whereas inferences drawn from laboratory studies in the artificial medium that most Drosophila researchers seem to use are typically limited. Unsurprisingly perhaps, the study showed that Drosophila melanogaster fared generally better in the artificial than the chosen natural medium (grape). Crucially, however, the bacterial symbionts modified both media differentially. Although common bacterial taxa were chosen, the particular bacteria isolated and used remain arbitrary, as there are many. I note that the main and strongest interactive effects between medium and bacterial type are apparent for the Enterobacteria, and they probably also strongly, if not exclusively, mediate the overall effect of the bacterial mixture.
While these specific data are novel, they are not very surprising. If we grow animals in different environments we can expect some detectable effects of these environments, including the bacterial (microbiome) environment, on the hosts life history. The standard and predicted [4] life history response of Drosophila melanogaster (but not all insects [3]) facing stressful nutritional environments, as apparently created by the Enterobacteria, is to extend development but come out smaller in the end. This is what happened here for the laboratory medium ([2]: Fig. 5). The biological interpretation is that individuals have more trouble ingesting and/or digesting the nutrients available (thus prolonging their foraging period and development), yet cannot convert the nutrients effectively into body size increments (hence emerging smaller). This is what the authors here refer to as developmental plasticity, which is ultimately nutritionally mediated. However, interestingly, a signal in the opposite direction was indicated for the bacterial mixture in the grape medium (flies emerging larger after accelerated development: Fig. 5), suggesting some positive effects on growth rate of the natural medium, perhaps related to grapes being a limited resource that needs to be escaped quickly [3]? The reversal of sexual size dimorphism across bacterial treatments in the grape environment detectable in Fig. 4 is interesting, too, though I don’t understand why this happens, and this is not discussed.
In general, more encompassing and increased questions in this context to be researched in the future could be: 1) are these effects predictable (not (yet) at this point, or so it seems); and 2) how strong are these environmental bacterial effects relative to other, more standard effects (e.g. relative to genetic variation, population variation, etc., or relative to other types of environmental effects like, say, temperature)? (3) It could further be asked why not natural but laboratory populations of Drosophila were used for this experiment, if the aim was to draw inferences for the wild situation. (4) Although Genotype x Environment effects are invoked in the Discussion, they were not tested here, lacking genetically different Drosophila families or populations. From an evolutionary standpoint, I consider this the greatest weakness of the study. I was also not too thrilled by the particular statistical analyses employed, though this ultimately does not negate the results. Nevertheless, this work is a good start in this huge field investigating the microbiome. In conclusion, I can recommend this paper after review by PCI Evol Biol.

References

[1] Kawecki, T. J. and Ebert, D. (2004) Conceptual issues in local adaptation. Ecology Letters 7: 1225-1241. doi: 10.1111/j.1461-0248.2004.00684.x
[2] Guilhot, R., Rombaut, A., Xuéreb, A., Howell, K. and Fellous, S. (2019). Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity. BioRxiv, 717702, v3 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/717702
[3] Blanckenhorn, W.U. (1999) Different growth responses to temperature and resource limitation in three fly species with similar life histories. Evolutionary Ecology 13: 395-409. doi: 10.1023/A:1006741222586
[4] Stearns, S. C. and Koella, J. (1986) The evolution of phenotypic plasticity in life history traits: predictions of reaction norms for age and size at maturity. Evolution 40: 893-914. doi: 10.1111/j.1558-5646.1986.tb00560.x

Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticityRobin Guilhot, Antoine Rombaut, Anne Xuéreb, Kate Howell, Simon Fellous<p>Environmentally acquired microbial symbionts could contribute to host adaptation to local conditions like vertically transmitted symbionts do. This scenario necessitates symbionts to have different effects in different environments. We investig...Adaptation, Evolutionary Ecology, Phenotypic Plasticity, Species interactionsWolf Blanckenhorn2019-02-13 15:22:23 View
02 Nov 2020
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Experimental evolution of virulence and associated traits in a Drosophila melanogaster – Wolbachia symbiosis

Temperature effects on virulence evolution of wMelPop Wolbachia in Drosophila melanogaster

Recommended by based on reviews by Shira Houwenhuyse and 3 anonymous reviewers

Monnin et al. [1] here studied how Drosophila populations are affected when exposed to a high virulent endosymbiotic wMelPop Wolbachia strain and why virulent vertically transmitting endosymbionts persist in nature. This virulent wMelPop strain has been described to be a blocker of dengue and other arboviral infections in arthropod vector species, such as Aedes aegypti. Whereas it can thus function as a mutualistic symbiont, it here acts as an antagonist along the mutualism-antagonism continuum symbionts operate. The wMelPop strain is not a natural occurring strain in Drosophila melanogaster and thus the start of this experiment can be seen as a novel host-pathogen association. Through experimental evolution of 17 generations, the authors studied how high temperature affects wMelPop Wolbachia virulence and Drosophila melanogaster survival. The authors used Drosophila strains that were selected for late reproduction, given that this should favor evolution to a lower virulence. Assumptions for this hypothesis are not given in the manuscript here, but it can indeed be assumed that energy that is assimilated to symbiont tolerance instead of reproduction may lead to reduced virulence evolution. This has equally been suggested by Reyserhove et al. [2] in a dynamics energy budget model tailored to Daphnia magna virulence evolution upon a viral infection causing White fat Cell disease, reconstructing changing environments through time.
Contrary to their expectations for vertically transmitting symbionts, the authors did not find a reduction in wMelPop Wolbachia virulence during the course of the experimental evolution experiment under high temperature. Important is what this learns for virulence evolution, also for currently horizontal transmitting disease epidemics (such as COVID-19). It mainly reflects that evolution of virulence for new host-pathogen associations is difficult to predict and that it may take multiple generations before optimal levels of virulence are reached [3,4]. These optimal levels of virulence will depend on trade-offs with other life history traits of the symbiont, but also on host demography, host heterogeneity, amongst others [5,6]. Multiple microbial interactions may affect the outcome of virulence evolution [7]. Given that no germ-free individuals were used, it can be expected that other components of the Drosophila microbiome may have played a role in the virulence evolution. In most cases, microbiota have been described as defensive or protective for virulent symbionts [8], but they may also have stimulated the high levels of virulence. Especially, given that upon higher temperatures, Wolbachia growth may have been increased, host metabolic demands increased [9], host immune responses affected and microbial communities changed [10]. This may have resulted in increased competitive interactions to retrieve host resources, sustaining high virulence levels of the symbiont.
A nice asset of this study is that the phenotypic results obtained in the experimental evolution set-up were linked with wMelPop density measurement and octomom copy number quantifications. Octomom is a specific 8-n genes region of the Wolbachia genome responsible for wMelPop virulence, so there is a link between the phenotypic and molecular functions of the involved symbiont. The authors found that density, octomom copy number and virulence were correlated to each other. An important note the authors address in their discussion is that, to exclude the possibility that octomom copy number has an effect on density, and density on virulence, the effect of these variables should be assessed independently of temperature and age. The obtained results are a valuable contribution to the ongoing debate on the relationship between wMelPop octomom copy number, density and virulence.

References

[1] Monnin, D., Kremer, N., Michaud, C., Villa, M., Henri, H., Desouhant, E. and Vavre, F. (2020) Experimental evolution of virulence and associated traits in a Drosophila melanogaster – Wolbachia symbiosis. bioRxiv, 2020.04.26.062265, ver. 4 peer-reviewed and recommended by PCI Evol Biol. doi: https://doi.org/10.1101/2020.04.26.062265
[2] Reyserhove, L., Samaey, G., Muylaert, K., Coppé, V., Van Colen, W., and Decaestecker, E. (2017). A historical perspective of nutrient change impact on an infectious disease in Daphnia. Ecology, 98(11), 2784-2798. doi: https://doi.org/10.1002/ecy.1994
[3] Ebert, D., and Bull, J. J. (2003). Challenging the trade-off model for the evolution of virulence: is virulence management feasible?. Trends in microbiology, 11(1), 15-20. doi: https://doi.org/10.1016/S0966-842X(02)00003-3
[4] Houwenhuyse, S., Macke, E., Reyserhove, L., Bulteel, L., and Decaestecker, E. (2018). Back to the future in a petri dish: Origin and impact of resurrected microbes in natural populations. Evolutionary Applications, 11(1), 29-41. doi: https://doi.org/10.1111/eva.12538
[5] Day, T., and Gandon, S. (2007). Applying population‐genetic models in theoretical evolutionary epidemiology. Ecology Letters, 10(10), 876-888. doi: https://doi.org/10.1111/j.1461-0248.2007.01091.x
[6] Alizon, S., Hurford, A., Mideo, N., and Van Baalen, M. (2009). Virulence evolution and the trade‐off hypothesis: history, current state of affairs and the future. Journal of evolutionary biology, 22(2), 245-259. doi: https://doi.org/10.1111/j.1420-9101.2008.01658.x
[7] Alizon, S., de Roode, J. C., and Michalakis, Y. (2013). Multiple infections and the evolution of virulence. Ecology letters, 16(4), 556-567. doi: https://doi.org/10.1111/ele.12076
[8] Decaestecker, E., and King, K. (2019). Red queen dynamics. Reference module in earth systems and environmental sciences, 3, 185-192. doi: https://doi.org/10.1016/B978-0-12-409548-9.10550-0
[9] Kirk, D., Jones, N., Peacock, S., Phillips, J., Molnár, P. K., Krkošek, M., and Luijckx, P. (2018). Empirical evidence that metabolic theory describes the temperature dependency of within-host parasite dynamics. PLoS biology, 16(2), e2004608. doi: https://doi.org/10.1371/journal.pbio.2004608
[10] Frankel-Bricker, J., Song, M. J., Benner, M. J., and Schaack, S. (2019). Variation in the microbiota associated with Daphnia magna across genotypes, populations, and temperature. Microbial ecology, 1-12. doi: https://doi.org/10.1007/s00248-019-01412-9

Experimental evolution of virulence and associated traits in a Drosophila melanogaster – Wolbachia symbiosisDavid Monnin, Natacha Kremer, Caroline Michaud, Manon Villa, Hélène Henri, Emmanuel Desouhant, Fabrice Vavre<p>Evolutionary theory predicts that vertically transmitted symbionts are selected for low virulence, as their fitness is directly correlated to that of their host. In contrast with this prediction, the Wolbachia strain wMelPop drastically reduces...Evolutionary Ecology, Experimental Evolution, Species interactionsEllen Decaestecker2020-04-29 19:16:56 View
02 May 2025
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Experimental evidence for short term directional selection of epigenetic trait variation

Transgenerationally-transmitted epigenetic variation responds to phenotypic selection – results from a novel selection methodology

Recommended by ORCID_LOGO based on reviews by Leandro Quadrana and Sophie Brunel Muguet

The breeder’s equation is a classical equation in evolutionary theory, and basically states that the response of a trait to selection is equal to the strength of selection on this trait multiplied by the heritability of the trait. There can be several reasons why reality does not conform to a narrow interpretation of this equation, but in spite of that, let us actually indulge in a broad interpretation of the equation. Typically, the heritability of a trait is interpreted to refer to the genetic basis of a trait (the additive genetic variance). However, a broad interpretation of the breeder’s equation would be that if selection acts on a trait and that trait is somehow heritable, we should expect to observe an evolutionary change in that trait. In other words, the source and mechanism of inheritance does not matter for the breeder’s equation to have applicability.

In this paper, Pujol et al. (2025) follow this rationale for epigenetic variation, and more specifically for differentially methylated regions in the model plant Arabidopsis thaliana. They used 120 lines which vary across 126 differentially methylated regions of the genome, but are genetically identical, thereby eliminating additive genetic variance from the heritability component of the breeder’s equation. Previous studies have already shown that these differentially methylated regions are associated with different phenotypes, suggesting they somehow functionally affect the development of the plants. Previous studies have also shown that these differentially methylated regions are stably transmitted across generation, i.e., that they are heritable. This predicts that if one selects for different phenotypes, there should be an evolutionary response in the phenotypes, and an associated shift in the differentially methylated regions that are responsible for the phenotypic variation.

By and large, this is what Pujol et al. (2025) found. They selected divergently on four different plants traits (biomass, rosette size, flowering time, and height at first fruit), in two different populations, and with two different selection strengths. For most traits they found a phenotypic shift, and this largely corresponded with associated shifts in the differentially methylated regions. The patterns were very congruent between the different selection strengths, and very similar for the two different populations. We can therefore confidently conclude that epigenetic variation has effects on fitness-relevant phenotypic traits, that therefore natural selection can act on this epigenetic variation, and if so that this would cause an evolutionary change in the phenotypes under selection and in the differentially methylated regions causing this phenotypic variation. I.e., the breeder’s equation can indeed by applied to more than just genetically heritable variation, it can also be applied to non-genetically heritable variation. 

While this seems like a very obvious result, there are still very few studies that show how selection on non-genetic heritable variation results in a between-generation shift in this non-genetic heritable variation. In that sense, this study can function as a case in favour of a broader interpretation of evolution; to refer to a heritable between-generation change in the composition of a population, independent of whether the heredity is genetic or non-genetic. Critics might say that this study has only limited validity, since the epigenetic variation has been artificially increased in the used plant lines, and may not reflect naturally occurring variation. Indeed, more studies on natural selection on epigenetic variation are called for, but these will have the added complication that they need to correct for genetic variation, which is often correlated to epigenetic variation. Here, the authors could exclude genetic variation by working with epigenetically different lines that were genetically identical.

The study stands out in yet another respect – it uses a highly unusual and apparently novel selection design (although the authors do not know for sure if their idea is actually novel). Typically, in a selection study only a subset of parents is allowed to reproduce out of the total set of potential parents. If one wants to select for different traits separately, or with different selection strengths, separate selection studies need to be undertaken. Here the authors took a different approach. They let all their parents reproduce (3 offspring per plant), and phenotyped all offspring. They then, virtually, selected for different traits or for different selection strengths in the parents by excluding from their dataset the offspring of parents that are selected not to reproduce – after they had actually already reproduced! It is almost as if selection acts with a time delay, destroying not only the selected parents but also their offspring. This has the benefit that a single dataset is generated (all phenotyped offspring of all parents), and then selection can be exerted as often as one wants, for example for distinct types of selection, or on different (combinations) of traits. While the initial effort to phenotype offspring of all potential parents is large, and exponentially so if multiple generations are selected, the subsequent evaluation of distinct types of selection on any of the phenotyped traits is virtually effortless. For example, the authors applied divergent selection, but could reuse their dataset to apply stabilising selection. This novel selection design may therefore be a very attractive approach for many other researchers.

References

Benoit Pujol, Mathieu Latutrie, Pierick Mouginot, Nelia Luviano- Aparicio, Jésaëlle Piquet, Sara Marin, and Stéphane Maury (2025) Experimental evidence for short term directional selection of epigenetic trait variation. Zenodo, ver.2 peer-reviewed and recommended by PCI Evolutionary Biology https://doi.org/10.5281/zenodo.15227609

Experimental evidence for short term directional selection of epigenetic trait variationBenoit Pujol, Mathieu Latutrie, Pierick Mouginot, Nelia Luviano- Aparicio, Jésaëlle Piquet, Sara Marin, and Stéphane Maury<p>Evolution by natural selection can occur when organisms harbor genetically inherited phenotypic variation, and phenotypic variants have differential fitness. Stable transgenerational epigenetic variation also exists for fitness-related traits a...Morphological Evolution, Non Genetic InheritancePim Edelaar2024-07-17 16:07:37 View
03 May 2020
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When does gene flow facilitate evolutionary rescue?

Reconciling the upsides and downsides of migration for evolutionary rescue

Recommended by ORCID_LOGO based on reviews by 3 anonymous reviewers

The evolutionary response of populations to changing or novel environments is a topic that unites the interests of evolutionary biologists, ecologists, and biomedical researchers [1]. A prominent phenomenon in this research area is evolutionary rescue, whereby a population that is otherwise doomed to extinction survives due to the spread of new or pre-existing mutations that are beneficial in the new environment. Scenarios of evolutionary rescue require a specific set of parameters: the absolute growth rate has to be negative before the rescue mechanism spreads, upon which the growth rate becomes positive. However, potential examples of its relevance exist (e.g., [2]). From a theoretical point of view, the technical challenge but also the beauty of evolutionary rescue models is that they combine the study of population dynamics (i.e., changes in the size of populations) and population genetics (i.e., changes in the frequencies in the population). Together, the potential relevance of evolutionary rescue in nature and the models' theoretical appeal has resulted in a suite of modeling studies on the subject in recent years.
In this manuscript [3], Tomasini and Peischl address a question that has been contentiously discussed in the literature: when does migration favor evolutionary rescue? They expand on past work (specifically, [4, 5]) by studying the influence of the interaction of the speed and severity of environmental change and the amount of dispersal on the probability of evolutionary rescue. They develop simple analytical results (complemented by simulations) for a haploid one-locus model of two populations connected by gene flow, where both populations deteriorate successively such that evolutionary rescue is required for the metapopulation to survive. For example, the authors derive a simple analytical condition demonstrating that migration between the subpopulations favors evolutionary rescue if environmental change occurs slowly across the two populations (which leaves time for the second population to serve as an immigration source), if the new environment is very harsh and/or if rescue mutations are strongly beneficial in the new environment. The latter conditions ensure that the rescue mutations can spread easily in the new environment without much competition with immigrating, maladapted, genotypes. This result is intuitive and connects between traditional single and multiple-deme models.
Altogether, Tomasini and Peischl present an extensive theoretical study and address also the effect of various tweaks to the model assumptions, such as asymmetries in gene flow and/or carrying capacities, and the effects of different density regulation and local growth rates. They successfully made an effort to explain and interpret their results for a general audience, such that also non-theoreticians should not be afraid to take a look at this manuscript.

References

[1] Bell, G. (2017). Evolutionary Rescue. Annual Review of Ecology, Evolution, and Systematics 48(1), 605-627. doi: 10.1146/annurev-ecolsys-110316-023011
[2] Oziolor, E. M., Reid, N. M., Yair, S. et al. (2019). Adaptive introgression enables evolutionary rescue from extreme environmental pollution. Science, 364(6439), 455-457. doi: 10.1126/science.aav4155
[3] Tomasini, M. and Peischl, S. (2020) When does gene flow facilitate evolutionary rescue? bioRxiv, 622142, ver. 5 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/622142
[4] Uecker, H., Otto, S. P., and Hermisson, J. (2014). Evolutionary rescue in structured populations. The American Naturalist, 183(1), E17-E35. doi: 10.1086/673914
[5] Tomasini, M., and Peischl, S. (2018). Establishment of locally adapted mutations under divergent selection. Genetics, 209(3), 885-895. doi: 10.1534/genetics.118.301104

When does gene flow facilitate evolutionary rescue?Matteo Tomasini, Stephan Peischl<p>Experimental and theoretical studies have highlighted the impact of gene flow on the probability of evolutionary rescue in structured habitats. Mathematical modelling and simulations of evolutionary rescue in spatially or otherwise structured p...Evolutionary Dynamics, Evolutionary Theory, Population Genetics / GenomicsClaudia Bank2019-05-22 11:12:13 View
23 Apr 2020
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How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridis

Selection on a single trait does not recapitulate the evolution of life-history traits seen during an invasion

Recommended by and based on reviews by 2 anonymous reviewers

Biological invasions are natural experiments, and often show that evolution can affect dynamics in important ways [1-3]. While we often think of invasions as a conservation problem stemming from anthropogenic introductions [4,5], biological invasions are much more commonplace than this, including phenomena as diverse as natural range shifts, the spread of novel pathogens, and the growth of tumors. A major question across all these settings is which set of traits determine the ability of a population to invade new space [6,7]. Traits such as: increased growth or reproductive rate, dispersal ability and ability to defend from predation often show large evolutionary shifts across invasion history [1,6,8]. Are such multi-trait shifts driven by selection on multiple traits, or a correlated response by multiple traits to selection on one? Resolving this question is important for both theoretical and practical reasons [9,10]. But despite the importance of this issue, it is not easy to perform the necessary manipulative experiments [9].
Foucaud et al. [11] tackled this issue by performing experimental evolution on source populations of the invasive ladybug Harmonia axyridis. The authors tested if selection on a single trait could generate correlated responses in other life history traits. Specifically, they used experimental evolution to impose divergent selection on female mass, and reproductive timing. After ten generations, they found that selection for weight did not affect almost any other life history trait. However, nine generations of selection for faster reproduction led to correlated phenotypic changes in developmental, reproduction and survival rate of populations, although not always in the direction we might have expected. Despite this correlated response, none of their selected lines were able to fully recapitulate the trait shifts seen in natural invasions of this species. This implies that selection during natural invasions is operating on multiple traits; a finding in agreement with our growing understanding of how selection acts during introduction and invasion [12,13].
Populations undergoing a colonization process may also be subject to a multitude of different selective pressures [14,15]. The authors expanded their work in this direction by testing whether food availability alters the observed correlations between life history traits. The pervasiveness of genotype by environment interactions observed also points to a role for multiple selective pressures in shaping the suite of life-history shifts observed in wild ladybug populations. The work from Foucaud and colleagues [11] adds to a small but growing list of important studies that use experimental evolution to investigate how life-history traits evolve, and how they evolve during invasions in particular.

References

[1] Sakai, A.K., Allendorf, F.W., Holt, J.S. et al. (2001). The population biology of invasive species. Annual review of ecology and systematics, 32(1), 305-332. doi: 10.1146/annurev.ecolsys.32.081501.114037
[2] Hairston Jr, N. G., Ellner, S. P., Geber, M. A., Yoshida, T. and Fox, J. A. (2005). Rapid evolution and the convergence of ecological and evolutionary time. Ecology letters, 8(10), 1114-1127. doi: 10.1111/j.1461-0248.2005.00812.x
[3] Chuang, A. and Peterson, C. R. (2016). Expanding population edges: theories, traits, and trade‐offs. Global change biology, 22(2), 494-512. doi: 10.1111/gcb.13107
[4] Whitney, K. D. and Gabler, C. A. (2008). Rapid evolution in introduced species,‘invasive traits’ and recipient communities: challenges for predicting invasive potential. Diversity and Distributions, 14(4), 569-580. doi: 10.1111/j.1472-4642.2008.00473.x
[5] Catullo, R. A., Llewelyn, J., Phillips, B. L. and Moritz, C. C. (2019). The Potential for Rapid Evolution under Anthropogenic Climate Change. Current Biology, 29(19), R996-R1007. doi: 10.1016/j.cub.2019.08.028
[6] Suarez, A. V. and Tsutsui, N. D. (2008). The evolutionary consequences of biological invasions. Molecular Ecology, 17(1), 351-360. doi: 10.1111/j.1365-294X.2007.03456.x
[7] Deforet, M., Carmona-Fontaine, C., Korolev, K. S. and Xavier, J. B. (2019). Evolution at the edge of expanding populations. The American Naturalist, 194(3), 291-305. doi: 10.1086/704594
[8] Phillips, B. L., Brown, G. P., and Shine, R. (2010). Life‐history evolution in range‐shifting populations. Ecology, 91(6), 1617-1627. doi: 10.1890/09-0910.1
[9] Colautti, R. I. and Lau, J. A. (2015). Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation. Molecular ecology, 24(9), 1999-2017. doi: 10.1111/mec.13162
[10] Szűcs, M., Melbourne, B. A., Tuff, T., Weiss‐Lehman, C. and Hufbauer, R. A. (2017). Genetic and demographic founder effects have long‐term fitness consequences for colonising populations. Ecology Letters, 20(4), 436-444. doi: 10.1111/ele.12743
[11] Foucaud, J., Hufbauer, R. A., Ravigné, V., Olazcuaga, L., Loiseau, A., Ausset, A., Wang, S., Zang, L.-S., Lemenager, N., Tayeh, A., Weyna, A., Gneux, P., Bonnet, E., Dreuilhe, V., Poutout, B., Estoup, A. and Facon, B. (2020). How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridis. bioRxiv, 849968 ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/849968
[12] Simons, A. M. (2003). Invasive aliens and sampling bias. Ecology Letters, 6(4), 278-280. doi: 10.1046/j.1461-0248.2003.00430.x
[13] Phillips, B. L. and Perkins, T. A. (2019). Spatial sorting as the spatial analogue of natural selection. Theoretical Ecology, 12(2), 155-163. doi: 10.1007/s12080-019-0412-9
[14] Lavergne, S. and Molofsky, J. (2007). Increased genetic variation and evolutionary potential drive the success of an invasive grass. Proceedings of the National Academy of Sciences, 104(10), 3883-3888. doi: 10.1073/pnas.0607324104
[15] Moran, E. V. and Alexander, J. M. (2014). Evolutionary responses to global change: lessons from invasive species. Ecology Letters, 17(5), 637-649. doi: 10.1111/ele.12262

How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridisJulien Foucaud, Ruth A. Hufbauer, Virginie Ravigné, Laure Olazcuaga, Anne Loiseau, Aurelien Ausset, Su Wang, Lian-Sheng Zang, Nicolas Lemenager, Ashraf Tayeh, Arthur Weyna, Pauline Gneux, Elise Bonnet, Vincent Dreuilhe, Bastien Poutout, Arnaud Est...<p>Experiments comparing native to introduced populations or distinct introduced populations to each other show that phenotypic evolution is common and often involves a suit of interacting phenotypic traits. We define such sets of traits that evol...Adaptation, Evolutionary Applications, Experimental Evolution, Life History, Quantitative GeneticsInês Fragata2019-11-29 07:07:00 View
03 Oct 2018
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Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plants

Are both very young and the very old plant lineages at heightened risk of extinction?

Recommended by based on reviews by Dan Greenberg and 1 anonymous reviewer

Human economic activity is responsible for the vast majority of ongoing extinction, but that does not mean lineages are being affected willy-nilly. For amphibians [1] and South African flowering plants [2], young species have a somewhat higher than expected chance of being threatened with extinction. In contrast, older Australian marsupial lineages seem to be more at risk [3]. Both of the former studies suggested that situations leading to peripheral isolation might simultaneously increase ongoing speciation and current threat via small geographic range, while the authors of the latter study suggested that older species might have evolved increasingly narrow niches. Here, Andrew Tanentzap and colleagues [4] dig deeper into the putative links between species age, niche breadth and threat status. Across 500-some plant genera worldwide, they find that, indeed, ""younger"" species (i.e. from younger and faster-diversifying genera) were more likely to be listed as imperiled by the IUCN, consistent with patterns for amphibians and African plants. Given this, results from their finer-level analyses of conifers are initially bemusing: here, ""older"" (i.e., on longer terminal branches) species were at higher risk. This would make conifers more like Australian marsupials, with the rest of the plants being more like amphibians. However, here where the data were more finely grained, the authors detected a second interesting pattern: using an intriguing matched-pair design, they detect a signal of conifer species niches seemingly shrinking as a function of age. The authors interpret this as consistent with increasing specialization, or loss of ancestral warm wet habitat, over paleontological time. It is true that conifers in general are older than plants more generally, with some species on branches that extend back many 10s of millions of years, and so a general loss of suitable habitat makes some sense. If so, both the pattern for all plants (small initial ranges heightening extinction) and the pattern for conifers (eventual increasing specialization or habitat contraction heightening extinction) could occur, each on a different time scale. As a coda, the authors detected no effect of age on threat status in palms; however, this may be both because palms have already lost species to climate-change induced extinction, and because they are thought to speciate more via long-distance dispersal and adaptive divergence then via peripheral isolation.
Given how quickly ranges can change, how hard it is to measure niche breadth, and the qualitatively different time scales governing past diversification and present-day extinction drivers, this is surely not the last word on the subject, even for plants. However, even the hint of a link between drivers of extinction in the Anthropocene and drivers of diversification through the ages is intellectually exciting and, perhaps, even, somehow, of practical importance.

References

[1] Greenberg, D. A., & Mooers, A. Ø. (2017). Linking speciation to extinction: Diversification raises contemporary extinction risk in amphibians. Evolution Letters, 1, 40–48. doi: 10.1002/evl3.4
[2] Davies, T. J., Smith, G. F., Bellstedt, D. U., Boatwright, J. S., Bytebier, B., Cowling, R. M., Forest, F., et al. (2011). Extinction risk and diversification are linked in a plant biodiversity hotspot. PLoS Biology, 9:e1000620. doi: 10.1371/journal.pbio.1000620
[3] Johnson, C. N., Delean S., & Balmford, A. (2002). Phylogeny and the selectivity of extinction in Australian marsupials. Animal Conservation, 5, 135–142. doi: 10.1017/S1367943002002196
[4] Tanentzap, A. J., Igea, J., Johnston, M. G., & Larcombe, M. G. (2018). Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plants. bioRxiv, 152215, ver. 5 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/152215

Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plantsAndrew J. Tanentzap, Javier Igea, Matthew G. Johnston, Matthew J. Larcombe<p>Extinction threatens many species, yet few factors predict this risk across the plant Tree of Life (ToL). Taxon age is one factor that may associate with extinction if occupancy of geographic and adaptive zones varies with time, but evidence fo...Macroevolution, Phylogenetics / Phylogenomics, Phylogeography & BiogeographyArne Mooers2018-02-01 21:01:19 View
14 Apr 2021
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Parasitic success and venom composition evolve upon specialization of parasitoid wasps to different host species

What makes a parasite successful? Parasitoid wasp venoms evolve rapidly in a host-specific manner

Recommended by based on reviews by Simon Fellous, alexandre leitão and 1 anonymous reviewer

Parasitoid wasps have developed different mechanisms to increase their parasitic success, usually at the expense of host survival (Fellowes and Godfray, 2000). Eggs of these insects are deposited inside the juvenile stages of their hosts, which in turn deploy several immune response strategies to eliminate or disable them (Yang et al., 2020). Drosophila melanogaster protects itself against parasitoid attacks through the production of specific elongated haemocytes called lamellocytes which form a capsule around the invading parasite (Lavine and Strand, 2002; Rizki and Rizki, 1992) and the subsequent activation of the phenol-oxidase cascade leading to the release of toxic radicals (Nappi et al., 1995). On the parasitoid side, robust responses have evolved to evade host immune defenses as for example the Drosophila-specific endoparasite Leptopilina boulardi, which releases venom during oviposition that modifies host behaviour (Varaldi et al., 2006) and inhibits encapsulation (Gueguen et al., 2011; Martinez et al., 2012).
Studies have shown that the wasp parasitic capacity is correlated to venom presence and its content (Colinet et al., 2009; Poirié et al., 2014), including that evolution of venom protein composition is driven by different levels of host susceptibility to infection (Cavigliasso et al., 2019). However, it had not been determined to this day, if and how parasitic range can affect venom protein composition and to which extent host specialization requires broad-spectrum factors or a plethora of specialized components.
These outstanding questions are now approached in a study by Cavigliasso and colleagues (Cavigliasso et al., 2021), where they perform experimental evolution of L. boulardi for 9 generations exposing it to different Drosophila host species and genetic backgrounds (two strains of D. melanogaster, D. simulans and D. yakuba). The authors tested whether the parasitic success of each selection regime was host-specific and how they influenced venom composition in parasitoids. For the first part, infection outcomes were assayed for each selection regime when cross-infecting different hosts. To get a finer measurement of the mechanisms under selection, the authors differentiated three phenotypes: overall parasitic success, encapsulation inhibition and escape from capsule. Throughout the course of experimental evolution, only encapsulation inhibition did not show an improved response upon selection on any host. Importantly, the cross-infection scenario revealed a clear specificity to the selected host for each evolved resistance.
As for venom composition, a trend of differential evolution was detected between host species, although a significant part of that was due to a larger differentiation in the D. yakuba regime, which showed a completely different directionality. Importantly, the authors could identify some of the specific proteins targeted by the several selection regimes, whether selected or counter-selected for. Interestingly, the D. yakuba regime is the only case where the key parasitoid protein LbSPNy (Colinet et al., 2009) was not counter-selected and the only regime in which the overall venom composition did not evolve towards the Ism strain, one of the two ancestral strains of L. boulardi used in the study. It is possible that these two results are correlated, since LbSPNy has been described to inhibit activation of the phenoloxidase cascade in D. yakuba and is one of the most abundant proteins in the ISy venom, making it a good target for selection (Colinet et al., 2013). The authors also discuss the possibility that this difference is related to the geographical distribution of the strains of L. boulardi, since each coincide with either D. melanogaster or D. yakuba.
This methodologically broad work by Cavigliasso and colleagues constitutes an important experimental contribution towards the understanding of how parasitoid adaptation to specific hosts is achieved at different phenotypic and mechanistic levels. It provides compelling evidence that venom composition evolves differently in response to specific parasitic ranges, particularly considering the evolutionary difference between the selective hosts. In line with this result, it is also concluded that the majority of venom proteins selected are lineage-specific, although a few broad-spectrum factors could also be detected. 
The question of whether parasitic range can affect venom composition and parasitic success is still open to more contributions. A potentially interesting long-term direction will be to use a similar setup of experimental evolution on the generalist L. heterotoma (Schlenke et al., 2007) . On a more immediate horizon, comparing the venom evolution of both L. heterotoma and L. boulardi under selection with different hosts and under cross-infection scenarios could reveal interesting patterns. The recent sequencing of the L. boulardi genome together with the vast number of studies addressing mechanisms of Drosophila resistance to parasitoid infection, will enable the thorough characterization of the genetic basis of host-parasitoid interactions and the deeper understanding of these ubiquitous and economically-relevant relationships.
 
*This recommendation text has been co-written with Tânia F. Paulo who is not a recommender of PCI Evol Biol

 

References

Cavigliasso, F., Mathé-Hubert, H., Gatti, J.-L., Colinet, D. and Poirié, M. (2021) Parasitic success and venom composition evolve upon specialization of parasitoid wasps to different host species. bioRxiv, 2020.10.24.353417, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2020.10.24.353417

Cavigliasso, F., Mathé-Hubert, H., Kremmer, L., Rebuf, C., Gatti, J.-L., Malausa, T., Colinet, D., Poiré, M. and  Léne. (2019). Rapid and Differential Evolution of the Venom Composition of a Parasitoid Wasp Depending on the Host Strain. Toxins, 11(629). https://doi.org/10.3390/toxins11110629

Colinet, D., Deleury, E., Anselme, C., Cazes, D., Poulain, J., Azema-Dossat, C., Belghazi, M., Gatti, J. L. and  Poirié, M. (2013). Extensive inter- and intraspecific venom variation in closely related parasites targeting the same host: The case of Leptopilina parasitoids of Drosophila. Insect Biochemistry and Molecular Biology, 43(7), 601–611. https://doi.org/10.1016/j.ibmb.2013.03.010

Colinet, D., Dubuffet, A., Cazes, D., Moreau, S., Drezen, J. M. and  Poirié, M. (2009). A serpin from the parasitoid wasp Leptopilina boulardi targets the Drosophila phenoloxidase cascade. Developmental and Comparative Immunology, 33(5), 681–689. https://doi.org/10.1016/j.dci.2008.11.013

Fellowes, M. D. E. and  Godfray, H. C. J. (2000). The evolutionary ecology of resistance to parasitoids by Drosophila. Heredity, 84(1), 1–8. https://doi.org/10.1046/j.1365-2540.2000.00685.x

Gueguen, G., Rajwani, R., Paddibhatla, I., Morales, J. and  Govind, S. (2011). VLPs of Leptopilina boulardi share biogenesis and overall stellate morphology with VLPs of the heterotoma clade. Virus Research, 160(1–2), 159–165. https://doi.org/10.1016/j.virusres.2011.06.005

Lavine, M. D. and  Strand, M. R. (2002). Insect hemocytes and their role in immunity. Insect Biochemistry and Molecular Biology, 32(10), 1295–1309. https://doi.org/10.1016/S0965-1748(02)00092-9

Martinez, J., Duplouy, A., Woolfit, M., Vavre, F., O’Neill, S. L. and  Varaldi, J. (2012). Influence of the virus LbFV and of Wolbachia in a host-parasitoid interaction. PloS One, 7(4), e35081. https://doi.org/10.1371/journal.pone.0035081

Nappi, A. J., Vass, E., Frey, F. and  Carton, Y. (1995). Superoxide anion generation in Drosophila during melanotic encapsulation of parasites. European Journal of Cell Biology, 68(4), 450–456.

Poirié, M., Colinet, D. and  Gatti, J. L. (2014). Insights into function and evolution of parasitoid wasp venoms. Current Opinion in Insect Science, 6, 52–60. https://doi.org/10.1016/j.cois.2014.10.004

Rizki, T. M. and  Rizki, R. M. (1992). Lamellocyte differentiation in Drosophila larvae parasitized by Leptopilina. Developmental and Comparative Immunology, 16(2–3), 103–110. https://doi.org/10.1016/0145-305X(92)90011-Z

Schlenke, T. A., Morales, J., Govind, S. and  Clark, A. G. (2007). Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster. PLoS Pathogens, 3(10), 1486–1501. https://doi.org/10.1371/journal.ppat.0030158

Varaldi, J., Petit, S., Boulétreau, M. and  Fleury, F. (2006). The virus infecting the parasitoid Leptopilina boulardi exerts a specific action on superparasitism behaviour. Parasitology, 132(Pt 6), 747–756. https://doi.org/10.1017/S0031182006009930

Yang, L., Qiu, L., Fang, Q., Stanley, D. W. and  Gong‐Yin, Y. (2020). Cellular and humoral immune interactions between Drosophila and its parasitoids. Insect Science. https://doi.org/10.1111/1744-7917.12863

 

Parasitic success and venom composition evolve upon specialization of parasitoid wasps to different host speciesFanny Cavigliasso, Hugo Mathé-Hubert, Jean-Luc Gatti, Dominique Colinet, Marylène Poirié<p>Female endoparasitoid wasps usually inject venom into hosts to suppress their immune response and ensure offspring development. However, the parasitoid’s ability to evolve towards increased success on a given host simultaneously with the evolut...Experimental Evolution, Species interactionsÉlio Sucena2020-10-26 15:00:55 View
03 Aug 2017
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Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradients

What doesn’t kill us makes us stronger: can Fisher’s Geometric model predict antibiotic resistance evolution?

Recommended by and ORCID_LOGO

The increasing number of reported cases of antibiotic resistance is one of today’s major public health concerns. Dealing with this threat involves understanding what drives the evolution of antibiotic resistance and investigating whether we can predict (and subsequently avoid or circumvent) it [1].
One of the most illustrative and common models of adaptation (and, hence, resistance evolution) is Fisher’s Geometric Model (FGM). The original model maps phenotypes to fitness, meaning that each point in the fitness landscape corresponds to a phenotype rather than a genotype. However, it has been shown that when mutations are numerous enough, FGM can also describe adaptive walks in genotype space [2]. Nevertheless, limitations have been highlighted, particularly when trying to study complex scenarios such as antibiotic resistance evolution [3].
Harmand et al. [4] incorporated three extensions to the FGM, which allowed them to match the mutational patterns of antibiotic resistance that they obtained from a screen across a gradient of drug concentrations. The implemented extensions took into account that: 1) only a subset of mutations may contribute to traits under selection, reflecting that not all regions in the genome affect the ability to resist antibiotics; 2) mutations that confer a fitness increase in one environment may not reflect a similar increase in others, if the selective constraints are different; and 3) different antibiotic concentrations may either constrain the maximum fitness that populations can reach (changing the height of the fitness peak) or change the rate of fitness increase with each mutation (changing the width/slope of the peak).
Traditionally, most empirical fitness landscape studies have focused on a subset of mutations obtained after laboratory evolution in specific conditions [5, 6]. The results obtained in Harmand et al. [4] indicate a potential shortcoming of studying these small fitness landscapes: rather than having a constrained evolutionary path to a resistant phenotype, as previously observed, their results suggest that antibiotic resistance can be the product of mutations in different regions of the genome. Returning to the fitness landscape perspective, this indicates that there are many alternative paths that can lead to the evolution of antibiotic resistance. This comparison points at a difficult challenge when aiming at developing a predictive framework for evolution: real-time experiments may indicate that evolution is likely to take similar and predictable paths because the strongest and most frequent mutations dictate the outcome, whereas systematic screens of mutants potentially indicate several paths, that may, however, not be relevant in nature. Only a combination of different experimental approaches with motivated theory as presented in Harmand et al. [4] will allow for a better understanding of where in this continuum evolution is taking place in nature, and to which degree we are able to interfere with it in order to slow down adaptation.

References

[1] Palmer AC, and Kishony R. 2013. Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nature Review Genetics 14: 243—248. doi: 10.1038/nrg3351

[2] Tenaillon O. 2014. The utility of Fisher’s geometric model in evolutionary genetics. Annual Review of Ecology, Evolution and Systematics 45: 179—201. doi: 10.1146/annurev-ecolsys-120213-091846

[3] Blanquart F and Bataillon T. 2016. Epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with Fisher’s geometric model? Genetics 203: 847—862. doi: 10.1534/genetics.115.182691

[4] Harmand N, Gallet R, Jabbour-Zahab R, Martin G and Lenormand T. 2017. Fisher’s geometrical model and the mutational patterns of antibiotic resistance across dose gradients. Evolution 71: 23—37. doi: 10.1111/evo.13111

[5] de Visser, JAGM, and Krug J. 2014. Empirical fitness landscapes and the predictability of evolution. Nature 15: 480—490. doi: 10.1038/nrg3744

[6] Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S and Kishony R. 2015. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nature Communications 6: 1—8. doi: 10.1038/ncomms8385

Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradientsNoémie Harmand, Romain Gallet, Roula Jabbour-Zahab, Guillaume Martin, Thomas Lenormand<p>Fisher's geometrical model (FGM) has been widely used to depict the fitness effects of mutations. It is a general model with few underlying assumptions that gives a large and comprehensive view of adaptive processes. It is thus attractive in se...AdaptationInês Fragata2017-08-01 16:06:02 View