Latest recommendations
Id | Title * | Authors * | Abstract * | Picture * | Thematic fields * ▲ | Recommender | Reviewers | Submission date | |
---|---|---|---|---|---|---|---|---|---|
11 Dec 2020
Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence dataGonche Danesh, Victor Virlogeux, Christophe Ramière, Caroline Charre, Laurent Cotte, Samuel Alizon https://doi.org/10.1101/689158Phylodynamics of hepatitis C virus reveals transmission dynamics within and between risk groups in LyonRecommended by David Rasmussen based on reviews by Chris Wymant and Louis DuPlessisGenomic epidemiology seeks to better understand the transmission dynamics of infectious pathogens using molecular sequence data. Phylodynamic methods have given genomic epidemiology new power to track the transmission dynamics of pathogens by combining phylogenetic analyses with epidemiological modeling. In recent year, applications of phylodynamics to chronic viral infections such as HIV and hepatitis C virus (HVC) have provided some of the best examples of how phylodynamic inference can provide valuable insights into transmission dynamics within and between different subpopulations or risk groups, allowing for more targeted interventions. References [1] Rasmussen, D. A., Volz, E. M., and Koelle, K. (2014). Phylodynamic inference for structured epidemiological models. PLoS Comput Biol, 10(4), e1003570. doi: https://doi.org/10.1371/journal.pcbi.1003570 | Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data | Gonche Danesh, Victor Virlogeux, Christophe Ramière, Caroline Charre, Laurent Cotte, Samuel Alizon | <p>Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fa... | Evolutionary Epidemiology, Phylogenetics / Phylogenomics | David Rasmussen | 2019-07-11 13:37:23 | View | ||
11 Sep 2017
POSTPRINT
Less effective selection leads to larger genomesTristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N. Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando and Christophe Douady https://doi.org/10.1101/gr.212589.116Colonisation of subterranean ecosystems leads to larger genome in waterlouse (Aselloidea)Recommended by Benoit Nabholz and Jochen B. W. WolfThe total amount of DNA utilized to store hereditary information varies immensely among eukaryotic organisms. Single copy genome sizes – disregarding differences due to ploidy - differ by more than three orders of magnitude ranging from a few million nucleotides (Mb) to hundreds of billions (Gb). With the ever-increasing availability of fully sequenced genomes we now know that most of the difference is due either to whole genome duplication or to variation in the abundance of repetitive elements. Regarding repetitive elements, the evolutionary forces underlying the large variation 'allowing' more or less elements in a genome remain largely elusive. A tentative correlation between an organism's complexity (however this may be adequately measured) and genome size, the so called C-value paradox [1], has long been dismissed. Studies testing for selection on secondary phenotypic effects associated with genome size (cell size, metabolic rates, nutrient availability) have yielded mixed results. Nonadaptive theories capitalizing on a role of deleterious insertion-deletion mutations and genetic drift as the main drivers have likewise received mixed support [2-3]. Overall, most evidence was derived from analyses across broad taxonomical scales [4-6]. Lefébure and colleagues [7] take a different approach. They confine their considerations to a homogeneous, restricted taxonomical group, isopod crustaceans of the superfamily Aselloidea. This taxonomic focus allows the authors to circumvent many of the confounding factors such as phylogenetic inertia, life history divergence and mutation rate variation that tend to trouble analyses across broad taxonomic timescales. Another important feature of the chosen system is the evolutionary independent transition of habitat use that has occurred at least 11 times. One group of species inhabits subterranean ecosystems (groundwater), another group thrives on surface water. Populations of the former live in low-energy habitats and are expected to be outnumbered by their surface dwelling relatives. Interestingly – and a precondition for the study - the groundwater species have significantly larger genomes (up to 137%). With this unique set-up, the authors are able to investigate the link between genome size and evolutionary forces related to a proxy of long-term population size by removing many of the confounding factors a priori. Upfront, we learn that the dN/dS ratio is higher in the groundwater species. This may either suggest prevalent positive selection or lower efficacy of purifying selection (relaxed constraint) in the group of species in which population sizes are expected to be low. Using a series of population genetic analyses the authors provide compelling evidence for the latter. Analyses are carefully conducted and include models for estimating the intensity and frequency of purifying and positive selection, the DoS (direction of selection) and α statistic. Next the authors also exclude the possibility that increased dN/dS of the subterranean groundwater species may be due to nonfunctionalization, which may result from the subterranean lifestyle. Overall, these analyses suggest relaxed constraint in smaller populations as the most plausible alternative to explain increased dN/dS ratios. In addition to the efficacy of selection, the authors estimate the timing of the ecological transition under the rationale that the amount of time a species may have been exposed to the subterranean habitat may reflect long term population sizes. To calibrate the 'colonization clock' they apply a neat trick based on the degree of degeneration of the opsin gene (as vision tends to get lost in these habitats). When finally testing which parameters may explain differences in genome size all factors – ecological status, selection efficiency as measured by dN/dS and colonization time - turned out to be significant predictors. Direct estimates of the short term effective population size Ne from polymorphism data, however, did not correlate with genome size. Ruling out the effect of other co-variates such as body size and growth rate the authors conclude that genome size was overall best predicted by long-term population size change upon habitat shift. In that the authors provide convincing evidence that the increase in genome size is linked to a decrease in long-term reduction of selection efficiency of subterranean species. Assuming a bias for insertion mutations over deletion mutations (which is usually the case in eukaryotes) this result is in agreement with the theory of mutational hazard [4-6]. This theory proposed by Michael Lynch postulates that the accumulation of non-functional DNA has a weak deleterious effect that can only be efficiently opposed by natural selection in species with high Ne. In conclusion, Lefébure and colleagues provide novel and welcome evidence supporting a 'neutralist' hypothesis of genome size evolution without the need to invoke an adaptive component. Methodologically, the study cautions against the common use of polymorphism-based estimates of Ne which are often obfuscated by transitory demographic change. Instead, alternative measures of selection efficacy linked to long-term population size may serve as better predictors of genome size. We hope that this study will stimulate additional work testing the link between Ne and genome size variation in other taxonomical groups [8-9]. Using genome sequences instead of the transcriptome approach applied here may concomitantly further our understanding of the molecular mechanisms underlying genome size change. References [1] Thomas, CA Jr. 1971. The genetic organization of chromosomes. Annual Review of Genetics 5: 237–256. doi: 10.1146/annurev.ge.05.120171.001321 [2] Ågren JA, Greiner S, Johnson MTJ, Wright SI. 2015. No evidence that sex and transposable elements drive genome size variation in evening primroses. Evolution 69: 1053–1062. doi: 10.1111/evo.12627 [3] Bast J, Schaefer I, Schwander T, Maraun M, Scheu S, Kraaijeveld K. 2016. No accumulation of transposable elements in asexual arthropods. Molecular Biology and Evolution 33: 697–706. doi: 10.1093/molbev/msv261 [4] Lynch M. 2007. The Origins of Genome Architecture. Sinauer Associates. [5] Lynch M, Bobay LM, Catania F, Gout JF, Rho M. 2011. The repatterning of eukaryotic genomes by random genetic drift. Annual Review of Genomics and Human Genetics 12: 347–366. doi: 10.1146/annurev-genom-082410-101412 [6] Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302: 1401–1404. doi: 10.1126/science.1089370 [7] Lefébure T, Morvan C, Malard F, François C, Konecny-Dupré L, Guéguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Der Sarkissian C, Charrier NP, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, and Douady CJ. 2017. Less effective selection leads to larger genomes. Genome Research 27: 1016-1028. doi: 10.1101/gr.212589.116 [8] Lower SS, Johnston JS, Stanger-Hall KF, Hjelmen CE, Hanrahan SJ, Korunes K, Hall D. 2017. Genome size in North American fireflies: Substantial variation likely driven by neutral processes. Genome Biolology and Evolution 9: 1499–1512. doi: 10.1093/gbe/evx097 [9] Sessegolo C, Burlet N, Haudry A. 2016. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biology Letters 12: 20160407. doi: 10.1098/rsbl.2016.0407 | Less effective selection leads to larger genomes | Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N. Pierre Charrier, David Eme, Florian Mermillod-Blondin, Lau... | <p>The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. Howe... | Evolutionary Theory, Genome Evolution, Molecular Evolution, Population Genetics / Genomics | Benoit Nabholz | 2017-09-08 09:39:23 | View | ||
06 Feb 2024
Can mechanistic constraints on recombination reestablishment explain the long-term maintenance of degenerate sex chromosomes?Thomas Lenormand, Denis Roze https://doi.org/10.1101/2023.02.17.528909New modelling results help understanding the evolution and maintenance of recombination suppression involving sex chromosomesRecommended by Jos Käfer based on reviews by 3 anonymous reviewersDespite advances in genomic research, many views of genome evolution are still based on what we know from a handful of species, such as humans. This also applies to our knowledge of sex chromosomes. We've apparently been too much used to the situation in which a highly degenerate Y chromosome coexists with an almost normal X chromosome to be able to fully grasp all the questions implied by this situation. Lately, many more sex chromosomes have been studied in other organisms, such as in plants, and the view is changing radically: there is a large diversity of situations, ranging from young highly divergent sex chromosomes to old ones that are so similar that they're hard to detect. Undoubtedly inspired by these recent findings, a few theoretical studies have been published around 2 years ago that put an entirely new light on the evolution of sex chromosomes. The differences between these models have however remained somewhat difficult to appreciate by non-specialists. In particular, the models by Lenormand & Roze (2022) and by Jay et al. (2022) seemed quite similar. Indeed, both rely on the same mechanism for initial recombination suppression: a ``lucky'' inversion, i.e. one with less deleterious mutations than the population average, encompassing the sex-determination locus, is initially selected. However, as it doesn't recombine, it will quickly accumulate deleterious mutations lowering its fitness. And it's at this point the models diverge: according to Lenormand & Roze (2022), nascent dosage compensation not only limits the deleterious effects on fitness by the ongoing degeneration, but it actually opposes recombination restoration as this would lead gene expression away from the optimum that has been reached. On the other hand, in the model by Jay et al. (2022), no additional ingredient is required: they argue that once an inversion had been fixed, reversions that restore recombination are extremely unlikely. This is what Lenormand & Roze (2024) now call a ``constraint'': in Jay et al.'s model, recombination restoration is impossible for mechanistic reasons. Lenormand & Roze (2024) argue such constraints cannot explain long-term recombination suppression. Instead, a mechanism should evolve to limit the negative fitness effects of recombination arrest, otherwise recombination is either restored, or the population goes extinct due to a dramatic drop in the fitness of the heterogametic sex. These two arguments work together: given the huge fitness cost of the lack of ongoing degeneration of the non-recombining Y, in the absence of compensatory mechanisms, there is a very strong selection for the restoration of recombination, so that even when restoration a priori is orders of magnitude less likely than inversion (leading to recombination suppression), it will eventually happen. One way the negative fitness effects of recombination suppression can be limited, is the way the authors propose in their own model: dosage compensation evolves through regulatory evolution right at the start of recombination suppression. This changes our classical, simplistic view that dosage compensation evolves in response to degeneration: rather, Lenormand & Roze (2024) argue, that degeneration can only happen when dosage compensation is effective. The reasoning is convincing and exposes the difference between the models to readers without a firm background in mathematical modelling. Although Lenormand & Roze (2024) target the "constraint theory", it seems likely that other theories for the maintenance of recombination suppression that don't imply the compensation of early degeneration are subject to the same criticism. Indeed, they mention the widely-cited "sexual antagonism" theory, in which mutations with a positive effect in males but a negative in females will select for recombination suppression that will link them to the sex-determining gene on the Y. However, once degeneration starts, the sexually-antagonistic benefits should be huge to overcome the negative effects of degeneration, and it's unlikely they'll be large enough. A convincing argument by Lenormand & Roze (2024) is that there are many ways recombination could be restored, allowing to circumvent the possible constraints that might be associated with reverting an inversion. First, reversions don't have to be exact to restore recombination. Second, the sex-determining locus can be transposed to another chromosome pair, or an entirely new sex-determining locus might evolve, leading to sex-chromosome turnover which has effectively been observed in several groups. These modelling studies raise important questions that need to be addressed with both theoretical and empirical work. First, is the regulatory hypothesis proposed by Lenormand & Roze (2022) the only plausible mechanism for the maintenance of long-term recombination suppression? The female- and male-specific trans regulators of gene expression that are required for this model, are they readily available or do they need to evolve first? Both theoretical work and empirical studies of nascent sex chromosomes will help to answer these questions. However, nascent sex chromosomes are difficult to detect and dosage compensation is difficult to reveal. Second, how many species today actually have "stable" recombination suppression? Maybe many species are in a transient phase, with different populations having different inversions that are either on their way to being fixed or starting to get counterselected. The models have now shown us some possibilities qualitatively but can they actually be quantified to be able to fit the data and to predict whether an observed case of recombination suppression is transient or stable? The debate will continue, and we need the active contribution of theoretical biologists to help clarify the underlying hypotheses of the proposed mechanisms. Conflict of interest statement: I did co-author a manuscript with D. Roze in 2023, but do not consider this a conflict of interest. The manuscript is the product of discussions that have taken place in a large consortium mainly in 2019. It furthermore deals with an entirely different topic of evolutionary biology. References Jay P, Tezenas E, Véber A, and Giraud T. (2022) Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes. PLoS Biol.;20:e3001698. https://doi.org/10.1371/journal.pbio.3001698 | Can mechanistic constraints on recombination reestablishment explain the long-term maintenance of degenerate sex chromosomes? | Thomas Lenormand, Denis Roze | <p style="text-align: justify;">Y and W chromosomes often stop recombining and degenerate. Most work on recombination suppression has focused on the mechanisms favoring recombination arrest in the short term. Yet, the long-term maintenance of reco... | Evolutionary Theory, Genome Evolution, Population Genetics / Genomics, Reproduction and Sex | Jos Käfer | 2023-10-27 21:52:06 | View | ||
25 Mar 2019
The joint evolution of lifespan and self-fertilisationThomas Lesaffre, Sylvain Billiard https://doi.org/10.1101/420877Evolution of selfing & lifespan 2.0Recommended by Thomas Bataillon based on reviews by 2 anonymous reviewersFlowering plants display a staggering diversity of both mating systems and life histories, ranging from almost exclusively selfers to obligate outcrossers, very short-lived annual herbs to super long lived trees. One pervasive pattern that has attracted considerable attention is the tight correlation that is found between mating systems and lifespan [1]. Until recently, theoretical explanations for these patterns have relied on static models exploring the consequences of several non-mutually exclusive important process: levels of inbreeding depression and ability to successfully were center stage. This make sense: successful colonization after long‐distance dispersal is far more likely to happen for self‐compatible than for self‐incompatible individuals in a sexually reproducing species. Furthermore, inbreeding depression (essentially a genetically driven phenomenon) and reproductive insurance are expected to shape the evolution of both mating system and lifespan. References | The joint evolution of lifespan and self-fertilisation | Thomas Lesaffre, Sylvain Billiard | <p>In Angiosperms, there exists a strong association between mating system and lifespan. Most self-fertilising species are short-lived and most predominant or obligate outcrossers are long-lived. This association is generally explained by the infl... | Evolutionary Theory, Life History, Reproduction and Sex | Thomas Bataillon | 2018-09-19 10:03:51 | View | ||
20 Nov 2017
Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selectionDiala Abu Awad and Denis Roze 10.1101/180000Understanding genetic variance, load, and inbreeding depression with selfingRecommended by Aneil F. Agrawal based on reviews by Frédéric Guillaume and 1 anonymous reviewerA classic problem in evolutionary biology is to understand the genetic variance in fitness. The simplest hypothesis is that variation exists, even in well-adapted populations, as a result of the balance between mutational input and selective elimination. This variation causes a reduction in mean fitness, known as the mutation load. Though mutation load is difficult to quantify empirically, indirect evidence of segregating genetic variation in fitness is often readily obtained by comparing the fitness of inbred and outbred offspring, i.e., by measuring inbreeding depression. Mutation-selection balance models have been studied as a means of understanding the genetic variance in fitness, mutation load, and inbreeding depression. Since their inception, such models have increased in sophistication, allowing us to ask these questions under more realistic and varied scenarios. The new theoretical work by Abu Awad and Roze [1] is a substantial step forward in understanding how arbitrary levels of self-fertilization affect variation, load and inbreeding depression under mutation-selection balance. References [1] Abu Awad D and Roze D. 2017. Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection. bioRxiv, 180000, ver. 4 of 17th November 2017. doi: 10.1101/180000 [2] Lande R. 1977. The influence of the mating system on the maintenance of genetic variability in polygenic characters. Genetics 86: 485–498. [3] Charlesworth D and Charlesworth B. 1987. Inbreeding depression and its evolutionary consequences. Annual Review of Ecology and Systematics. 18: 237–268. doi: 10.1111/10.1146/annurev.es.18.110187.001321 [4] Lande R and Porcher E. 2015. Maintenance of quantitative genetic variance under partial self-fertilization, with implications for the evolution of selfing. Genetics 200: 891–906. doi: 10.1534/genetics.115.176693 [5] Roze D. 2015. Effects of interference between selected loci on the mutation load, inbreeding depression, and heterosis. Genetics 201: 745–757. doi: 10.1534/genetics.115.178533 [6] Martin G and Lenormand T. 2006. A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species. Evolution 60: 893–907. doi: 10.1111/j.0014-3820.2006.tb01169.x [7] Martin G, Elena SF and Lenormand T. 2007. Distributions of epistasis in microbes fit predictions from a fitness landscape model. Nature Genetics 39: 555–560. doi: 10.1038/ng1998 | Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection | Diala Abu Awad and Denis Roze | The mating system of a species is expected to have important effects on its genetic diversity. In this paper, we explore the effects of partial selfing on the equilibrium genetic variance Vg, mutation load L and inbreeding depression δ under stabi... | Evolutionary Theory, Population Genetics / Genomics, Quantitative Genetics, Reproduction and Sex | Aneil F. Agrawal | 2017-08-26 09:29:20 | View | ||
28 Sep 2020
Evolution and genetic architecture of disassortative mating at a locus under heterozygote advantageLudovic Maisonneuve, Mathieu Joron, Mathieu Chouteau and Violaine Llaurens https://doi.org/10.1101/616409Evolutionary insights into disassortative mating and its association to an ecologically relevant supergeneRecommended by Charles Mullon based on reviews by Tom Van Dooren and 2 anonymous reviewersHeliconius butterflies are famous for their colorful wing patterns acting as a warning of their chemical defenses [1]. Most species are involved in Müllerian mimicry assemblies, as predators learn to associate common wing patterns with unpalatability and preferentially target rare variants. Such positive-frequency dependent selection homogenizes wing patterns at different localities, and in several species, all individuals within a community belong to the same morph [2]. In this respect, H. numata stands out. This species shows stable local polymorphism across multiple localities, with local populations home to up to seven distinct morphs [2]. Although a balance between migration and local positive-frequency dependent selection can allow some degree of local polymorphism, theory suggests that this occurs only when migration is within a narrow window [3]. References [1] Merrill, R M, K K Dasmahapatra, J W Davey, D D Dell'Aglio, J J Hanly, B Huber, C D Jiggins, et al. (2015). The Diversification of Heliconius butterflies: What Have We Learned in 150 Years? Journal of Evolutionary Biology 28 (8), 1417–38. https://doi.org/10.1111/jeb.12672. | Evolution and genetic architecture of disassortative mating at a locus under heterozygote advantage | Ludovic Maisonneuve, Mathieu Joron, Mathieu Chouteau and Violaine Llaurens | <p>The evolution of mate preferences may depend on natural selection acting on the mating cues and on the underlying genetic architecture. While the evolution of assortative mating with respect to locally adapted traits has been well-characterized... | Evolutionary Theory, Population Genetics / Genomics, Reproduction and Sex, Sexual Selection | Charles Mullon | 2019-10-29 09:55:18 | View | ||
17 Feb 2020
Epistasis, inbreeding depression and the evolution of self-fertilizationDiala Abu Awad and Denis Roze https://doi.org/10.1101/809814Epistasis and the evolution of selfingRecommended by Sylvain Gandon based on reviews by Nick Barton and 1 anonymous reviewerThe evolution of selfing results from a balance between multiple evolutionary forces. Selfing provides an "automatic advantage" due to the higher efficiency of selfers to transmit their genes via selfed and outcrossed offspring. Selfed offspring, however, may suffer from inbreeding depression. In principle the ultimate evolutionary outcome is easy to predict from the relative magnitude of these two evolutionary forces [1,2]. Yet, several studies explicitly taking into account the genetic architecture of inbreeding depression noted that these predictions are often too restrictive because selfing can evolve in a broader range of conditions [3,4]. References [1] Holsinger, K. E., Feldman, M. W., and Christiansen, F. B. (1984). The evolution of self-fertilization in plants: a population genetic model. The American Naturalist, 124(3), 446-453. doi: 10.1086/284287 | Epistasis, inbreeding depression and the evolution of self-fertilization | Diala Abu Awad and Denis Roze | <p>Inbreeding depression resulting from partially recessive deleterious alleles is thought to be the main genetic factor preventing self-fertilizing mutants from spreading in outcrossing hermaphroditic populations. However, deleterious alleles may... | Evolutionary Theory, Quantitative Genetics, Reproduction and Sex | Sylvain Gandon | 2019-10-18 09:29:41 | View | ||
12 Feb 2024
How do plant RNA viruses overcome the negative effect of Muller s ratchet despite strong transmission bottlenecks?Guillaume Lafforgue, Marie Lefebvre, Thierry Michon, Santiago F. Elena https://doi.org/10.1101/2023.08.01.550272How to survive the mutational meltdown: lessons from plant RNA virusesRecommended by Kavita Jain based on reviews by Brent Allman, Ana Morales-Arce and 1 anonymous reviewerAlthough most mutations are deleterious, the strongly deleterious ones do not spread in a very large population as their chance of fixation is very small. Another mechanism via which the deleterious mutations can be eliminated is via recombination or sexual reproduction. However, in a finite asexual population, the subpopulation without any deleterious mutation will eventually acquire a deleterious mutation resulting in the reduction of the population size or in other words, an increase in the genetic drift. This, in turn, will lead the population to acquire deleterious mutations at a faster rate eventually leading to a mutational meltdown. This irreversible (or, at least over some long time scales) accumulation of deleterious mutations is especially relevant to RNA viruses due to their high mutation rate, and while the prior work has dealt with bacteriophages and RNA viruses, the study by Lafforgue et al. [1] makes an interesting contribution to the existing literature by focusing on plants. In this study, the authors enquire how despite the repeated increase in the strength of genetic drift, how the RNA viruses manage to survive in plants. Following a series of experiments and some numerical simulations, the authors find that as expected, after severe bottlenecks, the fitness of the population decreases significantly. But if the bottlenecks are followed by population expansion, the Muller’s ratchet can be halted due to the genetic diversity generated during population growth. They hypothesize this mechanism as a potential way by which the RNA viruses can survive the mutational meltdown. As a theoretician, I find this investigation quite interesting and would like to see more studies addressing, e.g., the minimum population growth rate required to counter the potential extinction for a given bottleneck size and deleterious mutation rate. Of course, it would be interesting to see in future work if the hypothesis in this article can be tested in natural populations. References [1] Guillaume Lafforgue, Marie Lefebvre, Thierry Michon, Santiago F. Elena (2024) How do plant RNA viruses overcome the negative effect of Muller s ratchet despite strong transmission bottlenecks? bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community In Evolutionary Biology | How do plant RNA viruses overcome the negative effect of Muller s ratchet despite strong transmission bottlenecks? | Guillaume Lafforgue, Marie Lefebvre, Thierry Michon, Santiago F. Elena | <p>Muller's ratchet refers to the irreversible accumulation of deleterious mutations in small populations, resulting in a decline in overall fitness. This phenomenon has been extensively observed in experiments involving microorganisms, including ... | Experimental Evolution, Genome Evolution | Kavita Jain | 2023-08-04 09:37:08 | View | ||
31 Jan 2018
Identifying drivers of parallel evolution: A regression model approachSusan F Bailey, Qianyun Guo, Thomas Bataillon https://doi.org/10.1101/118695A new statistical tool to identify the determinant of parallel evolutionRecommended by Stephanie Bedhomme based on reviews by Bastien Boussau and 1 anonymous reviewerIn experimental evolution followed by whole genome resequencing, parallel evolution, defined as the increase in frequency of identical changes in independent populations adapting to the same environment, is often considered as the product of similar selection pressures and the parallel changes are interpreted as adaptive. References [1] Bailey SF, Guo Q and Bataillon T (2018) Identifying drivers of parallel evolution: A regression model approach. bioRxiv 118695, ver. 4 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/118695 [2] Lang GI, Rice DP, Hickman, MJ, Sodergren E, Weinstock GM, Botstein D, and Desai MM (2013) Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500: 571–574. doi: 10.1038/nature12344 | Identifying drivers of parallel evolution: A regression model approach | Susan F Bailey, Qianyun Guo, Thomas Bataillon | <p>This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100045). Parallel evolution, defined as identical changes arising in independent populations, is often attributed... | Experimental Evolution, Molecular Evolution | Stephanie Bedhomme | 2017-03-22 14:54:48 | View | ||
14 Apr 2021
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 https://doi.org/10.1101/2020.10.24.353417What makes a parasite successful? Parasitoid wasp venoms evolve rapidly in a host-specific mannerRecommended by Élio Sucena based on reviews by Simon Fellous, alexandre leitão and 1 anonymous reviewerParasitoid 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).
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 species | Fanny 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 interactions | Élio Sucena | 2020-10-26 15:00:55 | View |
MANAGING BOARD
Guillaume Achaz
Juan Arroyo
Trine Bilde
Dustin Brisson
Marianne Elias
Inês Fragata
Matteo Fumagalli
Tatiana Giraud
Frédéric Guillaume
Ruth Hufbauer
Sara Magalhaes
Caroline Nieberding
Michael David Pirie
Tanja Pyhäjärvi
Tanja Schwander
Alejandro Gonzalez Voyer