Latest recommendations
Id | Title * | Authors * ▲ | Abstract * | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
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05 Feb 2019
The quiescent X, the replicative Y and the AutosomesGuillaume Achaz, Serge Gangloff, Benoit Arcangioli https://doi.org/10.1101/351288Replication-independent mutations: a universal signature ?Recommended by Nicolas Galtier based on reviews by Marc Robinson-Rechavi and Robert LanfearMutations are the primary source of genetic variation, and there is an obvious interest in characterizing and understanding the processes by which they appear. One particularly important question is the relative abundance, and nature, of replication-dependent and replication-independent mutations - the former arise as cells replicate due to DNA polymerization errors, whereas the latter are unrelated to the cell cycle. A recent experimental study in fission yeast identified a signature of mutations in quiescent (=non-replicating) cells: the spectrum of such mutations is characterized by an enrichment in insertions and deletions (indels) compared to point mutations, and an enrichment of deletions compared to insertions [2]. References [1] Achaz, G., Gangloff, S., and Arcangioli, B. (2019). The quiescent X, the replicative Y and the Autosomes. BioRxiv, 351288, ver. 3 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/351288 | The quiescent X, the replicative Y and the Autosomes | Guillaume Achaz, Serge Gangloff, Benoit Arcangioli | <p>From the analysis of the mutation spectrum in the 2,504 sequenced human genomes from the 1000 genomes project (phase 3), we show that sexual chromosomes (X and Y) exhibit a different proportion of indel mutations than autosomes (A), ranking the... | Bioinformatics & Computational Biology, Genome Evolution, Human Evolution, Molecular Evolution, Population Genetics / Genomics, Reproduction and Sex | Nicolas Galtier | 2018-07-25 10:37:48 | 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 | ||
13 Apr 2023
The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variationGustavo V Barroso, Julien Y Dutheil https://doi.org/10.1101/2021.09.16.460667An unusual suspect: the mutation landscape as a determinant of local variation in nucleotide diversityRecommended by Fernando Racimo based on reviews by David Castellano and 1 anonymous reviewerSometimes, important factors for explaining biological processes fall through the cracks, and it is only through careful modeling that their importance eventually comes out to light. In this study, Barroso and Dutheil introduce a new method based on the sequentially Markovian coalescent (SMC, Marjoran and Wall 2006) for jointly estimating local recombination and coalescent rates along a genome. Unlike previous SMC-based methods, however, their method can also co-estimate local patterns of variation in mutation rates. This is a powerful improvement which allows them to tackle questions about the reasons for the extensive variation in nucleotide diversity across the chromosomes of a species - a problem that has plagued the minds of population geneticists for decades (Begun and Aquadro 1992, Andolfatto 2007, McVicker et al., 2009, Pouyet and Gilbert 2021). The authors find that variation in de novo mutation rates appears to be the most important factor in determining nucleotide diversity in Drosophila melanogaster. Though seemingly contradicting previous attempts at addressing this problem (Comeron 2014), they take care to investigate and explain why that might be the case. Barroso and Dutheil have also taken care to carefully explain the details of their new approach and have carried a very thorough set of analyses comparing competing explanations for patterns of nucleotide variation via causal modeling. The reviewers raised several issues involving choices made by the authors in their analysis of variance partitioning, the proper evaluation of the role of linked selection and the recombination rate estimates emerging from their model. These issues have all been extensively addressed by the authors, and their conclusions seem to remain robust. The study illustrates why the mutation landscape should not be ignored as an important determinant of local variation in genetic diversity, and opens up questions about the generalizability of these results to other organisms. REFERENCES Andolfatto, P. (2007). Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome research, 17(12), 1755-1762. https://doi.org/10.1101/gr.6691007 Barroso, G. V., & Dutheil, J. Y. (2021). The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation. bioRxiv, 2021.09.16.460667, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.09.16.460667 Begun, D. J., & Aquadro, C. F. (1992). Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature, 356(6369), 519-520. https://doi.org/10.1038/356519a0 Comeron, J. M. (2014). Background selection as baseline for nucleotide variation across the Drosophila genome. PLoS Genetics, 10(6), e1004434. https://doi.org/10.1371/journal.pgen.1004434 Marjoram, P., & Wall, J. D. (2006). Fast" coalescent" simulation. BMC genetics, 7, 1-9. https://doi.org/10.1186/1471-2156-7-16 McVicker, G., Gordon, D., Davis, C., & Green, P. (2009). Widespread genomic signatures of natural selection in hominid evolution. PLoS genetics, 5(5), e1000471. https://doi.org/10.1371/journal.pgen.1000471 Pouyet, F., & Gilbert, K. J. (2021). Towards an improved understanding of molecular evolution: the relative roles of selection, drift, and everything in between. Peer Community Journal, 1, e27. https://doi.org/10.24072/pcjournal.16 | The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation | Gustavo V Barroso, Julien Y Dutheil | <p style="text-align: justify;">What shapes the distribution of nucleotide diversity along the genome? Attempts to answer this question have sparked debate about the roles of neutral stochastic processes and natural selection in molecular evolutio... | Bioinformatics & Computational Biology, Population Genetics / Genomics | Fernando Racimo | 2022-10-30 07:52:07 | View | ||
19 Jul 2021
Host phenology can drive the evolution of intermediate virulence strategies in some obligate-killer parasitesHannelore MacDonald, Erol Akçay, Dustin Brisson https://doi.org/10.1101/2021.03.13.435259Modelling parasitoid virulence evolution with seasonalityRecommended by Samuel Alizon based on reviews by Alex Best and 2 anonymous reviewersThe harm most parasites cause to their host, i.e. the virulence, is a mystery because host death often means the end of the infectious period. For obligate killer parasites, or “parasitoids”, that need to kill their host to transmit to other hosts the question is reversed. Indeed, more rapid host death means shorter generation intervals between two infections and mathematical models show that, in the simplest settings, natural selection should always favour more virulent strains (Levin and Lenski, 1983). Adding biological details to the model modifies this conclusion and, for instance, if the relationship between the infection duration and the number of parasites transmission stages produced in a host is non-linear, strains with intermediate levels of virulence can be favoured (Ebert and Weisser 1997). Other effects, such as spatial structure, could yield similar effects (Lion and van Baalen, 2007). In their study, MacDonald et al. (2021) explore another type of constraint, which is seasonality. Earlier studies, such as that by Donnelly et al. (2013) showed that this constraint can affect virulence evolution but they had focused on directly transmitted parasites. Using a mathematical model capturing the dynamics of a parasitoid, MacDonald et al. (2021) show if two main assumptions are met, namely that at the end of the season only transmission stages (or “propagules”) survive and that there is a constant decay of these propagules with time, then strains with intermediate levels of virulence are favoured. Practically, the authors use delay differential equations and an adaptive dynamics approach to identify evolutionary stable strategies. As expected, the longer the short the season length, the higher the virulence (because propagule decay matters less). The authors also identify a non-linear relationship between the variation in host development time and virulence. Generally, the larger the variation, the higher the virulence because the parasitoid has to kill its host before the end of the season. However, if the variation is too wide, some hosts become physically impossible to use for the parasite, whence a decrease in virulence. Finally, MacDonald et ali. (2021) show that the consequence of adding trade-offs between infection duration and the number of propagules produced is in line with earlier studies (Ebert and Weisser 1997). These mathematical modelling results provide testable predictions for using well-described systems in evolutionary ecology such as daphnia parasitoids, baculoviruses, or lytic phages. Reference Donnelly R, Best A, White A, Boots M (2013) Seasonality selects for more acutely virulent parasites when virulence is density dependent. Proc R Soc B, 280, 20122464. https://doi.org/10.1098/rspb.2012.2464 Ebert D, Weisser WW (1997) Optimal killing for obligate killers: the evolution of life histories and virulence of semelparous parasites. Proc R Soc B, 264, 985–991. https://doi.org/10.1098/rspb.1997.0136 Levin BR, Lenski RE (1983) Coevolution in bacteria and their viruses and plasmids. In: Futuyma DJ, Slatkin M eds. Coevolution. Sunderland, MA, USA: Sinauer Associates, Inc., 99–127. Lion S, van Baalen M (2008) Self-structuring in spatial evolutionary ecology. Ecol. Lett., 11, 277–295. https://doi.org/10.1111/j.1461-0248.2007.01132.x MacDonald H, Akçay E, Brisson D (2021) Host phenology can drive the evolution of intermediate virulence strategies in some obligate-killer parasites. bioRxiv, 2021.03.13.435259, ver. 8 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.03.13.435259 | Host phenology can drive the evolution of intermediate virulence strategies in some obligate-killer parasites | Hannelore MacDonald, Erol Akçay, Dustin Brisson | <p style="text-align: justify;">The traditional mechanistic trade-offs resulting in a negative correlation between transmission and virulence are the foundation of nearly all current theory on the evolution of parasite virulence. Several ecologica... | Evolutionary Dynamics, Evolutionary Ecology, Evolutionary Epidemiology, Evolutionary Theory | Samuel Alizon | 2021-03-14 13:47:33 | View | ||
15 Sep 2022
Bimodal breeding phenology in the Parsley Frog Pelodytes punctatus as a bet-hedging strategy in an unpredictable environment despite strong priority effectsHelene Jourdan-Pineau, Pierre-Andre Crochet, Patrice David https://doi.org/10.1101/2022.02.24.481784Spreading the risk of reproductive failure when the environment is unpredictable and ephemeralRecommended by Gabriele Sorci based on reviews by Thomas Haaland and Zoltan RadaiMany species breed in environments that are unpredictable, for instance in terms of the availability of resources needed to raise the offspring. Organisms might respond to such spatial and temporal unpredictability by adopting plastic responses to adjust their reproductive investment according to perceived cues of environmental quality. Some species such as the amphibians might also face the problem of ephemeral habitats, when the ponds where they breed have a chance of drying up before metamorphosis has occurred. In this case, maximizing long-term fitness might involve a strategy of spreading the risk, even though the reproductive success of a single reproductive bout might be lower. Understanding how animals (and plants) get adapted to stochastic environments is particularly crucial in the current context of rapid environmental changes. In this article, Jourdan-Pineau et al. report the results of field surveys of the Parsley Frog (Pelodytes punctatus) in Southern France. This frog has peculiar breeding phenology with females breeding in autumn and spring. The authors provide quite an extensive amount of information on the reproductive success of eggs laid in each season and the possible ecological factors accounting for differences between seasons. Although the presence of interspecific competitors and predators does not seem to account for pond-specific reproductive success, the survival of tadpoles hatching from eggs laid in spring is severely impaired when tadpoles from the autumn cohort have managed to survive. This intraspecific competition takes the form of a “priority” effect where tadpoles from the autumn cohort outcompete the smaller larvae from the spring cohort. Given this strong priority effect, one might tentatively predict that females laying in spring should avoid ponds with tadpoles from the autumn cohort. Surprisingly, however, the authors did not find any evidence for such avoidance, which might indicate strong constraints on the availability of ponds where females might possibly lay. Assuming that each female can indeed lay both in autumn and spring, how is this bimodal phenology maintained? Would not be worthier to allocate all the eggs to the autumn (or the spring) laying season? Eggs laid in autumn and spring have to face different environmental hazards, reducing their hatching success and the probability to produce metamorphs (for instance, tadpoles hatching from eggs laid in autumn have to overwinter which might be a particularly risky phase). Jourdan-Pineau and coworkers addressed this question by adapting a bet-hedging model that was initially developed to investigate the strategy of allocation into seed dormancy of annual plants (Cohen 1966) to the case of the bimodal phenology of the Parsley Frog. By feeding the model with the parameter values obtained from the field surveys, they found that the two breeding strategies (laying in autumn and in spring) can coexist as long as the probability of breeding success in the autumn cohort is between 20% and 80% (the range of values allowing the coexistence of a bimodal phenology shrinking a little bit when considering that frogs can reproduce 5 times during their lifespan instead of three times). This paper provides a very nice illustration of the importance of combining approaches (here field monitoring to gather data that can be used to feed models) to understand the evolution of peculiar breeding strategies. Although future work should attempt to gather individual-based data (in addition to population data), this work shows that spreading the risk can be an adaptive strategy in environments characterized by strong stochastic variation. References Cohen D (1966) Optimizing reproduction in a randomly varying environment. Journal of Theoretical Biology, 12, 119–129. https://doi.org/10.1016/0022-5193(66)90188-3 Jourdan-Pineau H., Crochet P.-A., David P. (2022) Bimodal breeding phenology in the Parsley Frog Pelodytes punctatus as a bet-hedging strategy in an unpredictable environment despite strong priority effects. bioRxiv, 2022.02.24.481784, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.02.24.481784 | Bimodal breeding phenology in the Parsley Frog Pelodytes punctatus as a bet-hedging strategy in an unpredictable environment despite strong priority effects | Helene Jourdan-Pineau, Pierre-Andre Crochet, Patrice David | <p style="text-align: justify;">When environmental conditions are unpredictable, expressing alternative phenotypes spreads the risk of failure, a mixed strategy called bet-hedging. In the southern part of its range, the Parsley Frog <em>Pelodytes ... | Adaptation, Evolutionary Ecology, Life History | Gabriele Sorci | 2022-02-28 11:53:00 | View | ||
17 Dec 2016
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Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling studyHerbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C https://doi.org/10.1093/ve/vew028Predicting HIV virulence evolution in response to widespread treatmentRecommended by Samuel Alizon and Roger KouyosIt is a classical result in the virulence evolution literature that treatments decreasing parasite replication within the host should select for higher replication rates, thus driving increased levels of virulence if the two are correlated. There is some evidence for this in vitro but very little in the field. HIV infections in humans offer a unique opportunity to go beyond the simple predictions that treatments should favour more virulent strains because many details of this host-parasite system are known, especially the link between set-point virus load, transmission rate and virulence. To tackle this question, Herbeck et al. [1] used a detailed individual-based model. This is original because it allows them to integrate existing knowledge from the epidemiology and evolution of HIV (e.g. recent estimates of the ‘heritability’ of set-point virus load from one infection to the next). This detailed model allows them to formulate predictions regarding the effect of different treatment policies; especially regarding the current policy switch away from treatment initiation based on CD4 counts towards universal treatment. The results show that, perhaps as expected from the theory, treatments based on the level of remaining host target cells (CD4 T cells) do not affect virulence evolution because they do not strongly affect the virulence level that maximizes HIV’s transmission potential. However, early treatments can lead to moderate increase in virulence within several years if coverage is high enough. These results seem quite robust to variation of all the parameters in realistic ranges. The great step forward in this model is the ability to obtain quantitative prediction regarding how a virus may evolve in response to public health policies. Here the main conclusion is that given our current knowledge in HIV biology, the risk of virulence evolution is perhaps more limited than expected from a direct application of virulence evolution model. Interestingly, the authors also conclude that recently observed increased in HIV virulence [2-3] cannot be explained by the impact of antiretroviral therapy alone; which raises the question about the main mechanism behind this increase. Finally, the authors make the interesting suggestion that “changing virulence is amenable to being monitored alongside transmitted drug resistance in sentinel surveillance”. References [1] Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C. 2016. Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study. Virus Evolution 2:vew028. doi: 10.1093/ve/vew028 [2] Herbeck JT, Müller V, Maust BS, Ledergerber B, Torti C, et al. 2012. Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS 26:193-205. doi: 10.1097/QAD.0b013e32834db418 [3] Pantazis N, Porter K, Costagliola D, De Luca A, Ghosn J, et al. 2014. Temporal trends in prognostic markers of HIV-1 virulence and transmissibility: an observational cohort study. Lancet HIV 1:e119-26. doi: 10.1016/s2352-3018(14)00002-2 | Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study | Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C | <p>There are global increases in the use of HIV antiretroviral therapy (ART), guided by clinical benefits of early ART initiation and the efficacy of treatment as prevention of transmission. Separately, it has been shown theoretically and empirica... | Bioinformatics & Computational Biology, Evolutionary Applications, Evolutionary Epidemiology | Samuel Alizon | 2016-12-16 20:54:08 | View | ||
20 Dec 2016
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Experimental Evolution of Gene Expression and Plasticity in Alternative Selective RegimesHuang Y, Agrawal AF https://doi.org/10.1371/journal.pgen.1006336Genetic adaptation counters phenotypic plasticity in experimental evolutionRecommended by Luis-Miguel Chevin and Stephanie BedhommeHow do phenotypic plasticity and adaptive evolution interact in a novel or changing environment? Does evolution by natural selection generally reinforce initially plastic phenotypic responses, or does it instead oppose them? And to what extent does evolution of a trait involve evolution of its plasticity? These questions have lied at the heart of research on phenotypic evolution in heterogeneous environments ever since it was realized that the environment is likely to affect the expression of many (perhaps most) characters of an individual. Importantly, this broad definition of phenotypic plasticity as change in the average phenotype of a given genotype in response to its environment of development (or expression) does not involve any statement about the adaptiveness of the plastic changes. Theory on the evolution of plasticity has devoted much effort to understanding how reaction norm should evolve under different regimes of environmental change in space and time, and depending on genetic constraints on reaction norm shapes. However on an empirically ground, the questions above have mostly been addressed for individual traits, often chosen a priori for their likeliness to exhibit adaptive plasticity, and we still lack more systematic answers. These can be provided by so-called ‘phenomic’ approaches, where a large number of traits are tracked without prior information on their biological or ecological function. A problem is that the number of phenotypic characters that can be measured in an organism is virtually infinite (and to some extent arbitrary), and that scaling issues makes it difficult to compare different sets of traits. Gene-expression levels offer a partial solution to this dilemma, as they can be considered as a very large number of traits (one per typed gene) that can be measured easily and uniformly (fold change in the number of reads in RNAseq). As for any traits, expression levels of different genes may be genetically correlated, to an extent that depends on their regulation mechanism: cis-regulatory sequences that only affect expression of neighboring genes are likely to cause independent gene expression, while more systematic modifiers of expression (e.g. trans-regulators such as transcription factors) may cause correlated genetic responses of the expression of many genes. Huang and Agrawal [1] have studied plasticity and evolution of gene expression level in young larvae of populations of Drosophila melanogaster that have evolved for about 130 generations under either a constant environment (salt or cadmium), or an environment that is heterogeneous in time or space (combining salt and cadmium). They report a wealth of results, of which we summarize the most striking here. First, among genes that (i) were initially highly plastic and (ii) evolved significant divergence in expression levels between constant environment treatments, the evolved divergence is predominantly in the opposite direction to the initial plastic response. This suggests that either plasticity was initially maladaptive, or the selective pressure changed during the evolutionary process (see below). This somewhat unexpected result strikingly mirrors that from a study published last year in Nature [2], where the same pattern was found for responses of guppies to the presence of predators. However, Huang and Agrawal [1] went beyond this study by deciphering the underlying mechanisms in several interesting ways. First, they showed that change in gene expression often occurred at genes close to SNPs with differentiated frequencies across treatments (but not at genes with differentiated SNPs in their coding sequences), suggesting that cis-regulatory sequences are involved. This is also suggested by the fact that changes in gene expression are mostly caused by the increased expression of only one allele at polymorphic loci, and is a first step towards investigating the genetic underpinnings of (co)variation in gene expression levels. Another interesting set of findings concerns evolution of plasticity in treatments with variable environments. To compare the gene-expression plasticity that evolved in these treatments to an expectation, the authors considered that the expression levels in populations maintained for a long time under constant salt or cadmium had reached an optimum. The differences between these expression levels were thus assumed to predict the level of plasticity that should evolve in a heterogeneous environment (with both cadmium and salt) under perfect environmental predictability. The authors showed that plasticity did evolve more in the expected direction in heterogeneous than in constant environments, resulting in better adapted final expression levels across environments. Taken collectively, these results provide an unprecedented set of patterns that are greatly informative on how plasticity and evolution interact in constant versus changing environments. But of course, interpretations in terms of adaptive versus maladaptive plasticity are more challenging, as the authors themselves admit. Even though environmentally determined gene expression is the basic mechanism underlying the phenotypic plasticity of most traits, it is extremely difficult to relate to more integrated phenotypes for which we can understand the selection pressures, especially in multicellular organisms. The authors have recently investigated evolutionary change of quantitative traits in these selected lines, so it might be possible to establish links between reaction norms for macroscopic traits to those for gene expression levels. Such an approach would also involve tracking gene expression throughout life, rather than only in young larvae as done here, thus putting phenotypic complexity back in the picture also for expression levels. Another difficulty is that a plastic response that was originally adaptive may be replaced by an opposite evolutionary response in the long run, without having to invoke initially maladaptive plasticity. For instance, the authors mention the possibility that a generic stress response is initially triggered by cadmium, but is eventually unnecessary and costly after evolution of genetic mechanisms for cadmium detoxification (a case of so-called genetic accommodation). In any case, this study by Huang and Agrawal [1], together with the one by Ghalambor et al. last year [2], reports novel and unexpected results, which are likely to stimulate researchers interested in plasticity and evolution in heterogeneous environments for the years to come. References [1] Huang Y, Agrawal AF. 2016. Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes. PLoS Genetics 12:e1006336. doi: 10.1371/journal.pgen.1006336 [2] Ghalambor CK, Hoke KL, Ruell EW, Fischer EK, Reznick DN, Hughes KA. 2015. Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature. Nature 525: 372-375. doi: 10.1038/nature15256 | Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes | Huang Y, Agrawal AF | <p>Little is known of how gene expression and its plasticity evolves as populations adapt to different environmental regimes. Expression is expected to evolve adaptively in all populations but only those populations experiencing environmental hete... | Adaptation, Experimental Evolution, Expression Studies, Phenotypic Plasticity | Luis-Miguel Chevin | 2016-12-20 09:04:15 | View | ||
20 Nov 2019
Distribution of iridescent colours in hummingbird communities results from the interplay between selection for camouflage and communicationHugo Gruson, Marianne Elias, Juan L. Parra, Christine Andraud, Serge Berthier, Claire Doutrelant, Doris Gomez https://doi.org/10.1101/586362Feathers iridescence sheds light on the assembly rules of humingbirds communitiesRecommended by Sébastien Lavergne based on reviews by 2 anonymous reviewersEcology needs rules stipulating how species distributions and ecological communities should be assembled along environmental gradients, but few rules have yet emerged in the ecological literature. The search of ecogeographical rules governing the spatial variation of birds colours has recently known an upsurge of interest in the litterature [1]. Most studies have, however, looked at pigmentary colours and not structural colours (e.g. iridescence), although it is know that color perception by animals (both birds and their predators) can be strongly influenced by light diffraction causing iridescence patterns on feathers. References [1] Delhey, K. (2019). A review of Gloger’s rule, an ecogeographical rule of colour: definitions, interpretations and evidence. Biological Reviews, 94(4), 1294–1316. doi: 10.1111/brv.12503 | Distribution of iridescent colours in hummingbird communities results from the interplay between selection for camouflage and communication | Hugo Gruson, Marianne Elias, Juan L. Parra, Christine Andraud, Serge Berthier, Claire Doutrelant, Doris Gomez | <p>Identification errors between closely related, co-occurring, species may lead to misdirected social interactions such as costly interbreeding or misdirected aggression. This selects for divergence in traits involved in species identification am... | Evolutionary Ecology, Macroevolution, Phylogeography & Biogeography, Sexual Selection, Species interactions | Sébastien Lavergne | 2019-03-29 17:23:20 | View | ||
02 May 2023
Host-symbiont-gene phylogenetic reconciliationHugo Menet, Alexia Nguyen Trung, Vincent Daubin, Eric Tannier https://doi.org/10.1101/2022.07.01.498457Reconciling molecular evolution and evolutionary ecology studies: a phylogenetic reconciliation method for gene-symbiont-host systemsRecommended by Emmanuelle Jousselin based on reviews by Vincent Berry and Catherine MatiasInteractions between species are a driving force in evolution. Many organisms host symbiotic partners that live all or part of their life in or on their host. Whether they are mutualistic or parasitic, these symbiotic associations impose strong selective pressures on both partners and affect their evolutionary trajectories. In fine, they can have a significant impact on the diversification patterns of both host and symbiont lineages, with symbiotic lineages sometimes speciating simultaneously with their hosts and/or switching from one host species to another. Long-term associations between species can also result in gene transfers between the involved organisms. Those lateral gene transfers are a source of ecological innovation but can obscure the phylogenetic signals and render the process of phylogenetic reconstructions complex (Lerat et al. 2003). Methods known as reconciliations explore similarities and differences between phylogenetic trees. They have been widely used to both compare the diversification patterns of hosts and symbionts and identify lateral gene transfers between species. Though the reconciliation approaches used in host/ symbiont and species/ gene phylogenetic studies are identical, they are always applied separately to solve either molecular evolution questions or investigate the evolution of ecological interactions. However, the two questions are often intimately linked and the current interest in multi-level systems (e.g. the holobiont concept) calls for a unique model that will take into account three-level nested organization (gene/symbiont/ host) where both symbiont and genes can transfer among hosts. Here Menet and collaborators (2023) provide such a model to produce three-level reconciliations. In order to do so, they extend the two-level reconciliation model implemented in “ALE” software (Szöllősi et al. 2013), one of the most used and proven reconciliation methods. Briefly, given a symbiont gene tree, a symbiont tree and a host tree, as in previous reconciliation models, the symbiont tree is mapped onto the host tree by mixing three types of events: Duplication, Transfer or Loss (DTL), with a possibility of the symbiont evolving temporarily outside the host phylogeny (in a “ghost” host lineage). The gene tree evolves similarly inside the symbiont tree, but horizontal transfers are constrained to symbionts co-occurring within the same host. Joint reconciliation scenarios are reconstructed and DTL event rates and likelihoods are estimated according to the model. As a nice addition, the authors propose a method to infer the symbiont phylogeny through amalgamation from gene trees and a host tree. The authors then explore the diverse possibilities offered by this method by testing it on both simulated datasets and biological datasets in order to check whether considering three nested levels is worthwhile. They convincingly show that three-level reconciliation has a better capacity to retrieve the symbiont donors and receivers of horizontal gene transfers, probably because transfers are constrained by additional elements relevant to the biological systems. Using, aphids, their obligate endosymbionts, and the symbiont genes involved in their nutritional functions, they identify horizontal gene transfers between aphid symbionts that are missed by two-level reconciliations but detected by expertise (Manzano-Marín et al. 2020). The other dataset presented here is on the human pathogen Helicobacter pylori, which history is supposed to reflect human migration. They use more than 1000 H. pylori gene families, and four populations, and use likelihood computations to compare different hypotheses on the diversification of the host. In summary, this study is a proof-of-concept of a 3-level reconciliation, where the authors manage to convey the applicability of their framework to many biological systems. Reported complexities, confirmed by reported running times, show that the method is computationally efficient. Without a doubt, the tool presented here will be very useful to evolutionary biologists who want to investigate multi-scale cophylogenies and it will move forward the study of associations between host and symbionts when symbiont genomic data are available. REFERENCES Lerat, E., Daubin, V., & Moran, N. A. (2003). From gene trees to organismal phylogeny in prokaryotes: the case of the γ-Proteobacteria. PLoS biology, 1(1), e19. Menet H, Trung AN, Daubin V, Tannier E (2023) Host-symbiont-gene phylogenetic reconciliation. bioRxiv, 2022.07.01.498457, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.07.01.498457 Szöllősi, G. J., Rosikiewicz, W., Boussau, B., Tannier, E., & Daubin, V. (2013). Efficient exploration of the space of reconciled gene trees. Systematic biology, 62(6), 901-912. | Host-symbiont-gene phylogenetic reconciliation | Hugo Menet, Alexia Nguyen Trung, Vincent Daubin, Eric Tannier | <p style="text-align: justify;"><strong>Motivation:</strong> Biological systems are made of entities organized at different scales e.g. macro-organisms, symbionts, genes...) which evolve in interaction.<br>These interactions range from indepe... | Bioinformatics & Computational Biology, Phylogenetics / Phylogenomics | Emmanuelle Jousselin | 2022-08-21 18:34:27 | View | ||
25 Jan 2023
Drivers of genomic landscapes of differentiation across Populus divergence gradientHuiying Shang, Martha Rendón-Anaya, Ovidiu Paun, View David L Field, Jaqueline Hess, Claus Vogl, Jianquan Liu, Pär K. Ingvarsson, Christian Lexer, Thibault Leroy https://doi.org/10.1101/2021.08.26.457771Shedding light on genomic divergence along the speciation continuumRecommended by Violaine Llaurens based on reviews by Camille Roux, Steven van Belleghem and 1 anonymous reviewerThe article “Drivers of genomic landscapes of differentiation across Populus divergence gradient” by Shang et al. describes an amazing dataset where genomic variations among 21 pairs of diverging poplar species are compared. Such comparisons are still quite rare and are needed to shed light on the processes shaping genomic divergence along the speciation gradient. Relying on two hundred whole-genome resequenced samples from 8 species that diverged from 1.3 to 4.8 million years ago, the authors aim at identifying the key factors involved in the genomic differentiation between species. They carried out a wide range of robust statistical tests aiming at characterizing the genomic differentiation along the genome of these species pairs. They highlight in particular the role of linked selection and gene flow in shaping the divergence along the genomes of species pairs. They also confirm the significance of introgression among species with a net divergence larger than the upper boundaries of the grey zone of speciation previously documented in animals (da from 0.005 to 0.02, Roux et al. 2016). Because these findings pave the way to research about the genomic mechanisms associated with speciation in species with allopatric and parapatric distributions, I warmingly recommend this article. References Roux C, Fraïsse C, Romiguier J, Anciaux Y, Galtier N, Bierne N (2016) Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence. PLOS Biology, 14, e2000234. https://doi.org/10.1371/journal.pbio.2000234 Shang H, Rendón-Anaya M, Paun O, Field DL, Hess J, Vogl C, Liu J, Ingvarsson PK, Lexer C, Leroy T (2023) Drivers of genomic landscapes of differentiation across Populus divergence gradient. bioRxiv, 2021.08.26.457771, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.08.26.457771 | Drivers of genomic landscapes of differentiation across Populus divergence gradient | Huiying Shang, Martha Rendón-Anaya, Ovidiu Paun, View David L Field, Jaqueline Hess, Claus Vogl, Jianquan Liu, Pär K. Ingvarsson, Christian Lexer, Thibault Leroy | <p style="text-align: justify;">Speciation, the continuous process by which new species form, is often investigated by looking at the variation of nucleotide diversity and differentiation across the genome (hereafter genomic landscapes). A key cha... | Population Genetics / Genomics, Speciation | Violaine Llaurens | 2021-09-06 14:12:27 | View |
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