Latest recommendations
Id | Title▼ | Authors | Abstract | Picture | Thematic fields | Recommender | Reviewers | Submission date | |
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03 Jun 2018
Cost of resistance: an unreasonably expensive conceptThomas Lenormand, Noemie Harmand, Romain Gallet https://doi.org/10.1101/276675Let’s move beyond costs of resistance!Recommended by Inês Fragata and Claudia Bank based on reviews by Danna Gifford, Helen Alexander and 1 anonymous reviewerThe increase in the prevalence of (antibiotic) resistance has become a major global health concern and is an excellent example of the impact of real-time evolution on human society. This has led to a boom of studies that investigate the mechanisms and factors involved in the evolution of resistance, and to the spread of the concept of "costs of resistance". This concept refers to the relative fitness disadvantage of a drug-resistant genotype compared to a non-resistant reference genotype in the ancestral (untreated) environment. In their paper, Lenormand et al. [1] discuss the history of this concept and highlight its caveats and limitations. The authors address both practical and theoretical problems that arise from the simplistic view of "costly resistance" and argue that they can be prejudicial for antibiotic resistance studies. For a better understanding, they visualize their points of critique by means of Fisher's Geometric model. The authors give an interesting historical overview of how the concept arose and speculate that it emerged (during the 1980s) in an attempt by ecologists to spread awareness that fitness can be environment-dependent, and because of the concept's parallels to trade-offs in life-history evolution. They then identify several problems that arise from the concept, which, besides the conceptual misunderstandings that they can cause, are important to keep in mind when designing experimental studies. The authors highlight and explain the following points: Lenormand et al.'s paper [1] is a timely perspective piece in light of the ever-increasing efforts to understand and tackle resistance evolution [2]. Although some readers may shy away from the rather theoretical presentation of the different points of concern, it will be useful for both theoretical and empirical readers by illustrating the misconceptions that can arise from the concept of the cost of resistance. Ultimately, the main lesson to be learned from this paper may not be to ban the term "cost of resistance" from one's vocabulary, but rather to realize that the successful fight against drug resistance requires more differential information than the measurement of fitness effects in a drug-treated vs. non-treated environment in the lab [3-4]. Specifically, a better integration of the ecological aspects of drug resistance evolution and maintenance is needed [5], and we are far from a general understanding of how environmental factors interact and influence an organism's (absolute and relative) fitness and the effect of resistance mutations. References [1] Lenormand T, Harmand N, Gallet R. 2018. Cost of resistance: an unreasonably expensive concept. bioRxiv 276675, ver. 3 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/276675 | Cost of resistance: an unreasonably expensive concept | Thomas Lenormand, Noemie Harmand, Romain Gallet | <p>The cost of resistance, or the fitness effect of resistance mutation in absence of the drug, is a very widepsread concept in evolutionary genetics and beyond. It has represented an important addition to the simplistic view that resistance mutat... | Adaptation, Evolutionary Applications, Evolutionary Ecology, Evolutionary Theory, Experimental Evolution, Genotype-Phenotype, Population Genetics / Genomics | Inês Fragata | 2018-03-09 02:22:07 | View | ||
16 Mar 2017
POSTPRINT
Correlated paternity measures mate monopolization and scales with the magnitude of sexual selectionDorken, ME and Perry LE 10.1111/jeb.13013Measurement of sexual selection in plants made easierRecommended by Emmanuelle Porcher and Mathilde DufaySexual selection occurs in flowering plants too. However it tends to be understudied in comparison to animal sexual selection, in part because the minuscule size and long dispersal distances of the individuals producing male gametes (pollen grains) seriously complicate the estimation of male siring success and thereby the measurement of sexual selection. Dorken and Perry [1] introduce a novel and clever approach to estimate sexual selection in plants, which bypasses the need for a direct quantification of absolute male mating success. This approach builds on the fact that the strength of sexual selection is directly related to the ability of individuals to monopolize mates [2]. In plants, mate monopolization can be assessed by examining the proportion of seeds produced by a given plant that are full-sibs, i.e. that share the same father. A nice feature of this proportion of full-sib seeds per maternal parent is it equals the coefficient of correlated paternity of Ritland [3], which can be readily obtained from the hundreds of plant mating system studies using genetic markers. A less desirable feature of the proportion of full sibs per maternal plant is that it is inversely related to population size, an effect that should be corrected for. The resulting index of mate monopolization is a simple product: (coefficient of correlated paternity)x(population size – 1). The authors test whether their index of mate monopolization is a good correlate of sexual selection, measured more traditionally as the selection differential on a trait influencing mating success, using a combination of theoretical and experimental approaches. Both approaches confirm that the two quantities are positively correlated, which suggests that the index of mate monopolization could be a convenient way to estimate the relative strength of sexual selection in flowering plants. These results call for further investigation, e.g. to verify that the effect of population size is well controlled for, or to assess the effects of non-random mating and inbreeding depression; however, this work paves the way for an expansion of sexual selection studies in flowering plants. References [1] Dorken ME and Perry LE. 2017. Correlated paternity measures mate monopolization and scales with the magnitude of sexual selection. Journal of Evolutionary Biology 30: 377-387 doi: 10.1111/jeb.13013 [2] Klug H, Heuschele J, Jennions M and Kokko H. 2010. The mismeasurement of sexual selection. Journal of Evolutionary Biology 23:447-462. doi: 10.1111/j.1420-9101.2009.01921.x [3] Ritland K. 1989. Correlated matings in the partial selfer Mimulus guttatus. Evolution 43:848-859. doi: 10.2307/2409312 | Correlated paternity measures mate monopolization and scales with the magnitude of sexual selection | Dorken, ME and Perry LE | Indirect measures of sexual selection have been criticized because they can overestimate the magnitude of selection. In particular, they do not account for the degree to which mating opportunities can be monopolized by individuals of the sex that ... | Sexual Selection | Emmanuelle Porcher | 2017-03-13 23:22:26 | View | ||
11 May 2023
Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineagesAlejandro Manzano-Marín, Armelle Coeur d'acier, Anne-Laure Clamens, Corinne Cruaud, Valérie Barbe, Emmanuelle Jousselin https://doi.org/10.1101/2022.08.28.505559Flexibility in Aphid Endosymbiosis: Dual Symbioses Have Evolved Anew at Least Six TimesRecommended by Olivier Tenaillon based on reviews by Alex C. C. Wilson and 1 anonymous reviewerIn this intriguing study (Manzano-Marín et al. 2022) by Alejandro Manzano-Marin and his colleagues, the association between aphids and their symbionts is investigated through meta-genomic analysis of new samples. These associations have been previously described as leading to fascinating genomic evolution in the symbiont (McCutcheon and Moran 2012). The bacterial genomes exhibit a significant reduction in size and the range of functions performed. They typically lose the ability to produce many metabolites or biobricks created by the host, and instead, streamline their metabolism by focusing on the amino acids that the host cannot produce. This level of co-evolution suggests a stable association between the two partners. However, the new data suggests a much more complex pattern as multiple independent acquisitions of co-symbionts are observed. Co-symbiont acquisition leads to a partition of the functions carried out on the bacterial side, with the new co-symbiont taking over some of the functions previously performed by Buchnera. In most cases, the new co-symbiont also brings the ability to produce B1 vitamin. Various facultative symbiotic taxa are recruited to be co-symbionts, with the frequency of acquisition related to the bacterial niche and lifestyle. REFERENCES Manzano-Marín, Alejandro, Armelle Coeur D’acier, Anne-Laure Clamens, Corinne Cruaud, Valérie Barbe, and Emmanuelle Jousselin. 2023. “Co-Obligate Symbioses Have Repeatedly Evolved across Aphids, but Partner Identity and Nutritional Contributions Vary across Lineages.” bioRxiv, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.08.28.505559. McCutcheon, John P., and Nancy A. Moran. 2012. “Extreme Genome Reduction in Symbiotic Bacteria.” Nature Reviews Microbiology 10 (1): 13–26. https://doi.org/10.1038/nrmicro2670. | Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages | Alejandro Manzano-Marín, Armelle Coeur d'acier, Anne-Laure Clamens, Corinne Cruaud, Valérie Barbe, Emmanuelle Jousselin | <p style="text-align: justify;">Aphids are a large family of phloem-sap feeders. They typically rely on a single bacterial endosymbiont, <em>Buchnera aphidicola</em>, to supply them with essential nutrients lacking in their diet. This association ... | Genome Evolution, Other, Species interactions | Olivier Tenaillon | 2022-11-16 10:13:37 | View | ||
21 Nov 2018
Convergent evolution as an indicator for selection during acute HIV-1 infectionFrederic Bertels, Karin J Metzner, Roland R Regoes https://doi.org/10.1101/168260Is convergence an evidence for positive selection?Recommended by Guillaume Achaz based on reviews by Jeffrey Townsend and 1 anonymous reviewerThe preprint by Bertels et al. [1] reports an interesting application of the well-accepted idea that positively selected traits (here variants) can appear several times independently; think about the textbook examples of flight capacity. Hence, the authors assume that reciprocally convergence implies positive selection. The methodology becomes then, in principle, straightforward as one can simply count variants in independent datasets to detect convergent mutations. References [1] Bertels, F., Metzner, K. J., & Regoes R. R. (2018). Convergent evolution as an indicator for selection during acute HIV-1 infection. BioRxiv, 168260, ver. 4 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/168260 | Convergent evolution as an indicator for selection during acute HIV-1 infection | Frederic Bertels, Karin J Metzner, Roland R Regoes | <p>Convergent evolution describes the process of different populations acquiring similar phenotypes or genotypes. Complex organisms with large genomes only rarely and only under very strong selection converge to the same genotype. In contrast, ind... | Bioinformatics & Computational Biology, Evolutionary Applications, Genome Evolution, Molecular Evolution | Guillaume Achaz | 2017-07-26 08:39:17 | View | ||
01 Sep 2021
Connectivity and selfing drives population genetic structure in a patchy landscape: a comparative approach of four co-occurring freshwater snail speciesJarne P., Lozano del Campo A., Lamy T., Chapuis E., Dubart M., Segard A., Canard E., Pointier J.-P., David P. https://hal.archives-ouvertes.fr/hal-03295242Determinants of population genetic structure in co-occurring freshwater snailsRecommended by Trine Bilde and Matteo Fumagalli based on reviews by 3 anonymous reviewersGenetic diversity is a key aspect of biodiversity and has important implications for evolutionary potential and thereby the persistence of species. Improving our understanding of the factors that drive genetic structure within and between populations is, therefore, a long-standing goal in evolutionary biology. However, this is a major challenge, because of the complex interplay between genetic drift, migration, and extinction/colonization dynamics on the one hand, and the biology and ecology of species on the other hand (Romiguier et al. 2014, Ellegren and Galtier 2016, Charlesworth 2003). Jarne et al. (2021) studied whether environmental and demographic factors affect the population genetic structure of four species of hermaphroditic freshwater snails in a similar way, using comparative analyses of neutral genetic microsatellite markers. Specifically, they investigated microsatellite variability of Hygrophila in almost 280 sites in Guadeloupe, Lesser Antilles, as part of a long-term survey experiment (Lamy et al. 2013). They then modelled the influence of the mating system, local environmental characteristics and demographic factors on population genetic diversity. Consistent with theoretical predictions (Charlesworth 2003), they detected higher genetic variation in two outcrossing species than in two selfing species, emphasizing the importance of the mating system in maintaining genetic diversity. The study further identified an important role of site connectivity, through its influences on effective population size and extinction/colonisation events. Finally, the study detects an influence of interspecific interactions caused by an ongoing invasion by one of the studied species on genetic structure, highlighting the indirect effect of changes in community composition and demography on population genetics. Jarne et al. (2021) could address the extent to which genetic structure is determined by demographic and environmental factors in multiple species given the remarkable sampling available. Additionally, the study system is extremely suitable to address this hypothesis as species’ habitats are defined and delineated. Whilst the authors did attempt to test for across-species correlations, further investigations on this matter are required. Moreover, the effect of interactions between factors should be appropriately considered in any modelling between genetic structure and local environmental or demographic features. The findings in this study contribute to improving our understanding of factors influencing population genetic diversity, and highlights the complexity of interacting factors, therefore also emphasizing the challenges of drawing general implications, additionally hampered by the relatively limited number of species studied. Jarne et al. (2021) provide an excellent showcase of an empirical framework to test determinants of genetic structure in natural populations. As such, this study can be an example for further attempts of comparative analysis of genetic diversity. References Charlesworth, D. (2003) Effects of inbreeding on the genetic diversity of populations. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 358, 1051-1070. doi: https://doi.org/10.1098/rstb.2003.1296 Ellegren, H. and Galtier, N. (2016) Determinants of genetic diversity. Nature Reviews Genetics, 17, 422-433. doi: https://doi.org/10.1038/nrg.2016.58 Jarne, P., Lozano del Campo, A., Lamy, T., Chapuis, E., Dubart, M., Segard, A., Canard, E., Pointier, J.-P. and David, P. (2021) Connectivity and selfing drives population genetic structure in a patchy landscape: a comparative approach of four co-occurring freshwater snail species. HAL, hal-03295242, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://hal.archives-ouvertes.fr/hal-03295242 Lamy, T., Gimenez, O., Pointier, J. P., Jarne, P. and David, P. (2013). Metapopulation dynamics of species with cryptic life stages. The American Naturalist, 181, 479-491. doi: https://doi.org/10.1086/669676 Romiguier, J., Gayral, P., Ballenghien, M. et al. (2014) Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature, 515, 261-263. doi: https://doi.org/10.1038/nature13685 | Connectivity and selfing drives population genetic structure in a patchy landscape: a comparative approach of four co-occurring freshwater snail species | Jarne P., Lozano del Campo A., Lamy T., Chapuis E., Dubart M., Segard A., Canard E., Pointier J.-P., David P. | <p style="text-align: justify;">The distribution of neutral genetic variation in subdivided populations is driven by the interplay between genetic drift, migration, local extinction and colonization. The influence of environmental and demographic ... | Adaptation, Evolutionary Dynamics, Population Genetics / Genomics, Reproduction and Sex, Species interactions | Trine Bilde | 2021-02-11 19:57:51 | View | ||
16 Dec 2022
Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depressionDiala Abu Awad, Donald Waller https://doi.org/10.1101/2021.12.16.473022Pseudo-overdominance: how linkage and selection can interact and oppose to purging of deleterious mutations.Recommended by Sylvain Glémin based on reviews by Yaniv Brandvain, Lei Zhao and 1 anonymous reviewerMost mutations affecting fitness are deleterious and they have many evolutionary consequences. The dynamics and consequences of deleterious mutations are a long-standing question in evolutionary biology and a strong theoretical background has already been developed, for example, to predict the mutation load, inbreeding depression or background selection. One of the classical results is that inbreeding helps purge partially recessive deleterious mutations by exposing them to selection in homozygotes. However, this mainly results from single-locus considerations. When interactions among several, more or less linked, deleterious mutations are taken into account, peculiar dynamics can emerge. One of them, called pseudo-overdominance (POD), corresponds to the maintenance in a population of two (or more) haplotype blocks composed of several recessive deleterious mutations in repulsion that mimics overdominance. Indeed, homozygote individuals for one of the haplotype blocks expose many deleterious mutations to selection whereas they are reciprocally masked in heterozygotes, leading to higher fitness of heterozygotes compared to both homozygotes. A related process, called associative overdominance (AOD) is the effect of such deleterious alleles in repulsion on the linked neutral variation that can be increased by AOD. Although this possibility has been recognized for a long time (Otha and Kimura 1969), it has been mainly considered an anecdotal process. Recently, both theoretical (Zhao and Charlesworth 2016) and genomic analyses (Gilbert et al. 2020) have renewed interest in such a process, suggesting that it could be important in weakly recombining regions of a genome. Donald Waller (2021) - one of the co-authors of the current work - also recently proposed that POD could be quantitatively important with broad implications, and could resolve some unexplained observations such as the maintenance of inbreeding depression in highly selfing species. Yet, a proper theoretical framework analysing the effect of inbreeding on POD was lacking. In this theoretical work, Diala Abu Awad and Donald Waller (2022) addressed this question through an elegant combination of analytical predictions and intensive multilocus simulations. They determined the conditions under which POD can be maintained and how long it could resist erosion by recombination, which removes the negative association between deleterious alleles (repulsion) at the core of the mechanism. They showed that under tight linkage, POD regions can persist for a long time and generate substantial segregating load and inbreeding depression, even under inbreeding, so opposing (for a while) to the purging effect. They also showed that background selection can affect the genomic structure of POD regions by rapidly erasing weak POD regions but maintaining strong POD regions (i.e with many tightly linked deleterious alleles). These results have several implications. They can explain the maintenance of inbreeding depression despite inbreeding (as anticipated by Waller 2021), which has implications for the evolution of mating systems. If POD can hardly emerge under high selfing, it can persist from an outcrossing ancestor long after the transition towards a higher selfing rate and could explain the maintenance of mixed mating systems(which is possible with true overdominance, see Uyenoyama and Waller 1991). The results also have implications for genomic analyses, pointing to regions of low or no recombination where POD could be maintained, generating both higher diversity and heterozygosity than expected and variance in fitness. As structural variations are likely widespread in genomes with possible effects on suppressing recombination (Mérot et al. 2020), POD regions should be checked more carefully in genomic analyses (see also Gilbert et al. 2020). Overall, this work should stimulate new theoretical and empirical studies, especially to assess how quantitatively strong and widespread POD can be. It also stresses the importance of properly considering genetic linkage genome-wide, and so the role of recombination landscapes in determining patterns of diversity and fitness effects. References
Awad DA, Waller D (2022) Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depression. bioRxiv, 2021.12.16.473022, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.12.16.473022 Gilbert KJ, Pouyet F, Excoffier L, Peischl S (2020) Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination. Current Biology, 30, 101-107.e3. https://doi.org/10.1016/j.cub.2019.11.063 Mérot C, Oomen RA, Tigano A, Wellenreuther M (2020) A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation. Trends in Ecology & Evolution, 35, 561–572. https://doi.org/10.1016/j.tree.2020.03.002 Ohta T, Kimura M (1969) Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics, 63, 229–238. https://doi.org/10.1093/genetics/63.1.229 Uyenoyama MK, Waller DM (1991) Coevolution of self-fertilization and inbreeding depression II. Symmetric overdominance in viability. Theoretical Population Biology, 40, 47–77. https://doi.org/10.1016/0040-5809(91)90046-I Waller DM (2021) Addressing Darwin’s dilemma: Can pseudo-overdominance explain persistent inbreeding depression and load? Evolution, 75, 779–793. https://doi.org/10.1111/evo.14189 Zhao L, Charlesworth B (2016) Resolving the Conflict Between Associative Overdominance and Background Selection. Genetics, 203, 1315–1334. https://doi.org/10.1534/genetics.116.188912 | Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depression | Diala Abu Awad, Donald Waller | <p style="text-align: justify;">Classical models that ignore linkage predict that deleterious recessive mutations should purge or fix within inbred populations, yet inbred populations often retain moderate to high segregating load. True overdomina... | Evolutionary Dynamics, Evolutionary Theory, Genome Evolution, Hybridization / Introgression, Population Genetics / Genomics, Reproduction and Sex | Sylvain Glémin | 2022-01-04 12:15:35 | View | ||
02 Feb 2024
Community structure of heritable viruses in a Drosophila-parasitoids complexJulien Varaldi, David Lepetit, Nelly Burlet, Camille Faber, Bérénice Baretje, Roland Allemand https://doi.org/10.1101/2023.07.29.551099The virome of a Drosophilidae-parasitoid communityRecommended by Ben Longdon based on reviews by 3 anonymous reviewersUnderstanding the factors that shape the virome of a host is key to understanding virus ecology and evolution (Obbard, 2018; French & Holmes, 2020). There is still much to learn about the diversity and distribution of viruses in a host community (Wille et al., 2019; Chen et al., 2023). The viruses of parasitoid wasps are well studied, and their viruses, or integrated viral genes, are known to suppress their insect host’s immune response to enhance parasitoid survival (Herniou et al., 2013; Coffman et al., 2022). Likewise, the insect virome is being increasingly well studied (Shi et al., 2016), with the virome of Drosophila species being particularly well characterised over the best part of the last century (L'Heritier & Teissier, 1937; L'Heritier, 1970; Brun & Plus, 1980; Longdon et al., 2010; Longdon et al., 2011; Longdon et al., 2012; Webster et al., 2015; Webster et al., 2016; Medd et al., 2018; Wallace et al., 2021). However, the viromes of parasitoids and their insect host communities have been less well studied (Leigh et al., 2018; Caldas-Garcia et al., 2023), and the inherent connectivity between parasitoids and their hosts provides an interesting system to study virus host range and cross-species transmission. Here, Varaldi et al (Varaldi et al., 2024) have examined the viruses associated with a community of nine Drosophilidae hosts and six parasitoids. Using both RNA and DNA sequencing of insects reared for two generations, they selected viruses that are maintained in the lab either via vertical transmission or contamination of rearing medium. From 55 pools of insects they found 53 virus-like sequences, 37 of which were novel. Parasitoids were host to nearly twice as many viruses as their Drosophila hosts, although they note this could be due to differences in the rearing temperatures of the hosts. They next quantified if species, year, season, or location played a role in structuring the virome, finding only a significant effect of host species, which explained just over 50% of the variation in virus distribution. No evidence was found of related species sharing more similar virus communities. Although looking at a limited number of species, this suggests that these viruses are not co-speciating or preferentially host switching between closely related species. Finally, they carried out crosses between lines of the parasitoid Leptopilina heterotoma that were infected and uninfected for a novel Iflavirus found in their sequencing data. They found evidence of high levels of maternal transmission and lower level horizontal transmission between wasp larvae parasitising the same host. No evidence of changes in parasitoid-induced mortality, developmental success or the sex ratio was found in iflavirus-infected parasitoids. Interestingly individuals infected with this RNA virus also contained viral DNA, but this did not appear to be integrated into the wasp genome. Overall, this work has taken the first steps in examining the community structure of the virome of parasitoids together with their Drosophilidae hosts. This work will not doubt stimulate follow-up studies to explore the evolution and ecology of these novel virus communities. References Brun G, Plus N (1980) The viruses of Drosophila. In: The genetics and biology of Drosophila eds Ashburner M & Wright TRF), pp. 625-702. Academic Press, New York. | Community structure of heritable viruses in a *Drosophila*-parasitoids complex | Julien Varaldi, David Lepetit, Nelly Burlet, Camille Faber, Bérénice Baretje, Roland Allemand | <p style="text-align: justify;">The diversity and phenotypic impacts related to the presence of heritable bacteria in insects have been extensively studied in the last decades. On the contrary, heritable viruses have been overlooked for several re... | Evolutionary Ecology, Species interactions | Ben Longdon | 2023-08-03 01:07:43 | View | ||
13 Nov 2023
Color polymorphism and conspicuousness do not increase speciation rates in LacertidsThomas de Solan, Barry Sinervo, Philippe Geniez, Patrice David, Pierre-André Crochet https://doi.org/10.1101/2023.02.15.528678Colour polymorphism does not increase diversification rates in lizardsRecommended by Alejandro Gonzalez Voyer based on reviews by 2 anonymous reviewersThe striking differences in species richness among lineages in the Tree of Life have long attracted much research interest. In particular, researchers have asked whether certain traits are associated with greater diversification, with a particular focus on traits under sexual selection given their direct link to mating isolation. Polymorphism, defined as the presence of co-occurring, heritable morphs within a population, has been proposed to influence diversification rates although the effect has been proposed as both promoting or alternatively impeding speciation. The effect of polymorphism may be positive, that is facilitating speciation if polymorphism allows to broaden the ecological niche, thus enabling range expansion, or enabling maintenance of populations in variable environments. Specialized ectomorphs have been observed in several species (e.g. Kusche et al. 2015, Lattanzio and Miles 2016, Whitney et al. 2018, Scali et al. 2016). Polymorphism may also facilitate speciation if a morph is lost during the colonization of a novel area or niche, resulting in rapid divergence of the remaining morphs and reproductive isolation from the ancestral population, known as the morph speciation hypothesis (West-Eberhard 1986, Corl et al. 2010). On the other hand, polymorphism may hamper speciation through disassortative maintaining by morph, which may maintain the polymorphism through the speciation process (Jamie and Meier 2020). An example of such a process is Heliconius numata where disassortative mate preferences based on color hampers ecological speciation (Chouteau et al. 2017). Previous evidence in birds and lizards suggests polymorphism favors diversification (Corl et al. 2010b, 2012, Hugall and Stuart-Fox 2012, Brock et al. 2021). Here, de Solan et al. (2023) test the effect of polymorphism on diversification in Lacertidae, a family of lizards containing more than 300 species distributed across Europe, Africa and Asia. The group offers a good model system to test the effect of polymorphism on speciation as it contains several species with colour polymorphism, sometimes present in both sexes but restricted to males when present in the flank. Using coloration data from the literature as well as photographs of live specimens for 295 species the authors tested whether the presence of polymorphism is associated with higher diversification rates. While undertaking their project, another group independently tackled the same question (Brock et al. 2021), using the same model system but coming to very different conclusions. Therefore, de Solan et al. (2023) decided to also contrast their results with those of Brock et al. (2021) to determine the factors responsible for the contrasting results of both studies. The latter I consider one of the strengths of the work, given the careful re-analyses to determine the causes of the discrepancies between both studies. De Solan et al. (2023) found no association between the presence of polymorphism and diversification rates, even though they used different analytical approaches. Thus, this study is interesting as it provides results that do not support a positive effect of polymorphism on species richness. The use of a phylogeny with more limited species sampling (García-Porta et al. 2019) implied that the authors had to manually add 75 species, of which 17 were added to the tree based on information from previously published trees and 68 were added at random locations within the genus. To control for potential biases the authors repeated the analyses using a sample of trees with the imputed taxa, results were broadly concordant across the set of trees. The careful re-analysis contrasting Brock et al. (2021) and de Solan et al. (2023) results suggests the difference is mainly due to a difference in how species were coded as presenting polymorphism, which differed between the two studies, as well as a difference in the package version used to run the state-dependent diversification models. Interestingly non-parametric analyses yielded similar results across both datasets. Garcia-Porta, J., Irisarri, I., Kirchner, M. et al. 2019. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards. Nature Communications. 10: 4077. https://doi.org/10.1038/s41467-019-11943-x de Solan T, Sinervo B, Geniez P, David P, Crochet P-A (2023) Colour polymorphism and conspicuousness do not increase speciation rates in Lacertids. bioRxiv, 2023.02.15.528678, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.02.15.528678 West-Eberhard, M.J. 1986. Alternative adaptations, speciation, and phylogeny (A review). Proceedings of the National Academy of Sciences. 83: 1388-1392. https://doi.org/10.1073/pnas.83.5.1388 | Color polymorphism and conspicuousness do not increase speciation rates in Lacertids | Thomas de Solan, Barry Sinervo, Philippe Geniez, Patrice David, Pierre-André Crochet | <p style="text-align: justify;">Conspicuous body colors and color polymorphism have been hypothesized to increase rates of speciation. Conspicuous colors are evolutionary labile, and often involved in intraspecific sexual signaling and thus may pr... | Evolutionary Ecology, Macroevolution, Speciation | Alejandro Gonzalez Voyer | 2023-02-22 10:05:03 | View | ||
18 Dec 2017
Co-evolution of virulence and immunosuppression in multiple infectionsTsukushi Kamiya, Nicole Mideo, Samuel Alizon 10.1101/149211Two parasites, virulence and immunosuppression: how does the whole thing evolve?Recommended by Sara Magalhaes based on reviews by 2 anonymous reviewersHow parasite virulence evolves is arguably the most important question in both the applied and fundamental study of host-parasite interactions. Typically, this research area has been progressing through the formalization of the problem via mathematical modelling. This is because the question is a complex one, as virulence is both affected and affects several aspects of the host-parasite interaction. Moreover, the evolution of virulence is a problem in which ecology (epidemiology) and evolution (changes in trait values through time) are tightly intertwined, generating what is now known as eco-evolutionary dynamics. Therefore, intuition is not sufficient to address how virulence may evolve. References [1] Anderson RM and May RM. 1982. Coevolution of hosts and parasites. Parasitology, 1982. 85: 411–426. doi: 10.1017/S0031182000055360 [2] Kamiya T, Mideo N and Alizon S. 2017. Coevolution of virulence and immunosuppression in multiple infections. bioRxiv, ver. 7 peer-reviewed by PCI Evol Biol, 149211. doi: 10.1101/139147 | Co-evolution of virulence and immunosuppression in multiple infections | Tsukushi Kamiya, Nicole Mideo, Samuel Alizon | Many components of the host-parasite interaction have been shown to affect the way virulence, that is parasite induced harm to the host, evolves. However, co-evolution of multiple traits is often neglected. We explore how an immunosuppressive mech... | Evolutionary Applications, Evolutionary Dynamics, Evolutionary Ecology, Evolutionary Epidemiology, Evolutionary Theory | Sara Magalhaes | 2017-06-13 16:49:45 | 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 |
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