Latest recommendations
Id | Title | Authors | Abstract | Picture▲ | Thematic fields | Recommender | Reviewers | Submission date | |
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05 Feb 2021
Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating beesArthur Weyna, Jonathan Romiguier https://doi.org/10.1101/2020.04.14.038893Multi-gene and lineage comparative assessment of the strength of selection in HymenopteraRecommended by Bertanne Visser based on reviews by Michael Lattorff and 1 anonymous reviewerGenetic variation is the raw material for selection to act upon and the amount of genetic variation present within a population is a pivotal determinant of a population’s evolutionary potential. A large effective population size, i.e., the ideal number of individuals experiencing the same amount of genetic drift and inbreeding as an actual population, Ne (Wright 1931, Crow 1954), thus increases the probability of long-term survival of a population. However, natural populations, as opposed to theoretical ones, rarely adhere to the requirements of an ideal panmictic population (Sjödin et al. 2005). A range of circumstances can reduce Ne, including the structuring of populations (through space and time, as well as age and developmental stages) and inbreeding (Charlesworth 2009). In mammals, species with a larger body mass (as a proxy for lower Ne) were found to have a higher rate of nonsynonymous nucleotide substitutions (that alter the amino acid sequence of a protein), as well as radical amino acid substitutions (altering the physicochemical properties of a protein) (Popadin et al. 2007). In general, low effective population sizes increase the chance of mutation accumulation and drift, while reducing the strength of selection (Sjödin et al. 2005). References Charlesworth, B. (2009). Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics, 10(3), 195-205. doi: https://doi.org/10.1038/nrg2526 | Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees | Arthur Weyna, Jonathan Romiguier | <p>With one of the highest number of parasitic, eusocial and pollinator species among all insect orders, Hymenoptera features a great diversity of lifestyles. At the population genetic level, such life-history strategies are expected to decrease e... | Behavior & Social Evolution, Genome Evolution, Life History, Molecular Evolution, Population Genetics / Genomics | Bertanne Visser | 2020-04-21 17:30:57 | View | ||
22 Jul 2019
Transgenerational plasticity of inducible defenses: combined effects of grand-parental, parental and current environmentsJuliette Tariel; Sandrine Plénet; Emilien Luquet https://doi.org/10.1101/589945Transgenerational plasticity through three generationsRecommended by Troy Day based on reviews by Stewart Plaistow and 1 anonymous reviewerOrganisms very often display phenotypic plasticity, whereby the expression of trait (or suite of traits) changes in a consistent way as a function of some environmental variable. Sometimes this plastic response remains labile and so the trait continues to respond to the environment throughout an organism’s life, but there are also many examples in which environmental conditions during a critical developmental window irreversibly set the stage for how a trait will be expressed later in life. References [1] West-Eberhard, M. J. (2003). Developmental plasticity and evolution. Oxford University Press. | Transgenerational plasticity of inducible defenses: combined effects of grand-parental, parental and current environments | Juliette Tariel; Sandrine Plénet; Emilien Luquet | <p>While an increasing number of studies highlights that parental environment shapes offspring phenotype (transgenerational plasticity TGP), TGP beyond the parental generation has received less attention. Studies suggest that TGP impacts populatio... | Adaptation, Evolutionary Ecology, Non Genetic Inheritance, Phenotypic Plasticity | Troy Day | 2019-03-29 09:31:53 | View | ||
06 Sep 2022
Masculinization of the X-chromosome in aphid soma and gonadsJulie Jaquiery, Jean-Christophe Simon, Stephanie Robin, Gautier Richard, Jean Peccoud, Helene Boulain, Fabrice Legeai, Sylvie Tanguy, Nathalie Prunier-Leterme, Gael Letrionnaire https://doi.org/10.1101/2021.08.13.453080Sex-biased gene expression is not tissue-specific in Pea AphidsRecommended by Charles Baer and Tanja Schwander based on reviews by Ann Kathrin Huylmans and 1 anonymous reviewerSexual antagonism (SA), wherein the fitness interests of the sexes do not align, is inherent to organisms with two (or more) sexes. SA leads to intra-locus sexual conflict, where an allele that confers higher fitness in one sex reduces fitness in the other [1, 2]. This situation leads to what has been referred to as "gender load", resulting from the segregation of SA alleles in the population. Gender load can be reduced by the evolution of sex-specific (or sex-biased) gene expression. A specific prediction is that gene-duplication can lead to sub- or neo-functionalization, in which case the two duplicates partition the function in the different sexes. The conditions for invasion by a SA allele differ between sex-chromosomes and autosomes, leading to the prediction that (in XY or XO systems) the X should accumulate recessive male-favored alleles and dominant female-favored alleles; similar considerations apply in ZW systems ([3, but see 4]. Aphids present an interesting special case, for several reasons: they have XO sex-determination, and three distinct reproductive morphs (sexual females, parthenogenetic females, and males). Previous theoretical work by the lead author predict that the X should be optimized for male function, which was borne out by whole-animal transcriptome analysis [5]. Here [6], the authors extend that work to investigate “tissue”-specific (heads, legs and gonads), sex-specific gene expression. They argue that, if intra-locus SA is the primary driver of sex-biased gene expression, it should be generally true in all tissues. They set up as an alternative the possibility that sex-biased gene expression could also be driven by dosage compensation. They cite references supporting their argument that "dosage compensation (could be) stronger in the brain", although the underlying motivation for that argument appears to be based on empirical evidence rather than theoretical predictions. At any rate, the results are clear: all tissues investigated show masculinization of the X. Further, X-linked copies of gene duplicates were more frequently male-biased than duplicated autosomal genes or X-linked single-copy genes. To sum up, this is a nice empirical study with clearly interpretable (and interpreted) results, the most obvious of which is the greater sex-biased expression in sexually-dimorphic tissues. Unfortunately, as the authors emphasize, there is no general theory by which SA, variable dosage-compensation, and meiotic sex chromosome inactivation can be integrated in a predictive framework. It is to be hoped that empirical studies such as this one will motivate deeper and more general theoretical investigations. References [1] Rice WR, Chippindale AK (2001) Intersexual ontogenetic conflict. Journal of Evolutionary Biology 14: 685-693. https://doi.org/10.1046/j.1420-9101.2001.00319.x [2] Bonduriansky R, Chenoweth SF (2009) Intralocus sexual conflict. Trends Ecol Evol 24: 280-288. https://doi.org/10.1016/j.tree.2008.12.005 [3] Rice WR. (1984) Sex chromosomes and the evolution of sexual dimorphism. Evolution 38: 735-742. https://doi.org/10.1086/595754 [4] Fry JD (2010) The genomic location of sexually antagonistic variation: some cautionary comments. Evolution 64: 1510-1516. https://doi.org/10.1111%2Fj.1558-5646.2009.00898.x [5] Jaquiéry J, Rispe C, Roze D, Legeai F, Le Trionnaire G, Stoeckel S, et al. (2013) Masculinization of the X Chromosome in the Pea Aphid. PLoS Genetics 9. https://doi.org/10.1371/journal.pgen.1003690 [6] Jaquiéry J, Simon J-C, Robin S, Richard G, Peccoud J, Boulain H, Legeai F, Tanguy S, Prunier-Leterme N, Le Trionnaire G (2022) Masculinization of the X-chromosome in aphid soma and gonads. bioRxiv, 2021.08.13.453080, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.08.13.453080 | Masculinization of the X-chromosome in aphid soma and gonads | Julie Jaquiery, Jean-Christophe Simon, Stephanie Robin, Gautier Richard, Jean Peccoud, Helene Boulain, Fabrice Legeai, Sylvie Tanguy, Nathalie Prunier-Leterme, Gael Letrionnaire | <p>Males and females share essentially the same genome but differ in their optimal values for many phenotypic traits, which can result in intra-locus conflict between the sexes. Aphids display XX/X0 sex chromosomes and combine unusual X chromosome... | Genetic conflicts, Genome Evolution, Reproduction and Sex | Charles Baer | 2021-08-16 08:56:08 | View | ||
06 Jun 2019
Multi-model inference of non-random mating from an information theoretic approachAntonio Carvajal-Rodríguez https://doi.org/10.1101/305730Tell me who you mate with, I’ll tell you what’s going onRecommended by Sara Magalhaes and Alexandre Courtiol based on reviews by Alexandre Courtiol and 2 anonymous reviewersThe study of sexual selection goes as far as Darwin himself. Since then, elaborate theories concerning both intra- and inter-sexual sexual have been developed, and elegant experiments have been designed to test this body of theory. It may thus come as a surprise that the community is still debating on the correct way to measure simple components of sexual selection, such as the Bateman gradient (i.e., the covariance between the number of matings and the number of offspring)[1,2], or to quantify complex behaviours such as mate choice (the non-random choice of individuals with particular characters as mates)[3,4] and their consequences. References [1] Bateman, A. J. (1948). Intra-sexual selection in Drosophila. Heredity, 2(3), 349-368. doi: 10.1038/hdy.1948.21 | Multi-model inference of non-random mating from an information theoretic approach | Antonio Carvajal-Rodríguez | <p>Non-random mating has a significant impact on the evolution of organisms. Here, I developed a modelling framework for discrete traits (with any number of phenotypes) to explore different models connecting the non-random mating causes (mate comp... | Evolutionary Ecology, Evolutionary Theory, Sexual Selection | Sara Magalhaes | 2019-02-08 19:24:03 | View | ||
14 Dec 2016
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High Rates of Species Accumulation in Animals with Bioluminescent Courtship DisplaysEllis EA, Oakley TH 10.1016/j.cub.2016.05.043Bioluminescent sexually selected traits as an engine for biodiversity across animal speciesRecommended by Astrid Groot and Carole SmadjaIn evolutionary biology, sexual selection is hypothesized to increase speciation rates in animals, as theory predicts that sexual selection will contribute to phenotypic diversification and affect rates of species accumulation at macro-evolutionary time scales. However, testing this hypothesis and gathering convincing evidence have proven difficult. Although some studies have shown a strong correlation between proxies of sexual selection and species diversity (mostly in birds), this relationship relies on some assumptions on the link between these proxies and the strength of sexual selection and is not detected in some other taxa, making taxonomically widespread conclusions impossible. In a recent study published in Current Biology [1], Ellis and Oakley provide strong evidence that bioluminescent sexual displays have driven high species richness in taxonomically diverse animal lineages, providing a crucial link between sexual selection and speciation. Ellis and Oakley [1] explored the scientific literature for well-resolved evolutionary trees with branches containing bioluminescent lineages and identified lineages that use light for courtship or camouflage in a wide range of marine and terrestrial taxa including insects, crustaceans, cephalopods, segmented worms, and fishes. The researchers counted the number of species in each bioluminescent clade and found that all groups with light-courtship displays had more species and faster rates of species accumulation than their non-luminous most closely related sister lineages or ancestors. In contrast, those groups that used bioluminescence for predator avoidance had a lower than expected rate of species richness on average. Nicely encompassing a diversity of taxa and neatly controlling for the rate of species accumulation of the encompassing clade, the results of Ellis and Oakley are clear-cut and provide the most comprehensive evidence to date for the hypothesis that sexual displays can act as drivers of speciation. One question this study incites is what is happening in terms of sexual selection in species displaying defensive bioluminescence or no bioluminescence at all: do those lineages use no mating signals at all or other mating signals that are less apparent, and will those experience lower levels of sexual selection than bioluminescent mating signals, i.e. consistent with Ellis and Oakley results? It would also be interesting to investigate the diversification rates in animal species using other modalities, such as chemical, acoustic or any other type of signals used by males, females or both sexes, to determine what types of sexual signals may be more generally drivers of speciation. References [1] Ellis EA, Oakley TH. 2016. High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays. Current Biology 26:1916–1921. doi: 10.1016/j.cub.2016.05.043 [2] Davis MP, Holcroft NI, Wiley EO, Sparks JS, Smith WL. 2014. Species-specific bioluminescence facilitates speciation in the deep sea. Marine Biology 161:11391148. doi: 10.1007/s00227-014-2406-x [3] Davis MP, Sparks JS, Smith WL. 2016. Repeated and Widespread Evolution of Bioluminescence in Marine Fishes. PLoS One 11:e0155154. doi: 10.1371/journal.pone.0155154 [4] Claes JM, Nilsson D-E, Mallefet J, Straube N. 2015. The presence of lateral photophores correlates with increased speciation in deep-sea bioluminescent sharks. Royal Society Open Science 2:150219. doi: 10.1098/rsos.150219 | High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays | Ellis EA, Oakley TH | One of the great mysteries of evolutionary biology is why closely related lineages accumulate species at different rates. Theory predicts that populations undergoing strong sexual selection will more quickly differentiate because of increased pote... | Adaptation, Evolutionary Ecology, Sexual Selection, Speciation | Astrid Groot | 2016-12-14 19:01:59 | View | ||
03 Oct 2023
The evolutionary dynamics of plastic foraging and its ecological consequences: a resource-consumer modelLéo Ledru, Jimmy Garnier, Océane Guillot, Erwan Faou, Camille Noûs, Sébastien Ibanez https://doi.org/10.32942/X2QG7MEvolution and consequences of plastic foraging behavior in consumer-resource ecosystemsRecommended by François Rousset based on reviews by 2 anonymous reviewersPlastic responses of organisms to their environment may be maladaptive in particular when organisms are exposed to new environments. Phenotypic plasticity may also have opposite effects on the adaptive response of organisms to environmental changes: whether phenotypic plasticity favors or hinders such adaptation depends on a balance between the ability of the population to respond to the change non-genetically in the short term, and the weakened genetic response to environmental change. These topics have received continued attention, particularly in the context of climate change (e.g., Chevin et al. 2013, Duputié et al., 2015, Vinton et al . 2022). In their work, Ledru et al. focus on the adaptive nature of plastic behavior and on its consequences in a consumer-resource ecosystem. As they emphasize, previous works have found that plastic foraging promotes community stability, but these did not consider plasticity as an evolving trait, so Ledru et al. set out to test whether this conclusion holds when both plastic foraging and niche traits of consumers and resources evolve (though ultimately, their new conclusions may not all depend on plasticity evolving). Along the way, they first seek to clarify when such plasticity will evolve, and how it affects the evolution of the niche diversity of consumers and resources, before turning to the question of consumer persistence. The model is rather complex, as three traits are allowed to evolve, and the resource uptake expressed through plastic behavior has its own dynamics affected by some form of social learning. Classically, in models of niche evolution, a consumer's efficiency in exploiting a resource characterized by a trait y (here, the resource's individual niche trait), has been described in terms of location-scale (typically Gaussian) kernels, with mean x (the consumer's individual niche trait) specifying the most efficiently exploited resource, and with variance characterizing individual niche breadth. The evolution of the variance has been considered in some previous models but is assumed to be fixed here. Rather, the new model considers the evolution of the distribution of resource traits, of the consumer's individual niche trait (which is not plastic), and of a "plastic foraging trait" that controls the relative time spent foraging plastically versus foraging randomly. When foraging plastically, the consumers modify their foraging effort towards the type of resource that maximizes their energy intake. in some previous models, the effect of variation in the extent of plastic foraging was already considered, but the evolution of allocation to a plastic foraging strategy versus random foraging was not considered. The model is formulated through reaction-diffusion equations, and its dynamics is investigated by numerical integration. Foraging plasticity readily evolves, when resources vary widely enough, competition for resources is strong, and the cost of plasticity is weak. This means in particular that a large individual niche width of consumers selects for increased plastic foraging, as the evolution of plastic foraging leads to reduced niche overlap between consumers. The evolution of plastic foraging itself generally, though not always, favors the diversification of the niche traits of consumers and of resources. There is thus a positive feedback loop between plastic foraging and resource diversity. Ledru et al. conclude that the total niche width of the consumer population should also correlate with the evolution of plastic foraging, an implication which they relate to the so-called niche variation hypothesis and to empirical tests of it. The joint evolution of the consumer's individual niche trait and plastic foraging trait generates a striking pattern within populations: consumers whose individual niche trait is at an edge of the resource distribution forage more plastically. The authors observe that this relatively simple prediction has not been subjected to any empirical test. Returning to the question of consumer persistence, Ledru et al. evaluate this persistence when consumer mortality increases, and in response to either gradual or sudden environmental changes. These different perturbations all reduce the benefits of plastic foraging. The effect of plastic foraging on stability are complex, being negative or positive effect depending on the type of disturbance, and in particular the ecosystem has a lower sustainable rate of environmental change in the presence of plastic foraging. However, allowing the evolutionary regression of plastic foraging then has a comparatively positive effect on persistence. Despite the substantial effort devoted to analyzing this complex model, relaxing some of its assumptions would likely reveal further complexities. Notably, the overall effect of plasticity on consumer persistence depends on effects already encountered in models of the adaptive response of single species to environmental change: a fast non-genetic response in the short term versus a weakened genetic response in the longer term. The overall balance between these opposite effects on adaptation may be difficult to predict robustly. In the case of a constant rate of environmental change, the results of the present model depend on a lag load between the trait changes of consumer and resource populations, and the extent of the lag may also depend on many factors, such as the extent of genetic variation (e.g., Bürger & Lynch, 1995) for niche traits in consumers and resources. Here, the same variance of mutational effects was assumed for all three evolving traits. Further, spatial environmental variation, a central issue in studies of adaptive responses to environmental changes (e.g., Parmesan, 2006, Zhu et al., 2012), was not considered. Finally, the rate of adjustment of effort by consumers with given niche trait and plastic foraging trait values was assumed proportional to the density of consumers with such trait values. This was justified as a way of accounting for the use of social cues during foraging, but to the extent that they occur, social effects could manifest themselves through other learning dynamics. In conclusion, Ledru et al. have addressed a broad range of questions, suggesting new empirical tests of behavioural patterns on one side, and recovering in the context of community response to environmental changes a complexity that could be expected from earlier works on adaptive responses of organisms but that has been overlooked by previous works on community effects of phenotypic plasticity. References Bürger, R. and Lynch, M. (1995), Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution, 49: 151-163. https://doi.org/10.1111/j.1558-5646.1995.tb05967.x Chevin, L.-M., Collins, S. and Lefèvre, F. (2013), Phenotypic plasticity and evolutionary demographic responses to climate change: taking theory out to the field. Funct Ecol, 27: 967-979. https://doi.org/10.1111/j.1365-2435.2012.02043.x Duputié, A., Rutschmann, A., Ronce, O. and Chuine, I. (2015), Phenological plasticity will not help all species adapt to climate change. Glob Change Biol, 21: 3062-3073. https://doi-org.inee.bib.cnrs.fr/10.1111/gcb.12914 Ledru, L., Garnier, J., Guillot, O., Faou, E., & Ibanez, S. (2023). The evolutionary dynamics of plastic foraging and its ecological consequences: a resource-consumer model. EcoEvoRxiv, ver. 4 peer-reviewed and recommended by Peer Community In Evolutionary Biology. https://doi.org/10.32942/X2QG7M Parmesan, C. (2006) Ecological and evolutionary responses to recent climate change Vinton, A.C., Gascoigne, S.J.L., Sepil, I., Salguero-Gómez, R., (2022) Plasticity’s role in adaptive evolution depends on environmental change components. Trends in Ecology & Evolution, 37: 1067-1078. Zhu, K., Woodall, C.W. and Clark, J.S. (2012), Failure to migrate: lack of tree range expansion in response to climate change. Glob Change Biol, 18: 1042-1052. https://doi.org/10.1111/j.1365-2486.2011.02571.x | The evolutionary dynamics of plastic foraging and its ecological consequences: a resource-consumer model | Léo Ledru, Jimmy Garnier, Océane Guillot, Erwan Faou, Camille Noûs, Sébastien Ibanez | <p style="text-align: justify;">Phenotypic plasticity has important ecological and evolutionary consequences. In particular, behavioural phenotypic plasticity such as plastic foraging (PF) by consumers, may enhance community stability. Yet little ... | Bioinformatics & Computational Biology, Evolutionary Dynamics, Evolutionary Ecology, Phenotypic Plasticity | François Rousset | 2023-03-25 12:04:08 | View | ||
16 Jun 2022
Sensory plasticity in a socially plastic beeRebecca A Boulton, Jeremy Field https://doi.org/10.1101/2022.01.29.478030Taking advantage of facultative sociality in sweat bees to study the developmental plasticity of antennal sense organs and its association with social phenotypeRecommended by Nadia Aubin-Horth based on reviews by Michael D Greenfield, Sylvia Anton and Lluís Socias-MartínezThe study of the evolution of sociality is closely associated with the study of the evolution of sensory systems. Indeed, group life and sociality necessitate that individuals recognize each other and detect outsiders, as seen in eusocial insects such as Hymenoptera. While we know that antennal sense organs that are involved in olfactory perception are found in greater densities in social species of that group compared to solitary hymenopterans, whether this among-species correlation represents the consequence of social evolution leading to sensory evolution, or the opposite, is still questioned. Knowing more about how sociality and sensory abilities covary within a species would help us understand the evolutionary sequence. Studying a species that shows social plasticity, that is facultatively social, would further allow disentangling the cause and consequence of social evolution and sensory systems and the implication of plasticity in the process. Boulton and Field (2022) studied a species of sweat bee that shows social plasticity, Halictus rubicundus. They studied populations at different latitudes in Great Britain: populations in the North are solitary, while populations in the south often show sociality, as they face a longer and warmer growing season, leading to the opportunity for two generations in a single year, a pre-condition for the presence of workers provisioning for the (second) brood. Using scanning electron microscope imaging, the authors compared the density of antennal sensilla types in these different populations (north, mid-latitude, south) to test for an association between sociality and olfactory perception capacities. They counted three distinct types of antennal sensilla: olfactory plates, olfactory hairs, and thermos/hygro-receptive pores, used to detect humidity, temperature and CO2. In addition, they took advantage of facultative sociality in this species by transplanting individuals from a northern population (solitary) to a southern location (where conditions favour sociality), to study how social plasticity is reflected (or not) in the density of antennal sensilla types. They tested the prediction that olfactory sensilla density is also developmentally plastic in this species. Their results show that antennal sensilla counts differ between the 3 studied regions (north, mid-latitude, south), but not as predicted. Individuals in the southern population were not significantly different from the mid-latitude and northern ones in their count of olfactory plates and they had less, not more, thermos/hygro receptors than mid-latitude and northern individuals. Furthermore, mid-latitude individuals had more olfactory hairs than the ones from the northern population and did not differ from southern ones. The prediction was that the individuals expressing sociality would have the highest count of these olfactory hairs. This unpredicted pattern based on the latitude of sampling sites may be due to the effect of temperature during development, which was higher in the mid-latitude site than in the southern one. It could also be the result of a genotype-by-environment interaction, where the mid-latitude population has a different developmental response to temperature compared to the other populations, a difference that is genetically determined (a different “reaction norm”). Reciprocal transplant experiments coupled with temperature measurements directly on site would provide interesting information to help further dissect this intriguing pattern. Interestingly, where a sweat bee developed had a significant effect on their antennal sensilla counts: individuals originating from the North that developed in the south after transplantation had significantly more olfactory hairs on their antenna than individuals from the same Northern population that developed in the North. This is in accordance with the prediction that the characteristics of sensory organs can also be plastic. However, there was no difference in antennal characteristics depending on whether these transplanted bees became solitary or expressed the social phenotype (foundress or worker). This result further supports the hypothesis that temperature affects development in this species and that these sensory characteristics are also plastic, although independently of sociality. Overall, the work of Boulton and Field underscores the importance of including phenotypic plasticity in the study of the evolution of social behaviour and provides a robust and fruitful model system to explore this further. References Boulton RA, Field J (2022) Sensory plasticity in a socially plastic bee. bioRxiv, 2022.01.29.478030, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.01.29.478030 | Sensory plasticity in a socially plastic bee | Rebecca A Boulton, Jeremy Field | <p style="text-align: justify;">The social Hymenoptera have contributed much to our understanding of the evolution of sensory systems. Attention has focussed chiefly on how sociality and sensory systems have evolved together. In the Hymenoptera, t... | Behavior & Social Evolution, Evolutionary Ecology, Phenotypic Plasticity | Nadia Aubin-Horth | 2022-02-02 11:34:49 | 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 | ||
13 Dec 2016
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Prezygotic isolation, mating preferences, and the evolution of chromosomal inversionsDagilis AJ, Kirkpatrick M 10.1111/evo.12954The spread of chromosomal inversions as a mechanism for reinforcementRecommended by Denis Roze and Thomas BroquetSeveral examples of chromosomal inversions carrying genes affecting mate choice have been reported from various organisms. Furthermore, inversions are also frequently involved in genetic isolation between populations or species. Past work has shown that inversions can spread when they capture not only some loci involved in mate choice but also loci involved in incompatibilities between hybridizing populations [1]. In this new paper [2], the authors derive analytical approximations for the selection coefficient associated with an inversion suppressing recombination between a locus involved in mate choice and one (or several) locus involved in Dobzhansky-Muller incompatibilities. Two mechanisms for mate choice are considered: assortative mating based on the allele present at a single locus, or a trait-preference model where one locus codes for the trait and another for the preference. The results show that such an inversion is generally favoured, the selective advantage associated with the inversion being strongest when hybridization is sufficiently frequent. Assuming pairwise epistatic interactions between loci involved in incompatibilities, selection for the inversion increases approximately linearly with the number of such loci captured by the inversion. This paper is a good read for several reasons. First, it presents the problem clearly (e.g. the introduction provides a clear and concise presentation of the issue and past work) and its crystal-clear writing facilitates the reader's understanding of theoretical approaches and results. Second, the analysis is competently done and adds to previous work by showing that very general conditions are expected to be favourable to the spread of the type of inversion considered here. And third, it provides food for thought about the role of inversions in the origin or the reinforcement of divergence between nascent species. One result of this work is that an inversion linked to pre-zygotic isolation "is favoured so long as there is viability selection against recombinant genotypes", suggesting that genetic incompatibilities must have evolved first and that inversions capturing mating preference loci may then enhance pre-existing reproductive isolation. However, the results also show that inversions are more likely to be favoured in hybridizing populations among which gene flow is still high, rather than in more strongly isolated populations. This matches the observation that inversions are more frequently observed between sympatric species than between allopatric ones. References [1] Trickett AJ, Butlin RK. 1994. Recombination Suppressors and the Evolution of New Species. Heredity 73:339-345. doi: 10.1038/hdy.1994.180 [2] Dagilis AJ, Kirkpatrick M. 2016. Prezygotic isolation, mating preferences, and the evolution of chromosomal inversions. Evolution 70: 1465–1472. doi: 10.1111/evo.12954 | Prezygotic isolation, mating preferences, and the evolution of chromosomal inversions | Dagilis AJ, Kirkpatrick M | Chromosomal inversions are frequently implicated in isolating species. Models have shown how inversions can evolve in the context of postmating isolation. Inversions are also frequently associated with mating preferences, a topic that has not been... | Adaptation, Evolutionary Theory, Genome Evolution, Hybridization / Introgression, Population Genetics / Genomics, Speciation | Denis Roze | 2016-12-13 22:11:54 | View | ||
17 Nov 2017
ABC random forests for Bayesian parameter inferenceLouis Raynal, Jean-Michel Marin, Pierre Pudlo, Mathieu Ribatet, Christian P. Robert, Arnaud Estoup https://arxiv.org/abs/1605.05537Machine learning methods are useful for Approximate Bayesian Computation in evolution and ecologyRecommended by Michael Blum based on reviews by Dennis Prangle and Michael BlumIt is my pleasure to recommend the paper by Raynal et al. [1] about using random forest for parameter inference. There are two reviews about the paper, one review written by Dennis Prangle and another review written by myself. Both reviews were positive and included comments that have been addressed in the current version of the preprint. The paper nicely shows that modern machine learning approaches are useful for Approximate Bayesian Computation (ABC) and more generally for simulation-driven parameter inference in ecology and evolution. The authors propose to consider the random forest approach, proposed by Meinshausen [2] to perform quantile regression. The numerical implementation of ABC with random forest, available in the abcrf package, is based on the RANGER R package that provides a fast implementation of random forest for high-dimensional data. According to my reading of the manuscript, there are 3 main advantages when using random forest (RF) for parameter inference with ABC. The first advantage is that RF can handle many summary statistics and that dimension reduction is not needed when using RF. The second advantage is very nicely displayed in Figure 5, which shows the main result of the paper. If correct, 95% posterior credibility intervals (C.I.) should contain 95% of the parameter values used in simulations. Figure 5 shows that posterior C.I. obtained with rejection are too large compared to other methods. By contrast, C.I. obtained with regression methods have been shrunken. However, the shrinkage can be excessive for the smallest tolerance rates, with coverage values that can be equal to 85% instead of the expected 95% value. The attractive property of RF is that C.I. have been shrunken but the coverage is of 100% resulting in a conservative decision about parameter values. The last advantage is that no hyperparameter should be chosen. It is a parameter free approach, which is desirable because of the potential difficulty of choosing an appropriate acceptance rate. The main drawback of the proposed approach concerns joint parameter inference. There are many settings where the joint parameter distribution is of interest and the proposed RF approach cannot handle that. In population genetics for example, estimation of the severity and of the duration of the bottleneck should be estimated jointly because of identifiability issues. The challenge of performing joint parameter inference with RF might constitute a useful research perspective. References [1] Raynal L, Marin J-M, Pudlo P, Ribatet M, Robert CP, Estoup A. 2017. ABC random forests for Bayesian parameter inference. arXiv 1605.05537v4, https://arxiv.org/pdf/1605.05537 | ABC random forests for Bayesian parameter inference | Louis Raynal, Jean-Michel Marin, Pierre Pudlo, Mathieu Ribatet, Christian P. Robert, Arnaud Estoup | This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http:// dx.doi.org/ 10.24072/ pci.evolbiol.100036). Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian infer... | Bioinformatics & Computational Biology, Evolutionary Applications, Other, Population Genetics / Genomics | Michael Blum | 2017-07-06 07:42:00 | View |
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