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26 Sep 2024
The impact of social complexity on the efficacy of natural selection in termitesCamille Roux, Alice Ha, Arthur Weyna, Morgan Lode, Jonathan Romiguier https://doi.org/10.1101/2024.04.26.591327Evolutionary trajectories of social transitions: Higher social complexity is associated with lower effective population size and reduced efficacy of selection in termitesRecommended by Trine Bilde based on reviews by 2 anonymous reviewersA comprehensive study by Roux et al 2024 investigates the impact of eusociality on the efficacy of natural selection in termites, with and additional focus on whether higher levels of social complexity are associated with lower effective population size (Ne) and relaxed purifying selection. Eusociality is characterized by a division of reproductive labor, cooperative care of offspring, and overlapping generations, and has evolved independently across various animal taxa with the most complex social systems found in Hymenoptera (bees, wasps, ants) and termites. Because reproduction is limited to a few individuals, this leads to a reduced effective population size (Ne), which impacts genome evolution. Smaller Ne increases the influence of genetic drift, weakening the efficiency of natural selection and allowing the accumulation of weakly deleterious mutations. This phenomenon, known as the "drift barrier," alters the mutation-selection balance in eusocial organisms. Studies in a range of social arthropods including ants, termites, crustaceans and spiders have shown an elevated ratio of nonsynonymous to synonymous substitutions (dN/dS), indicating relaxed purifying selection due to small Ne. In termite species with complex social structures, such as those with large colonies and high caste specialization, there are reports of higher dN/dS ratios compared to simpler social species. This suggests that higher social complexity, reflected in traits like nesting strategies and developmental pathways, further reduces Ne and the effectiveness of natural selection. The authors address these hypotheses by exploring the genomic impact of eusociality in termites (Isoptera) taking two approaches: First, they analyze transcriptome data from 66 Blattodea species and calculate the ratio of non-synonymous to synonymous mutations (dN/dS) as an indicator of natural selection efficiency and effective population size. They analyses reveal an increased dN/dS ratio in termites compared to other Blattodea species, reinforcing the notion that convergent evolution toward eusociality significantly reduces effective population size and weakens natural selection efficiency across the genome. Additionally, a comparison of 68 termite transcriptomes shows that this effect is more pronounced in species with higher social complexity. This is exciting as it advances our understanding of how increasing complexity in social organization decreases Ne and the efficiency of natural selection. The study substantiates the notion that social transitions follow evolutionary trajectories where lower and Ne and increasing drift have negative consequences for genome evolution (Ma et al 2024). References Camille Roux, Alice Ha, Arthur Weyna, Morgan Lode, Jonathan Romiguier (2024) The impact of social complexity on the efficacy of natural selection in termites. bioRxiv, ver.2 peer-reviewed and recommended by PCI Evol Biol. https://doi.org/10.1101/2024.04.26.591327 Jilong Ma, Jesper Bechsgaard, Anne Aagaard, Palle Villesen, Trine Bilde, Mikkel Heide Schierup (2024) Sociality in spiders is an evolutionary dead-end. | The impact of social complexity on the efficacy of natural selection in termites | Camille Roux, Alice Ha, Arthur Weyna, Morgan Lode, Jonathan Romiguier | <p style="text-align: justify;">In eusocial species, reproduction is monopolized by a few reproductive individuals. From the perspective of population genetics, this implies that the effective population size (Ne<em>)</em> of these organisms is li... | Molecular Evolution | Trine Bilde | 2024-04-30 12:10:20 | View | ||
26 Aug 2024
Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid Ludwigia grandiflora subsp. hexapetala in western EuropeSolenn Stoeckel, Ronan Becheler, Luis Portillo-Lemus, Marilyne Harang, Anne-Laure Besnard, Gilles Lassalle, Romain Causse-Védrines, Sophie Michon-Coudouel, Daniel J. Park, Bernard J. Pope, Eric J. Petit, Dominique Barloy https://doi.org/10.1101/2024.03.21.586104Mixed reproduction modes explain a high genetic diversity in the invasive plant Ludwigia grandiflora subsp. hexapetala in western EuropeRecommended by Ines Alvarez based on reviews by Rubén Torices and 2 anonymous reviewersThe introduction of Ludwigia species as ornamental plants in both North America and Europe dates back almost two centuries, during which time they expanded as naturalized and later invasive species in these territories (Dandelot et al. 2005, Okada et al. 2009). Repeated deliberate or non-deliberate introductions over time of this species complex that can hybridize has given rise to an evolutionarily complex scenario, which is compounded by the difficulty in delimiting some of these species and by the diversity of their modes of reproduction. Dandelot (2004) and Dandelot et al. (2005) determined the presence of two Ludwigia taxa in France, L. peploides subsp. montevidensis (Spreng.) P.H.Raven (here after Lpm), and L. grandiflora subsp. hexapetala (Hook. & Arn.) G.L.Nesom & Kartesz (here after Lgh), based on their cytotypes (2n = 16, and 2n = 80, respectively) and without evidence of hybridization between them. Furthermore, despite a predominantly vegetative reproduction observed for both species, they differed in their breeding systems. While Lpm is self-compatible and produce a high number of viable seeds in all populations, Lgh is self-incompatible and its populations may drastically differ in seed viability (Dandelot 2004). Several years later, Portillo-Lemus et al. (2021) determined that the differences in seed production between some populations of Lgh are due to the existence of a heteromorphic reproductive system in this taxon, involving a self-incompatible morph (long-style morph; hereafter L-morph), and a self-compatible morph (short-style morph: hereafter S-morph). Moreover, Portillo-Lemus et al. (2022) observed that self-pollen in the L-morph flowers stop growing lately (i.e., in the ovarian area) without fertilizing the ovules, concluding that a late-acting self-incompatible system (hereafter, LSI) is present in this morph. At this point, it is relevant to understand the possible interactions between populations of different morphs in Lgh, and the implications that they may have on their expansive success in non-native areas in order to develop more effective management plans. To achieve this goal, Stoeckel et al. (2024) analyzed the population genetics in 53 Lgh populations in western Europe (without finding any Lpm population in the sampling area), 40 of which exclusively presented the L-morph and 13 the S-morph. This fact offered the opportunity to compare and interpret the differences between populations of different morphs in Lgh. Other previous works on genetic diversity of Lgh in peripatric or non-native areas pointed to a high clonality and an extremely low genetic diversity (Okada et al. 2009, Armitage et al. 2013), concluding in a monoclonal or few ancestral original clones for these invasive populations. However, the investigations of Stoeckel et al. (2024) found a high genetic diversity in all populations of Lgh studied despite their predominant clonal reproduction. Interestingly, they found that sexual reproduction is also present, not only in the S-morph by selfing, but also in the L-morph, although limited and preferably by allogamy. They discuss the advantages and drawbacks of the different modes of reproduction observed in Lgh populations, the interactions among them, and the implications that both, the scarcely documented LSI (Gibbs 2014) and selfing, have in the reproductive success and in the maintenance of the high genetic diversity observed in Lgh in western Europe. The contrasting results with the previous ones (Okada et al. 2009, Armitage et al. 2013) stress the relevance of using appropriate markers and analyses to assess the genetic diversity in autoployploid species, as well as the necessity of knowing the modes of reproduction in the populations studied for an optimal interpretation of the genetic metrics. The approach of the study by Stoeckel et al. (2024) had the challenge of having found suitable markers to deal with a taxon of complex origin such as Lgh, whose genome is compound by a set of autotetraploid chromosomes shared with Lpm and traces of ancient hybridizations of other diploid lineages (Barloy et al. 2024). Using RAD-Seq, Stoeckel et al. (2024) generated an original set of 36 polymorphic SNPs shared between Lgh and Lpm ensuring that these SNPs belong to the tetraploid part of the Lgh genome derived from Lpm. Another interesting contribution of this work is the exhaustive analysis of several genetic descriptors (indexes) and the interpretative guide they provide for each of them in relation to the different modes of reproduction of the study system. Finally, they propose a pair of very useful synthetic indices (i.e., clonality index and selfing index), since they allow to classify populations according to their levels of clonality and selfing. Stoeckel et al. (2024) conclude the relevance that selfing and LSI populations, and the hybridization between them may have on the expansion and success of invasive plant species, and the necessity to know the modes of reproduction of these populations jointly with their genetic diversity in order to develop appropriate management plans. This study raises new questions such as the modes of reproduction and genetic diversity and structure have other Lgh populations, both invasive and native, and the dynamics of these populations under different future scenarios. References Armitage, J. D., Könyves, K., Bailey, J. P., David, J. C., & Culham, A. (2013). A molecular, morphological and cytological investigation of the identity of non-native Ludwigia (Onagraceae) populations in Britain. New Journal of Botany, 3(2), 88–95. https://doi.org/10.1179/2042349713Y.0000000023 Barloy, D., Lemus, L. P.-, Krueger-Hadfield, S. A., Huteau, V., & Coriton, O. (2024). Genomic relationships among diploid and polyploid species of the genus Ludwigia L. section Jussiaea using a combination of cytogenetic, morphological, and crossing investigations. ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.01.02.522458 Dandelot, S. (2004). Les Ludwigia spp. invasives du Sud de la France: Historique, Biosystématique, Biologie et Ecologie [PhD thesis, Aix-Marseille 3]. https://www.theses.fr/2004AIX30052 Dandelot, S., Verlaque, R., Dutartre, A., & Cazaubon, A. (2005). Ecological, dynamic and taxonomic problems due to Ludwigia (Onagraceae) in France. Hydrobiologia, 551(1), 131–136. https://doi.org/10.1007/s10750-005-4455-0 Gibbs, P. E. (2014). Late-acting self-incompatibility – the pariah breeding system in flowering plants. New Phytologist, 203(3), 717–734. https://doi.org/10.1111/nph.12874 Okada, M., Grewell, B. J., & Jasieniuk, M. (2009). Clonal spread of invasive Ludwigia hexapetala and L. grandiflora in freshwater wetlands of California. Aquatic Botany, 91(3), 123–129. https://doi.org/10.1016/j.aquabot.2009.03.006 Portillo Lemus, L. O., Bozec, M., Harang, M., Coudreuse, J., Haury, J., Stoeckel, S., & Barloy, D. (2021). Self-incompatibility limits sexual reproduction rather than environmental conditions in an invasive water primrose. Plant-Environment Interactions, 2(2), 74–86. https://doi.org/10.1002/pei3.10042 Portillo Lemus, L. O., Harang, M., Bozec, M., Haury, J., Stoeckel, S., & Barloy, D. (2022). Late-acting self-incompatible system, preferential allogamy and delayed selfing in the heteromorphic invasive populations of Ludwigia grandiflora subsp. hexapetala. Peer Community Journal, 2. https://doi.org/10.24072/pcjournal.108 Stoeckel, S., Becheler, R., Portillo-Lemus, L., Harang, M., Besnard, A.-L., Lassalle, G., Causse-Védrines, R., Michon-Coudouel, S., Park D. J., Pope, B. J., Petit, E. J. & Barloy, D. (2024) Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid Ludwigia grandiflora subsp. hexapetala in western Europe. biorxiv, ver.4 peer-reviewed and recommended by PCI Evol Biol https://doi.org/10.1101/2024.03.21.586104 | Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid *Ludwigia grandiflora* subsp. hexapetala in western Europe | Solenn Stoeckel, Ronan Becheler, Luis Portillo-Lemus, Marilyne Harang, Anne-Laure Besnard, Gilles Lassalle, Romain Causse-Védrines, Sophie Michon-Coudouel, Daniel J. Park, Bernard J. Pope, Eric J. Petit, Dominique Barloy | <p>Reproductive mode, i.e., the proportion of individuals produced by clonality, selfing and outcrossing in populations, determines how hereditary material is transmitted through generations. It shapes genetic diversity and its structure over time... | Evolutionary Applications, Evolutionary Ecology, Population Genetics / Genomics, Reproduction and Sex | Ines Alvarez | 2024-03-25 10:33:17 | View | ||
24 May 2024
mtDNA "Nomenclutter" and its Consequences on the Interpretation of Genetic DataVladimir Bajić, Vanessa Hava Schulmann, Katja Nowick https://doi.org/10.1101/2023.11.19.567721Resolving the clutter of naming “Eve’s” descendantsRecommended by Torsten Günther based on reviews by Nicole Huber, Joshua Daniel Rubin and 1 anonymous reviewerNature is complicated and humans often resort to categorization into simplified groups in order to comprehend and manage complex systems. The human mitochondrial genome and its phylogeny are quite complex. Many of those ~16600 base pairs mutated as humans spread across the planet and the resulting phylogeny can be used to illustrate many different aspects of human history and evolution. But it has too many branches and sub-branches to comprehend, which is why major lineages are considered haplogroups. On the highest level, these haplogroups receive capital letters which are then followed by integers and lowercase letters to designate a more fine-scale structure. This nomenclature even inspired semi-fictional literature, such as Bryan Sykes’ “The Seven Daughters of Eve” [1] from 2001 which includes fictional narratives for each of seven “clan mothers” representing seven major European haplogroups (e.g. Helene representing haplogroup H and Tara representing haplogroup T). But apart from categorizing things, humans also like to make exceptions to rules. For instance, not all haplogroup names consist only of letters and numbers but also special characters. And not everything seems logical or intuitive: the deepest split does not include haplogroup A but the most basal lineage is L0. The main letters also do not represent the same level of the tree structure, Sykes’ Katrine representing haplogroup K should not be considered a “daughter of Eve” but (at best) a granddaughter as K is a sub-haplogroup of U (represented by Ursula). This system and the number of haplogroups have not just reached a point where everything has become incredibly complicated despite supposedly simplifying categories. The inherent arbitrariness can also have serious effects on downstream analysis and the interpretation of results depending on how and on what level the authors of a specific study decide to group their individuals. This situation of potential biases introduced through the choice of haplogroup groupings is the motivation for the study by Bajić, Schulmann and Nowick who are using the quite fitting term “nomenclutter” in their title [2]. They are raising an important issue in the inconsistencies introduced by the practice of somewhat arbitrary haplotype groupings which varies across studies and has no common standards in place making comparisons between studies virtually impossible. The study shows that the outcome of certain standard analyses and the interpretation of results are very sensitive to the decision on how to group the different haplotypes. This effect is especially pronounced for populations of African ancestry where the haplotype nomenclature would cut the phylogenetic tree at higher levels and the definition of different lineages is generally more coarse than for other populations. But the authors go beyond pointing out this issue, they also suggest solutions. Instead of grouping sequences by their haplogroup code, one could use “algorithm-based groupings” based on the sequence similarity itself or cutting the phylogenetic tree at a common level of the hierarchy. The analysis of the authors shows that this reduces potential biases substantially. But even such groupings would not be without the influence of the user or researcher’s choices as different parameters have to be set to define the level at which groupings are conducted. The authors propose a neat solution, lifting this issue to be resolved during future updates of the mitochondrial haplogroup nomenclature and the phylogeny. Ideally, the research community could agree on centrally defined haplogroup grouping levels (called “macro-”, “meso-”, and “micro-haplogroups” by the authors) which would all represent different scales of events in human history (from global, continental to local). Classifications like that could be provided through central databases and the classifications could be added to commonly used tools for that purpose. If everyone used these groupings, studies would be a lot more comparable and more fine-scale investigations could still resort to the sequences and the tree itself to avoid all grouping. The experts who reviewed the study have all highlighted its importance of pointing at a very relevant issue. It will take a community effort to improve practices and the current status of this research area. This study provides an important first step and it should be in everyone’s interest to resolve the “nomenclutter”. References 1. Sykes B. (2001) The seven daughters of Eve: the science that reveals our genetic ancestry. 1st American ed. New York: Norton. 2. Bajić V, Schulmann VH, Nowick K. (2024) mtDNA “Nomenclutter” and its Consequences on the Interpretation of Genetic Data. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.11.19.567721 | mtDNA "Nomenclutter" and its Consequences on the Interpretation of Genetic Data | Vladimir Bajić, Vanessa Hava Schulmann, Katja Nowick | <p style="text-align: justify;">Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into h... | Bioinformatics & Computational Biology, Human Evolution, Other, Phylogenetics / Phylogenomics, Phylogeography & Biogeography, Population Genetics / Genomics | Torsten Günther | 2023-11-20 11:16:36 | View | ||
25 Jun 2024
Taking fear back into the Marginal Value Theorem: the risk-MVT and optimal boldnessVincent Calcagno, Frederic Grognard, Frederic M Hamelin, Ludovic Mailleret https://doi.org/10.1101/2023.10.31.564970Applying the marginal value theorem when risk affects foraging behaviorRecommended by Stephen Proulx based on reviews by Taom Sakal and 1 anonymous reviewerForaging has been long been studied from an economic perspective, where the costs and benefits of foraging decisions are measured in terms of a single currency of energy which is then taken as a proxy for fitness. A mainstay foraging theory is Charnov’s Marginal Value Theorem (Charnov, 1976), or MVT, which includes a graphical interpretation and has been applied to an enormous range topics in behavioral ecology (Menezes , 2022). Empirical studies often find that animals deviate from MVT, sometimes in that they predictably stay longer than the optimal time. One explanation for this comes from state based models of behavior (Nonacs 2001) Now Calcgano and colleagues (2024) set out to extend and unify foraging models that include various aspects of risk to the foragers, and propose using a risk MVT, or rMVT. They consider three types of risk that foragers face, disturbance, escape, and death. Disturbance represents scenarios where the forager is either physically interrupted in their foraging, or stops foraging temporarily because of the presence of a predator (i.e. a fear response). Such a disturbance can be thought of as altering the gain function for resources acquired while foraging in the patch, allowing the rMVT to be applied in a familiar way with only a reinterpretation of the gain function. In the escape scenarios, foragers are forced to leave a patch because of predator behavior, and therefore artificially decrease their foraging time as compared with their desired foraging time. Now, optimization can be calculated based on this expected time foraging, which means that in effect the forager compensates for the reduced time in the patch by modifying their view of how long they will actually forage. Finally they consider scenarios where risk may result in death, and further divide this into two cases, one where foraging returns are instantaneously converted to fitness, and another where they are only converted in between foraging bouts. This represents an important case to consider, because the total number of foraging trips now depends on the rate of predator attack. In these scenarios, the boldness of the forager is decreased and they become more risk-averse. The authors find that under the disturbance and escape scenarios, patch residence time can actually go up with risk. This is in effect because they are depleting the patch less per unit time, because a larger fraction of time is taken up with avoiding predators. In terms of field applications, this may differ from what is typically considered as risk, since harassment by conspecifics has the same disturbance effect as predator avoidance behaviors. Most experiments on foraging are done in the absence of risk or signals of risk, i.e. in laboratory or otherwise controlled environments. The rMVT predictions deviate from non-risk scenarios in complex ways, in that the patch residence time may increase or decrease under risk. It is also important to note that foragers have evolved their foraging strategies in response to the risk profiles that they have historically experienced, and therefore experiments lacking risk may still show that foragers alter their behavior from the MVT predictions in a way that reflects historical levels of risk. References Calcagno, V., Grognard, F., Hamelin, F.M. and Mailleret, L. (2024). Taking fear back into the Marginal Value Theorem: the risk-MVT and optimal boldness. bioRxiv, 2023.10.31.564970, ver. 3 peer-reviewed and recommended by PCI Evolutionary Biology. https://doi.org/10.1101/2023.10.31.564970 Charnov E. (1976). Optimal foraging the marginal value theorem. Theor Popul Biol. 9, 129–136. Menezes, JFS (2022).The marginal value theorem as a special case of the ideal free distribution. Ecological Modelling 468:109933. https://doi.org/10.1016/j.ecolmodel.2022.109933 Nonacs, P. 2001. State dependent behavior and the Marginal Value Theorem. Behavioral Ecology 12(1) 71–83. https://doi.org/10.1093/oxfordjournals.beheco.a000381 | Taking fear back into the Marginal Value Theorem: the risk-MVT and optimal boldness | Vincent Calcagno, Frederic Grognard, Frederic M Hamelin, Ludovic Mailleret | <p>Foragers exploiting heterogeneous habitats must make strategic movement decisions in order to maximize fitness. Foraging theory has produced very general formalizations of the optimal patch-leaving decisions rational individuals should make. On... | Adaptation, Behavior & Social Evolution, Evolutionary Ecology, Evolutionary Theory, Life History | Stephen Proulx | 2023-11-03 13:25:16 | 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 | ||
01 Mar 2024
Rapid life-history evolution reinforces competitive asymmetry between invasive and resident speciesElodie Chapuis, Philippe Jarne, Patrice David https://doi.org/10.1101/2023.10.25.563987The evolution of a hobo snailRecommended by Ben Phillips based on reviews by David Reznick and 2 anonymous reviewersAt the very end of a paper entitled "Copepodology for the ornithologist" Hutchinson (1951) pointed out the possibility of 'fugitive species'. A fugitive species, said Hutchinson, is one that we would typically think of as competitively inferior. Wherever it happens to live it will eventually be overwhelmed by competition from another species. We would expect it to rapidly go extinct but for one reason: it happens to be a much better coloniser than the other species. Now all we need to explain its persistence is a dose of space and a little disturbance: a world in which there are occasional disturbances that cause local extinction of the dominant species. Now, argued Hutchinson, we have a recipe for persistence, albeit of a harried kind. As Hutchinson put it, fugitive species "are forever on the move, always becoming extinct in one locality as they succumb to competition, and always surviving as they reestablish themselves in some other locality." It is a fascinating idea, not just because it points to an interesting strategy, but also because it enriches our idea of competition: competition for space can be just as important as competition for time. Hutchinson's idea was independently discovered with the advent of metapopulation theory (Levins 1971; Slatkin 1974) and since then, of course, ecologists have gone looking, and they have unearthed many examples of species that could be said to have a fugitive lifestyle. These fugitive species are out there, but we don't often get to see them evolve. In their recent paper, Chapuis et al. (2024) make a convincing case that they have seen the evolution of a fugitive species. They catalog the arrival of an invasive freshwater snail on Guadeloupe in the Lesser Antilles, and they wonder what impact this snail's arrival might have on a native freshwater snail. This is a snail invasion, so it has been proceeding at a majestic pace, allowing the researchers to compare populations of the native snail that are completely naive to the invader with those that have been exposed to the invader for either a relatively short period (<20 generations) or longer periods (>20 generations). They undertook an extensive set of competition assays on these snails to find out which species were competitively superior and how the native species' competitive ability has evolved over time. Against naive populations of the native, the invasive snail turns out to be unequivocally the stronger competitor. (This makes sense; it probably wouldn't have been able to invade if it wasn't.) So what about populations of the native snail that have been exposed for longer, that have had time to adapt? Surprisingly these populations appear to have evolved to become even weaker competitors than they already were. So why is it that the native species has not simply been driven extinct? Drawing on their previous work on this system, the authors can explain this situation. The native species appears to be the better coloniser of new habitats. Thus, it appears that the arrival of the invasive species has pushed the native species into a different place along the competition-colonisation axis. It has sacrificed competitive ability in favour of becoming a better coloniser; it has become a fugitive species in its own backyard. This is a really nice empirical study. It is a large lab study, but one that makes careful sampling around a dynamic field situation. Thus, it is a lab study that informs an earlier body of fieldwork and so reveals a fascinating story about what is happening in the field. We are left not only with a particularly compelling example of character displacement towards a colonising phenotype but also with something a little less scientific: the image of a hobo snail, forever on the run, surviving in the spaces in between. References Chapuis E, Jarne P, David P (2024) Rapid life-history evolution reinforces competitive asymmetry between invasive and resident species. bioRxiv, 2023.10.25.563987, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.10.25.563987 Hutchinson, G.E. (1951) Copepodology for the Ornithologist. Ecology 32: 571–77. https://doi.org/10.2307/1931746 Levins, R., and D. Culver. (1971) Regional Coexistence of Species and Competition between Rare Species. Proceedings of the National Academy of Sciences 68, no. 6: 1246–48. https://doi.org/10.1073/pnas.68.6.1246. Slatkin, Montgomery. (1974) Competition and Regional Coexistence. Ecology 55, no. 1: 128–34. https://doi.org/10.2307/1934625. | Rapid life-history evolution reinforces competitive asymmetry between invasive and resident species | Elodie Chapuis, Philippe Jarne, Patrice David | <p style="text-align: justify;">Biological invasions by phylogenetically and ecologically similar competitors pose an evolutionary challenge to native species. Cases of character displacement following invasions suggest that they can respond to th... | Evolutionary Ecology, Life History, Species interactions | Ben Phillips | 2023-10-26 15:49:33 | View | ||
14 Feb 2024
Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structureJun Ishigohoka, Karen Bascón-Cardozo, Andrea Bours, Janina Fuß, Arang Rhie, Jacquelyn Mountcastle, Bettina Haase, William Chow, Joanna Collins, Kerstin Howe, Marcela Uliano-Silva, Olivier Fedrigo, Erich D. Jarvis, Javier Pérez-Tris, Juan Carlos Illera, Miriam Liedvogel https://doi.org/10.1101/2021.12.22.473882Discerning the causes of local deviations in genetic variation: the effect of low-recombination regionsRecommended by Matteo Fumagalli based on reviews by Claire Merot and 1 anonymous reviewerIn this study, Ishigohoka and colleagues tackle an important, yet often overlooked, question on the causes of genetic variation. While genome-wide patterns represent population structure, local variation is often associated with selection. Authors propose that an alternative cause for variation in individual loci is reduced recombination rate. To test this hypothesis, authors perform local Principal Component Analysis (PCA) (Li & Ralph, 2019) to identify local deviations in population structure in the Eurasian blackcap (Sylvia atricapilla) (Ishigohoka et al. 2022). This approach is typically used to detect chromosomal rearrangements or any long region of linked loci (e.g., due to reduced recombination or selection) (Mérot et al. 2021). While other studies investigated the effect of low recombination on genetic variation (Booker et al. 2020), here authors provide a comprehensive analysis of the effect of recombination to local PCA patterns both in empirical and simulated data sets. Findings demonstrate that low recombination (and not selection) can be the sole explanatory variable for outlier windows. The study also describes patterns of genetic variation along the genome of Eurasian blackcaps, localising at least two polymorphic inversions (Ishigohoka et al. 2022). Further investigations on the effect of model parameters (e.g., window sizes and thresholds for defining low-recombining regions), as well as the use of powerful neutrality tests are in need to clearly assess whether outlier regions experience selection and reduced recombination, and to what extent. References Booker, T. R., Yeaman, S., & Whitlock, M. C. (2020). Variation in recombination rate affects detection of outliers in genome scans under neutrality. Molecular Ecology, 29 (22), 4274–4279. https://doi.org/10.1111/mec.15501 Ishigohoka, J., Bascón-Cardozo, K., Bours, A., Fuß, J., Rhie, A., Mountcastle, J., Haase, B., Chow, W., Collins, J., Howe, K., Uliano-Silva, M., Fedrigo, O., Jarvis, E. D., Pérez-Tris, J., Illera, J. C., Liedvogel, M. (2022) Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure. bioRxiv 2021.12.22.473882, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.12.22.473882 Li, H., & Ralph, P. (2019). Local PCA Shows How the Effect of Population Structure Differs Along the Genome. Genetics, 211 (1), 289–304. https://doi.org/10.1534/genetics.118.301747 Mérot, C., Berdan, E. L., Cayuela, H., Djambazian, H., Ferchaud, A.-L., Laporte, M., Normandeau, E., Ragoussis, J., Wellenreuther, M., & Bernatchez, L. (2021). Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly. Molecular Biology and Evolution, 38 (9), 3953–3971. https://doi.org/10.1093/molbev/msab143 | Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure | Jun Ishigohoka, Karen Bascón-Cardozo, Andrea Bours, Janina Fuß, Arang Rhie, Jacquelyn Mountcastle, Bettina Haase, William Chow, Joanna Collins, Kerstin Howe, Marcela Uliano-Silva, Olivier Fedrigo, Erich D. Jarvis, Javier Pérez-Tris, Juan Carlos Il... | <p>Genetic variation of the entire genome represents population structure, yet individual loci can show distinct patterns. Such deviations identified through genome scans have often been attributed to effects of selection instead of randomness. Th... | Genome Evolution, Molecular Evolution, Population Genetics / Genomics | Matteo Fumagalli | 2023-10-13 11:58:47 | View | ||
31 May 2024
Cross-tolerance evolution is driven by selection of heat tolerance in Drosophila subobscuraLuis E. Castañeda https://www.doi.org/10.1101/2023.09.05.556367Evolution of cross-tolerance: a mechanism to cope with climate change?Recommended by Pedro Simões based on reviews by Marina Stamenkovic-Radak and 1 anonymous reviewerUnderstanding how populations evolve under thermal stress and how this process shapes the response of other stress responses is an important research topic in the context of thermal adaptation and climate change. In a thermal experimental evolution study in Drosophila subobscura, Castañeda (2024) addressed the correlated responses to selection for increasing knockdown temperature in different resistance traits, either directly related to thermal stress (e.g. knockdown time at different temperatures and CTmax) or not (e.g. desiccation and starvation resistance). The author found that the evolution of higher knockdown temperature did in fact lead to correlated responses in other stress traits. While such correlations might be expected for the thermal stress traits measured (knockdown time and CTmax), it was perhaps less expectable for desiccation and starvation resistance. However, the general occurrence of correlated evolutionary responses between stressors has been previously described, namely in Drosophila (e.g. see Bubliy and Loeschcke 2005), pointing to a possible genetic link between distinct (thermal) stress traits. There are however some features that make the findings of this study rather appealing. First, the evidence that the correlated stress responses depend on the intensity of thermal selection (i.e. the warming rate) and on the sex of the organisms. Second, correlated patterns of both desiccation and starvation resistance highlight the possibility of the evolution of a cross-tolerance response, which might positively impact on population ability to evolve under sustained stressful environments (Rodgers and Gomez Izasa 2023). However, it is important to point out that the correlated patterns between these two resistance traits (desiccation and starvation) were not exactly consistent. In fact, the negative correlated response observed for female starvation resistance is thought provoking and argues again a general scenario of cross-tolerance. While these findings are a step forward for a more multifaceted understanding of thermal adaptation in the context of stressful environments, they also highlight the need for further studies of thermal adaptation namely 1) addressing the underlying physiological and genomic mechanisms that link male and female heat tolerance and the response to other stress resistance traits (namely starvation resistance); 2) testing the extent to which cross-resistance patterns can be generalized to different thermal selection contexts and populations. In addition, this study also opens new questions considering the scope of correlated evolution to other stress traits, that might be relevant in diverse ecological scenarios. For instance, does selection towards higher heat resistance lead to correlated evolution of cold resistance? And under which circumstances (e.g. different heat selection intensities)? In fact, the occurrence of a positive (or negative) correlation cold and heat stress responses is a topic of high interest, with relevant ecological implications particularly considering the increased thermal fluctuations in natural environments because of climate warming. Cross-tolerance between cold and heat stress responses has been described (Singh 2022, Rodgers and Gomez Izasa 2023). On the other hand, negative correlations (i.e. trade-offs) between these stress traits (Stazione et al. 2020; Schou et al 2022) can impact negatively on populations’ ability to withstand thermal variability. As climatic changes proceed leading to increasing environmental variability, empirical studies such as that of Castañeda (2024) are critical in the pursue for a multivariate perspective on trait evolution in scenarios of climate change adaptation. Understanding how tolerance to different environmental stressors may evolve and which factors can act as drivers of that variation will ultimately enable better forecasts of climate change effects on biodiversity in nature. References Castañeda, LE. Cross-tolerance evolution is driven by selection on heat tolerance in Drosophila subobscura. Biorxiv, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology (2024). https://www.doi.org/10.1101/2023.09.05.556367 Bubliy, OA, Loeschcke, V. Correlated responses to selection for stress resistance and longevity in a laboratory population of Drosophila melanogaster. J Evol Biol. 18(4):789-803 (2005). https://www.doi.org/10.1111/j.1420-9101.2005.00928.x. Rodgers, EM, Gomez Isaza, DF. The mechanistic basis and adaptive significance of cross-tolerance: a 'pre-adaptation' to a changing world? J Exp Biol. 226(11):jeb245644 (2023). https://www.doi.org/10.1242/jeb.245644. Schou, MF, Engelbrecht, A, Brand, Z, Svensson, EI, Cloete, S, Cornwallis, CK. Evolutionary trade-offs between heat and cold tolerance limit responses to fluctuating climates. Sci Adv. 8(21):eabn9580 (2022). https://www.doi.org/10.1126/sciadv.abn9580. Singh, K, Arun Samant, M, Prasad, NG. Evolution of cross-tolerance in Drosophila melanogaster as a result of increased resistance to cold stress. Sci Rep. 12(1):19536 (2022). https://www.doi.org/10.1038/s41598-022-23674-z. Stazione, L, Norry, FM, Gomez, FH, Sambucetti, P. Heat knockdown resistance and chill-coma recovery as correlated responses to selection on mating success at high temperature in Drosophila buzzatii. Ecol Evol. 10(4):1998-2006 (2020). https://www.doi.org/10.1002/ece3.6032. | Cross-tolerance evolution is driven by selection of heat tolerance in *Drosophila subobscura* | Luis E. Castañeda | <p>The evolution of heat tolerance is a crucial mechanism for the adaptive response to global warming, but it depends on the genetic variance carried by populations and on the intensity of thermal stress in nature. Experimental selection studies h... | Adaptation, Experimental Evolution | Pedro Simões | 2023-10-02 14:13:02 | View | ||
28 Mar 2024
Gene expression is the main driver of purifying selection in large penguin populationsEmiliano Trucchi, Piergiorgio Massa, Francesco Giannelli, Thibault Latrille, Flavia A.N. Fernandes, Lorena Ancona, Nils Chr Stenseth, Joan Ferrer Obiol, Josephine Paris, Giorgio Bertorelle, Celine Le Bohec https://doi.org/10.1101/2023.08.08.552445Purifying selection on highly expressed genes in PenguinsRecommended by Bruce Rannala based on reviews by Tanja Pyhäjärvi and 1 anonymous reviewerGiven the general importance of protein expression levels, in cells it is widely accepted that gene expression levels are often a target of natural selection and that most mutations affecting gene expression levels are therefore likely to be deleterious [1]. However, it is perhaps less obvious that the strength of selection on the regulated genes themselves may be influenced by their expression levels. This might be due to harmful effects of misfolded proteins, for example, when higher protein concentrations exist in cells [2]. Recent studies have suggested that highly expressed genes accumulate fewer deleterious mutations; thus a positive relationship appears to exist between gene expression levels and the relative strength of purifying selection [3]. The recommended paper by Trucchi et al. [4] examines the relationship between gene expression, purifying selection and a third variable -- effective population size -- in populations of two species of penguin with different population sizes, the Emperor penguin (Aptenodytes forsteri) and the King penguin (A. patagonicus). Using transcriptomic data and computer simulations modeling selection, they examine patterns of nonsynonymous and synonymous segregating polymorphisms (p) across genes in the two populations, concluding that even in relatively small populations purifying selection has an important effect in eliminating deleterious mutations. References 1] Gilad Y, Oshlack A, and Rifkin SA. 2006. Natural selection on gene expression. Trends in Genetics 22: 456-461. https://doi.org/10.1016/j.tig.2006.06.002 [4] Trucchi E, Massa P, Giannelli F, Latrille T, Fernandes FAN, Ancona L, Stenseth NC, Obiol JF, Paris J, Bertorelle G, and Le Bohec, C. 2023. Gene expression is the main driver of purifying selection in large penguin populations. bioRxiv 2023.08.08.552445, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.08.08.552445
| Gene expression is the main driver of purifying selection in large penguin populations | Emiliano Trucchi, Piergiorgio Massa, Francesco Giannelli, Thibault Latrille, Flavia A.N. Fernandes, Lorena Ancona, Nils Chr Stenseth, Joan Ferrer Obiol, Josephine Paris, Giorgio Bertorelle, Celine Le Bohec | <p style="text-align: justify;">Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate ... | Bioinformatics & Computational Biology, Evolutionary Dynamics, Evolutionary Theory, Population Genetics / Genomics | Bruce Rannala | 2023-08-09 17:53:03 | 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 |
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