|Id||Title||Authors||Abstract||Picture||Thematic fields▲||Recommender||Reviewers||Submission date|
03 Aug 2017
Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradientsNoémie Harmand, Romain Gallet, Roula Jabbour-Zahab, Guillaume Martin, Thomas Lenormand 10.1111/evo.13111
What doesn’t kill us makes us stronger: can Fisher’s Geometric model predict antibiotic resistance evolution?Recommended by Inês Fragata and Claudia Bank
The increasing number of reported cases of antibiotic resistance is one of today’s major public health concerns. Dealing with this threat involves understanding what drives the evolution of antibiotic resistance and investigating whether we can predict (and subsequently avoid or circumvent) it .
 Palmer AC, and Kishony R. 2013. Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nature Review Genetics 14: 243—248. doi: 10.1038/nrg3351
 Tenaillon O. 2014. The utility of Fisher’s geometric model in evolutionary genetics. Annual Review of Ecology, Evolution and Systematics 45: 179—201. doi: 10.1146/annurev-ecolsys-120213-091846
 Blanquart F and Bataillon T. 2016. Epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with Fisher’s geometric model? Genetics 203: 847—862. doi: 10.1534/genetics.115.182691
 Harmand N, Gallet R, Jabbour-Zahab R, Martin G and Lenormand T. 2017. Fisher’s geometrical model and the mutational patterns of antibiotic resistance across dose gradients. Evolution 71: 23—37. doi: 10.1111/evo.13111
 de Visser, JAGM, and Krug J. 2014. Empirical fitness landscapes and the predictability of evolution. Nature 15: 480—490. doi: 10.1038/nrg3744
 Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S and Kishony R. 2015. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nature Communications 6: 1—8. doi: 10.1038/ncomms8385
|Fisher's geometrical model and the mutational patterns of antibiotic resistance across dose gradients||Noémie Harmand, Romain Gallet, Roula Jabbour-Zahab, Guillaume Martin, Thomas Lenormand||Fisher's geometrical model (FGM) has been widely used to depict the fitness effects of mutations. It is a general model with few underlying assumptions that gives a large and comprehensive view of adaptive processes. It is thus attractive in sever...||Adaptation||Inês Fragata||2017-08-01 16:06:02||View|
14 Mar 2017
Evolution of multiple sensory systems drives novel egg-laying behavior in the fruit pest Drosophila suzukiiMarianthi Karageorgi, Lasse B. Bräcker, Sébastien Lebreton, Caroline Minervino, Matthieu Cavey, K.P. Siju, Ilona C. Grunwald Kadow, Nicolas Gompel, Benjamin Prud’homme https://doi.org/10.1016/j.cub.2017.01.055
A valuable work lying at the crossroad of neuro-ethology, evolution and ecology in the fruit pest Drosophila suzukiiRecommended by Arnaud Estoup and Ruth Arabelle Hufbauer
Adaptations to a new ecological niche allow species to access new resources and circumvent competitors and are hence obvious pathways of evolutionary success. The evolution of agricultural pest species represents an important case to study how a species adapts, on various timescales, to a novel ecological niche. Among the numerous insects that are agricultural pests, the ability to lay eggs (or oviposit) in ripe fruit appears to be a recurrent scenario. Fruit flies (family Tephritidae) employ this strategy, and include amongst their members some of the most destructive pests (e.g., the olive fruit fly Bactrocera olea or the medfly Ceratitis capitata). In their ms, Karageorgi et al.  studied how Drosophila suzukii, a new major agricultural pest species that recently invaded Europe and North America, evolved the novel behavior of laying eggs into undamaged fresh fruit. The close relatives of D. suzukii lay their eggs on decaying plant substrates, and thus this represents a marked change in host use that links to substantial economic losses to the fruit industry. Although a handful of studies have identified genetic changes causing new behaviors in various species, the question of the evolution of behavior remains a largely uncharted territory. The study by Karageorgi et al.  represents an original and most welcome contribution in this domain for a non-model species. Using clever behavioral experiments to compare D. suzukii to several related Drosophila species, and complementing those results with neurogenetics and mutant analyses using D. suzukii, the authors nicely dissect the sensory changes at the origin of the new egg-laying behavior. The experiments they describe are easy to follow, richly illustrate through figures and images, and particularly well designed to progressively decipher the sensory bases driving oviposition of D. suzukii on ripe fruit. Altogether, Karageorgi et al.’s  results show that the egg-laying substrate preference of D. suzukii has considerably evolved in concert with its morphology (especially its enlarged, serrated ovipositor that enables females to pierce the skin of many ripe fruits). Their observations clearly support the view that the evolution of traits that make D. suzukii an agricultural pest included the modification of several sensory systems (i.e. mechanosensation, gustation and olfaction). These differences between D. suzukii and its close relatives collectively underlie a radical change in oviposition behavior, and were presumably instrumental in the expansion of the ecological niche of the species. The authors tentatively propose a multi-step evolutionary scenario from their results with the emergence of D. suzukii as a pest species as final outcome. Such formalization represents an interesting evolutionary model-framework that obviously would rely upon further data and experiments to confirm and refine some of the evolutionary steps proposed, especially the final and recent transition of D. suzukii from non-invasive to invasive species.
 Karageorgi M, Bräcker LB, Lebreton S, Minervino C, Cavey M, Siju KP, Grunwald Kadow IC, Gompel N, Prud’homme B. 2017. Evolution of multiple sensory systems drives novel egg-laying behavior in the fruit pest Drosophila suzukii. Current Biology, 27: 1-7. doi: 10.1016/j.cub.2017.01.055
|Evolution of multiple sensory systems drives novel egg-laying behavior in the fruit pest Drosophila suzukii||Marianthi Karageorgi, Lasse B. Bräcker, Sébastien Lebreton, Caroline Minervino, Matthieu Cavey, K.P. Siju, Ilona C. Grunwald Kadow, Nicolas Gompel, Benjamin Prud’homme||The rise of a pest species represents a unique opportunity to address how species evolve new behaviors and adapt to novel ecological niches. We address this question by studying the egg-laying behavior of Drosophila suzukii, an invasive agricultur...||Adaptation, Behavior & Social Evolution, Evo-Devo, Evolutionary Applications, Evolutionary Ecology, Expression Studies, Genotype-Phenotype, Macroevolution, Molecular Evolution||Arnaud Estoup||2017-03-13 17:42:00||View|
15 Dec 2016
Limiting opportunities for cheating stabilizes virulence in insect parasitic nematodesShapiro-Ilan D. and B. Raymond doi:10.1111/eva.12348
Application of kin theory to long-standing problem in nematode production for biocontrolRecommended by Thomas Sappington and Ruth Arabelle Hufbauer
Much research effort has been extended toward developing systems for managing soil inhabiting insect pests of crops with entomopathogenic nematodes as biocontrol agents. Although small plot or laboratory experiments may suggest a particular insect pest is vulnerable to management in this way, it is often difficult to scale-up nematode production for application at the field- and farm scale to make such a tactic viable. Part of the problem is that entomopathogenic nematode strains must be propagated by serial passage in vivo, because storage by freezing decreases fitness. At the same time, serial propagation results in loss of virulence (ability to infect) over generations in the laboratory, a phenomenon called attenuation.
To probe the underlying reasons for development of attenuation, as a prerequisite to designing strategies to mitigate it, Shapiro-Ilan and Raymond  turned to evolutionary theory of social conflict as a possible explanatory framework. Virulence of entomopathogenic nematodes depends on a combination of virulence factors, like various proteases, secreted by both the nematode and symbiotic bacteria to overcome host defenses. Attenuation is characterized in part by a reduced production of these factors. Invasion of a host involves simultaneous attack by a group of nematodes ("cooperators"), which together neutralize host defenses enough to allow individuals to successfully invade. "Cheaters" in the invading population can avoid the metabolic costs of producing virulence factors while reaping the benefits of infecting the host made vulnerable by the cooperators in the population. The authors hypothesize that an increase in frequency of cheaters may contribute to attenuation of virulence during serial propagation in the laboratory. The evolutionary dynamics of cheater frequency in a population have been explored in many contexts as part of kin selection theory. Cheaters can increase in a population by outcompeting cooperators in a host if overall relatedness within the invading population is low. Conversely, frequency of altruism, or costly cooperation, increases in a population if relatedness is high, which is enhanced by low effective dispersal. However, a population that is too isolated can suffer from inbreeding effects, and competition will occur mainly among relatives, which decreases the fitness benefits of altruism.
Shapiro-Ilan and Raymond  tested changes in virulence and reproductive output in a serially propagated entomopathogenic nematode, Heterorhabditis floridensis. They compared lines of high or low relatedness, manipulated via multiplicity of infection (MOI) rates (where a low dose of nematodes gives high relatedness and a high dose gives low relatedness); and under global or local competition, manipulated by pooling populations emerging from all or only two host cadavers per generation, respectively. As predicted, treatments of high relatedness (low MOI) and global competition had the greatest level of reproduction, while all lines of low relatedness (high MOI) evolved decreased reproduction and decreased virulence, which led to extinction. The key finding was that lines in the high relatedness (low MOI) and low (local) competition treatment exhibited the most stable virulence through the 12 generations tested. Thus, to minimize attenuation of virulence while maintaining fitness of recently isolated entomopathogenic nematodes, the authors recommend insect hosts be inoculated with low doses of nematodes from inocula pools from as few cadavers as possible.
The application of evolutionary theory, with a clever experimental design, to an important problem in pest management makes this paper particularly noteworthy.
 Shapiro-Ilan D, Raymond B. 2016. Limiting opportunities for cheating stabilizes virulence in insect parasitic nematodes. Evolutionary Applications 9:462-470. doi: 10.1111/eva.12348
|Limiting opportunities for cheating stabilizes virulence in insect parasitic nematodes||Shapiro-Ilan D. and B. Raymond||Cooperative secretion of virulence factors by pathogens can lead to social conflict when cheating mutants exploit collective secretion, but do not contribute to it. If cheats outcompete cooperators within hosts, this can cause loss of virulence....||Adaptation, Behavior & Social Evolution, Evolutionary Applications, Evolutionary Dynamics, Evolutionary Ecology, Evolutionary Epidemiology, Evolutionary Theory, Experimental Evolution, Population Genetics / Genomics, Reproduction and Sex||Thomas Sappington||2016-12-15 18:33:39||View|
18 Nov 2020
A demogenetic agent based model for the evolution of traits and genome architecture under sexual selectionLouise Chevalier, François de Coligny, Jacques Labonne https://doi.org/10.1101/2020.04.01.014514
Sexual selection goes dynamicRecommended by Michael D Greenfield based on reviews by Frédéric Guillaume and 1 anonymous reviewer
150 years after Darwin published ‘Descent of man and selection in relation to sex’ (Darwin, 1871), the evolutionary mechanism that he laid out in his treatise continues to fascinate us. Sexual selection is responsible for some of the most spectacular traits among animals, and plants, and it appeals to our interest in all things reproductive and sexual (Bell, 1982). In addition, sexual selection poses some of the more intractable problems in evolutionary biology: Its realm encompasses traits that are subject to markedly different selection pressures, particularly when distinct, yet associated, traits tend to be associated with males, e.g. courtship signals, and with females, e.g. preferences (cf. Ah-King & Ahnesjo, 2013). While separate, such traits cannot evolve independently of each other (Arnqvist & Rowe, 2005), and complex feedback loops and correlations between them are predicted (Greenfield et al., 2014). Traditionally, sexual selection has been modelled under simplifying assumptions, and quantitative genetic approaches that avoided evolutionary dynamics have prevailed. New computing methods may be able to free the field from these constraints, and a trio of theoreticians (Chevalier, De Coligny & Labonne 2020) describe here a novel application of a ‘demo-genetic agent (or individual) based model’, a mouthful hereafter termed DG-ABM, for arriving at a holistic picture of the sexual selection trajectory. The application is built on the premise that traits, e.g. courtship, preference, gamete investment, competitiveness for mates, can influence the genetic architecture, e.g. correlations, of those traits. In turn, the genetic architecture can influence the expression and evolvability of the traits. Much of this influence occurs via demographic features, i.e. social environment, generated by behavioral interactions during sexual advertisement, courtship, mate guarding, parental care, post-mating dispersal, etc.
Ah-King, M. and Ahnesjo, I. 2013. The ‘sex role’ concept: An overview and evaluation Evolutionary Biology, 40, 461-470. doi: https://doi.org/10.1007/s11692-013-9226-7
|A demogenetic agent based model for the evolution of traits and genome architecture under sexual selection||Louise Chevalier, François de Coligny, Jacques Labonne||<p>Sexual selection has long been known to favor the evolution of mating behaviors such as mate preference and competitiveness, and to affect their genetic architecture, for instance by favoring genetic correlation between some traits. Reciprocall...||Adaptation, Behavior & Social Evolution, Evolutionary Dynamics, Evolutionary Theory, Life History, Population Genetics / Genomics, Sexual Selection||Michael D Greenfield||2020-04-02 14:44:25||View|
13 Dec 2018
A behavior-manipulating virus relative as a source of adaptive genes for parasitoid waspsD. Di Giovanni, D. Lepetit, M. Boulesteix, M. Ravallec, J. Varaldi https://doi.org/10.1101/342758
Genetic intimacy of filamentous viruses and endoparasitoid waspsRecommended by Ignacio Bravo based on reviews by Alejandro Manzano Marín and 1 anonymous reviewer
Viruses establish intimate relationships with the cells they infect. The virocell is a novel entity, different from the original host cell and beyond the mere combination of viral and cellular genetic material. In these close encounters, viral and cellular genomes often hybridise, combine, recombine, merge and excise. Such chemical promiscuity leaves genomics scars that can be passed on to descent, in the form of deletions or duplications and, importantly, insertions and back and forth exchange of genetic material between viruses and their hosts.
 Di Giovanni, D., Lepetit, D., Boulesteix, M., Ravallec, M., & Varaldi, J. (2018). A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps. bioRxiv, 342758, ver. 5 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/342758
|A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps||D. Di Giovanni, D. Lepetit, M. Boulesteix, M. Ravallec, J. Varaldi||<p>To circumvent host immune response, numerous hymenopteran endo-parasitoid species produce virus-like structures in their reproductive apparatus that are injected into the host together with the eggs. These viral-like structures are absolutely n...||Adaptation, Behavior & Social Evolution, Genetic conflicts, Genome Evolution||Ignacio Bravo||2018-07-18 15:59:14||View|
13 Dec 2016
Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)Lamichhaney S, Fan G, Widemo F, Gunnarsson U, Thalmann DS, Hoeppner MP, Kerje S, Gustafson U, Shi C, Zhang H, et al. doi:10.1038/ng.3430
Supergene Control of a Reproductive PolymorphismRecommended by Thomas Flatt and Laurent Keller
Two back-to-back papers published earlier this year in Nature Genetics provide compelling evidence for the control of a male reproductive polymorphism in a wading bird by a "supergene", a cluster of tightly linked genes [1-2]. The bird in question, the ruff (Philomachus pugnax), has a rather unusual reproductive system that consists of three distinct types of males ("reproductive morphs"): aggressive "independents" who represent the majority of males; a smaller fraction of non-territorial "satellites" who are submissive towards "independents"; and "faeders" who mimic females and are rare. Previous work has shown that the male morphs differ in major aspects of mating and aggression behavior, plumage coloration and body size, and that – intriguingly – this complex multi-trait polymorphism is apparently controlled by a single autosomal Mendelian locus with three alleles . To uncover the genetic control of this polymorphism two independent teams, led by Terry Burke  and Leif Andersson , have set out to analyze the genomes of male ruffs. Using a combination of genomics and genetics, both groups managed to pin down the supergene locus and map it to a non-recombining, 4.5 Mb large inversion which arose 3.8 million years ago. While "independents" are homozygous for the ancestral uninverted sequence, "satellites" and "faeders" carry evolutionarily divergent, dominant alternative haplotypes of the inversion. Thus, as in several other notable cases, for example the supergene control of disassortative mating, aggressiveness and plumage color in white-throated sparrows , of mimicry in Heliconius and Papilio butterflies [5-6], or of social structure in ants , an inversion – behaving as a single "locus" – underpins the mechanistic basis of the supergene. More generally, and beyond inversions, a growing number of studies now shows that selection can favor the evolution of suppressed recombination, thereby leading to the emergence of clusters of tightly linked loci which can then control – presumably due to polygenic gene action – a suite of complex phenotypes [8-10]. A largely unresolved question in this field concerns the identity of the causative alleles and loci within a given supergene. Recent progress on this question has been made for example in Papilio polytes butterflies where a mimicry supergene has been found to involve – surprisingly – only a single but large gene: multiple mimicry alleles in the doublesex gene are maintained in strong linkage disequilibrium via an inversion. It will clearly be of great interest to see future examples of such a fine-scale genetic dissection of supergenes. In conclusion, we were impressed by the data and analyses of Küpper et al.  and Lamichhaney et al. : both papers beautifully illustrate how genomics and evolutionary ecology can be combined to make new, exciting discoveries. Both papers will appeal to readers with an interest in supergenes, inversions, the interplay of selection and recombination, or the genetic control of complex phenotypes.
 Küpper C, Stocks M, Risse JE, dos Remedios N, Farrell LL, McRae SB, Morgan TC, Karlionova N, Pinchuk P, Verkuil YI, et al. 2016. A supergene determines highly divergent male reproductive morphs in the ruff. Nature Genetics 48:79-83. doi: 10.1038/ng.3443
 Lamichhaney S, Fan G, Widemo F, Gunnarsson U, Thalmann DS, Hoeppner MP, Kerje S, Gustafson U, Shi C, Zhang H, et al. 2016. Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nature Genetics 48:84-88. doi: 10.1038/ng.3430
 Lank DB, Smith CM, Hanotte O, Burke T, Cooke F. 1995. Genetic polymorphism for alternative mating behaviour in lekking male ruff Philomachus pugnax. Nature 378:59-62. doi: 10.1038/378059a0
 Tuttle Elaina M, Bergland Alan O, Korody Marisa L, Brewer Michael S, Newhouse Daniel J, Minx P, Stager M, Betuel A, Cheviron Zachary A, Warren Wesley C, et al. 2016. Divergence and Functional Degradation of a Sex Chromosome-like Supergene. Current Biology 26:344-350. doi: 10.1016/j.cub.2015.11.069
 Joron M, Frezal L, Jones RT, Chamberlain NL, Lee SF, Haag CR, Whibley A, Becuwe M, Baxter SW, Ferguson L, et al. 2011. Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. Nature 477:203-206. doi: 10.1038/nature10341
 Kunte K, Zhang W, Tenger-Trolander A, Palmer DH, Martin A, Reed RD, Mullen SP, Kronforst MR. 2014. doublesex is a mimicry supergene. Nature 507:229-232. doi: 10.1038/nature13112
 Wang J, Wurm Y, Nipitwattanaphon M, Riba-Grognuz O, Huang Y-C, Shoemaker D, Keller L. 2013. A Y-like social chromosome causes alternative colony organization in fire ants. Nature 493:664-668. doi: 10.1038/nature11832
 Thompson MJ, Jiggins CD. 2014. Supergenes and their role in evolution. Heredity 113:1-8. doi: 10.1038/hdy.2014.20
 Schwander T, Libbrecht R, Keller L. 2014. Supergenes and Complex Phenotypes. Current Biology 24:R288-R294. doi: 10.1016/j.cub.2014.01.056
 Charlesworth D. 2015. The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex adaptations. Evolutionary Applications 9:74-90. doi: 10.1111/eva.12291
|Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)||Lamichhaney S, Fan G, Widemo F, Gunnarsson U, Thalmann DS, Hoeppner MP, Kerje S, Gustafson U, Shi C, Zhang H, et al.||The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females1, 2, 3, 4. This bird has one of the most remarkable mating systems in the animal kingdom, comprising three different male morphs (...||Adaptation, Behavior & Social Evolution, Genotype-Phenotype, Life History, Population Genetics / Genomics, Quantitative Genetics, Reproduction and Sex||Thomas Flatt||2016-12-13 17:46:54||View|
16 Nov 2022
Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in miceCarole M. Smadja, Etienne Loire, Pierre Caminade, Dany Severac, Mathieu Gautier, Guila Ganem https://doi.org/10.1101/2022.07.21.500634
Tinder in mice: A match made with the sense of smellRecommended by Christelle Fraïsse based on reviews by Ludovic Claude Maisonneuve, Angeles de Cara and 1 anonymous reviewer
Differentiation-based genome scans lie at the core of speciation and adaptation genomics research. Dating back to Lewontin & Krakauer (1973), they have become very popular with the advent of genomics to identify genome regions of enhanced differentiation relative to neutral expectations. These regions may represent genetic barriers between divergent lineages and are key for studying reproductive isolation. However, genome scan methods can generate a high rate of false positives, primarily if the neutral population structure is not accounted for (Bierne et al. 2013). Moreover, interpreting genome scans can be challenging in the context of secondary contacts between diverging lineages (Bierne et al. 2011), because the coupling between different components of reproductive isolation (local adaptation, intrinsic incompatibilities, mating preferences, etc.) can occur readily, thus preventing the causes of differentiation from being determined.
Smadja and collaborators (2022) applied a sophisticated genome scan for trait association (BAYPASS, Gautier 2015) to underlie the genetic basis of a polygenetic behaviour: assortative mating in hybridizing mice. My interest in this neat study mainly relies on two reasons. First, the authors used an ingenious geographical setting (replicate pairs of “Choosy” versus “Non-Choosy” populations) with multi-way comparisons to narrow down the list of candidate regions resulting from BAYPASS. The latter corrects for population structure, handles cost-effective pool-seq data and allows for gene-based analyses that aggregate SNP signals within a gene. These features reinforce the set of outlier genes detected; however, not all are expected to be associated with mating preference.
The second reason why this study is valuable to me is that Smadja et al. (2022) complemented the population genomic approach with functional predictions to validate the genetic signal. In line with previous behavioural and chemical assays on the proximal mechanisms of mating preferences, they identified multiple olfactory and vomeronasal receptor genes as highly significant candidates. Therefore, combining genomic signals with functional analyses is a clever way to provide insights into the causes of reproductive isolation, especially when multiple barriers are involved. This is typically true for reinforcement (Butlin & Smadja 2018), suspected to occur in these mice because, in that case, assortative mating (a prezygotic barrier) evolves in response to the cost of hybridization (for example, due to hybrid inviability).
As advocated by the authors, their study paves the way for future work addressing the genetic basis of reinforcement, a trait of major evolutionary importance for which we lack empirical data. They also make a compelling case using complementary approaches that olfactory and vomeronasal receptors have a central role in mammal speciation.
Bierne N, Welch J, Loire E, Bonhomme F, David P (2011) The coupling hypothesis: why genome scans may fail to map local adaptation genes. Mol Ecol 20: 2044–2072. https://doi.org/10.1111/j.1365-294X.2011.05080.x
Bierne N, Roze D, Welch JJ (2013) Pervasive selection or is it…? why are FST outliers sometimes so frequent? Mol Ecol 22: 2061–2064. https://doi.org/10.1111/mec.12241
Butlin RK, Smadja CM (2018) Coupling, Reinforcement, and Speciation. Am Nat 191:155–172. https://doi.org/10.1086/695136
Gautier M (2015) Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates. Genetics 201:1555–1579. https://doi.org/10.1534/genetics.115.181453
Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of selective neutrality of polymorphisms. Genetics 74: 175–195. https://doi.org/10.1093/genetics/74.1.175
Smadja CM, Loire E, Caminade P, Severac D, Gautier M, Ganem G (2022) Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in mice. bioRxiv, 2022.07.21.500634, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.07.21.500634
|Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in mice||Carole M. Smadja, Etienne Loire, Pierre Caminade, Dany Severac, Mathieu Gautier, Guila Ganem||<p>Deciphering the genetic bases of behavioural traits is essential to understanding how they evolve and contribute to adaptation and biological diversification, but it remains a substantial challenge, especially for behavioural traits with polyge...||Adaptation, Behavior & Social Evolution, Genotype-Phenotype, Speciation||Christelle Fraïsse||2022-07-25 11:54:52||View|
22 May 2023
Weak seed banks influence the signature and detectability of selective sweepsKevin Korfmann, Diala Abu Awad, Aurélien Tellier https://doi.org/10.1101/2022.04.26.489499
New insights into the dynamics of selective sweeps in seed-banked speciesRecommended by Renaud Vitalis based on reviews by Guillaume Achaz, Jere Koskela, William Shoemaker and Simon Boitard
Many organisms across the Tree of life have the ability to produce seeds, eggs, cysts, or spores, that can remain dormant for several generations before hatching. This widespread adaptive trait in bacteria, fungi, plants and animals, has a significant impact on the ecology, population dynamics and population genetics of species that express it (Evans and Dennehy 2005).
In population genetics, and despite the recognition of its evolutionary importance in many empirical studies, few theoretical models have been developed to characterize the evolutionary consequences of this trait on the level and distribution of neutral genetic diversity (see, e.g., Kaj et al. 2001; Vitalis et al. 2004), and also on the dynamics of selected alleles (see, e.g., Živković and Tellier 2018). However, due to the complexity of the interactions between evolutionary forces in the presence of dormancy, the fate of selected mutations in their genomic environment is not yet fully understood, even from the most recently developed models.
In a comprehensive article, Korfmann et al. (2023) aim to fill this gap by investigating the effect of germ banking on the probability of (and time to) fixation of beneficial mutations, as well as on the shape of the selective sweep in their vicinity. To this end, Korfmann et al. (2023) developed and released their own forward-in-time simulator of genome-wide data, including neutral and selected polymorphisms, that makes use of Kelleher et al.’s (2018) tree sequence toolkit to keep track of gene genealogies.
The originality of Korfmann et al.’s (2023) study is to provide new quantitative results for the effect of dormancy on the time to fixation of positively selected mutations, the shape of the genomic landscape in the vicinity of these mutations, and the temporal dynamics of selective sweeps. Their major finding is the prediction that germ banking creates narrower signatures of sweeps around positively selected sites, which are detectable for increased periods of time (as compared to a standard Wright-Fisher population).
The availability of Korfmann et al.’s (2023) code will allow a wider range of parameter values to be explored, to extend their results to the particularities of the biology of many species. However, as they chose to extend the haploid coalescent model of Kaj et al. (2001), further development is needed to confirm the robustness of their results with a more realistic diploid model of seed dormancy.
Evans, M. E. K., and J. J. Dennehy (2005) Germ banking: bet-hedging and variable release from egg and seed dormancy. The Quarterly Review of Biology, 80(4): 431-451. https://doi.org/10.1086/498282
Kaj, I., S. Krone, and M. Lascoux (2001) Coalescent theory for seed bank models. Journal of Applied Probability, 38(2): 285-300. https://doi.org/10.1239/jap/996986745
Kelleher, J., K. R. Thornton, J. Ashander, and P. L. Ralph (2018) Efficient pedigree recording for fast population genetics simulation. PLoS Computational Biology, 14(11): e1006581. https://doi.org/10.1371/journal.pcbi.1006581
Korfmann, K., D. Abu Awad, and A. Tellier (2023) Weak seed banks influence the signature and detectability of selective sweeps. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.04.26.489499
Vitalis, R., S. Glémin, and I. Olivieri (2004) When genes go to sleep: the population genetic consequences of seed dormancy and monocarpic perenniality. American Naturalist, 163(2): 295-311. https://doi.org/10.1086/381041
Živković, D., and A. Tellier (2018). All but sleeping? Consequences of soil seed banks on neutral and selective diversity in plant species. Mathematical Modelling in Plant Biology, 195-212. https://doi.org/10.1007/978-3-319-99070-5_10
|Weak seed banks influence the signature and detectability of selective sweeps||Kevin Korfmann, Diala Abu Awad, Aurélien Tellier||<p style="text-align: justify;">Seed banking (or dormancy) is a widespread bet-hedging strategy, generating a form of population overlap, which decreases the magnitude of genetic drift. The methodological complexity of integrating this trait impli...||Adaptation, Bioinformatics & Computational Biology, Evolutionary Applications, Evolutionary Ecology, Genome Evolution, Life History, Population Genetics / Genomics||Renaud Vitalis||2022-05-23 13:01:57||View|
10 Jul 2019
Population genomics supports clonal reproduction and multiple gains and losses of parasitic abilities in the most devastating nematode plant pestGeorgios D. Koutsovoulos, Eder Marques, Marie-Jeanne Arguel, Laurent Duret, Andressa C.Z. Machado, Regina M.D.G. Carneiro, Djampa K. Kozlowski, Marc Bailly-Bechet, Philippe Castagnone-Sereno, Erika V.S. Albuquerque, Etienne G.J. Danchin https://doi.org/10.1101/362129
The scandalous pestRecommended by Nicolas Galtier based on reviews by 2 anonymous reviewers
Koutsovoulos et al.  have generated and analysed the first population genomic dataset in root-knot nematode Meloidogyne incognita. Why is this interesting? For two major reasons. First, M. incognita has been documented to be apomictic, i.e., to lack any form of sex. This is a trait of major evolutionary importance, with implications on species adaptive potential. The study of genome evolution in asexuals is fascinating and has the potential to inform on the forces governing the evolution of sex and recombination. Even small amounts of sex, however, are sufficient to restore most of the population genetic properties of true sexuals . Because rare events of sex can remain undetected in the field, to confirm asexuality in M. incognita using genomic data is an important step. The second reason why M. incognita is of interest is that this nematode is one of the most harmful pests currently living on earth. M. incognita feeds on the roots of many cultivated plants, including tomato, bean, and cotton, and has been of major agricultural importance for decades. A number of races were defined based on host specificity. These have played a key role in attempts to control the dynamic of M. incognita populations via crop rotations. Races and management strategies so far lack any genetic basis, hence the second major interest of this study.
 Koutsovoulos, G. D., Marques, E., Arguel, M. J., Duret, L., Machado, A. C. Z., Carneiro, R. M. D. G., Kozlowski, D. K., Bailly-Bechet, M., Castagnone-Sereno, P., Albuquerque, E. V., & Danchin, E. G. J. (2019). Population genomics supports clonal reproduction and multiple gains and losses of parasitic abilities in the most devastating nematode plant pest. bioRxiv, 362129, ver. 5, peer-reviewed and recommended by Peer Community in Evolutionary Biology. doi: 10.1101/362129
|Population genomics supports clonal reproduction and multiple gains and losses of parasitic abilities in the most devastating nematode plant pest||Georgios D. Koutsovoulos, Eder Marques, Marie-Jeanne Arguel, Laurent Duret, Andressa C.Z. Machado, Regina M.D.G. Carneiro, Djampa K. Kozlowski, Marc Bailly-Bechet, Philippe Castagnone-Sereno, Erika V.S. Albuquerque, Etienne G.J. Danchin||<p>The most devastating nematodes to worldwide agriculture are the root-knot nematodes with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seem surprising given its supposed obli...||Adaptation, Bioinformatics & Computational Biology, Evolutionary Ecology, Genome Evolution, Genotype-Phenotype, Molecular Evolution, Phylogenetics / Phylogenomics, Population Genetics / Genomics, Reproduction and Sex||Nicolas Galtier||2018-08-24 09:02:33||View|
18 May 2018
Modularity of genes involved in local adaptation to climate despite physical linkageKatie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken, Kathryn Hodgins https://doi.org/10.1101/202481
Differential effect of genes in diverse environments, their role in local adaptation and the interference between genes that are physically linkedRecommended by Sebastian Ernesto Ramos-Onsins based on reviews by Tanja Pyhäjärvi and 1 anonymous reviewer
The genome of eukaryotic species is a complex structure that experience many different interactions within itself and with the surrounding environment. The genetic architecture of a phenotype (that is, the set of genetic elements affecting a trait of the organism) plays a fundamental role in understanding the adaptation process of a species to, for example, different climate environments, or to its interaction with other species. Thus, it is fundamental to study the different aspects of the genetic architecture of the species and its relationship with its surronding environment. Aspects such as modularity (the number of genetic units and the degree to which each unit is affecting a trait of the organism), pleiotropy (the number of different effects that a genetic unit can have on an organism) or linkage (the degree of association between the different genetic units) are essential to understand the genetic architecture and to interpret the effects of selection on the genome. Indeed, the knowledge of the different aspects of the genetic architecture could clarify whether genes are affected by multiple aspects of the environment or, on the contrary, are affected by only specific aspects [1,2].
The work performed by Lotterhos et al.  sought to understand the genetic architecture of the adaptation to different environments in lodgepole pine (Pinus contorta), considering as candidate SNPs those previously detected as a result of its extreme association patterns to different environmental variables or to extreme population differentiation. This consideration is very important because the study is only relevant if the studied markers are under the effect of selection. Otherwise, the genetic architecture of the adaptation to different environments would be masked by other (neutral) kind of associations that would be difficult to interpret [4,5]. In order to understand the relationship between genetic architecture and adaptation, it is relevant to detect the association networks of the candidate SNPs with climate variables (a way to measure modularity) and if these SNPs (and loci) are affected by single or multiple environments (a way to measure pleiotropy).
The authors used co-association networks, an innovative approach in this field, to analyse the interaction between the environmental information and the genetic polymorphism of each individual. This methodology is more appropriate than other multivariate methods - such as analysis based on principal components - because it is possible to cluster SNPs based on associations with similar environmental variables. In this sense, the co-association networks allowed to both study the genetic and physical linkage between different co-associations modules but also to compare two different models of evolution: a Modular environmental response architecture (specific genes are affected by specific aspects of the environment) or a Universal pleiotropic environmental response architecture (all genes are affected by all aspects of the environment). The representation of different correlations between allelic frequency and environmental factors (named galaxy biplots) are especially informative to understand the effect of the different clusters on specific aspects of the environment (for example, the co-association network ‘Aridity’ shows strong associations with hot/wet versus cold/dry environments).
The analysis performed by Lotterhos et al. , although it has some unavoidable limitations (e.g., only extreme candidate SNPs are selected, limiting the results to the stronger effects; the genetic and physical map is incomplete in this species), includes relevant results and also implements new methodologies in the field. To highlight some of them: the preponderance of a Modular environmental response architecture (evolution in separated modules), the detection of physical linkage among SNPs that are co-associated with different aspects of the environment (which was unexpected a priori), the implementation of co-association networks and galaxy biplots to see the effect of modularity and pleiotropy on different aspects of environment. Finally, this work contains remarkable introductory Figures and Tables explaining unambiguously the main concepts  included in this study. This work can be treated as a starting point for many other future studies in the field.
 Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperone FG, Toomajian C, Roux F & Bergelson J. 2011. Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83–86. doi: 10.1126/science.1209244
|Modularity of genes involved in local adaptation to climate despite physical linkage||Katie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken, Kathryn Hodgins||<p>Background: Physical linkage among genes shaped by different sources of selection is a fundamental aspect of genetic architecture. Theory predicts that evolution in complex environments selects for modular genetic architectures and high recombi...||Adaptation, Bioinformatics & Computational Biology, Genome Evolution||Sebastian Ernesto Ramos-Onsins||2017-10-15 19:21:57||View|
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