Latest recommendations
| Id | Title * | Authors * | Abstract * ▲ | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
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16 Nov 2022
Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in miceTinder in mice: A match made with the sense of smellRecommended by Christelle Fraïsse based on reviews by Angeles de Cara, Ludovic Claude Maisonneuve ? 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 | ||
05 Aug 2020
Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognitaDNA transposons drive genome evolution of the root-knot nematode Meloidogyne incognitaRecommended by Ines Alvarez based on reviews by Daniel Vitales and 2 anonymous reviewers
Duplications, mutations and recombination may be considered the main sources of genomic variation and evolution. In addition, sexual recombination is essential in purging deleterious mutations and allowing advantageous allelic combinations to occur (Glémin et al. 2019). However, in parthenogenetic asexual organisms, variation cannot be explained by sexual recombination, and other mechanisms must account for it. Although it is known that transposable elements (TE) may influence on genome structure and gene expression patterns, their role as a primary source of genomic variation and rapid adaptability has received less attention. An important role of TE on adaptive genome evolution has been documented for fungal phytopathogens (Faino et al. 2016), suggesting that TE activity might explain the evolutionary dynamics of this type of organisms. References [1] Bessereau J-L. 2006. Transposons in C. elegans. WormBook. 10.1895/wormbook.1.70.1 | Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita | Djampa KL Kozlowski, Rahim Hassanaly-Goulamhoussen, Martine Da Rocha, Georgios D Koutsovoulos, Marc Bailly-Bechet, Etienne GJ Danchin | <p>Despite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant ... | | Adaptation, Bioinformatics & Computational Biology, Genome Evolution, Molecular Evolution, Population Genetics / Genomics, Reproduction and Sex | Ines Alvarez | 2020-05-04 11:43:14 | ||
05 Jun 2018
Pleistocene climate change and the formation of regional species poolsRecent assembly of European biogeographic species poolRecommended by Fabien Condamine based on reviews by 3 anonymous reviewersBiodiversity is unevenly distributed over time, space and the tree of life [1]. The fact that regions are richer than others as exemplified by the latitudinal diversity gradient has fascinated biologists as early as the first explorers travelled around the world [2]. Provincialism was one of the first general features of land biotic distributions noted by famous nineteenth century biologists like the phytogeographers J.D. Hooker and A. de Candolle, and the zoogeographers P.L. Sclater and A.R. Wallace [3]. When these explorers travelled among different places, they were struck by the differences in their biotas (e.g. [4]). The limited distributions of distinctive endemic forms suggested a history of local origin and constrained dispersal. Much biogeographic research has been devoted to identifying areas where groups of organisms originated and began their initial diversification [3]. Complementary efforts found evidence of both historical barriers that blocked the exchange of organisms between adjacent regions and historical corridors that allowed dispersal between currently isolated regions. The result has been a division of the Earth into a hierarchy of regions reflecting patterns of faunal and floral similarities (e.g. regions, subregions, provinces). Therefore a first ensuing question is: “how regional species pools have been assembled through time and space?”, which can be followed by a second question: “what are the ecological and evolutionary processes leading to differences in species richness among species pools?”. To address these questions, the study of Calatayud et al. [5] developed and performed an interesting approach relying on phylogenetic data to identify regional and sub-regional pools of European beetles (using the iconic ground beetle genus Carabus). Specifically, they analysed the processes responsible for the assembly of species pools, by comparing the effects of dispersal barriers, niche similarities and phylogenetic history. They found that Europe could be divided in seven modules that group zoogeographically distinct regions with their associated faunas, and identified a transition zone matching the limit of the ice sheets at Last Glacial Maximum (19k years ago). Deviance of species co-occurrences across regions, across sub-regions and within each region was significantly explained, primarily by environmental niche similarity, and secondarily by spatial connectivity, except for northern regions. Interestingly, southern species pools are mostly separated by dispersal barriers, whereas northern species pools are mainly sorted by their environmental niches. Another important finding of Calatayud et al. [5] is that most phylogenetic structuration occurred during the Pleistocene, and they show how extreme recent historical events (Quaternary glaciations) can profoundly modify the composition and structure of geographic species pools, as opposed to studies showing the role of deep-time evolutionary processes. The study of biogeographic assembly of species pools using phylogenies has never been more exciting and promising than today. Catalayud et al. [5] brings a nice study on the importance of Pleistocene glaciations along with geographical barriers and niche-based processes in structuring the regional faunas of European beetles. The successful development of powerful analytical tools in recent years, in conjunction with the rapid and massive increase in the availability of biological data (including molecular phylogenies, fossils, georeferrenced occurrences and ecological traits), will allow us to disentangle complex evolutionary histories. Although we still face important limitations in data availability and methodological shortcomings, the last decade has witnessed an improvement of our understanding of how historical and biotic triggers are intertwined on shaping the Earth’s stupendous biological diversity. I hope that the Catalayud et al.’s approach (and analytical framework) will help movement in that direction, and that it will provide interesting perspectives for future investigations of other regions. Applied to a European beetle radiation, they were able to tease apart the relative contributions of biotic (niche-based processes) versus abiotic (geographic barriers and climate change) factors. References [1] Rosenzweig ML. 1995. Species diversity in space and time. Cambridge: Cambridge University Press. | Pleistocene climate change and the formation of regional species pools | Joaquín Calatayud, Miguel Á. Rodríguez, Rafael Molina-Venegas, María Leo, José Luís Hórreo, Joaquín Hortal | <p>Despite the description of bioregions dates back from the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring... | | Phylogeography & Biogeography | Fabien Condamine | 2017-06-14 07:30:32 | ||
07 Aug 2023
Pollen-feeding delays reproductive senescence and maintains toxicity of Heliconius eratoImpact of pollen-feeding on egg-laying and cyanogenic glucoside abundance in red postman butterfliesRecommended by Adriana Briscoe based on reviews by Carol Boggs, Caroline Mueller and 1 anonymous reviewerGrowth, development and reproduction in animals are all limited by dietary nutrients. Expansion of an organism’s diet to sources not accessible to closely related species reduces food competition, and eases the constraints of nutrient-limited diets. Adult butterflies are herbivorous insects known to feed primarily on nectar from flowers, which is rich in sugars but poor in amino acids. Only certain species in the genus Heliconius are known to also feed on pollen, which is especially rich in amino acids, and is known to prolong their lives by several months. The ability to digest pollen in Heliconius has been linked to specialized feeding behaviors (Krenn et al. 2009) and extra-oral digestion using enzymes, possibly including duplicated copies of cocoonase (Harpel et al. 2016; Smith et al. 2016 and 2018), a protease used by some moths to digest silk upon eclosion from their cocoons. In this reprint, Pinheiro de Castro and colleagues investigated the impact of artificial and natural diets on egg-laying ability, body weight, and cyanogenic glucoside abundance in adult Heliconius erato butterflies of both sexes. Previous studies (Dunlap-Pianka et al. 1981) in H. charithonia demonstrated that access to dietary pollen led to extended egg-laying ability among adult female butterflies compared to females deprived of pollen, and compared to Dryas iulia females which feed only on nectar. In the current study, Pinheiro de Castro et al. (2023) examine the impact of diet on both young and old H. erato, over a longer period of time than the earlier work, highlighting the importance of extending the time period over which effects are evaluated. In addition to extending egg-laying ability in older females, the authors found that pollen in the diet appeared to maintain older female body weight, presumably because the pollen contained nutrients depleted during egg-laying. The authors then investigated the effects of nutrition on the production of cyanogenic glycoside defenses. Heliconius are aposematic butterflies that sequester cyanide-forming defense chemicals from food plants as larvae or synthesize these compounds de novo. The authors found the abundance of cyanogenic glycosides to be significantly greater in butterflies with access to pollen, but again only in older females. Curiously, field studies of male and female H. charithonia butterflies found that females in the wild collected more pollen than males (Mendoza-Cuenca and Macías-Ordóñez 2005). Taken together, these new findings raise the intriguing possibility that females collect more pollen than males, in part, because pollen has a bigger impact on female survival and reproduction. A small limitation of the study is the use of wing length, rather than body weight, at the zero time point. But the trend is clear in both males and females, and it adds supporting detail to the efficacy of pollen feeding as an unusual strategy for increasing fertility and survival in Heliconius butterflies.
References | Pollen-feeding delays reproductive senescence and maintains toxicity of Heliconius erato | Erika C. Pinheiro de Castro, Josie McPherson, Glennis Jullian, Anniina L. K. Mattila, Søren Bak, Stephen Montgomery, Chris Jiggins | <p>Dietary shifts may act to ease energetic constraints and allow organisms to optimise life-history traits. Heliconius butterflies differ from other nectar-feeders due to their unique ability to digest pollen, which provides a reliable source of ... | | Evolutionary Ecology, Life History | Adriana Briscoe | 2023-02-07 12:59:54 | ||
07 Sep 2018
Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineagesGenomic parallelism in adaptation to orthogonal environments in sea horsesRecommended by Yaniv Brandvain based on reviews by 2 anonymous reviewersStudies in speciation genomics have revealed that gene flow is quite common, and that despite this, species can maintain their distinct environmental adaptations. Although researchers are still elucidating the genomic mechanisms by which species maintain their adaptations in the face of gene flow, this often appears to involve few diverged genomic regions in otherwise largely undifferentiated genomes. In this preprint [1], Riquet and colleagues investigate the genetic structuring and patterns of parallel evolution in the long-snouted seahorse. References [1] Riquet, F., Liautard-Haag, C., Woodall, L., Bouza, C., Louisy, P., Hamer, B., Otero-Ferrer, F., Aublanc, P., Béduneau, V., Briard, O., El Ayari, T., Hochscheid, S. Belkhir, K., Arnaud-Haond, S., Gagnaire, P.-A., Bierne, N. (2018). Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages. bioRxiv, 161786, ver. 4 recommended and peer-reviewed by PCI Evol Biol. doi: 10.1101/161786 | Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages | Florentine Riquet, Cathy Liautard-Haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, Bojan Hamer, Francisco Otero-Ferrer, Philippe Aublanc, Vickie Béduneau, Olivier Briard, Tahani El Ayari, Sandra Hochscheid, Khalid Belkhir, Sophie Arnaud-Haond, Pi... | <p>Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the la... | | Hybridization / Introgression, Molecular Evolution, Population Genetics / Genomics, Speciation | Yaniv Brandvain | Kathleen Lotterhos, Sarah Fitzpatrick | 2017-07-11 13:12:40 | |
24 Mar 2023
Domestication of different varieties in the cheese-making fungus Geotrichum candidumDiverse outcomes in cheese fungi domesticationRecommended by Christelle Fraïsse based on reviews by Delphine Sicard and 1 anonymous reviewer
Domestication is a complex process that imprints the demography and the genomes of domesticated populations, enforcing strong selective pressures on traits favourable to humans, e.g. for food production [1]. Domestication has been quite intensely studied in plants and animals, but less so in micro-organisms such as fungi, despite their assets (e.g. their small genomes and tractability in the lab). This elegant study by Bennetot and collaborators [2] on the cheese-making fungus Geotrichum candidum adds to the mounting body of studies in the genomics of fungi, proving they are excellent models in evolutionary biology for studying adaptation and drift in eukaryotes [3]. Bennetot et al. newly showed with whole genome sequences that all G. candidum strains isolated from cheese form a monophyletic clade subdivided into three genetically differentiated populations with several admixed strains, while the wild strains sampled from diverse geographic locations form a sister clade. This suggests the wild progenitor was not sampled in the present study and calls for future exciting work on the domestication history of the G. candidum fungus. The authors scanned the genomes for footprints of adaptation to the cheese environment and identified promising candidates, such as a gene involved in iron uptake (this element is limiting in cheese). Their functional genome analysis also provides evidence for higher contents of transposable elements in cheese-making strains, likely due to relaxed selection during the domestication process. This paper is particularly impressive in that the authors complemented the population genomic approach with the phenotypic characterization of the strains and tested their ability to outcompete common fungal food spoilers. The authors convincingly showed that cheese-making strains display phenotypic differences relative to wild relatives for multiple traits such as slower growth, lower proteolysis activity and a greater amount of volatiles attractive to consumers, these phenotypes being beneficial for cheese making. Finally, this work is particularly inspiring because it thoroughly discusses convergent evolution during domestication in different cheese-associated fungi. Indeed, studying populations experiencing similar environmental pressures is fundamental to understanding whether evolution is repeatable [4]. For instance, all three cheese populations of G. candidum exhibit a lower genetic diversity than wild populations. However, only one population displays a stronger domestication syndrome, resembling the Penicillium camemberti situation [5]. Furthermore, different cheese-making practices may have led to varying situations with clonal lineages in non-Roquefort P. roqueforti and P. camemberti [5, 6], while the cheese-making G. candidum populations still harbour some diversity. In a nutshell, Bennetot's study makes an important contribution to evolutionary biology and highlights the value of diversifying our model organisms toward under-represented clades. REFERENCES [1] Diamond J (2002) Evolution, consequences and future of plant and animal domestication. Nature 418: 700–707. https://doi.org/10.1038/nature01019 [2] Bennetot B, Vernadet J-P, Perkins V, Hautefeuille S, Rodríguez de la Vega RC, O’Donnell S, Snirc A, Grondin C, Lessard M-H, Peron A-C, Labrie S, Landaud S, Giraud T, Ropars J (2023) Domestication of different varieties in the cheese-making fungus Geotrichum candidum. bioRxiv, 2022.05.17.492043, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.05.17.492043 [3] Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, de Vienne DM, Rodríguez de la Vega RC, Branco S, Giraud T (2014) Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol. Ecol. 23: 753–773. https://doi.org/10.1111/mec.12631 [4] Bolnick DI, Barrett RD, Oke KB, Rennison DJ, Stuart YE (2018) (Non)Parallel evolution. Ann. Rev. Ecol. Evol. Syst. 49: 303–330. https://doi.org/10.1146/annurev-ecolsys-110617-062240 [5] Ropars J, Didiot E, Rodríguez de la Vega RC, Bennetot B, Coton M, Poirier E, Coton E, Snirc A, Le Prieur S, Giraud T (2020) Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties. Current Biol. 30: 4441–4453.e4. https://doi.org/10.1016/j.cub.2020.08.082 [6] Dumas, E, Feurtey, A, Rodríguez de la Vega, RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A, Giraud T (2020) Independent domestication events in the blue-cheese fungus Penicillium roqueforti. Mol Ecol. 29: 2639–2660. https://doi.org/10.1111/mec.15359 | Domestication of different varieties in the cheese-making fungus *Geotrichum candidum* | Bastien Bennetot, Jean-Philippe Vernadet, Vincent Perkins, Sophie Hautefeuille, Ricardo C. Rodríguez de la Vega, Samuel O’Donnell, Alodie Snirc, Cécile Grondin, Marie-Hélène Lessard, Anne-Claire Peron, Steve Labrie, Sophie Landaud, Tatiana Giraud,... | <p>Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions. <em>Geotrichum candidum... | | Adaptation, Genome Evolution, Population Genetics / Genomics | Christelle Fraïsse | 2022-08-12 20:50:42 | ||
12 Apr 2017
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Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoesVectors as motors (of virus evolution)Recommended by Frédéric Fabre and Benoit MouryMany viruses are transmitted by biological vectors, i.e. organisms that transfer the virus from one host to another. Dengue virus (DENV) is one of them. Dengue is a mosquito-borne viral disease that has rapidly spread around the world since the 1940s. One recent estimate indicates 390 million dengue infections per year [1]. As many arthropod-borne vertebrate viruses, DENV has to cross several anatomical barriers in the vector, to multiply in its body and to invade its salivary glands before getting transmissible. As a consequence, vectors are not passive carriers but genuine hosts of the viruses that potentially have important effects on the composition of virus populations and, ultimately, on virus epidemiology and virulence. Within infected vectors, virus populations are expected to acquire new mutations and to undergo genetic drift and selection effects. However, the intensity of these evolutionary forces and the way they shape virus genetic diversity are poorly known. In their study, Lequime et al. [2] finely disentangled the effects of genetic drift and selection on DENV populations during their infectious cycle within mosquito (Aedes aegypti) vectors. They evidenced that the genetic diversity of viruses within their vectors is shaped by genetic drift, selection and vector genotype. The experimental design consisted in artificial acquisition of purified virus by mosquitoes during a blood meal. The authors monitored the diversity of DENV populations in Ae. aegypti individuals at different time points by high-throughput sequencing (HTS). They estimated the intensity of genetic drift and selection effects exerted on virus populations by comparing the DENV diversity at these sampling time points with the diversity in the purified virus stock (inoculum). Disentangling the effects of genetic drift and selection remains a methodological challenge because both evolutionary forces operate concomitantly and both reduce genetic diversity. However, selection reduces diversity in a reproducible manner among experimental replicates (here, mosquito individuals): the fittest variants are favoured at the expense of the weakest ones. In contrast, genetic drift reduces diversity in a stochastic manner among replicates. Genetic drift acts equally on all variants irrespectively of their fitness. The strength of genetic drift is frequently evaluated with the effective population size Ne: the lower Ne, the stronger the genetic drift [3]. The estimation of the effective population size of DENV populations by Lequime et al. [2] was based on single-nucleotide polymorphisms (SNPs) that were (i) present both in the inoculum and in the virus populations sampled at the different time points and (ii) that were neutral (or nearly-neutral) and therefore subjected to genetic drift only and insensitive to selection. As expected for viruses that possess small and constrained genomes, such neutral SNPs are extremely rare. Starting from a set of >1800 SNPs across the DENV genome, only three SNPs complied with the neutrality criteria and were enough represented in the sequence dataset for a precise Ne estimation. Using the method described by Monsion et al. [4], Lequime et al. [2] estimated Ne values ranging from 5 to 42 viral genomes (95% confidence intervals ranged from 2 to 161 founding viral genomes). Consequently, narrow bottlenecks occurred at the virus acquisition step, since the blood meal had allowed the ingestion of ca. 3000 infectious virus particles, on average. Interestingly, bottleneck sizes did not differ between mosquito genotypes. Monsion et al.’s [4] formula provides only an approximation of Ne. A corrected formula has been recently published [5]. We applied this exact Ne formula to the means and variances of the frequencies of the three neutral markers estimated before and after the bottlenecks (Table 1 in [2]), and nearly identical Ne estimates were obtained with both formulas. Selection intensity was estimated from the dN/dS ratio between the nonsynonymous and synonymous substitution rates using the HTS data on DENV populations. DENV genetic diversity increased following initial infection but was restricted by strong purifying selection during virus expansion in the midgut. Again, no differences were detected between mosquito genotypes. However and importantly, significant differences in DENV genetic diversity were detected among mosquito genotypes. As they could not be related to differences in initial genetic drift or to selection intensity, the authors raise interesting alternative hypotheses, including varying rates of de novo mutations due to differences in replicase fidelity or differences in the balancing selection regime. Interestingly, they also suggest that this observation could simply result from a methodological issue linked to the detection threshold of low-frequency SNPs. References [1] Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, Drake JM, et al. 2013. The global distribution and burden of dengue. Nature 496: 504–7 doi: 10.1038/nature12060 [2] Lequime S, Fontaine A, Gouilh MA, Moltini-Conclois I and Lambrechts L. 2016. Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes. PloS Genetics 12: e1006111 doi: 10.1371/journal.pgen.1006111 [3] Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics 10: 195-205 doi: 10.1038/nrg2526 [4] Monsion B, Froissart R, Michalakis Y and Blanc S. 2008. Large bottleneck size in cauliflower mosaic virus populations during host plant colonization. PloS Pathogens 4: e1000174 doi: 10.1371/journal.ppat.1000174 [5] Thébaud G and Michalakis Y. 2016. Comment on ‘Large bottleneck size in cauliflower mosaic virus populations during host plant colonization’ by Monsion et al. (2008). PloS Pathogens 12: e1005512 doi: 10.1371/journal.ppat.1005512 | Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes | Lequime S, Fontaine A, Gouilh MA, Moltini-Conclois I and Lambrechts L | <p>Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically... | | Evolutionary Dynamics, Molecular Evolution, Population Genetics / Genomics | Frédéric Fabre | 2017-04-10 14:26:04 | ||
19 Feb 2018
Genomic imprinting mediates dosage compensation in a young plant XY systemDosage compensation by upregulation of maternal X alleles in both males and females in young plant sex chromosomesRecommended by Tatiana Giraud and Judith Mank based on reviews by 3 anonymous reviewersSex chromosomes evolve as recombination is suppressed between the X and Y chromosomes. The loss of recombination on the sex-limited chromosome (the Y in mammals) leads to degeneration of both gene expression and gene content for many genes [1]. Loss of gene expression or content from the Y chromosome leads to differences in gene dose between males and females for X-linked genes. Because expression levels are often correlated with gene dose [2], these hemizygous genes have a lower expression levels in the heterogametic sex. This in turn disrupts the stoichiometric balance among genes in protein complexes that have components on both the sex chromosomes and autosomes [3], which could have serious deleterious consequences for the heterogametic sex. References | Genomic imprinting mediates dosage compensation in a young plant XY system | Aline Muyle, Niklaus Zemp, Cecile Fruchard, Radim Cegan, Jan Vrana, Clothilde Deschamps, Raquel Tavares, Franck Picard, Roman Hobza, Alex Widmer, Gabriel Marais | <p>During the evolution of sex chromosomes, the Y degenerates and its expression gets reduced relative to the X and autosomes. Various dosage compensation mechanisms that recover ancestral expression levels in males have been described in animals.... | | Bioinformatics & Computational Biology, Expression Studies, Genome Evolution, Molecular Evolution, Reproduction and Sex | Tatiana Giraud | 2017-09-20 20:39:46 | ||
24 Oct 2019
Testing host-plant driven speciation in phytophagous insects : a phylogenetic perspectivePhylogenetic approaches for reconstructing macroevolutionary scenarios of phytophagous insect diversificationRecommended by Hervé Sauquet based on reviews by Brian O'Meara and 1 anonymous reviewerPlant-animal interactions have long been identified as a major driving force in evolution. However, only in the last two decades have rigorous macroevolutionary studies of the topic been made possible, thanks to the increasing availability of densely sampled molecular phylogenies and the substantial development of comparative methods. In this extensive and thoughtful perspective [1], Jousselin and Elias thoroughly review current hypotheses, data, and available macroevolutionary methods to understand how plant-insect interactions may have shaped the diversification of phytophagous insects. First, the authors review three main hypotheses that have been proposed to lead to host-plant driven speciation in phytophagous insects: the ‘escape and radiate’, ‘oscillation’, and ‘musical chairs’ scenarios, each with their own set of predictions. Jousselin and Elias then synthesize a vast core of recent studies on different clades of insects, where explicit phylogenetic approaches have been used. In doing so, they highlight heterogeneity in both the methods being used and predictions being tested across these studies and warn against the risk of subjective interpretation of the results. Lastly, they advocate for standardization of phylogenetic approaches and propose a series of simple tests for the predictions of host-driven speciation scenarios, including the characterization of host-plant range history and host breadth history, and diversification rate analyses. This helpful review will likely become a new point of reference in the field and undoubtedly help many researchers formalize and frame questions of plant-insect diversification in future studies of phytophagous insects. References [1] Jousselin, E., Elias, M. (2019). Testing Host-Plant Driven Speciation in Phytophagous Insects: A Phylogenetic Perspective. arXiv, 1910.09510, ver. 1 peer-reviewed and recommended by PCI Evol Biol. https://arxiv.org/abs/1910.09510v1 | Testing host-plant driven speciation in phytophagous insects : a phylogenetic perspective | Emmanuelle Jousselin, Marianne Elias | <p>During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation. Phytophagous ... | | Macroevolution, Phylogenetics / Phylogenomics, Speciation, Species interactions | Hervé Sauquet | 2019-02-25 17:31:33 | ||
21 Nov 2019
Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticityNutrition-dependent effects of gut bacteria on growth plasticity in Drosophila melanogasterRecommended by Wolf Blanckenhorn based on reviews by Pedro Simões and 1 anonymous reviewerIt is well known that the rearing environment has strong effects on life history and fitness traits of organisms. Microbes are part of every environment and as such likely contribute to such environmental effects. Gut bacteria are a special type of microbe that most animals harbor, and as such they are part of most animals’ environment. Such microbial symbionts therefore likely contribute to local adaptation [1]. The main question underlying the laboratory study by Guilhot et al. [2] was: How much do particular gut bacteria affect the organismal phenotype, in terms of life history and larval foraging traits, of the fruit fly Drosophila melanogaster, a common laboratory model species in biology? References [1] Kawecki, T. J. and Ebert, D. (2004) Conceptual issues in local adaptation. Ecology Letters 7: 1225-1241. doi: 10.1111/j.1461-0248.2004.00684.x | Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity | Robin Guilhot, Antoine Rombaut, Anne Xuéreb, Kate Howell, Simon Fellous | <p>Environmentally acquired microbial symbionts could contribute to host adaptation to local conditions like vertically transmitted symbionts do. This scenario necessitates symbionts to have different effects in different environments. We investig... | | Adaptation, Evolutionary Ecology, Phenotypic Plasticity, Species interactions | Wolf Blanckenhorn | 2019-02-13 15:22:23 |
