|2020-02-17 ||Epistasis, inbreeding depression and the evolution of self-fertilization|
Diala Abu Awad and Denis Roze
Recommended by Sylvain Gandon based on reviews by Nick Barton and 1 anonymous reviewer
Epistasis and the evolution of selfing
The evolution of selfing results from a balance between multiple evolutionary forces. Selfing provides an "automatic advantage" due to the higher efficiency of selfers to transmit their genes via selfed and outcrossed offspring. Selfed offspring, however, may suffer from inbreeding depression. In principle the ultimate evolutionary outcome is easy to predict from the relative magnitude of these two evolutionary forces [1,2]. Yet, several studies explicitly taking into account the genetic archite...
|2020-01-23 ||A novel workflow to improve multi-locus genotyping of wildlife species: an experimental set-up with a known model system|
Gillingham, Mark A. F., Montero, B. Karina, Wilhelm, Kerstin, Grudzus, Kara, Sommer, Simone and Santos, Pablo S. C.
Recommended by François Rousset based on reviews by Thomas Bigot, Sebastian Ernesto Ramos-Onsins and Helena Westerdahl
Improving the reliability of genotyping of multigene families in non-model organisms
The reliability of published scientific papers has been the topic of much recent discussion, notably in the biomedical sciences . Although small sample size is regularly pointed as one of the culprits, big data can also be a concern. The advent of high-throughput sequencing, and the processing of sequence data by opaque bioinformatics workflows, mean that sequences with often high error rates are produced, and that exact but slow analyses are not feasible.
The troubles with bioinformatics ...
|2020-01-20 ||A young age of subspecific divergence in the desert locust Schistocerca gregaria, inferred by ABC Random Forest|
Marie-Pierre Chapuis, Louis Raynal, Christophe Plantamp, Christine N. Meynard, Laurence Blondin, Jean-Michel Marin, Arnaud Estoup
Recommended by Takeshi Kawakami and Concetta Burgarella based on reviews by Michael D Greenfield and 2 anonymous reviewers
Estimating recent divergence history: making the most of microsatellite data and Approximate Bayesian Computation approaches
The present-day distribution of extant species is the result of the interplay between their past population demography (e.g., expansion, contraction, isolation, and migration) and adaptation to the environment. Shedding light on the timing and magnitude of key demographic events helps identify potential drivers of such events and interaction of those drivers, such as life history traits and past episodes of environmental shifts. The understanding of the key factors driving species evolution give...
|2020-01-10 ||Probabilities of tree topologies with temporal constraints and diversification shifts|
Recommended by Nicolas Lartillot based on reviews by Amaury Lambert, Dominik Schrempf and 1 anonymous reviewer
Fitting diversification models on undated or partially dated trees
Phylogenetic trees can be used to extract information about the process of diversification that has generated them. The most common approach to conduct this inference is to rely on a likelihood, defined here as the probability of generating a dated tree T given a diversification model (e.g. a birth-death model), and then use standard maximum likelihood. This idea has been explored extensively in the context of the so-called diversification studies, with many variants for the models and for the q...
|2019-12-09 ||Systematics and geographical distribution of Galba species, a group of cryptic and worldwide freshwater snails|
Pilar Alda, Manon Lounnas, Antonio Alejandro Vázquez, Rolando Ayaqui, Manuel Calvopina, Maritza Celi-Erazo, Robert Dillon, Luisa Carolina González Ramírez, Eric S. Loker, Jenny Muzzio-Aroca, Alberto Orlando Nárvaez, Oscar Noya, Andrés Esteban Pereira, Luiggi Martini Robles, Richar Rodríguez-Hidalgo, Nelson Uribe, Patrice David, Philippe Jarne, Jean-Pierre Pointier, Sylvie Hurtrez-Boussès
Recommended by Fabien Condamine based on reviews by Christelle Fraïsse, Pavel Matos and Niklas Wahlberg
The challenge of delineating species when they are hidden
The science of naming species (taxonomy) has been renewed with the developments of molecular sequencing, digitization of museum specimens, and novel analytical tools. However, naming species can be highly subjective, sometimes considered as an art , because it is based on human-based criteria that vary among taxonomists. Nonetheless, taxonomists often argue that species names are hypotheses, which are therefore testable and refutable as new evidence is provided. This challenge comes with a mo...
|2019-12-09 ||Trait-specific trade-offs prevent niche expansion in two parasites|
Eva JP Lievens, Yannis Michalakis, Thomas Lenormand
Recommended by Frédéric Guillaume based on reviews by Seth Barribeau, Anne Duplouy and Cindy Gidoin
Trade-offs in fitness components and ecological source-sink dynamics affect host specialisation in two parasites of Artemia shrimps
Ecological specialisation, especially among parasites infecting a set of host species, is ubiquitous in nature. Host specialisation can be understood as resulting from trade-offs in parasite infectivity, virulence and growth. However, it is not well understood how variation in these trade-offs shapes the overall fitness trade-off a parasite faces when adapting to multiple hosts. For instance, it is not clear whether a strong trade-off in one fitness component may sufficiently constrain the evolu...
|2019-11-26 ||Pleiotropy or linkage? Their relative contributions to the genetic correlation of quantitative traits and detection by multi-trait GWA studies|
Jobran Chebib and Frédéric Guillaume
Recommended by Kathleen Lotterhos based on reviews by Pär Ingvarsson and 1 anonymous reviewer
Understanding the effects of linkage and pleiotropy on evolutionary adaptation
Genetic correlations among traits are ubiquitous in nature. However, we still have a limited understanding of the genetic architecture of trait correlations. Some genetic correlations among traits arise because of pleiotropy - single mutations or genotypes that have effects on multiple traits. Other genetic correlations among traits arise because of linkage among mutations that have independent effects on different traits. Teasing apart the differential effects of pleiotropy and linkage on trait...
|2019-11-21 ||Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity|
Robin Guilhot, Antoine Rombaut, Anne Xuéreb, Kate Howell, Simon Fellous
Recommended by Wolf Blanckenhorn based on reviews by Pedro Simões and 1 anonymous reviewer
Nutrition-dependent effects of gut bacteria on growth plasticity in Drosophila melanogaster
It 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 . The main question underlying the laboratory study by Guilhot et al.  was: How ...
|2019-11-20 ||Distribution of iridescent colours in hummingbird communities results from the interplay between selection for camouflage and communication|
Hugo Gruson, Marianne Elias, Juan L. Parra, Christine Andraud, Serge Berthier, Claire Doutrelant, Doris Gomez
Recommended by Sébastien Lavergne based on reviews by 2 anonymous reviewers
Feathers iridescence sheds light on the assembly rules of humingbirds communities
Ecology needs rules stipulating how species distributions and ecological communities should be assembled along environmental gradients, but few rules have yet emerged in the ecological literature. The search of ecogeographical rules governing the spatial variation of birds colours has recently known an upsurge of interest in the litterature . Most studies have, however, looked at pigmentary colours and not structural colours (e.g. iridescence), although it is know that color perception by ani...
|2019-11-07 ||New insights into the population genetics of partially clonal organisms: when seagrass data meet theoretical expectations|
Arnaud-Haond, Sophie, Stoeckel, Solenn, and Bailleul, Diane
Recommended by Olivier J Hardy based on reviews by Stacy Krueger-Hadfield, Ludwig TRIEST and 1 anonymous reviewer
Inferring rates of clonal versus sexual reproduction from population genetics data
In partially clonal organisms, genetic markers are often used to characterize the genotypic diversity of populations and infer thereof the relative importance of clonal versus sexual reproduction. Most studies report a measure of genotypic diversity based on a ratio, R, of the number of distinct multilocus genotypes over the sample size, and qualitatively interpret high / low R as indicating the prevalence of sexual / clonal reproduction. However, a theoretical framework allowing to quantify the...
|2019-10-24 ||Testing host-plant driven speciation in phytophagous insects : a phylogenetic perspective |
Emmanuelle Jousselin, Marianne Elias
Recommended by Hervé Sauquet based on reviews by Brian O'Meara and 1 anonymous reviewer
Phylogenetic approaches for reconstructing macroevolutionary scenarios of phytophagous insect diversification
Plant-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 , Jousselin and Elias thoroughly review current hypotheses, data, and available macroevolutionary methods to unders...
|2019-10-22 ||Geographic variation in adult and embryonic desiccation tolerance in a terrestrial-breeding frog|
Rudin-Bitterli, T, Evans, J. P. and Mitchell, N. J.
Recommended by Ben Phillips based on reviews by Juan Diego Gaitan-Espitia, Jennifer Nicole Lohr and 1 anonymous reviewer
Tough as old boots: amphibians from drier habitats are more resistant to desiccation, but less flexible at exploiting wet conditions
Species everywhere are facing rapid climatic change, and we are increasingly asking whether populations will adapt, shift, or perish . There is a growing realisation that, despite limited within-population genetic variation, many species exhibit substantial geographic variation in climate-relevant traits. This geographic variation might play an important role in facilitating adaptation to climate change [2,3].
Much of our understanding of geographic variation in climate-relevant traits com...
|2019-10-08 ||Strong habitat and weak genetic effects shape the lifetime reproductive success in a wild clownfish population|
Océane C. Salles, Glenn R. Almany, Michael L. Berumen, Geoffrey P. Jones, Pablo Saenz-Agudelo, Maya Srinivasan, Simon Thorrold, Benoit Pujol, Serge Planes
Recommended by Philip Munday based on reviews by Juan Diego Gaitan-Espitia and Loeske Kruuk
Habitat variation of wild clownfish population shapes selfrecruitment more than genetic effects
Estimating the genetic and environmental components of variation in reproductive success is crucial to understanding the adaptive potential of populations to environmental change. To date, the heritability of lifetime reproductive success (fitness) has been estimated in a handful of wild animal population, mostly in mammals and birds, but has never been estimated for a marine species. The primary reason that such estimates are lacking in marine species is that most marine organisms have a disper...
|2019-09-13 ||Deceptive combined effects of short allele dominance and stuttering: an example with Ixodes scapularis, the main vector of Lyme disease in the U.S.A.|
Thierry De Meeûs, Cynthia T. Chan, John M. Ludwig, Jean I. Tsao, Jaymin Patel, Jigar Bhagatwala, and Lorenza Beati
Recommended by Aurelien Tellier based on reviews by Martin Husemann, Eric Petit and 2 anonymous reviewers
New curation method for microsatellite markers improves population genetics analyses
Genetic markers are used for in modern population genetics/genomics to uncover the past neutral and selective history of population and species. Besides Single Nucleotide Polymorphisms (SNPs) obtained from whole genome data, microsatellites (or Short Tandem Repeats, SSR) have been common markers of choice in numerous population genetics studies of non-model species with large sample sizes . Microsatellites can be used to uncover and draw inference of the past population demography (e.g. expan...
|2019-09-04 ||The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates|
Solenn Stoeckel, Barbara Porro, Sophie Arnaud-Haond
Recommended by Myriam Heuertz based on reviews by David Macaya-Sanz, Marcela Van Loo and 1 anonymous reviewer
How to estimate clonality from genetic data: use large samples and consider the biology of the species
Population geneticists frequently use the genetic and genotypic information of a population sample of individuals to make inferences on the reproductive system of a species. The detection of clones, i.e. individuals with the same genotype, can give information on whether there is clonal (vegetative) reproduction in the species. If clonality is detected, population geneticists typically use genotypic richness R, the number of distinct genotypes relative to the sample size, to estimate the rate of...
|2019-08-28 ||Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals|
Marjolaine Rousselle, Paul Simion, Marie-Ka Tilak, Emeric Figuet, Benoit Nabholz, Nicolas Galtier
Recommended by Georgii Bazykin based on reviews by David Enard, Konstantin Popadin and 1 anonymous reviewer
To tinker, evolution needs a supply of spare parts
Is evolution adaptive? Not if there is no variation for natural selection to work with. Theory predicts that how fast a population can adapt to a new environment can be limited by the supply of new mutations coming into it. This supply, in turn, depends on two things: how often mutations occur and in how many individuals. If there are few mutations, or few individuals in whom they can originate, individuals will be mostly identical in their DNA, and natural selection will be impotent.
|2019-07-22 ||Transgenerational plasticity of inducible defenses: combined effects of grand-parental, parental and current environments|
Juliette Tariel; Sandrine Plénet; Emilien Luquet
Recommended by Troy Day based on reviews by Stewart Plaistow and 1 anonymous reviewer
Transgenerational plasticity through three generations
Organisms very often display phenotypic plasticity, whereby the expression of trait (or suite of traits) changes in a consistent way as a function of some environmental variable. Sometimes this plastic response remains labile and so the trait continues to respond to the environment throughout an organism’s life, but there are also many examples in which environmental conditions during a critical developmental window irreversibly set the stage for how a trait will be expressed later in life.
|2019-07-10 ||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
Recommended by Nicolas Galtier based on reviews by 2 anonymous reviewers
The scandalous pest
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 ...
|2019-06-11 ||A bird’s white-eye view on neosex chromosome evolution|
Thibault Leroy, Yoann Anselmetti, Marie-Ka Tilak, Sèverine Bérard, Laura Csukonyi, Maëva Gabrielli, Céline Scornavacca, Borja Milá, Christophe Thébaud, Benoit Nabholz
Recommended by Kateryna Makova based on reviews by Gabriel Marais, Melissa Wilson and 1 anonymous reviewer
Young sex chromosomes discovered in white-eye birds
Recent advances in next-generation sequencing are allowing us to uncover the evolution of sex chromosomes in non-model organisms. This study  represents an example of this application to birds of two Sylvioidea species from the genus Zosterops (commonly known as white-eyes). The study is exemplary in the amount and types of data generated and in the thoroughness of the analysis applied. Both male and female genomes were sequenced to allow the authors to identify sex-chromosome specific scaf...
|2019-06-06 ||Multi-model inference of non-random mating from an information theoretic approach|
Recommended by Sara Magalhaes and Alexandre Courtiol based on reviews by Alexandre Courtiol and 2 anonymous reviewers
Tell me who you mate with, I’ll tell you what’s going on
The study of sexual selection goes as far as Darwin himself. Since then, elaborate theories concerning both intra- and inter-sexual sexual have been developed, and elegant experiments have been designed to test this body of theory. It may thus come as a surprise that the community is still debating on the correct way to measure simple components of sexual selection, such as the Bateman gradient (i.e., the covariance between the number of matings and the number of offspring)[1,2], or to quantify ...
|2019-06-04 ||Thermal regimes, but not mean temperatures, drive patterns of rapid climate adaptation at a continent-scale: evidence from the introduced European earwig across North America|
Jean-Claude Tourneur, Joël Meunier
Recommended by Fabien Aubret based on reviews by Eric Gangloff and Ben Phillips
Temperature variance, rather than mean, drives adaptation to local climate
Climate change is impacting eco-systems worldwide and driving many populations to move, adapt or go extinct. It is increasingly appreciated, for example, that species may adjust their phenology in response to climate change, although empirical data is scarce. In this preprint , Tourneur and Meunier report an impressive sampling effort in which life-history traits were measured across introduced populations of earwig in North America. The authors examine whether variation in life-history acr...
|2019-06-03 ||Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network|
Maud Irène Tenaillon, Khawla Sedikki, Maeva Mollion, Martine Le Guilloux, Elodie Marchadier, Adrienne Ressayre, Christine Dillmann
Recommended by Tanja Pyhäjärvi based on reviews by Laura Shannon and 2 anonymous reviewers
Early and late flowering gene expression patterns in maize
Artificial selection experiments are key experiments in evolutionary biology. The demonstration that application of selective pressure across multiple generations results in heritable phenotypic changes is a tangible and reproducible proof of the evolution by natural selection.
Artificial selection experiments are used to evaluate the joint effects of selection on multiple traits, their genetic covariances and differences in responses in different environments. Most studies on artificial sele...
|2019-05-06 ||When sinks become sources: adaptive colonization in asexuals|
Florian Lavigne, Guillaume Martin, Yoann Anciaux, Julien Papaïx, Lionel Roques
Recommended by François Blanquart and Florence Débarre based on reviews by 3 anonymous reviewers
Fisher to the rescue
The ability of a population to adapt to a new niche is an important phenomenon in evolutionary biology. The colonisation of a new volcanic island by plant species; the colonisation of a host treated by antibiotics by a-resistant strain; the Ebola virus transmitting from bats to humans and spreading epidemically in Western Africa, are all examples of a population invading a new niche, adapting and eventually establishing in this new environment.
Adaptation to a new niche can be studied using s...
|2019-03-28 ||Ancient tropical extinctions contributed to the latitudinal diversity gradient|
Andrea S. Meseguer, Fabien Condamine
Recommended by Joaquín Hortal and Juan Arroyo based on reviews by Juan Arroyo, Joaquin Calatayud, Joaquín Hortal, Arne Mooers and 2 anonymous reviewers
One (more) step towards a dynamic view of the Latitudinal Diversity Gradient
The Latitudinal Diversity Gradient (LDG) has fascinated natural historians, ecologists and evolutionary biologists ever since  described it about 200 years ago . Despite such interest, agreement on the origin and nature of this gradient has been elusive. Several tens of hypotheses and models have been put forward as explanations for the LDG [2-3], that can be grouped in ecological, evolutionary and historical explanations  (see also ). These explanations can be reduced to no less tha...
|2019-03-25 ||The joint evolution of lifespan and self-fertilisation|
Thomas Lesaffre, Sylvain Billiard
Recommended by Thomas Bataillon based on reviews by 2 anonymous reviewers
Evolution of selfing & lifespan 2.0
Flowering plants display a staggering diversity of both mating systems and life histories, ranging from almost exclusively selfers to obligate outcrossers, very short-lived annual herbs to super long lived trees. One pervasive pattern that has attracted considerable attention is the tight correlation that is found between mating systems and lifespan . Until recently, theoretical explanations for these patterns have relied on static models exploring the consequences of several non-mutually exc...
|2019-02-15 ||Architectural traits constrain the evolution of unisexual flowers and sexual segregation within inflorescences: an interspecific approach|
Rubén Torices, Ana Afonso, Arne A. Anderberg, José M. Gómez and Marcos Méndez
Recommended by Juan Arroyo based on reviews by 3 anonymous reviewers
Sometimes, sex is in the head
Plants display an amazing diversity of reproductive strategies with and without sex. This diversity is particularly remarkable in flowering plants, as highlighted by Charles Darwin, who wrote several botanical books scrutinizing plant reproduction. One particularly influential work concerned floral variation . Darwin recognized that flowers may present different forms within a single population, with or without sex specialization. The number of species concerned is small, but they display rec...
|2019-02-08 ||Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes|
Anouk Willemsen, Marta Félez-Sánchez, and Ignacio G. Bravo
Recommended by Hirohisa Kishino based on reviews by Leonardo de Oliveira Martins and 1 anonymous reviewer
E5, the third oncogene of Papillomavirus
Papillomaviruses (PVs) infect almost all mammals and possibly amniotes and bony fishes. While most of them have no significant effects on the hosts, some induce physical lesions. Phylogeny of PVs consists of a few crown groups , among which AlphaPVs that infect primates including human have been well studied. They are associated to largely different clinical manifestations: non-oncogenic PVs causing anogenital warts, oncogenic and non-oncogenic PVs causing mucosal lesions, and non-oncogenic P...
|2019-02-05 ||The quiescent X, the replicative Y and the Autosomes|
Guillaume Achaz, Serge Gangloff, Benoit Arcangioli
Recommended by Nicolas Galtier based on reviews by Robert Lanfear and Marc Robinson-Rechavi
Replication-independent mutations: a universal signature ?
Mutations are the primary source of genetic variation, and there is an obvious interest in characterizing and understanding the processes by which they appear. One particularly important question is the relative abundance, and nature, of replication-dependent and replication-independent mutations - the former arise as cells replicate due to DNA polymerization errors, whereas the latter are unrelated to the cell cycle. A recent experimental study in fission yeast identified a signature of mutatio...
|2019-01-13 ||Why cooperation is not running away|
Félix Geoffroy, Nicolas Baumard, Jean-Baptiste André
Recommended by Erol Akcay based on reviews by 2 anonymous reviewers
A nice twist on partner choice theory
In this paper, Geoffroy et al.  deal with partner choice as a mechanism of maintaining cooperation, and argues that rather than being unequivocally a force towards improved payoffs to everyone through cooperation, partner choice can lead to “over-cooperation” where individuals can evolve to invest so much in cooperation that the costs of cooperating partially or fully negate the benefits from it. This happens when partner choice is consequential and effective, i.e., when interactions are ...
|2019-01-10 ||Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce|
Jun Chen, Lili Li, Pascal Milesi, Gunnar Jansson, Mats Berlin, Bo Karlsson, Jelena Aleksic, Giovanni G Vendramin, Martin Lascoux
Recommended by Jason Holliday based on reviews by 2 anonymous reviewers
Disentangling the recent and ancient demographic history of European spruce species
Genetic diversity in temperate and boreal forests tree species has been strongly affected by late Pleistocene climate oscillations [2,3,5], but also by anthropogenic forces. Particularly in Europe, where a long history of human intervention has re-distributed species and populations, it can be difficult to know if a given forest arose through natural regeneration and gene flow or through some combination of natural and human-mediated processes. This uncertainty can confound inferences of the cau...
|2019-01-02 ||Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica|
Michael D. Pirie, Martha Kandziora, Nicolai M. Nuerk, Nicholas C. Le Maitre, Ana Laura Mugrabi de Kuppler, Berit Gehrke, Edward G.H. Oliver, and Dirk U. Bellstedt
Recommended by Andrea S. Meseguer based on reviews by Florian Boucher, Simon Joly and 2 anonymous reviewers
The colonization history of largely isolated habitats
The build-up of biodiversity is the result of in situ speciation and immigration, with the interplay between geographical distance and ecological suitability determining the probability of an organism to establish in a new area. The relative contribution of these factors have long interested biogeographers, in particular to explain the distribution of organisms adapted to habitats that remained largely isolated, such as the colonization of oceanic islands or land waters. The focus of this study ...
|2018-12-13 ||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
Recommended by Ignacio Bravo based on reviews by Alejandro Manzano-Marín and 1 anonymous reviewer
Genetic intimacy of filamentous viruses and endoparasitoid wasps
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 ...
|2018-12-13 ||Separate the wheat from the chaff: genomic analysis of local adaptation in the red coral Corallium rubrum|
Pratlong M, Haguenauer A, Brener K, Mitta G, Toulza E, Garrabou J, Bensoussan N, Pontarotti P, Aurelle D
Recommended by Guillaume Achaz based on reviews by Lucas Gonçalves da Silva and 1 anonymous reviewer
Pros and Cons of local adaptation scans
The preprint by Pratlong et al.  is a well thought quest for genomic regions involved in local adaptation to depth in a species a red coral living the Mediterranean Sea. It first describes a pattern of structuration and then attempts to find candidate genes involved in local adaptation by contrasting deep with shallow populations. Although the pattern of structuration is clear and meaningful, the candidate genomic regions involved in local adaptation remain to be confirmed. Two external revie...
|2018-11-21 ||Convergent evolution as an indicator for selection during acute HIV-1 infection|
Frederic Bertels, Karin J Metzner, Roland R Regoes
Recommended by Guillaume Achaz based on reviews by Jeffrey Townsend and 2 anonymous reviewers
Is convergence an evidence for positive selection?
The preprint by Bertels et al.  reports an interesting application of the well-accepted idea that positively selected traits (here variants) can appear several times independently; think about the textbook examples of flight capacity. Hence, the authors assume that reciprocally convergence implies positive selection. The methodology becomes then, in principle, straightforward as one can simply count variants in independent datasets to detect convergent mutations.
In this preprint, the ...
|2018-11-16 ||Fine-grained habitat-associated genetic connectivity in an admixed population of mussels in the small isolated Kerguelen Islands|
Christelle Fraïsse, Anne Haguenauer, Karin Gerard, Alexandra Anh-Thu Weber, Nicolas Bierne, Anne Chenuil
Recommended by Marianne Elias based on reviews by Thomas Broquet and Tatiana Giraud
Introgression from related species reveals fine-scale structure in an isolated population of mussels and causes patterns of genetic-environment associations
Assessing population connectivity is central to understanding population dynamics, and is therefore of great importance in evolutionary biology and conservation biology. In the marine realm, the apparent absence of physical barriers, large population sizes and high dispersal capacities of most organisms often result in no detectable structure, thereby hindering inferences of population connectivity. In a review paper, Gagnaire et al.  propose several ideas to improve detection of population c...
|2018-11-09 ||Field evidence for manipulation of mosquito host selection by the human malaria parasite, Plasmodium falciparum|
Amelie Vantaux, Franck Yao, Domonbabele FdS Hien, Edwige Guissou, Bienvenue K Yameogo, Louis-Clement Gouagna, Didier Fontenille, Francois Renaud, Frederic Simard, Carlo Constantini, Frederic Thomas, Karine Mouline, Benjamin Roche, Anna Cohuet, Kounbobr R Dabire, Thierry Lefevre
Recommended by Alison Duncan based on reviews by Ricardo S. Ramiro, Olivier Restif and 1 anonymous reviewer
Malaria host manipulation increases probability of mosquitoes feeding on humans
Parasites can manipulate their host’s behaviour to ensure their own transmission. These manipulated behaviours may be outside the range of ordinary host activities , or alter the crucial timing and/or location of a host’s regular activity. Vantaux et al show that the latter is true for the human malaria parasite, Plasmodium falciparum . They demonstrate that three species of Anopheles mosquito were 24% more likely to choose human hosts, rather than other vertebrates, for their bloo...
|2018-10-03 ||Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plants|
Andrew J. Tanentzap, Javier Igea, Matthew G. Johnston, Matthew J. Larcombe
Recommended by Arne Mooers based on reviews by Dan Greenberg and 1 anonymous reviewer
Are both very young and the very old plant lineages at heightened risk of extinction?
Human economic activity is responsible for the vast majority of ongoing extinction, but that does not mean lineages are being affected willy-nilly. For amphibians  and South African flowering plants , young species have a somewhat higher than expected chance of being threatened with extinction. In contrast, older Australian marsupial lineages seem to be more at risk . Both of the former studies suggested that situations leading to peripheral isolation might simultaneously increase on...
|2018-09-07 ||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, Pierre-Alexandre Gagnaire, Nicolas Bierne
Recommended by Yaniv Brandvain based on reviews by 2 anonymous reviewers
Genomic parallelism in adaptation to orthogonal environments in sea horses
Studies 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 , Riquet and colleagues investigate the genetic structuring and patterns of...
|2018-08-08 ||Sexual selection and inbreeding: two efficient ways to limit the accumulation of deleterious mutations|
E. Noël, E. Fruitet, D. Lelaurin, N. Bonel, A. Ségard, V. Sarda, P. Jarne and P. David
Recommended by Charles Baer based on reviews by 2 anonymous reviewers
Inbreeding compensates for reduced sexual selection in purging deleterious mutations
Two evolutionary processes have been shown in theory to enhance the effects of natural selection in purging deleterious mutations from a population (here ""natural"" selection is defined as ""selection other than sexual selection""). First, inbreeding, especially self-fertilization, facilitates the removal of deleterious recessive alleles, the effects of which are largely hidden from selection in heterozygotes when mating is random. Second, sexual selection can facilitate the removal of delete...
|2018-07-06 ||Variation in competitive ability with mating system, ploidy and range expansion in four Capsella species|
Xuyue Yang, Martin Lascoux and Sylvain Glémin
Recommended by Sylvain Billiard and Henrique Teotonio based on reviews by Yaniv Brandvain, Henrique Teotonio and 1 anonymous reviewer
When ecology meets genetics: Towards an integrated understanding of mating system transitions and diversity
In the 19th century, C. Darwin and F. Delpino engaged in a debate about the success of species with different reproduction modes, with the later favouring the idea that monoecious plants capable of autonomous selfing could spread more easily than dioecious plants (or self-incompatible hermaphroditic plants) if cross-pollination opportunities were limited . Since then, debate has never faded about how natural selection is responsible for transitions to selfing and can explain the diversity and...
|2018-06-12 ||Transgenerational cues about local mate competition affect offspring sex ratios in the spider mite Tetranychus urticae|
Alison B. Duncan, Cassandra Marinosci, Céline Devaux, Sophie Lefèvre, Sara Magalhães, Joanne Griffin, Adeline Valente, Ophélie Ronce, Isabelle Olivieri
Recommended by Dries Bonte based on reviews by 2 anonymous reviewers
Maternal effects in sex-ratio adjustment
Optimal sex ratios have been topic of extensive studies so far. Fisherian 1:1 proportions of males and females are known to be optimal in most (diploid) organisms, but many deviations from this golden rule are observed. These deviations not only attract a lot of attention from evolutionary biologists but also from population ecologists as they eventually determine long-term population growth. Because sex ratios are tightly linked to fitness, they can be under strong selection or plastic in resp...
|2018-06-05 ||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
Recommended by Fabien Condamine based on reviews by 3 anonymous reviewers
Recent assembly of European biogeographic species pool
Biodiversity is unevenly distributed over time, space and the tree of life . 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 . 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. Wa...
|2018-06-05 ||The dynamics of preferential host switching: host phylogeny as a key predictor of parasite prevalence and distribution|
Jan Engelstaedter & Nicole Fortuna
Recommended by Lucy Weinert based on reviews by Damien de Vienne and Nathan Medd
Shift or stick? Untangling the signatures of biased host switching, and host-parasite co-speciation
Many emerging diseases arise by parasites switching to new host species, while other parasites seem to remain with same host lineage for very long periods of time, even over timescales where an ancestral host species splits into two or more new species. The ability to understand these dynamics would form an important part of our understanding of infectious disease.
Experiments are clearly important for understanding these processes, but so are comparative studies, investigating the variation...
|2018-06-03 ||Cost of resistance: an unreasonably expensive concept|
Thomas Lenormand, Noemie Harmand, Romain Gallet
Recommended by Inês Fragata and Claudia Bank based on reviews by Helen Alexander, Danna Gifford and 1 anonymous reviewer
Let’s move beyond costs of resistance!
The increase in the prevalence of (antibiotic) resistance has become a major global health concern and is an excellent example of the impact of real-time evolution on human society. This has led to a boom of studies that investigate the mechanisms and factors involved in the evolution of resistance, and to the spread of the concept of "costs of resistance". This concept refers to the relative fitness disadvantage of a drug-resistant genotype compared to a non-resistant reference genotype in the ...
|2018-05-18 ||Modularity of genes involved in local adaptation to climate despite physical linkage|
Katie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken, Kathryn Hodgins
Recommended by Sebastian Ernesto Ramos-Onsins based on reviews by Tanja Pyhäjärvi and 1 anonymous reviewer
Differential effect of genes in diverse environments, their role in local adaptation and the interference between genes that are physically linked
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 gene...
|2018-03-19 ||Natural selection on plasticity of thermal traits in a highly seasonal environment|
Leonardo Bacigalupe, Juan Diego Gaitan-Espitia, Aura M Barria, Avia Gonzalez-Mendez, Manuel Ruiz-Aravena, Mark Trinder, Barry Sinervo
Recommended by Wolf Blanckenhorn based on reviews by Nadia Aubin-Horth, Wolf Blanckenhorn and Dries Bonte
Is thermal plasticity itself shaped by natural selection? An assessment with desert frogs
It is well known that climatic factors – most notably temperature, season length, insolation and humidity – shape the thermal niche of organisms on earth through the action of natural selection. But how is this achieved precisely? Much of thermal tolerance is actually mediated by phenotypic plasticity (as opposed to genetic adaptation). A prominent expectation is that environments with greater (daily and/or annual) thermal variability select for greater plasticity, i.e. better acclimation ca...
|2018-02-28 ||Insects and incest: sib-mating tolerance in natural populations of a parasitoid wasp|
Marie Collet, Isabelle Amat, Sandrine Sauzet, Alexandra Auguste, Xavier Fauvergue, Laurence Mouton, Emmanuel Desouhant
Recommended by Caroline Nieberding and Bertanne Visser based on reviews by 2 anonymous reviewers
Incestuous insects in nature despite occasional fitness costs
Inbreeding, or mating between relatives, generally lowers fitness . Mating between genetically similar individuals can result in higher levels of homozygosity and consequently a higher frequency with which recessive disease alleles may be expressed within a population. Reduced fitness as a consequence of inbreeding, or inbreeding depression, can vary between individuals, sexes, populations and species , but remains a pervasive challenge for many organisms with small local population sizes,...
|2018-02-19 ||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
Recommended by Tatiana Giraud and Judith Mank based on reviews by 3 anonymous reviewers
Dosage compensation by upregulation of maternal X alleles in both males and females in young plant sex chromosomes
Sex 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 . 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 , these hemizygous genes have a lower expression leve...
|2018-02-09 ||Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak|
Simon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
Recommended by Samuel Alizon based on reviews by Christian Althaus, Chris Wymant and 1 anonymous reviewer
Simulating the effect of public health interventions using dated virus sequences and geographical data
Perhaps because of its deadliness, the 2013-2016 Ebola Virus (EBOV) epidemics in West-Africa has led to unprecedented publication and sharing of full virus genome sequences. This was both rapid (90 full genomes were shared within weeks ) and important (more than 1500 full genomes have been released overall ). Furthermore, the availability of the metadata (especially GPS location) has led to depth analyses of the geographical spread of the epidemics .
In their work, Dellicour et al. [...
|2018-01-31 ||Identifying drivers of parallel evolution: A regression model approach|
Susan F Bailey, Qianyun Guo, Thomas Bataillon
Recommended by Stephanie Bedhomme based on reviews by Bastien Boussau and 1 anonymous reviewer
A new statistical tool to identify the determinant of parallel evolution
In experimental evolution followed by whole genome resequencing, parallel evolution, defined as the increase in frequency of identical changes in independent populations adapting to the same environment, is often considered as the product of similar selection pressures and the parallel changes are interpreted as adaptive.
However, theory predicts that heterogeneity both in mutation rate and selection intensity across the genome can trigger patterns of parallel evolution. It is thus important...
|2017-12-20 ||Renewed diversification following Miocene landscape turnover in a Neotropical butterfly radiation|
Nicolas Chazot, Keith R. Willmott, Gerardo Lamas, André V.L. Freitas, Florence Piron-Prunier, Carlos F. Arias, James Mallet, Donna Lisa De-Silva, Marianne Elias
Recommended by Richard H Ree based on reviews by Delano Lewis and 1 anonymous reviewer
The influence of environmental change over geological time on the tempo and mode of biological diversification, revealed by Neotropical butterflies
The influence of environmental change over geological time on the tempo and mode of biological diversification is a hot topic in biogeography. Of central interest are questions about where, when, and how fast lineages proliferated, suffered extinction, and migrated in response to tectonic events, the waxing and waning of dominant biomes, etc. In this context, the dynamic conditions of the Miocene have received much attention, from studies of many clades and biogeographic regions. Here, Chazot et...
|2017-12-18 ||Co-evolution of virulence and immunosuppression in multiple infections|
Tsukushi Kamiya, Nicole Mideo, Samuel Alizon
Recommended by Sara Magalhaes based on reviews by 2 anonymous reviewers
Two parasites, virulence and immunosuppression: how does the whole thing evolve?
How parasite virulence evolves is arguably the most important question in both the applied and fundamental study of host-parasite interactions. Typically, this research area has been progressing through the formalization of the problem via mathematical modelling. This is because the question is a complex one, as virulence is both affected and affects several aspects of the host-parasite interaction. Moreover, the evolution of virulence is a problem in which ecology (epidemiology) and evolution (...
|2017-12-05 ||Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data|
Emeric Figuet, Marion Ballenghien, Nicolas Lartillot, Nicolas Galtier
Recommended by Bruce Rannala based on reviews by Bruce Rannala and 1 anonymous reviewer
Predicting small ancestors using contemporary genomes of large mammals
Recent methodological developments and increased genome sequencing efforts have introduced the tantalizing possibility of inferring ancestral phenotypes using DNA from contemporary species. One intriguing application of this idea is to exploit the apparent correlation between substitution rates and body size to infer ancestral species' body sizes using the inferred patterns of substitution rate variation among species lineages based on genomes of extant species .
The recommended paper by F...
|2017-11-20 ||Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection|
Diala Abu Awad and Denis Roze
Recommended by Aneil F. Agrawal based on reviews by Frédéric Guillaume and 1 anonymous reviewer
Understanding genetic variance, load, and inbreeding depression with selfing
A classic problem in evolutionary biology is to understand the genetic variance in fitness. The simplest hypothesis is that variation exists, even in well-adapted populations, as a result of the balance between mutational input and selective elimination. This variation causes a reduction in mean fitness, known as the mutation load. Though mutation load is difficult to quantify empirically, indirect evidence of segregating genetic variation in fitness is often readily obtained by comparing the f...
|2017-11-17 ||ABC random forests for Bayesian parameter inference|
Louis Raynal, Jean-Michel Marin, Pierre Pudlo, Mathieu Ribatet, Christian P. Robert, Arnaud Estoup
Recommended by Michael Blum based on reviews by Michael Blum and Dennis Prangle
Machine learning methods are useful for Approximate Bayesian Computation in evolution and ecology
It is my pleasure to recommend the paper by Raynal et al.  about using random forest for parameter inference. There are two reviews about the paper, one review written by Dennis Prangle and another review written by myself. Both reviews were positive and included comments that have been addressed in the current version of the preprint.
The paper nicely shows that modern machine learning approaches are useful for Approximate Bayesian Computation (ABC) and more generally for simulation-dri...
|2017-11-13 ||Epidemiological trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen population|
Frederic Suffert, Henriette Goyeau, Ivan Sache, Florence Carpentier, Sandrine Gelisse, David Morais, Ghislain Delestre
Recommended by Benoit Moury based on reviews by Benoit Moury and 1 anonymous reviewer
The pace of pathogens’ adaptation to their host plants
Because of their shorter generation times and larger census population sizes, pathogens are usually ahead in the evolutionary race with their hosts. The risks linked to pathogen adaptation are still exacerbated in agronomy, where plant and animal populations are not freely evolving but depend on breeders and growers, and are usually highly genetically homogeneous. As a consequence, the speed of pathogen adaptation is crucial for agriculture sustainability. Unraveling the time scale required for ...
|2017-11-10 ||Rates of Molecular Evolution Suggest Natural History of Life History Traits and a Post-K-Pg Nocturnal Bottleneck of Placentals|
Wu J, Yonezawa T, Kishino H.
Recommended by Nicolas Galtier and Belinda Chang
A new approach to DNA-aided ancestral trait reconstruction in mammals
Reconstructing ancestral character states is an exciting but difficult problem. The fossil record carries a great deal of information, but it is incomplete and not always easy to connect to data from modern species. Alternatively, ancestral states can be estimated by modelling trait evolution across a phylogeny, and fitting to values observed in extant species. This approach, however, is heavily dependent on the underlying assumptions, and typically results in wide confidence intervals.
|2017-11-07 ||MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers|
Cédric Chauve, Akbar Rafiey, Adrian A. Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J Szöllosi, Vincent Daubin, and Eric Tannier
Recommended by Tatiana Giraud and Toni Gabaldon based on reviews by Mukul Bansal, Alexandros Stamatakis and 2 anonymous reviewers
Dating nodes in a phylogeny using inferred horizontal gene transfers
Dating nodes in a phylogeny is an important problem in evolution and is typically performed by using molecular clocks and fossil age estimates . The manuscript by Chauve et al.  reports a novel method, which uses lateral gene transfers to help ordering nodes in a species tree. The idea is that a lateral gene transfer can only occur between two species living at the same time, which indirectly informs on node relative ages in a phylogeny: the donor species cannot be more recent than the r...
|2017-10-06 ||Evolutionary analysis of candidate non-coding elements regulating neurodevelopmental genes in vertebrates|
Francisco J. Novo
Recommended by Marc Robinson-Rechavi based on reviews by Charles Danko and Marc Robinson-Rechavi
Combining molecular information on chromatin organisation with eQTLs and evolutionary conservation provides strong candidates for the evolution of gene regulation in mammalian brains
In this manuscript , Francisco J. Novo proposes candidate non-coding genomic elements regulating neurodevelopmental genes.
What is very nice about this study is the way in which public molecular data, including physical interaction data, is used to leverage recent advances in our understanding to molecular mechanisms of gene regulation in an evolutionary context. More specifically, evolutionarily conserved non coding sequences are combined with enhancers from the FANTOM5 project, DNAse ...
|2017-10-05 ||Using Connectivity To Identify Climatic Drivers Of Local Adaptation|
Stewart L. Macdonald, John Llewelyn, Ben Phillips
Recommended by Ruth Arabelle Hufbauer based on reviews by Ruth Arabelle Hufbauer and Thomas Lenormand
A new approach to identifying drivers of local adaptation
Local adaptation, the higher fitness a population achieves in its local “home” environment relative to other environments is a crucial phase in the divergence of populations, and as such both generates and maintains diversity. Local adaptation is enhanced by selection and genetic variation in the relevant traits, and decreased by gene flow and genetic drift.
Demonstrating local adaptation is laborious, and is typically done with a reciprocal transplant design , documenting repeated g...
|2017-09-29 ||Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent|
Michael D. Pirie, Paul J. M. Maas, Rutger A. Wilschut, Heleen Melchers-Sharrott & Lars W. Chatrou
Recommended by Hervé Sauquet based on reviews by Thomas Couvreur and Hervé Sauquet
Unravelling the history of Neotropical plant diversification
South American rainforests, particularly the Tropical Andes, have been recognized as the hottest spot of plant biodiversity on Earth, while facing unprecedented threats from human impact [1,2]. Considerable research efforts have recently focused on unravelling the complex geological, bioclimatic, and biogeographic history of the region [3,4]. While many studies have addressed the question of Neotropical plant diversification using parametric methods to reconstruct ancestral areas and patterns of...
|2017-09-26 ||Lacking conservation genomics in the giant Galápagos tortoise|
Etienne Loire, Nicolas Galtier
Recommended by Michael C. Fontaine based on reviews by 4 anonymous reviewers
A genomic perspective is needed for the re-evaluation of species boundaries, evolutionary trajectories and conservation strategies for the Galápagos giant tortoises
Genome-wide data obtained from even a small number of individuals can provide unprecedented levels of detail about the evolutionary history of populations and species , determinants of genetic diversity , species boundaries and the process of speciation itself . Loire and Galtier  present a clear example, using the emblematic Galápagos giant tortoise (Chelonoidis nigra), of how multi-species comparative population genomic approaches can provide valuable insights about population s...
|2017-09-20 ||An interaction between cancer progression and social environment in Drosophila|
Erika H. Dawson, Tiphaine P.M. Bailly, Julie Dos Santos , Céline Moreno, Maëlle Devilliers, Brigitte Maroni, Cédric Sueur, Andreu Casali, Beata Ujvari, Frederic Thomas, Jacques Montagne, Frederic Mery
Recommended by Ana Rivero based on reviews by Silvie Huijben and Ana Rivero
Cancer and loneliness in Drosophila
Drosophila flies may not be perceived as a quintessentially social animal, particularly when compared to their eusocial hymenopteran cousins. Although they have no parental care, division of labour or subfertile caste, fruit flies nevertheless exhibit an array of social phenotypes that are potentially comparable to those of their highly social relatives. In the wild, Drosophila adults cluster around food resources where courtship, mating activity and oviposition occur. Recent work has shown ...
|2017-09-11 ||Less effective selection leads to larger genomes|
Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N. Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando and Christophe Douady
Recommended by Benoit Nabholz and Jochen B. W. Wolf
Colonisation of subterranean ecosystems leads to larger genome in waterlouse (Aselloidea)
The total amount of DNA utilized to store hereditary information varies immensely among eukaryotic organisms. Single copy genome sizes – disregarding differences due to ploidy - differ by more than three orders of magnitude ranging from a few million nucleotides (Mb) to hundreds of billions (Gb). With the ever-increasing availability of fully sequenced genomes we now know that most of the difference is due either to whole genome duplication or to variation in the abundance of repetitive elemen...
|2017-08-03 ||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
Recommended by Inês Fragata and Claudia Bank
What doesn’t kill us makes us stronger: can Fisher’s Geometric model predict antibiotic resistance evolution?
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 .
One of the most illustrative and common models of adaptation (and, hence, resistance evolution) is Fisher’s Geometric Model (FGM). The original model maps phenotypes to fitness, meaning that ea...
|2017-07-31 ||Selection on morphological traits and fluctuating asymmetry by a fungal parasite in the yellow dung fly|
Wolf U. Blanckenhorn
Recommended by Rodrigo Medel based on reviews by Rodrigo Medel and 1 anonymous reviewer
Parasite-mediated selection promotes small body size in yellow dung flies
Body size has long been considered as one of the most important organismic traits influencing demographical processes, population size, and evolution of life history strategies [1, 2]. While many studies have reported a selective advantage of large body size, the forces that determine small-sized organisms are less known, and reports of negative selection coefficients on body size are almost absent at present. This lack of knowledge is unfortunate as climate change and energy demands in stressfu...
|2017-07-12 ||Assortment of flowering time and defense alleles in natural Arabidopsis thaliana populations suggests co-evolution between defense and vegetative lifespan strategies|
Glander S, He F, Schmitz G, Witten A, Telschow A, de Meaux J
Recommended by Xavier Picó based on reviews by Xavier Picó and Rafa Rubio de Casas
Towards an integrated scenario to understand evolutionary patterns in A. thaliana
Nobody can ignore that a full understanding of evolution requires an integrated approach from both conceptual and methodological viewpoints. Although some life-history traits, e.g. flowering time, have long been receiving more attention than others, in many cases because the former are more workable than the latter, we must acknowledge that our comprehension about how evolution works is strongly biased and limited. In the Arabidopsis community, such an integration is making good progress as an...
|2017-07-12 ||Despite reproductive interference, the net outcome of reproductive interactions among spider mite species is not necessarily costly|
Salomé H. Clemente, Inês Santos, Rita Ponce, Leonor R. Rodrigues, Susana A. M. Varela and Sara Magalhães
Recommended by Vincent Calcagno based on reviews by Michael D Greenfield and Joël Meunier
The pros and cons of mating with strangers
Interspecific matings are by definition rare events in nature, but when they occur they can be very important, and not only because they might condition gene flow between species. Even when such matings have no genetic consequence, for instance if they do not yield any fertile hybrid offspring, they can still have an impact on the population dynamics of the species involved . Such atypical pairings between heterospecific partners are usually regarded as detrimental or undesired; as ...
|2017-07-07 ||Negative frequency-dependent selection is frequently confounding|
Recommended by Ignacio Bravo based on reviews by David Baltrus and 2 anonymous reviewers
Unmasking the delusive appearance of negative frequency-dependent selection
Explaining the processes that maintain polymorphisms in a population has been a fundamental line of research in evolutionary biology. One of the main mechanisms identified that preserves genetic diversity is negative frequency-dependent selection (NFDS), which constitutes a powerful framework for interpreting the presence of persistent polymorphisms. Nevertheless, a number of patterns that are often explained by invoking NFDS may also be compatible with, and possibly more easily explained by, di...
|2017-06-12 ||Evolution and manipulation of vector host choice|
Recommended by Samuel Alizon based on reviews by Samuel Alizon and Nicole Mideo
Modelling the evolution of how vector-borne parasites manipulate the vector's host choice
Many parasites can manipulate their hosts, thus increasing their transmission to new hosts . This is particularly the case for vector-borne parasites, which can alter the feeding behaviour of their hosts. However, predicting the optimal strategy is not straightforward because three actors are involved and the interests of the parasite may conflict with that of the vector. There are few models that consider the evolution of host manipulation by parasites [but see 2-4], but there are virtually ...
|2017-05-22 ||Can Ebola Virus evolve to be less virulent in humans?|
Mircea T. Sofonea, Lafi Aldakak, Luis Fernando Boullosa, Samuel Alizon
Recommended by Virginie Ravigné and François Blanquart based on reviews by François Blanquart and Virginie Ravigné
A new hypothesis to explain Ebola's high virulence
The tragic 2014-2016 Ebola outbreak that resulted in more than 28,000 cases and 11,000 deaths in West Africa  has been a surprise to the scientific community. Before 2013, the Ebola virus (EBOV) was known to produce recurrent outbreaks in remote villages near tropical rainforests in Central Africa, never exceeding a few hundred cases with very high virulence. Both EBOV’s ability to circulate for several months in large urban human populations and its important mutation rate sugges...
|2017-04-12 ||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
Recommended by Frédéric Fabre and Benoit Moury
Vectors as motors (of virus evolution)
Many 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 . 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 gett...
|2017-04-03 ||Things softly attained are long retained: Dissecting the Impacts of Selection Regimes on Polymorphism Maintenance in Experimental Spatially Heterogeneous Environments|
Romain Gallet, Rémy Froissart, Virginie Ravigné
Recommended by Stephanie Bedhomme based on reviews by Joachim Hermisson and 2 anonymous reviewers
Experimental test of the conditions of maintenance of polymorphism under hard and soft selection
Theoretical work, initiated by Levene (1953)  and Dempster (1955) , suggests that within a given environment, the way populations are regulated and contribute to the next generation is a key factor for the maintenance of local adaptation polymorphism. In this theoretical context, hard selection describes the situation where the genetic composition of each population affects its contribution to the next generation whereas soft selection describes the case where the contribution of...
|2017-03-31 ||Human adaptation of Ebola virus during the West African outbreak|
Urbanowicz, R.A., McClure, C.P., Sakuntabhai, A., Sall, A.A., Kobinger, G., Müller, M.A., Holmes, E.C., Rey, F.A., Simon-Loriere, E., and Ball, J.K.
Recommended by Sylvain Gandon and Sébastien Lion
Ebola evolution during the 2013-2016 outbreak
The Ebola virus (EBOV) epidemic that started in December 2013 resulted in around 28,000 cases and more than 11,000 deaths. Since the emergence of the disease in Zaire in 1976 the virus had produced a number of outbreaks in Africa but until 2013 the reported numbers of human cases had never risen above 500. Could this exceptional epidemic size be due to the spread of a human-adapted form of the virus?
The large mutation rate of the virus [1-2] may indeed introduce massive amounts of genetic va...
|2017-03-16 ||Correlated paternity measures mate monopolization and scales with the magnitude of sexual selection|
Dorken, ME and Perry LE
Recommended by Emmanuelle Porcher and Mathilde Dufay
Measurement of sexual selection in plants made easier
Sexual selection occurs in flowering plants too. However it tends to be understudied in comparison to animal sexual selection, in part because the minuscule size and long dispersal distances of the individuals producing male gametes (pollen grains) seriously complicate the estimation of male siring success and thereby the measurement of sexual selection. Dorken and Perry  introduce a novel and clever approach to estimate sexual selection in plants, which bypasses the need for a direct quantif...
|2017-03-14 ||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
Recommended by Arnaud Estoup and Ruth Arabelle Hufbauer
A valuable work lying at the crossroad of neuro-ethology, evolution and ecology in the fruit pest Drosophila suzukii
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 th...
|2017-01-24 ||Birth of a W sex chromosome by horizontal transfer of Wolbachia bacterial symbiont genome|
Sébastien Leclercq, Julien Thézé, Mohamed Amine Chebbi, Isabelle Giraud, Bouziane Moumen, Lise Ernenwein, Pierre Grève, Clément Gilbert, and Richard Cordaux
Recommended by Gabriel Marais and Sylvain Charlat
A newly evolved W(olbachia) sex chromosome in pillbug!
In some taxa such as fish and arthropods, closely related species can have different mechanisms of sex determination and in particular different sex chromosomes, which implies that new sex chromosomes are constantly evolving . Several models have been developed to explain this pattern but empirical data are lacking and the causes of the fast sex chromosome turn over remain mysterious [2-4]. Leclerq et al.  in a paper that just came out in PNAS have focused on one possible explanation: *W...
|2017-01-18 ||Associative Mechanisms Allow for Social Learning and Cultural Transmission of String Pulling in an Insect|
Alem S, Perry CJ, Zhu X, Loukola OJ, Ingraham T, Søvik E, Chittka L
Recommended by Caroline Nieberding and Jacques J. M. van Alphen
Culture in Bumblebees
This is an original paper  addressing the question whether cultural transmission occurs in insects and studying the mechanisms of such transmission. Often, culture-like phenomena require relatively sophisticated learning mechanisms, for example imitation and/or teaching. In insects, seemingly complex processes of social information acquisition, can sometimes instead be mediated by relatively simple learning mechanisms suggesting that cultural processes may not necessarily require sophisticate...
|2016-12-20 ||Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes|
Huang Y, Agrawal AF
Recommended by Luis-Miguel Chevin and Stephanie Bedhomme
Genetic adaptation counters phenotypic plasticity in experimental evolution
How do phenotypic plasticity and adaptive evolution interact in a novel or changing environment? Does evolution by natural selection generally reinforce initially plastic phenotypic responses, or does it instead oppose them? And to what extent does evolution of a trait involve evolution of its plasticity?
These questions have lied at the heart of research on phenotypic evolution in heterogeneous environments ever since it was realized that the environment is likely to affect the expression of m...
|2016-12-19 ||Geographic body size variation in the periodical cicadas Magicicada: implications for life cycle divergence and local adaptation|
Koyama T, Ito H, Kakishima S, Yoshimura J, Cooley JR, Simon C, Sota T
Recommended by Wolf Blanckenhorn and Thomas Flatt
Megacicadas show a temperature-mediated converse Bergmann cline in body size (larger in the warmer south) but no body size difference between 13- and 17-year species pairs
Periodical cicadas are a very prominent insect group in North America that are known for their large size, good looks, and loud sounds. However, they are probably known best to evolutionary ecologists because of their long juvenile periods of 13 or 17 years (prime numbers!), which they spend in the ground. Multiple related species living in the same area are often coordinated in emerging as adults during the same year, thereby presumably swamping any predators specialized on eating them.
|2016-12-17 ||Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study|
Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C
Recommended by Samuel Alizon and Roger Kouyos
Predicting HIV virulence evolution in response to widespread treatment
It is a classical result in the virulence evolution literature that treatments decreasing parasite replication within the host should select for higher replication rates, thus driving increased levels of virulence if the two are correlated. There is some evidence for this in vitro but very little in the field. HIV infections in humans offer a unique opportunity to go beyond the simple predictions that treatments should favour more virulent strains because many details of this host-parasite syste...
|2016-12-16 ||Evolutionary robotics simulations help explain why reciprocity is rare in nature.|
André J-B, Nolfi S
Recommended by Michael D Greenfield and Joël Meunier
Simulated robots and the evolution of reciprocity
Of the various forms of cooperative and altruistic behavior, reciprocity remains the most contentious. Humans certainly exhibit reciprocity – under certain circumstances – and various non-human animals behave in ways suggesting that they do as well. Thus, evolutionary biologists have sought to explain why non-relatives might engage in altruistic transactions when a substantial delay occurs between helping and compensation; i.e. an individual may be a donor today and a beneficiary tomorrow,...
|2016-12-16 ||Spatiotemporal microbial evolution on antibiotic landscapes|
Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, Kishony R
Recommended by Daniel Rozen and Arjan de Visser
A poster child for experimental evolution
Evolution is usually studied via two distinct approaches: by inferring evolutionary processes from relatedness patterns among living species or by observing evolution in action in the laboratory or field. A recent study by Baym and colleagues in Science  has now combined these approaches by taking advantage of the pattern left behind by spatially evolving bacterial populations.
Evolution is often considered too slow to see, and can only be inferred by studying patterns of relatedness usin...
|2016-12-15 ||Limiting opportunities for cheating stabilizes virulence in insect parasitic nematodes|
Shapiro-Ilan D. and B. Raymond
Recommended by Thomas Sappington and Ruth Arabelle Hufbauer
Application of kin theory to long-standing problem in nematode production for biocontrol
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 propaga...
|2016-12-15 ||Basidiomycete yeasts in the cortex of ascomycete macrolichens|
Spribille T, Tuovinen V, Resl P, et al.
Recommended by Enric Frago and Benoit Facon
New partner at the core of macrolichen diversity
It has long been known that most multicellular eukaryotes rely on microbial partners for a variety of functions including nutrition, immune reactions and defence against enemies. Lichens are probably the most popular example of a symbiosis involving a photosynthetic microorganism (an algae, a cyanobacteria or both) living embedded within the filaments of a fungus (usually an ascomycete). The latter is the backbone structure of the lichen, whereas the former provides photosynthetic products. Lich...
|2016-12-14 ||High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays|
Ellis EA, Oakley TH
Recommended by Astrid Groot and Carole Smadja
Bioluminescent sexually selected traits as an engine for biodiversity across animal species
In evolutionary biology, sexual selection is hypothesized to increase speciation rates in animals, as theory predicts that sexual selection will contribute to phenotypic diversification and affect rates of species accumulation at macro-evolutionary time scales. However, testing this hypothesis and gathering convincing evidence have proven difficult. Although some studies have shown a strong correlation between proxies of sexual selection and species diversity (mostly in birds), this relationship...
|2016-12-14 ||Evolution of resistance to single and combined floral phytochemicals by a bumble bee parasite|
Palmer-Young EC, Sadd BM, Adler LS
Recommended by Alison Duncan and Sara Magalhaes
The medicinal value of phytochemicals is hindered by pathogen evolution of resistance
As plants cannot run from their enemies, natural selection has favoured the evolution of diverse chemical compounds (phytochemicals) to protect them against herbivores and pathogens. This provides an opportunity for plant feeders to exploit these compounds to combat their own enemies. Indeed, it is widely known that herbivores use such compounds as protection against predators . Recently, this reasoning has been extended to pathogens, and elegant studies have shown that some herbivores feed o...
|2016-12-14 ||The Red Queen lives: epistasis between linked resistance loci|
Metzger CMJA, Luijckx P, Bento G, Mariadassou M, Ebert D.
Recommended by Adele Mennerat and Thierry Lefèvre
Evidence of epistasis provides further support to the Red Queen theory of host-parasite coevolution
According to the Red Queen theory of antagonistic host-parasite coevolution, adaptation of parasites to the most common host genotype results in negative frequency-dependent selection whereby rare host genotypes are favoured. Assuming that host resistance relies on a genetic host-parasite (mis)match involving several linked loci, then recombination appears as much more efficient than parthenogenesis in generating new resistant host genotypes. This has long been proposed to explain one of the big...
|2016-12-13 ||Prezygotic isolation, mating preferences, and the evolution of chromosomal inversions|
Dagilis AJ, Kirkpatrick M
Recommended by Denis Roze and Thomas Broquet
The spread of chromosomal inversions as a mechanism for reinforcement
Several examples of chromosomal inversions carrying genes affecting mate choice have been reported from various organisms. Furthermore, inversions are also frequently involved in genetic isolation between populations or species. Past work has shown that inversions can spread when they capture not only some loci involved in mate choice but also loci involved in incompatibilities between hybridizing populations . In this new paper , the authors derive analytical approximations for the select...
|2016-12-13 ||Addicted? Reduced host resistance in populations with defensive symbionts|
Martinez J, Cogni R, Cao C, Smith S, Illingworth CJR & Jiggins FM
Recommended by Ana Rivero and Natacha Kremer
Hooked on Wolbachia
This very nice paper by Martinez et al.  provides further evidence, if further evidence was needed, of the extent to which heritable microorganisms run the evolutionary show.
Wolbachia is an ubiquitous endosymbiont of arthropods who has been recently shown to protect its hosts against viral infections. Here, Martinez et al. are able to show that this multifaceted heritable symbiont weakens selective pressures induced by viruses on host immune genes. In a series of very elegant experim...
|2016-12-13 ||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.
Recommended by Thomas Flatt and Laurent Keller
Supergene Control of a Reproductive Polymorphism
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 "sat...
|2016-12-13 ||A supergene determines highly divergent male reproductive morphs in the ruff|
Küpper C, Stocks M, Risse JE, dos Remedios N, Farrell LL, McRae SB, Morgan TC, Karlionova N, Pinchuk P, Verkuil YI, et al.
Recommended by Thomas Flatt and Laurent Keller
Supergene Control of a Reproductive Polymorphism
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 "sat...
|2016-12-13 ||Repeated replacements of an intrabacterial symbiont in the tripartite nested mealybug symbiosis|
Husnik F, McCutcheon JP
Recommended by Emmanuelle Jousselin and Fabrice Vavre
Obligate dependence does not preclude changing partners in a Russian dolls symbiotic system
Symbiotic associations with bacterial partners have facilitated important evolutionary transitions in the life histories of eukaryotes. For instance, many insects have established long-term interactions with intracellular bacteria that provide them with essential nutrients lacking in their diet. However, despite the high level of interdependency among organisms involved in endosymbiotic systems, examples of symbiont replacements along the evolutionary history of insect hosts are numerous.