|Id||Title||Authors||Abstract||Picture||Thematic fields||Recommender||Reviewers||Submission date|
12 Jun 2018
Transgenerational cues about local mate competition affect offspring sex ratios in the spider mite Tetranychus urticaeAlison B. Duncan, Cassandra Marinosci, Céline Devaux, Sophie Lefèvre, Sara Magalhães, Joanne Griffin, Adeline Valente, Ophélie Ronce, Isabelle Olivieri https://doi.org/10.1101/240127
Maternal effects in sex-ratio adjustmentRecommended by Dries Bonte based on reviews by 2 anonymous reviewers
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 response to changing demographic conditions. Hamilton  pointed out that an equality of the sex ratio breaks down when there is local competition for mates. Competition for mates can be considered as a special case of local resource competition. In short, this theory predicts females to adjust their offspring sex ratio conditional on cues indicating the level of local mate competition that their sons will experience. When cues indicate high levels of LMC mothers should invest more resources in the production of daughters to maximise their fitness, while offspring sex ratios should be closer to 50:50 when cues indicate low levels of LMC.
 Hamilton, W. D. (1967). Extraordinary Sex Ratios. Science, 156(3774), 477–488. doi: 10.1126/science.156.3774.477
|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||<p>In structured populations, competition between closely related males for mates, termed Local Mate Competition (LMC), is expected to select for female-biased offspring sex ratios. However, the cues underlying sex allocation decisions remain poor...||Evolutionary Ecology, Life History||Dries Bonte||2017-12-29 16:10:32||View|
05 Jun 2018
Pleistocene climate change and the formation of regional species poolsJoaquín Calatayud, Miguel Á. Rodríguez, Rafael Molina-Venegas, María Leo, José Luís Hórreo, Joaquín Hortal https://doi.org/10.1101/149617
Recent assembly of European biogeographic species poolRecommended by Fabien Condamine based on reviews by 3 anonymous reviewers
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. Wallace . When these explorers travelled among different places, they were struck by the differences in their biotas (e.g. ). 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 . 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.  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.  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.  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.
 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||View|
05 Jun 2018
The dynamics of preferential host switching: host phylogeny as a key predictor of parasite prevalence and distributionJan Engelstaedter & Nicole Fortuna https://doi.org/10.1101/209254
Shift or stick? Untangling the signatures of biased host switching, and host-parasite co-speciationRecommended by Lucy Weinert based on reviews by Damien de Vienne and Nathan Medd
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 that we find in nature. Such comparative data do show strong signs of non-randomness, and this suggests that the epidemiological and ecological processes might be predictable, at least in part. For example, when we map patterns of parasite presence/absence onto host phylogenies, we often find that certain host clades harbour many more parasites than expected, or that closely-related hosts harbour closely-related parasites. Nevertheless, it remains difficult to interpret these patterns to make inferences about ecological and epidemiological processes. This is partly because non-random associations can arise in multiple ways. For example, parasites might be inherited from the common ancestor of related hosts, or might switch to new hosts, but preferentially establish on novel hosts that are closely related to their existing host. Infection might also influence the shape of host phylogeny, either by increasing the rate of host extinction or, conversely, increasing the rate of speciation (as with manipulative symbionts that might induce reproductive isolation).
These various processes have, by and large, been studied in isolation, but the model introduced by Engelstädter and Fortuna , makes an important first step towards studying them together. Without such combined analyses, we will not be able to tell if the processes have their own unique signatures, or whether the same sort of non-randomness can arise in multiple ways.
A major finding of the work is that the size of a host clade can be an important determinant of its overall infection level. This had been shown in previous work, assuming that the host phylogeny was fixed, but the current paper shows that it extends also to situations where host extinction and speciation takes place at a comparable rate to host shifting. This finding, then, calls into question the natural assumption that a clade of host species that is highly parasite ridden, must have some genetic or ecological characteristic that makes them particularly prone to infection, arguing that the clade size, rather than any characteristic of the clade members, might be the important factor. It will be interesting to see whether this prediction about clade size is borne out with comparative studies.
Another feature of the study is that the framework is naturally extendable, to include further processes, such as the influence of parasite presence on extinction or speciation rates. No doubt extensions of this kind will form the basis of important future work.
 Engelstädter J and Fortuna NZ. 2018. The dynamics of preferential host switching: host phylogeny as a key predictor of parasite prevalence and distribution. bioRxiv 209254 ver. 5 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/209254
|The dynamics of preferential host switching: host phylogeny as a key predictor of parasite prevalence and distribution||Jan Engelstaedter & Nicole Fortuna||<p>New parasites commonly arise through host-shifts, where parasites from one host species jump to and become established in a new host species. There is much evidence that the probability of host-shifts decreases with increasing phylogenetic dist...||Bioinformatics & Computational Biology, Evolutionary Epidemiology, Evolutionary Theory, Macroevolution, Phylogenetics / Phylogenomics, Species interactions||Lucy Weinert||2017-10-30 02:06:06||View|
03 Jun 2018
Cost of resistance: an unreasonably expensive conceptThomas Lenormand, Noemie Harmand, Romain Gallet https://doi.org/10.1101/276675
Let’s move beyond costs of resistance!Recommended by Inês Fragata and Claudia Bank based on reviews by Danna Gifford, Helen Alexander and 1 anonymous reviewer
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 ancestral (untreated) environment.
In their paper, Lenormand et al.  discuss the history of this concept and highlight its caveats and limitations. The authors address both practical and theoretical problems that arise from the simplistic view of "costly resistance" and argue that they can be prejudicial for antibiotic resistance studies. For a better understanding, they visualize their points of critique by means of Fisher's Geometric model.
The authors give an interesting historical overview of how the concept arose and speculate that it emerged (during the 1980s) in an attempt by ecologists to spread awareness that fitness can be environment-dependent, and because of the concept's parallels to trade-offs in life-history evolution. They then identify several problems that arise from the concept, which, besides the conceptual misunderstandings that they can cause, are important to keep in mind when designing experimental studies.
The authors highlight and explain the following points:
Lenormand et al.'s paper  is a timely perspective piece in light of the ever-increasing efforts to understand and tackle resistance evolution . Although some readers may shy away from the rather theoretical presentation of the different points of concern, it will be useful for both theoretical and empirical readers by illustrating the misconceptions that can arise from the concept of the cost of resistance. Ultimately, the main lesson to be learned from this paper may not be to ban the term "cost of resistance" from one's vocabulary, but rather to realize that the successful fight against drug resistance requires more differential information than the measurement of fitness effects in a drug-treated vs. non-treated environment in the lab [3-4]. Specifically, a better integration of the ecological aspects of drug resistance evolution and maintenance is needed , and we are far from a general understanding of how environmental factors interact and influence an organism's (absolute and relative) fitness and the effect of resistance mutations.
 Lenormand T, Harmand N, Gallet R. 2018. Cost of resistance: an unreasonably expensive concept. bioRxiv 276675, ver. 3 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/276675
|Cost of resistance: an unreasonably expensive concept||Thomas Lenormand, Noemie Harmand, Romain Gallet||<p>The cost of resistance, or the fitness effect of resistance mutation in absence of the drug, is a very widepsread concept in evolutionary genetics and beyond. It has represented an important addition to the simplistic view that resistance mutat...||Adaptation, Evolutionary Applications, Evolutionary Ecology, Evolutionary Theory, Experimental Evolution, Genotype-Phenotype, Population Genetics / Genomics||Inês Fragata||2018-03-09 02:22:07||View|
18 May 2018
Modularity of genes involved in local adaptation to climate despite physical linkageKatie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken, Kathryn Hodgins https://doi.org/10.1101/202481
Differential effect of genes in diverse environments, their role in local adaptation and the interference between genes that are physically linkedRecommended by Sebastian Ernesto Ramos-Onsins based on reviews by Tanja Pyhäjärvi and 1 anonymous reviewer
The genome of eukaryotic species is a complex structure that experience many different interactions within itself and with the surrounding environment. The genetic architecture of a phenotype (that is, the set of genetic elements affecting a trait of the organism) plays a fundamental role in understanding the adaptation process of a species to, for example, different climate environments, or to its interaction with other species. Thus, it is fundamental to study the different aspects of the genetic architecture of the species and its relationship with its surronding environment. Aspects such as modularity (the number of genetic units and the degree to which each unit is affecting a trait of the organism), pleiotropy (the number of different effects that a genetic unit can have on an organism) or linkage (the degree of association between the different genetic units) are essential to understand the genetic architecture and to interpret the effects of selection on the genome. Indeed, the knowledge of the different aspects of the genetic architecture could clarify whether genes are affected by multiple aspects of the environment or, on the contrary, are affected by only specific aspects [1,2].
The work performed by Lotterhos et al.  sought to understand the genetic architecture of the adaptation to different environments in lodgepole pine (Pinus contorta), considering as candidate SNPs those previously detected as a result of its extreme association patterns to different environmental variables or to extreme population differentiation. This consideration is very important because the study is only relevant if the studied markers are under the effect of selection. Otherwise, the genetic architecture of the adaptation to different environments would be masked by other (neutral) kind of associations that would be difficult to interpret [4,5]. In order to understand the relationship between genetic architecture and adaptation, it is relevant to detect the association networks of the candidate SNPs with climate variables (a way to measure modularity) and if these SNPs (and loci) are affected by single or multiple environments (a way to measure pleiotropy).
The authors used co-association networks, an innovative approach in this field, to analyse the interaction between the environmental information and the genetic polymorphism of each individual. This methodology is more appropriate than other multivariate methods - such as analysis based on principal components - because it is possible to cluster SNPs based on associations with similar environmental variables. In this sense, the co-association networks allowed to both study the genetic and physical linkage between different co-associations modules but also to compare two different models of evolution: a Modular environmental response architecture (specific genes are affected by specific aspects of the environment) or a Universal pleiotropic environmental response architecture (all genes are affected by all aspects of the environment). The representation of different correlations between allelic frequency and environmental factors (named galaxy biplots) are especially informative to understand the effect of the different clusters on specific aspects of the environment (for example, the co-association network ‘Aridity’ shows strong associations with hot/wet versus cold/dry environments).
The analysis performed by Lotterhos et al. , although it has some unavoidable limitations (e.g., only extreme candidate SNPs are selected, limiting the results to the stronger effects; the genetic and physical map is incomplete in this species), includes relevant results and also implements new methodologies in the field. To highlight some of them: the preponderance of a Modular environmental response architecture (evolution in separated modules), the detection of physical linkage among SNPs that are co-associated with different aspects of the environment (which was unexpected a priori), the implementation of co-association networks and galaxy biplots to see the effect of modularity and pleiotropy on different aspects of environment. Finally, this work contains remarkable introductory Figures and Tables explaining unambiguously the main concepts  included in this study. This work can be treated as a starting point for many other future studies in the field.
 Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperone FG, Toomajian C, Roux F & Bergelson J. 2011. Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83–86. doi: 10.1126/science.1209244
|Modularity of genes involved in local adaptation to climate despite physical linkage||Katie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken, Kathryn Hodgins||<p>Background: Physical linkage among genes shaped by different sources of selection is a fundamental aspect of genetic architecture. Theory predicts that evolution in complex environments selects for modular genetic architectures and high recombi...||Adaptation, Bioinformatics & Computational Biology, Genome Evolution||Sebastian Ernesto Ramos-Onsins||2017-10-15 19:21:57||View|
19 Mar 2018
Natural selection on plasticity of thermal traits in a highly seasonal environmentLeonardo Bacigalupe, Juan Diego Gaitan-Espitia, Aura M Barria, Avia Gonzalez-Mendez, Manuel Ruiz-Aravena, Mark Trinder, Barry Sinervo https://doi.org/10.1101/191825
Is thermal plasticity itself shaped by natural selection? An assessment with desert frogsRecommended by Wolf Blanckenhorn based on reviews by Dries Bonte, Wolf Blanckenhorn and Nadia Aubin-Horth
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 capacity. Thus, plasticity might be selected per se.
A Chilean group around Leonardo Bacigalupe assessed natural selection in the wild in one marginal (and extreme) population of the four-eyed frog Pleurodema thaul (Anura: Leptodactylidae) in an isolated oasis in the Atacama Desert, permitting estimation of mortality without much potential of confounding it with migration . Several thermal traits were considered: CTmax – the critical maximal temperature; CTmin – the critical minimum temperature; Tpref – preferred temperature; Q10 – thermal sensitivity of metabolism; and body mass. Animals were captured in the wild and subsequently assessed for thermal traits in the laboratory at two acclimation temperatures (10° & 20°C), defining the plasticity in all traits as the difference between the traits at the two acclimation temperatures. Thereafter the animals were released again in their natural habitat and their survival was monitored over the subsequent 1.5 years, covering two breeding seasons, to estimate viability selection in the wild. The authors found and conclude that, aside from larger body size increasing survival (an unsurprising result), plasticity does not seem to be systematically selected directly, while some of the individual traits show weak signs of selection.
Despite limited sample size (ca. 80 frogs) investigated in only one marginal but very seasonal population, this study is interesting because selection on plasticity in physiological thermal traits, as opposed to selection on the thermal traits themselves, is rarely investigated. The study thus also addressed the old but important question of whether plasticity (i.e. CTmax-CTmin) is a trait by itself or an epiphenomenon defined by the actual traits (CTmax and CTmin) [2-5]. Given negative results, the main question could not be ultimately solved here, so more similar studies should be performed.
 Bacigalupe LD, Gaitan-Espitia, JD, Barria AM, Gonzalez-Mendez A, Ruiz-Aravena M, Trinder M & Sinervo B. 2018. Natural selection on plasticity of thermal traits in a highly seasonal environment. bioRxiv 191825, ver. 5 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/191825
|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||<p>For ectothermic species with broad geographical distributions, latitudinal/altitudinal variation in environmental temperatures (averages and extremes) are expected to shape the evolution of physiological tolerances and the acclimation capacity ...||Adaptation, Evolutionary Ecology, Phenotypic Plasticity||Wolf Blanckenhorn||2017-09-22 23:17:40||View|
28 Feb 2018
Insects and incest: sib-mating tolerance in natural populations of a parasitoid waspMarie Collet, Isabelle Amat, Sandrine Sauzet, Alexandra Auguste, Xavier Fauvergue, Laurence Mouton, Emmanuel Desouhant https://doi.org/10.1101/169268
Incestuous insects in nature despite occasional fitness costsRecommended by Caroline Nieberding and Bertanne Visser based on reviews by 2 anonymous reviewers
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, including humans . But all is not lost for individuals within small populations, because an array of mechanisms can be employed to evade the negative effects of inbreeding , including sib-mating avoidance and dispersal [5, 6].
Despite thorough investigation of inbreeding and sib-mating avoidance in the laboratory, only very few studies have ventured into the field besides studies on vertebrates and eusocial insects. The study of Collet et al.  is a surprising exception, where the effect of male density and frequency of relatives on inbreeding avoidance was tested in the laboratory, after which robust field collections and microsatellite genotyping were used to infer relatedness and dispersal in natural populations. The parasitic wasp Venturia canescens is an excellent model system to study inbreeding, because mating success was previously found to decrease with increasing relatedness between mates in the laboratory  and this species thus suffers from inbreeding depression [9–11]. The authors used an elegant design combining population genetics and model simulations to estimate relatedness of mating partners in the field and compared that with a theoretical distribution of potential mate encounters when random mating is assumed. One of the most important findings of this study is that mating between siblings is not avoided in this species in the wild, despite negative fitness effects when inbreeding does occur. Similar findings were obtained for another insect species, the field cricket Gryllus campestris , which leaves us to wonder whether inbreeding tolerance could be more common in nature than currently appreciated.
The authors further looked into sex-specific dispersal patterns between two patches located a few hundred meters apart. Females were indeed shown to be more related within a patch, but no genetic differences were observed between males, suggesting that V. canescens males more readily disperse. Moreover, microsatellite data at 18 different loci did not reveal genetic differentiation between populations approximately 300 kilometers apart. Gene flow is thus occurring over considerable distances, which could play an important role in the ability of this species to avoid negative fitness consequences of inbreeding in nature.
Another interesting aspect of this work is that discrepancies were found between laboratory- and field-based data. What is the relevance of laboratory-based experiments if they cannot predict what is happening in the wild? Many, if not most, biologists (including us) bring our model system into the laboratory to control, at least to some extent, the plethora of environmental factors that could potentially affect our system (in ways that we do not want). Most behavioral studies on mating patterns and sexual selection are conducted in standardized laboratory conditions, but sexual selection is in essence social selection, because an individual’s fitness is partly determined by the phenotype of its social partners (i.e. the social environment) . The social environment may actually dictate the expression of female mate choice and it is unclear how potential laboratory-induced social biases affect mating outcome. In V. canescens, findings using field-caught individuals paint a completely opposite picture of what was previously shown in the laboratory, i.e. sib-avoidance is not taking place in the field. It is likely that density, level of relatedness, sex ratio in the field, and/or the size of experimental arenas in the lab are all factors affecting mate selectivity, as we have previously shown in a butterfly [14–16]. If females, for example, typically only encounter a few males in sequence in the wild, it may be problematic for them to express choosiness when confronted simultaneously with two or more males in the laboratory. A recent study showed that, in the wild, female moths take advantage of staying in groups to blur male choosiness . It is becoming more and more clear that what we observe in the laboratory may not actually reflect what is happening in nature . Instead of ignoring the species-specific life history and ecological features of our favorite species when conducting lab experiments, we suggest that it is time to accept that we now have the theoretical foundations to tease apart what in this “environmental noise” actually shapes sexual selection in nature. Explicitly including ecology in studies on sexual selection will allow us to make more meaningful conclusions, i.e. rather than “this is what may happen in the wild”, we would be able to state “this is what often happens in nature”.
 Charlesworth D & Willis JH. 2009. The genetics of inbreeding depression. Nat. Rev. Genet. 10: 783–796. doi: 10.1038/nrg2664
|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||<p>This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100047) 1. Sib-mating avoidance is a pervasive behaviour that likely evolves in species subject to inbreeding dep...||Behavior & Social Evolution, Evolutionary Ecology, Sexual Selection||Caroline Nieberding||2017-07-28 09:23:20||View|
19 Feb 2018
Genomic imprinting mediates dosage compensation in a young plant XY systemAline Muyle, Niklaus Zemp, Cecile Fruchard, Radim Cegan, Jan Vrana, Clothilde Deschamps, Raquel Tavares, Franck Picard, Roman Hobza, Alex Widmer, Gabriel Marais https://doi.org/10.1101/179044
Dosage 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 reviewers
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 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 , which could have serious deleterious consequences for the heterogametic sex.
|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||View|
09 Feb 2018
Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreakSimon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey https://doi.org/10.1101/163691
Simulating the effect of public health interventions using dated virus sequences and geographical dataRecommended by Samuel Alizon based on reviews by Christian Althaus, Chris Wymant and 1 anonymous reviewer
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 .
 Gire et al. 2014. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345: 1369–1372. doi: 10.1126/science.1259657.
|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||<p>This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100046). The recent Ebola virus (EBOV) outbreak in West Africa witnessed considerable efforts to obtain viral genom...||Phylogenetics / Phylogenomics, Phylogeography & Biogeography||Samuel Alizon||2017-09-30 13:49:57||View|
31 Jan 2018
Identifying drivers of parallel evolution: A regression model approachSusan F Bailey, Qianyun Guo, Thomas Bataillon https://doi.org/10.1101/118695
A new statistical tool to identify the determinant of parallel evolutionRecommended by Stephanie Bedhomme based on reviews by Bastien Boussau and 1 anonymous reviewer
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.
 Bailey SF, Guo Q and Bataillon T (2018) Identifying drivers of parallel evolution: A regression model approach. bioRxiv 118695, ver. 4 peer-reviewed by Peer Community In Evolutionary Biology. doi: 10.1101/118695
 Lang GI, Rice DP, Hickman, MJ, Sodergren E, Weinstock GM, Botstein D, and Desai MM (2013) Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500: 571–574. doi: 10.1038/nature12344
|Identifying drivers of parallel evolution: A regression model approach||Susan F Bailey, Qianyun Guo, Thomas Bataillon||<p>This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100045). Parallel evolution, defined as identical changes arising in independent populations, is often attributed...||Experimental Evolution, Molecular Evolution||Stephanie Bedhomme||2017-03-22 14:54:48||View|
Michael David Pirie
Alejandro Gonzalez Voyer