Latest recommendations
Id | Title * | Authors * | Abstract * | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
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27 Jul 2020
![]() Evolution of the DAN gene family in vertebratesJuan C. Opazo, Federico G. Hoffmann, Kattina Zavala, Scott V. Edwards https://doi.org/10.1101/794404An evolutionary view of a biomedically important gene familyRecommended by Kateryna Makova based on reviews by 2 anonymous reviewersThis manuscript [1] investigates the evolutionary history of the DAN gene family—a group of genes important for embryonic development of limbs, kidneys, and left-right axis speciation. This gene family has also been implicated in a number of diseases, including cancer and nephropathies. DAN genes have been associated with the inhibition of the bone morphogenetic protein (BMP) signaling pathway. Despite this detailed biochemical and functional knowledge and clear importance for development and disease, evolution of this gene family has remained understudied. The diversification of this gene family was investigated in all major groups of vertebrates. The monophyly of the gene members belonging to this gene family was confirmed. A total of five clades were delineated, and two novel lineages were discovered. The first lineage was only retained in cephalochordates (amphioxus), whereas the second one (GREM3) was retained by cartilaginous fish, holostean fish, and coelanth. Moreover, the patterns of chromosomal synteny in the chromosomal regions harboring DAN genes were investigated. Additionally, the authors reconstructed the ancestral gene repertoires and studied the differential retention/loss of individual gene members across the phylogeny. They concluded that the ancestor of gnathostome vertebrates possessed eight DAN genes that underwent differential retention during the evolutionary history of this group. During radiation of vertebrates, GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major vertebrate groups. At the same time, GREM3, CER1, and DAND5 were differentially lost in some vertebrate lineages. At least two DAN genes were present in the common ancestor of vertebrates, and at least three DAN genes were present in the common ancestor of chordates. Therefore the patterns of retention and diversification in this gene family appear to be complex. Evolutionary slowdown for the DAN gene family was observed in mammals, suggesting selective constraints. Overall, this article puts the biomedical importance of the DAN family in the evolutionary perspective. References [1] Opazo JC, Hoffmann FG, Zavala K, Edwards SV (2020) Evolution of the DAN gene family in vertebrates. bioRxiv, 794404, ver. 3 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/794404 | Evolution of the DAN gene family in vertebrates | Juan C. Opazo, Federico G. Hoffmann, Kattina Zavala, Scott V. Edwards | <p>The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogene... | ![]() | Molecular Evolution | Kateryna Makova | 2019-10-15 16:43:13 | View | |
25 Jun 2020
![]() Transcriptional differences between the two host strains of Spodoptera frugiperda (Lepidoptera: Noctuidae)Marion Orsucci, Yves Moné, Philippe Audiot, Sylvie Gimenez, Sandra Nhim, Rima Naït-Saïdi, Marie Frayssinet, Guillaume Dumont, Jean-Paul Boudon, Marin Vabre, Stéphanie Rialle, Rachid Koual, Gael J. Kergoat, Rodney N. Nagoshi, Robert L. Meagher, Emmanuelle d'Alencon, Nicolas Nègre https://doi.org/10.1101/263186Speciation through selection on mitochondrial genes?Recommended by Astrid Groot based on reviews by Heiko Vogel and Sabine HaennigerWhether speciation through ecological specialization occurs has been a thriving research area ever since Mayr (1942) stated this to play a central role. In herbivorous insects, ecological specialization is most likely to happen through host plant differentiation (Funk et al. 2002). Therefore, after Dorothy Pashley had identified two host strains in the Fall armyworm (FAW), Spodoptera frugiperda, in 1988 (Pashley 1988), researchers have been trying to decipher the evolutionary history of these strains, as this seems to be a model species in which speciation is currently occurring through host plant specialization. Even though FAW is a generalist, feeding on many different host plant species (Pogue 2002) and a devastating pest in many crops, Pashley identified a so-called corn strain and a so-called rice strain in Puerto Rico. Genetically, these strains were found to differ mostly in an esterase, although later studies showed additional genetic differences and markers, mostly in the mitochondrial COI and the nuclear TPI. Recent genomic studies showed that the two strains are overall so genetically different (2% of their genome being different) that these two strains could better be called different species (Kergoat et al. 2012). So far, the most consistent differences between the strains have been their timing of mating activities at night (Schoefl et al. 2009, 2011; Haenniger et al. 2019) and hybrid incompatibilities (Dumas et al. 2015; Kost et al. 2016). Whether and to what extent host plant preference or performance contributed to the differentiation of these sympatrically occurring strains has remained unclear. References [1] Dumas, P. et al. (2015). Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?. Genetica, 143(3), 305-316. doi: 10.1007/s10709-015-9829-2 | Transcriptional differences between the two host strains of Spodoptera frugiperda (Lepidoptera: Noctuidae) | Marion Orsucci, Yves Moné, Philippe Audiot, Sylvie Gimenez, Sandra Nhim, Rima Naït-Saïdi, Marie Frayssinet, Guillaume Dumont, Jean-Paul Boudon, Marin Vabre, Stéphanie Rialle, Rachid Koual, Gael J. Kergoat, Rodney N. Nagoshi, Robert L. Meagher, Emm... | <p>Spodoptera frugiperda, the fall armyworm (FAW), is an important agricultural pest in the Americas and an emerging pest in sub-Saharan Africa, India, East-Asia and Australia, causing damage to major crops such as corn, sorghum and soybean. While... | ![]() | Adaptation, Evolutionary Ecology, Expression Studies, Life History, Speciation | Astrid Groot | 2018-05-09 13:04:34 | View | |
18 Jun 2020
![]() Towards an improved understanding of molecular evolution: the relative roles of selection, drift, and everything in betweenFanny Pouyet and Kimberly J. Gilbert https://doi.org/10.48550/arXiv.1909.11490Molecular evolution through the joint lens of genomic and population processes.Recommended by Guillaume Achaz based on reviews by Benoit Nabholz and 1 anonymous reviewerIn their perspective article, F Pouyet and KJ Gilbert (2020), propose an interesting overview of all the processes that sculpt patterns of molecular evolution. This well documented article covers most (if not all) important facets of the recurrent debate that has marked the history of molecular evolution: the relative importance of natural selection and neutral processes (i.e. genetic drift). I particularly enjoyed reading this review, that instead of taking a clear position on the debate, catalogs patiently every pieces of information that can help understand how patterns we observed at the genome level, can be understood from a selectionnist point of view, from a neutralist one, and, to quote their title, from "everything in between". The review covers the classical objects of interest in population genetics (genetic drift, selection, demography and structure) but also describes several genomic processes (meiotic drive, linked selection, gene conversion and mutation processes) that obscure the interpretation of these population processes. The interplay between all these processes is very complex (to say the least) and have resulted in many cases in profound confusions while analyzing data. It is always very hard to fully acknowledge our ignorance and we have many times payed the price of model misspecifications. This review has the grand merit to improve our awareness in many directions. Being able to cover so many aspects of a wide topic, while expressing them simply and clearly, connecting concepts and observations from distant fields, is an amazing "tour de force". I believe this article constitutes an excellent up-to-date introduction to the questions and problems at stake in the field of molecular evolution and will certainly also help established researchers by providing them a stimulating overview supported with many relevant references. References [1] Pouyet F, Gilbert KJ (2020) Towards an improved understanding of molecular evolution: the relative roles of selection, drift, and everything in between. arXiv:1909.11490 [q-bio]. ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. url:https://arxiv.org/abs/1909.11490 | Towards an improved understanding of molecular evolution: the relative roles of selection, drift, and everything in between | Fanny Pouyet and Kimberly J. Gilbert | <p>A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus compreh... | ![]() | Genome Evolution, Population Genetics / Genomics | Guillaume Achaz | 2019-09-26 10:58:10 | View | |
20 May 2020
![]() How much does Ne vary among species?Nicolas Galtier, Marjolaine Rousselle https://doi.org/10.1101/861849Further questions on the meaning of effective population sizeRecommended by Martin Lascoux based on reviews by 3 anonymous reviewersIn spite of its name, the effective population size, Ne, has a complex and often distant relationship to census population size, as we usually understand it. In truth, it is primarily an abstract concept aimed at measuring the amount of genetic drift occurring in a population at any given time. The standard way to model random genetic drift in population genetics is the Wright-Fisher model and, with a few exceptions, definitions of the effective population size stems from it: “a certain model has effective population size, Ne, if some characteristic of the model has the same value as the corresponding characteristic for the simple Wright-Fisher model whose actual size is Ne” (Ewens 2004). Since Sewall Wright introduced the concept of effective population size in 1931 (Wright 1931), it has flourished and there are today numerous definitions of it depending on the process being examined (genetic diversity, loss of alleles, efficacy of selection) and the characteristic of the model that is considered. These different definitions of the effective population size were generally introduced to address specific aspects of the evolutionary process. One aspect that has been hotly debated since the first estimates of genetic diversity in natural populations were published is the so-called Lewontin’s paradox (1974). Lewontin noted that the observed variation in heterozygosity across species was much smaller than one would expect from the neutral expectations calculated with the actual size of the species. References Brandvain Y, Wright SI (2016) The Limits of Natural Selection in a Nonequilibrium World. Trends in Genetics, 32, 201–210. doi: 10.1016/j.tig.2016.01.004 | How much does Ne vary among species? | Nicolas Galtier, Marjolaine Rousselle | <p>Genetic drift is an important evolutionary force of strength inversely proportional to *Ne*, the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a d... | ![]() | Bioinformatics & Computational Biology, Genome Evolution, Molecular Evolution, Population Genetics / Genomics | Martin Lascoux | 2019-12-08 00:11:00 | View | |
18 May 2020
![]() The insertion of a mitochondrial selfish element into the nuclear genome and its consequencesJulien Y. Dutheil, Karin Münch, Klaas Schotanus, Eva H. Stukenbrock and Regine Kahmann https://doi.org/10.1101/787044Some evolutionary insights into an accidental homing endonuclease passage from mitochondria to the nucleusRecommended by Sylvain Charlat based on reviews by Jan Engelstaedter and Yannick WurmNot all genetic elements composing genomes are there for the benefit of their carrier. Many have no consequences on fitness, or too mild ones to be eliminated by selection, and thus stem from neutral processes. Many others are indeed the product of selection, but one acting at a different level, increasing the fitness of some elements of the genome only, at the expense of the “organism” as a whole. These can be called selfish genetic elements, and come into a wide variety of flavours [1], illustrating many possible means to cheat with “fair” reproductive processes such as meiosis, and thus get overrepresented in the offspring of their hosts. Producing copies of itself through transposition is one such strategy; a very successful one indeed, explaining a large part of the genomic content of many organisms. Killing non carrier gametes following meiosis in heterozygous carriers is another one. Less know and less common is the ability of some elements to turn heterozygous carriers into homozygous ones, that will thus transmit the selfish elements to all offspring instead of half. This is achieved by nucleic sequences encoding so-called “Homing endonucleases” (HEs). These proteins tend to induce double strand breaks of DNA specifically in regions homologous to their own insertion sites. The recombination machinery is such that the intact homologous region, that is, the one carrying the HE sequence, is then used as a template for the reparation of the break, resulting in the effective conversion of a non-carrier allele into a carrier allele. Such elements can also occur in the mitochondrial genomes of organisms where mitochondria are not strictly transmitted by one parent only, offering mitochondrial HEs some opportunities for “homing” into new non carrier genomes. This is the case in yeasts, where HEs were first reported [2,3]. References [1] Burt, A., and Trivers, R. (2006). Genes in Conflict: The Biology of Selfish Genetic Elements. Belknap Press. | The insertion of a mitochondrial selfish element into the nuclear genome and its consequences | Julien Y. Dutheil, Karin Münch, Klaas Schotanus, Eva H. Stukenbrock and Regine Kahmann | <p>Homing endonucleases (HE) are enzymes capable of cutting DNA at highly specific target sequences, the repair of the generated double-strand break resulting in the insertion of the HE-encoding gene ("homing" mechanism). HEs are present in all th... | ![]() | Genome Evolution, Molecular Evolution | Sylvain Charlat | 2019-09-30 20:34:23 | View | |
14 May 2020
![]() Potential adaptive divergence between subspecies and populations of snapdragon plants inferred from QST – FST comparisonsSara Marin, Anaïs Gibert, Juliette Archambeau, Vincent Bonhomme, Mylène Lascoste and Benoit Pujol https://doi.org/10.5281/zenodo.3628168From populations to subspecies… to species? Contrasting patterns of local adaptation in closely-related taxa and their potential contribution to species divergenceRecommended by Emmanuelle Porcher based on reviews by Sophie Karrenberg, Santiago C. Gonzalez-Martinez and 1 anonymous reviewerElevation gradients are convenient and widely used natural setups to study local adaptation, particularly in these times of rapid climate change [e.g. 1]. Marin and her collaborators [2] did not follow the mainstream, however. Instead of tackling adaptation to climate change, they used elevation gradients to address another crucial evolutionary question [3]: could adaptation to altitude lead to ecological speciation, i.e. reproductive isolation between populations in spite of gene flow? More specifically, they examined how much local adaptation to environmental variation differed among closely-related, recently diverged subspecies. They studied several populations of two subspecies of snapdragon (Antirrhinum majus), with adjacent geographical distributions. Using common garden experiments and the classical, but still useful, QST-FST comparison, they demonstrate contrasting patterns of local adaptation to altitude between the two subspecies, with several traits under divergent selection in A. majus striatum but none in A. majus pseudomajus. These differences in local adaptation may contribute to species divergence, and open many stimulating questions on the underlying mechanisms, such as the identity of environmental drivers or contribution of reproductive isolation involving flower color polymorphism. References [1] Anderson, J. T., and Wadgymar, S. M. (2020). Climate change disrupts local adaptation and favours upslope migration. Ecology letters, 23(1), 181-192. doi: 10.1111/ele.13427 | Potential adaptive divergence between subspecies and populations of snapdragon plants inferred from QST – FST comparisons | Sara Marin, Anaïs Gibert, Juliette Archambeau, Vincent Bonhomme, Mylène Lascoste and Benoit Pujol | <p>Phenotypic divergence among natural populations can be explained by natural selection or by neutral processes such as drift. Many examples in the literature compare putatively neutral (FST) and quantitative genetic (QST) differentiation in mult... | ![]() | Adaptation, Evolutionary Ecology, Genotype-Phenotype, Morphological Evolution, Quantitative Genetics | Emmanuelle Porcher | 2018-08-05 15:34:30 | View | |
05 May 2020
![]() Meta-population structure and the evolutionary transition to multicellularityCaroline J Rose, Katrin Hammerschmidt, Yuriy Pichugin and Paul B Rainey https://doi.org/10.1101/407163The ecology of evolutionary transitions to multicellularityRecommended by Dustin Brisson based on reviews by 2 anonymous reviewersThe evolutionary transition to multicellular life from free-living, single-celled ancestors has occurred independently in multiple lineages [1-5]. This evolutionary transition to cooperative group living can be difficult to explain given the fitness advantages enjoyed by the non-cooperative, single-celled organisms that still numerically dominate life on earth [1,6,7]. Although several hypotheses have been proposed to explain the transition to multicellularity, a common theme is the abatement of the efficacy of natural selection among the single cells during the free-living stage and the promotion of the efficacy of selection among groups of cells during the cooperative stage, an argument reminiscent of those from George Williams’ seminal book [8,9]. The evolution of life cycles appears to be a key step in the transition to multicellularity as it can align fitness advantages of the single-celled 'reproductive' stage with that of the cooperative 'organismal' stage [9-12]. That is, the evolution of life cycles allows natural selection to operate over timescales longer than that of the doubling time of the free-living cells [13]. Despite the importance of this issue, identifying the range of ecological conditions that reduce the importance of natural selection at the single-celled, free-living stage and increase the importance of selection among groups of cooperating cells has not been addressed empirically. References [1] Maynard Smith, J. and Szathmáry, E. (1995). The Major Transitions in Evolution. Oxford, UK: Freeman. p 346. | Meta-population structure and the evolutionary transition to multicellularity | Caroline J Rose, Katrin Hammerschmidt, Yuriy Pichugin and Paul B Rainey | <p>The evolutionary transition to multicellularity has occurred on numerous occasions, but transitions to complex life forms are rare. While the reasons are unclear, relevant factors include the intensity of within- versus between-group selection ... | ![]() | Adaptation, Evolutionary Dynamics, Experimental Evolution | Dustin Brisson | 2019-04-04 12:26:36 | View | |
03 May 2020
![]() When does gene flow facilitate evolutionary rescue?Matteo Tomasini, Stephan Peischl https://doi.org/10.1101/622142Reconciling the upsides and downsides of migration for evolutionary rescueRecommended by Claudia BankThe evolutionary response of populations to changing or novel environments is a topic that unites the interests of evolutionary biologists, ecologists, and biomedical researchers [1]. A prominent phenomenon in this research area is evolutionary rescue, whereby a population that is otherwise doomed to extinction survives due to the spread of new or pre-existing mutations that are beneficial in the new environment. Scenarios of evolutionary rescue require a specific set of parameters: the absolute growth rate has to be negative before the rescue mechanism spreads, upon which the growth rate becomes positive. However, potential examples of its relevance exist (e.g., [2]). From a theoretical point of view, the technical challenge but also the beauty of evolutionary rescue models is that they combine the study of population dynamics (i.e., changes in the size of populations) and population genetics (i.e., changes in the frequencies in the population). Together, the potential relevance of evolutionary rescue in nature and the models' theoretical appeal has resulted in a suite of modeling studies on the subject in recent years. References [1] Bell, G. (2017). Evolutionary Rescue. Annual Review of Ecology, Evolution, and Systematics 48(1), 605-627. doi: 10.1146/annurev-ecolsys-110316-023011 | When does gene flow facilitate evolutionary rescue? | Matteo Tomasini, Stephan Peischl | <p>Experimental and theoretical studies have highlighted the impact of gene flow on the probability of evolutionary rescue in structured habitats. Mathematical modelling and simulations of evolutionary rescue in spatially or otherwise structured p... | ![]() | Evolutionary Dynamics, Evolutionary Theory, Population Genetics / Genomics | Claudia Bank | 2019-05-22 11:12:13 | View | |
23 Apr 2020
![]() How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridisJulien Foucaud, Ruth A. Hufbauer, Virginie Ravigné, Laure Olazcuaga, Anne Loiseau, Aurelien Ausset, Su Wang, Lian-Sheng Zang, Nicolas Lemenager, Ashraf Tayeh, Arthur Weyna, Pauline Gneux, Elise Bonnet, Vincent Dreuilhe, Bastien Poutout, Arnaud Estoup, Benoit Facon https://doi.org/10.1101/849968Selection on a single trait does not recapitulate the evolution of life-history traits seen during an invasionRecommended by Inês Fragata and Ben Phillips based on reviews by 2 anonymous reviewersBiological invasions are natural experiments, and often show that evolution can affect dynamics in important ways [1-3]. While we often think of invasions as a conservation problem stemming from anthropogenic introductions [4,5], biological invasions are much more commonplace than this, including phenomena as diverse as natural range shifts, the spread of novel pathogens, and the growth of tumors. A major question across all these settings is which set of traits determine the ability of a population to invade new space [6,7]. Traits such as: increased growth or reproductive rate, dispersal ability and ability to defend from predation often show large evolutionary shifts across invasion history [1,6,8]. Are such multi-trait shifts driven by selection on multiple traits, or a correlated response by multiple traits to selection on one? Resolving this question is important for both theoretical and practical reasons [9,10]. But despite the importance of this issue, it is not easy to perform the necessary manipulative experiments [9]. References [1] Sakai, A.K., Allendorf, F.W., Holt, J.S. et al. (2001). The population biology of invasive species. Annual review of ecology and systematics, 32(1), 305-332. doi: 10.1146/annurev.ecolsys.32.081501.114037 | How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridis | Julien Foucaud, Ruth A. Hufbauer, Virginie Ravigné, Laure Olazcuaga, Anne Loiseau, Aurelien Ausset, Su Wang, Lian-Sheng Zang, Nicolas Lemenager, Ashraf Tayeh, Arthur Weyna, Pauline Gneux, Elise Bonnet, Vincent Dreuilhe, Bastien Poutout, Arnaud Est... | <p>Experiments comparing native to introduced populations or distinct introduced populations to each other show that phenotypic evolution is common and often involves a suit of interacting phenotypic traits. We define such sets of traits that evol... | ![]() | Adaptation, Evolutionary Applications, Experimental Evolution, Life History, Quantitative Genetics | Inês Fragata | 2019-11-29 07:07:00 | View | |
03 Apr 2020
Evolution at two time-frames: ancient and common origin of two structural variants involved in local adaptation of the European plaice (Pleuronectes platessa)Alan Le Moan, Dorte Bekkevold, Jakob Hemmer-Hansen https://doi.org/10.1101/662577Genomic structural variants involved in local adaptation of the European plaiceRecommended by Maren Wellenreuther based on reviews by 3 anonymous reviewersAwareness has been growing that structural variants in the genome of species play a fundamental role in adaptive evolution and diversification [1]. Here, Le Moan and co-authors [2] report empirical genomic-wide SNP data on the European plaice (Pleuronectes platessa) across a major environmental transmission zone, ranging from the North Sea to the Baltic Sea. Regions of high linkage disequilibrium suggest the presence of two structural variants that appear to have evolved 220 kya. These two putative structural variants show weak signatures of isolation by distance when contrasted against the rest of the genome, but the frequency of the different putative structural variants appears to co-vary in some parts of the studied range with the environment, indicating the involvement of both selective and neutral processes. This study adds to the mounting body of evidence that structural genomic variants harbour significant information that allows species to respond and adapt to the local environmental context. References [1] Wellenreuther, M., Mérot, C., Berdan, E., & Bernatchez, L. (2019). Going beyond SNPs: the role of structural genomic variants in adaptive evolution and species diversification. Molecular ecology, 28(6), 1203-1209. doi: 10.1111/mec.15066 | Evolution at two time-frames: ancient and common origin of two structural variants involved in local adaptation of the European plaice (Pleuronectes platessa) | Alan Le Moan, Dorte Bekkevold, Jakob Hemmer-Hansen | <p>Changing environmental conditions can lead to population diversification through differential selection on standing genetic variation. Structural variant (SV) polymorphisms provide examples of ancient alleles that in time become associated with... | Adaptation, Hybridization / Introgression, Population Genetics / Genomics, Speciation | Maren Wellenreuther | 2019-07-13 12:44:01 | View |
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