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Gouy M.,CNRS Biometry and Evolutionary Biology Laboratory | Guindon S.,CNRS Montpellier Laboratory of Informatics, Robotics and Microelectronics | Guindon S.,University of Auckland | Gascuel O.,CNRS Montpellier Laboratory of Informatics, Robotics and Microelectronics
Molecular Biology and Evolution | Year: 2010

We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo-win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.

Peres-Neto P.R.,University of Quebec at Montréal | Leibold M.A.,University of Texas at Austin | Dray S.,CNRS Biometry and Evolutionary Biology Laboratory
Ecology | Year: 2012

Patterns in biodiversity and species coexistence are the result of multiple interacting processes including evolutionary history, trait variation, species interactions, dispersal, environmental variation, and landscape heterogeneity. Exploring patterns of biodiversity across space is perhaps the best integrative method (in contrast to the scarcity of temporal data) to interpret the influence of these multiple and interactive effects in determining community assembly, but it is still underdeveloped. Two emerging fields, metacommunity ecology and community phylogenetics, have been making relevant, though rather independent, progress toward understanding how communities are assembled in space. Our main goals were twofold. First, we described a heuristical framework to merge these two fields into "metacommunity phylogenetics." The main goal of this framework is to provide a way to think about how niche properties of species arranged across the environment and different spatial scales influence the process of community assembly. Second, we developed an analytical framework to link niche properties based on trait and phylogenetics to environmental and spatial variation. In order to assess the performance of the framework, we used extensive computer simulations of community assembly to show that the procedure is robust under a variety of scenarios. © 2012 by the Ecological Society of America.

Kvikstad E.M.,CNRS Biometry and Evolutionary Biology Laboratory | Duret L.,CNRS Biometry and Evolutionary Biology Laboratory
Molecular Biology and Evolution | Year: 2014

Elucidating the mechanisms of mutation accumulation and fixation is critical to understand the nature of genetic variation and its contribution to genome evolution. Of particular interest is the effect of insertions and deletions (indels) on the evolution of genome landscapes. Recent population-scaled sequencing efforts provide unprecedented data for analyzing the relative impact of selection versus nonadaptive forces operating on indels. Here, we combined McDonald-Kreitman tests with the analysis of derived allele frequency spectra to investigate the dynamics of allele fixation of short (1-50 bp) indels in the human genome. Our analyses revealed apparently higher fixation probabilities for insertions than deletions. However, this fixation bias is not consistent with either selection or biased gene conversion and varies with local mutation rate, being particularly pronounced at indel hotspots. Furthermore, we identified an unprecedented number of loci with evidence for multiple indel events in the primate phylogeny. Even in nonrepetitive sequence contexts (a priori not prone to indel mutations), such loci are 60-fold more frequent than expected according to a model of uniform indel mutation rate. This provides evidence of as yet unidentified cryptic indel hotspots. We propose that indel homoplasy, at known and cryptic hotspots, produces systematic errors in determination of ancestral alleles via parsimony and advise caution interpreting classic selection tests given the strong heterogeneity in indel rates across the genome. These results will have great impact on studies seeking to infer evolutionary forces operating on indels observed in closely related species, because such mutations are traditionally presumed homoplasy-free. © 2013 The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Agrebi R.,Aix - Marseille University | Wartel M.,Aix - Marseille University | Brochier-Armanet C.,CNRS Biometry and Evolutionary Biology Laboratory | Mignot T.,Aix - Marseille University
Nature Reviews Microbiology | Year: 2015

Studying the evolution of macromolecular assemblies is important to improve our understanding of how complex cellular structures evolved, and to identify the functional building blocks that are involved. Recent studies suggest that the macromolecular complexes that are involved in two distinct processes in Myxococcus xanthus-surface motility and sporulation-are derived from an ancestral polysaccharide capsule assembly system. In this Opinion article, we argue that the available data suggest that the motility machinery evolved from this capsule assembly system following a gene duplication event, a change in carbohydrate polymer specificity and the acquisition of additional proteins by the motility complex, all of which are key features that distinguish the motility and sporulation systems. Furthermore, the presence of intermediates of these systems in bacterial genomes suggests a testable evolutionary model for their emergence and spread. © 2015 Macmillan Publishers Limited. All rights reserved.

Gout J.F.,CNRS Biometry and Evolutionary Biology Laboratory
PLoS genetics | Year: 2010

The understanding of selective constraints affecting genes is a major issue in biology. It is well established that gene expression level is a major determinant of the rate of protein evolution, but the reasons for this relationship remain highly debated. Here we demonstrate that gene expression is also a major determinant of the evolution of gene dosage: the rate of gene losses after whole genome duplications in the Paramecium lineage is negatively correlated to the level of gene expression, and this relationship is not a byproduct of other factors known to affect the fate of gene duplicates. This indicates that changes in gene dosage are generally more deleterious for highly expressed genes. This rule also holds for other taxa: in yeast, we find a clear relationship between gene expression level and the fitness impact of reduction in gene dosage. To explain these observations, we propose a model based on the fact that the optimal expression level of a gene corresponds to a trade-off between the benefit and cost of its expression. This COSTEX model predicts that selective pressure against mutations changing gene expression level or affecting the encoded protein should on average be stronger in highly expressed genes and hence that both the frequency of gene loss and the rate of protein evolution should correlate negatively with gene expression. Thus, the COSTEX model provides a simple and common explanation for the general relationship observed between the level of gene expression and the different facets of gene evolution.

Kafer J.,CNRS Biometry and Evolutionary Biology Laboratory | Mousset S.,CNRS Biometry and Evolutionary Biology Laboratory
Systematic Biology | Year: 2014

Comparing species richness in sister clades that differ in a character state is one of the ways to study factors influencing diversification. While most of its applications have focussed on traits that increase diversification, some have been used to study the association of a trait with lower species richness, e.g., the occurrence of dioecy in flowering plants. We show here, using simulations and an analytical model, that the null expectation of equal species richness that is generally used in sister clade comparisons is wrong in the case of a derived trait occurring independently from speciation: one should expect fewer species in the clade with the derived character state when there is no difference in diversification rates. This is due to the waiting time for the derived state to appear, which causes it to occur more often on longer branches. This has the important implication that the probability for a clade to possess the derived state depends on the tree geometry, and thus on species richness: species-poorer clades are more likely to possess the derived state. We develop a statistical test for sister clade comparisons to study the effect of a derived character state. Applying it to a data set of dioecious clades, we find that we cannot confirm earlier work that concluded that dioecy decreases diversification; on the contrary, it seems to be associated to higher species richness than expected. [angiosperms; dioecy; diversification; sister clades; species richness.] © 2014 The Author(s).

Lesecque Y.,CNRS Biometry and Evolutionary Biology Laboratory | Mouchiroud D.,CNRS Biometry and Evolutionary Biology Laboratory | Duret L.,CNRS Biometry and Evolutionary Biology Laboratory
Molecular Biology and Evolution | Year: 2013

GC-biased gene conversion (gBGC) is a process associated with recombination that favors the transmission of GC alleles over AT alleles during meiosis. gBGC plays a major role in genome evolution in many eukaryotes. However, the molecular mechanisms of gBGC are still unknown. Different steps of the recombination process could potentially cause gBGC: the formation of double-strand breaks (DSBs), the invasion of the homologous or sister chromatid, and the repair of mismatches in heteroduplexes. To investigate these models, we analyzed a genome-wide data set of crossovers (COs) and noncrossovers (NCOs) in Saccharomyces cerevisiae. We demonstrate that the overtransmission of GC alleles is specific to COs and that it occurs among conversion tracts in which all alleles are converted from the same donor haplotype. Thus, gBGC results from a process that leads to long-patch repair. We show that gBGC is associated with longer tracts and that it is driven by the nature (GC or AT) of the alleles located at the extremities of the tract. These observations invalidate the hypotheses that gBGC is due to the base excision repair machinery or to a bias in DSB formation and suggest that in S. cerevisiae, gBGC is caused by the mismatch repair (MMR) system. We propose that the presence of nicks on both DNA strands during CO resolution could be the cause of the bias in MMR activity. Our observations are consistent with the hypothesis that gBGC is a nonadaptive consequence of a selective pressure to limit the mutation rate in mitotic cells. © The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Lemaitre J.-F.,CNRS Biometry and Evolutionary Biology Laboratory | Gaillard J.-M.,CNRS Biometry and Evolutionary Biology Laboratory
Behavioral Ecology | Year: 2013

Understanding causes of between-sex differences in survival patterns is a long-standing challenge in evolutionary biology. Interspecific differences in male allocation to sexual competition have been suggested to shape species-specific patterns of male adult survival and actuarial senescence, and thereby the extent of between-sex differences in these parameters. Sexual competition is complex and involves both competition for gaining mating (i.e., precopulatory competition) and competition for fertilization opportunities (i.e., postcopulatory competition). However, to date, studies seeking for a relationship between allocation to precopulatory competition and male absolute adult survival have led to contrasting results and the influence of postcopulatory competition on these parameters has never been yet investigated. To fill the gap, we performed a comparative study in large herbivores using median lifespan (i.e., age at which only half of the initial cohort is still alive) and actuarial intensity of senescence (i.e., number of years elapsed between the median lifespan and the age where only one-tenth of the initial cohort is still alive). As expected, we found a lower adult survival and a stronger actuarial intensity of senescence in males than in females. Conversely, we did not find any evidence that variation in male allocation to pre-and/or postcopulatory traits explain between-species differences of both absolute and relative adult survival and intensity of actuarial senescence. These results challenge the idea that allocation to specific traits associated with sexual competition is responsible for between-sex differences in survival and senescence patterns generally reported in mammals. © The Author 2012.

Gamelon M.,CNRS Biometry and Evolutionary Biology Laboratory
Biology letters | Year: 2013

To maximize long-term average reproductive success, individuals can diversify the phenotypes of offspring produced within a reproductive event by displaying the 'coin-flipping' tactic. Wild boar (Sus scrofa scrofa) females have been reported to adopt this tactic. However, whether the magnitude of developmental plasticity within a litter depends on stochasticity in food resources has not been yet investigated. From long-term monitoring, we found that juvenile females produced similar-sized fetuses within a litter independent of food availability. By contrast, adult females adjusted their relative allocation to littermates to the amount of food resources, by providing a similar allocation to all littermates in years of poor food resources but producing highly diversified offspring phenotypes within a litter in years of abundant food resources. By minimizing sibling rivalry, such a plastic reproductive tactic allows adult wild boar females to maximize the number of littermates for a given breeding event.

Valeix M.,CNRS Biometry and Evolutionary Biology Laboratory
Journal of Tropical Ecology | Year: 2011

As the dry season progresses in arid and semi-arid ecosystems, rain-fed surface water sources become depleted, forcing most animals to concentrate in the immediate vicinity of the few remaining permanent sources of drinking water. This study investigates the temporal dynamics of use of water-holes by nine African large-herbivore species in the dry season in the semi-arid savanna of Hwange National Park, Zimbabwe, and particularly how annual rainfall influences this temporal dynamics. Two contrasting years in terms of annual rainfall were compared: 2003 (a drought - 362.6 mm) and 2004 (average rainfall - 695.8 mm). In 2003, water-holes were used far more intensively and the level of aggregation of herbivores at water-holes was significantly higher. The temporal dynamics of water-hole use in the dry season differed between the two years: in 2003, the peak of water-hole use started much earlier and lasted 3 mo. Elephants and grazers showed the largest difference in use of water-holes between 2003 and 2004 supporting the suggestion that browsers are less water dependent. This study suggests that annual rainfall should be taken into account when predicting the peak of the dry season. © Copyright 2011 Cambridge University Press.

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