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Brachi B.,University of Chicago | Meyer C.G.,University of Chicago | Villoutreix R.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Platt A.,Temple University | And 4 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

The "mustard oil bomb" is a major defense mechanism in the Brassicaceae, which includes crops such as canola and the model plant Arabidopsis thaliana. These plants produce and store blends of amino acid-derived secondary metabolites called glucosinolates. Upon tissue rupture by natural enemies, the myrosinase enzyme hydrolyses glucosinolates, releasing defense molecules. Brassicaceae display extensive variation in the mixture of glucosinolates that they produce. To investigate the genetics underlying natural variation in glucosinolate profiles, we conducted a large genomewide association study of 22 methionine-derived glucosinolates using A. thaliana accessions from across Europe. We found that 36% of among accession variation in overall glucosinolate profile was explained by genetic differentiation at only three known loci from the glucosinolate pathway. Glucosinolate-related SNPs were up to 490-fold enriched in the extreme tail of the genome-wide FST scan, indicating strong selection on loci controlling this pathway. Glucosinolate profiles displayed a striking longitudinal gradient with alkenyl and hydroxyalkenyl glucosinolates enriched in the West. We detected a significant contribution of glucosinolate loci toward general herbivore resistance and lifetime fitness in common garden experiments conducted in France, where accessions are enriched in hydroxyalkenyls. In addition to demonstrating the adaptive value of glucosinolate profile variation, we also detected long-distance linkage disequilibrium at two underlying loci, GS-OH and GS-ELONG. Locally cooccurring alleles at these loci display epistatic effects on herbivore resistance and fitness in ecologically realistic conditions. Together, our results suggest that natural selection has favored a locally adaptive configuration of physically unlinked loci in Western Europe.

Cramer B.D.,University of Iowa | Vandenbroucke T.R.A.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Vandenbroucke T.R.A.,Ghent University | Ludvigson G.A.,University of Kansas
Earth-Science Reviews | Year: 2015

The ability to resolve the stratigraphic record of Earth history is critical to understanding past global change events and the range of natural variability within the global paleoclimate. The geosphere-hydrosphere-atmosphere-biosphere system operates on geologically very short time scales and we must be able to resolve the stratigraphic record of past events on similar time scales if we are to understand the cause-and-effect relationships operating within the system. Global resolution ≤. 100. kyr is commonly available when evaluating events from the Cenozoic Era, but such resolution is less common for older portions of Earth history. The introduction of High-Resolution Event Stratigraphy (HiRES) more than two decades ago revolutionized the ability to resolve the Mesozoic and Cenozoic stratigraphic records of global change, and a similar revolution is currently underway for the Paleozoic as well. Here, we review the application of the principles of HiRES to the Paleozoic stratigraphic record with examples from the Silurian System, discuss the quantification of chronostratigraphic uncertainty, and highlight the current deep-time Earth history revolution that has the potential to open the entire Phanerozoic record to the evaluation of short time scale global climate dynamics. © 2014 Elsevier B.V.

Ozkan R.,Turkish Petroleum Corporation | Vachard D.,CNRS Evolution, Ecology, and Paleonthology Laboratory
Revue de Micropaleontologie | Year: 2015

A complete Devonian sequence is well exposed in the eastern Taurides, forming more than 1000 m-thick succession of carbonate and siliciclastic sediments. The carbonate succession, stratigraphically ranging from Middle Devonian to early Late Devonian and mostly comprising limestones, dolomitic limestones and reefal limestones, contains abundant and diverse assemblages of foraminifers, corals, stromatoporoids, calcareous algae, bivalves, brachiopods, ostracods, and conodonts. The limestone samples collected from a more closely sampled stratigraphic section have been investigated for their foraminiferal content. The micropalaeontological analyses carried out on these samples have revealed the presence of an early Frasnian foraminiferal assemblage including predominantly unilocular parathuramminid species and multilocular forms of the genera Nanicella, Paratikhinella and Semitextularia? and further indicated the presence of a new genus and a new species Halevikia deveciae n. gen. n. sp. which appears as an important phylogenetic and stratigraphic transitional taxon between the families Baituganellidae n. fam. and Tournayellinidae, the phylogenetic potentiality of which during the Late Devonian is currently probably underestimated. © 2015 Elsevier Masson SAS.

Vekemans X.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Poux C.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Goubet P.M.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Castric V.,CNRS Evolution, Ecology, and Paleonthology Laboratory
Journal of Evolutionary Biology | Year: 2014

Evolutionary transitions between mating systems have occurred repetitively and independently in flowering plants. One of the most spectacular advances of the recent empirical literature in the field was the discovery of the underlying genetic machinery, which provides the opportunity to retrospectively document the scenario of the outcrossing to selfing transitions in a phylogenetic perspective. In this review, we explore the literature describing patterns of polymorphism and molecular evolution of the locus controlling self-incompatibility (S-locus) in selfing species of the Brassicaceae family in order to document the transition from outcrossing to selfing, a retrospective approach that we describe as the 'mating system genes approach'. The data point to strikingly contrasted scenarios of transition from outcrossing to selfing. We also perform original analyses of the fully sequenced genomes of four species showing self-compatibility, to compare the orthologous S-locus region with that of functional S-locus haplotypes. Phylogenetic analyses suggest that all species we investigated evolved independently towards loss of self-incompatibility, and in most cases almost intact sequences of either of the two S-locus genes suggest that these transitions occurred relatively recently. The S-locus region in Aethionema arabicum, representing the most basal lineage of Brassicaceae, showed unusual patterns so that our analysis could not determine whether self-incompatibility was lost secondarily, or evolved in the core Brassicaceae after the split with this basal lineage. Although the approach we detail can only be used when mating system genes have been identified in a clade, we suggest that its integration with phylogenetic and population genetic approaches should help determine the main routes of this predominant mating system shift in plants. © 2014 European Society For Evolutionary Biology.

Touzet P.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Meyer E.H.,Max Planck Institute of Molecular Plant Physiology
Mitochondrion | Year: 2014

Cytoplasmic male sterility (CMS) is a common feature encountered in plant species. It is the result of a genomic conflict between the mitochondrial and the nuclear genomes. CMS is caused by mitochondrial encoded factors which can be counteracted by nuclear encoded factors restoring male fertility. Despite extensive work, the molecular mechanism of male sterility still remains unknown. Several studies have suggested the involvement of respiration on the disruption of pollen production through an energy deficiency. By comparing recent works on CMS and respiratory mutants, we suggest that the "ATP hypothesis" might not be as obvious as previously suggested. © 2014 Elsevier B.V. and Mitochondria Research Society.

Santure A.W.,University of Sheffield | De Cauwer I.,University of Sheffield | De Cauwer I.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Robinson M.R.,University of Sheffield | And 3 more authors.
Molecular Ecology | Year: 2013

Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade-off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker-based approaches - chromosome partitioning, quantitative trait locus (QTL) mapping and a genome-wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome-wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait. © 2013 John Wiley & Sons Ltd.

Touzet P.,CNRS Evolution, Ecology, and Paleonthology Laboratory
Advances in Botanical Research | Year: 2012

Gynodioecy is a breeding system frequently encountered in flowering plants. It consists of the co-occurrence of hermaphrodites and females in populations. Gynodioecy is generally under nuclear-cytoplasmic control, which involves mitochondrial sterilizing genes and nuclear genes that restore male fertility. Sterilizing mitochondrial genomes have been described in crops in which cytoplasmic male sterility (CMS) is cryptic, i.e. not maintained in populations of wild relative species. However, the isolation of sterilizing genes has led to the definition of a profile that can help to find candidate genes in CMSs found in gynodioecious species. We discuss the expected effect of two alternative evolutionary dynamics of gynodioecy on mitochondrial diversity and describe the pattern of diversity observed at the gene and genome levels. On the basis of whole sequence analyses of mitochondrial genomes in beet and maize, we suggest that CMS mitochondrial genomes might exhibit a faster evolution rate, and a clue to its cause might be found in male sterility itself. © 2012 Elsevier Ltd.

Brachi B.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Aime C.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Glorieux C.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Cuguen J.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Roux F.,CNRS Evolution, Ecology, and Paleonthology Laboratory
PLoS ONE | Year: 2012

Phenological traits often show variation within and among natural populations of annual plants. Nevertheless, the adaptive value of post-anthesis traits is seldom tested. In this study, we estimated the adaptive values of pre- and post-anthesis traits in two stressful environments (water stress and interspecific competition), using the selfing annual species Arabidopsis thaliana. By estimating seed production and by performing laboratory natural selection (LNS), we assessed the strength and nature (directional, disruptive and stabilizing) of selection acting on phenological traits in A. thaliana under the two tested stress conditions, each with four intensities. Both the type of stress and its intensity affected the strength and nature of selection, as did genetic constraints among phenological traits. Under water stress, both experimental approaches demonstrated directional selection for a shorter life cycle, although bolting time imposes a genetic constraint on the length of the interval between bolting and anthesis. Under interspecific competition, results from the two experimental approaches showed discrepancies. Estimation of seed production predicted directional selection toward early pre-anthesis traits and long post-anthesis periods. In contrast, the LNS approach suggested neutrality for all phenological traits. This study opens questions on adaptation in complex natural environment where many selective pressures act simultaneously. © 2012 Brachi et al.

Roux C.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Pauwels M.,CNRS Evolution, Ecology, and Paleonthology Laboratory | Ruggiero M.-V.,Stazione Zoologica Anton Dohrn | Charlesworth D.,University of Edinburgh | And 2 more authors.
Molecular Biology and Evolution | Year: 2013

Balancing selection can maintain different alleles over long evolutionary times. Beyond this direct effect on the molecular targets of selection, balancing selection is also expected to increase neutral polymorphism in linked genome regions, in inverse proportion to their genetic map distances from the selected sites. The genes controlling plant self-incompatibility are subject to one of the strongest forms of balancing selection, and they show clear signatures of balancing selection. The genome region containing those genes (the S-locus) is generally described as nonrecombining, and the physical size of the region with low recombination has recently been established in a few species. However, the size of the region showing the indirect footprints of selection due to linkage to the S-locus is only roughly known. Here, we improved estimates of this region by surveying synonymous polymorphism and estimating recombination rates at 12 flanking region loci at known physical distances from the S-locus region boundary, in two closely related self-incompatible plants Arabidopsis halleri and A. lyrata. In addition to studying more loci than previous studies and using known physical distances, we simulated an explicit demographic scenario for the divergence between the two species, to evaluate the extent of the genomic region whose diversity departs significantly from neutral expectations. At the closest flanking loci, we detected signatures of both recent and ancient indirect effects of selection on the S-locus flanking genes, finding ancestral polymorphisms shared by both species, as well as an excess of derived mutations private to either species. However, these effects are detected only in a physically small region, suggesting that recombination in the flanking regions is sufficient to quickly break up linkage disequilibrium with the S-locus. Our approach may be useful for distinguishing cases of ancient versus recently evolved balancing selection in other systems. © The Author(s) 2012.

Leducq J.-B.,Montpellier University | Leducq J.-B.,CNRS Evolution, Ecology, and Paleonthology Laboratory
G3 (Bethesda, Md.) | Year: 2014

Self-incompatibility (SI) is a genetic system that prevents self-fertilization in many Angiosperms. Although plants from the Brassicaceae family present an apparently unique SI system that is ancestral to the family, investigations at the S-locus responsible for SI have been mostly limited to two distinct lineages (Brassica and Arabidopsis-Capsella, respectively). Here, we investigated SI in a third deep-branching lineage of Brassicaceae: the tribe Biscutelleae. By coupling sequencing of the SI gene responsible for pollen recognition (SRK) with phenotypic analyses based on controlled pollinations, we identified 20 SRK-like sequences functionally linked to 13 S-haplotypes in 21 individuals of Biscutella neustriaca and 220 seedlings. We found two genetic and phylogenetic features of SI in Biscutelleae that depart from patterns observed in the reference Arabidopsis clade: (1) SRK-like sequences cluster into two main phylogenetic lineages interspersed within the many SRK lineages of Arabidopsis; and (2) some SRK-like sequences are transmitted by linked pairs, suggesting local duplication within the S-locus. Strikingly, these features also were observed in the Brassica clade but probably evolved independently, as the two main SRK clusters in Biscutella are distinct from those in Brassica. In the light of our results and of what has been previously observed in other Brassicaceae, we discuss the ecological and evolutionary implications on SI plant populations of the high diversity and the complex dominance relationships we found at the S-locus in Biscutelleae. Copyright © 2014 Leducq et al.

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