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Article
Open AccessIdentification of constrained sequence elements across 239 primate genomes
Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory ele...
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Article
Competition and coevolution drive the evolution and the diversification of CRISPR immunity
The diversity of resistance challenges the ability of pathogens to spread and to exploit host populations. Yet, how this host diversity evolves over time remains unclear because it depends on the interplay bet...
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Article
Open AccessVariation of the adaptive substitution rate between species and within genomes
The importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness e...
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polyDFE: Inferring the Distribution of Fitness Effects and Properties of Beneficial Mutations from Polymorphism Data
The possible evolutionary trajectories a population can follow is determined by the fitness effects of new mutations. Their relative frequencies are best specified through a distribution of fitness effects (DF...
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Article
The fitness landscape of the codon space across environments
Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role ...
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Article
Joint impact of competition, summer precipitation, and maternal effects on survival and reproduction in the perennial Hieracium umbellatum
Most studies on consequences of environmental change focus on evolutionary and phenotypic plastic responses, but parental effects represent an additional mechanism by which organisms respond to their local env...
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Article
Open AccessHeterogeneity in effective population size and its implications in conservation genetics and animal breeding
Effective population size (N e ) is defined as the size of an idealized population undergoing the same rate of genetic drift as the population under stu...
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Article
Open AccessContrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicagogenus (L.)
Gene duplications are a molecular mechanism potentially mediating generation of functional novelty. However, the probabilities of maintenance and functional divergence of duplicated genes are shaped by selecti...
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Article
Open AccessMolecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula
We studied patterns of molecular adaptation in the wild Mediterranean legume Medicago truncatula. We focused on two phenotypic traits that are not functionally linked: flowering time and perception of symbiotic m...
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Open AccessAdaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago
The NODULATION RECEPTOR KINASE (NORK) gene encodes a Leucine-Rich Repeat (LRR)-containing receptor-like protein and controls the infection by symbiotic rhizobia and endomycorrhizal fungi in Legumes. The occurrenc...
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Open AccessMicrosatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula
Exploiting genetic diversity requires previous knowledge of the extent and structure of the variation occurring in a species. Such knowledge can in turn be used to build a core-collection, i.e. a subset of acc...
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Article
Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria
The extent to which a population diverges from its ancestor through adaptive evolution depends on variation supplied by novel beneficial mutations. Extending earlier work1,2, recent theory makes two predictions t...
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Article
Molecular Evolution and Positive Selection of the Symbiotic Gene NORK in Medicago truncatula
Understanding the selective constraints of partner specificity in mutually beneficial symbiosis is a significant, yet largely unexplored, prospect of evolutionary biology. These selective constraints can be ex...
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Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations?
Empirical estimates of genome-wide mutation rates and of the distribution of mutational effects are needed to illuminate various topics ranging from evolutionary biology to conservation. Methods for inferring ...
