Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations.
PeerJ 4:e1910 (2016)
Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey (L. planeri) show a low reproductive isolation but have highly distinct life histories, the former being p...
Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl.
Molecular Ecology 23(22):5508 (2014)
Gradients of variation--or clines--have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact betw...
Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis.
Molecular Ecology 23(20):5089 (2014)
Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops has recently been detected despite notoriously high levels of selfing in these species. Here, we assess and model the spread of wheat alleles into natural populations of the barbed goatgrass (Aegilo...
Regulation of 11β-hydroxysteroid dehydrogenase type 2 by microRNA.
Hypertension 64(4):860 (2014)
The enzyme 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2) is selectively expressed in aldosterone target tissues, conferring aldosterone selectivity for the mineralocorticoid receptor. A diminished activity causes salt-sensitive hypertension. The mechanism of the variable and distinct 11β-hy...
Sex-chromosome turnovers: the hot-potato model.
American Naturalist 183(1):140 (2014)
Sex-determining systems often undergo high rates of turnover but for reasons that remain largely obscure. Two recent evolutionary models assign key roles, respectively, to sex-antagonistic (SA) mutations occurring on autosomes and to deleterious mutations accumulating on sex chromosomes. These t...
Independent polled mutations leading to complex gene expression differences in cattle.
PLoS ONE 9(3):e93435 (2014)
The molecular regulation of horn growth in ruminants is still poorly understood. To investigate this process, we collected 1019 hornless (polled) animals from different cattle breeds. High-density SNP genotyping confirmed the presence of two different polled associated haplotypes in Simmental an...
Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine.
PLoS ONE 9(11):e110436 (2014)
Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these method...
Sex-chromosome turnovers induced by deleterious mutation load.
Evolution 67(3):635 (2013)
In sharp contrast with mammals and birds, many cold-blooded vertebrates present homomorphic sex chromosomes. Empirical evidence supports a role for frequent turnovers, which replace nonrecombining sex chromosomes before they have time to decay. Three main mechanisms have been proposed for such t...
The balanced lethal system of crested newts: a ghost of sex chromosomes past?
American Naturalist 180(6):E174 (2012)
Balanced lethal systems are more than biological curiosities: as theory predicts, they should quickly be eliminated through the joint forces of recombination and selection. That such systems might become fixed in natural populations poses a challenge to evolutionary theory. Here we address the c...
The evolution of XY recombination: sexually antagonistic selection versus deleterious mutation load.
Evolution 66(10):3155 (2012)
Recombination arrest between X and Y chromosomes, driven by sexually antagonistic genes, is expected to induce their progressive differentiation. However, in contrast to birds and mammals (which display the predicted pattern), most cold-blooded vertebrates have homomorphic sex chromosomes. Two m...
On the maintenance of sex chromosome polymorphism by sex-antagonistic selection.
American Naturalist 178(4):515 (2011)
Complex sex determination systems are a priori unstable and require specific selective forces for their maintenance. Analytical derivations suggest that sex antagonistic selection may play such a role, but this assumes absence of recombination between the sex-determining and sex-antagonistic gen...
Temperature-dependent turnovers in sex-determination mechanisms: a quantitative model.
Evolution 65(1):64 (2011)
Sex determination is often seen as a dichotomous process: individual sex is assumed to be determined either by genetic (genotypic sex determination, GSD) or by environmental factors (environmental sex determination, ESD), most often temperature (temperature sex determination, TSD). We endorse an...
ABCtoolbox: a versatile toolkit for approximate Bayesian computations.
BMC Bioinformatics 11:116 (2010)
The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. Th...
quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation.
quantiNemo is an individual-based, genetically explicit stochastic simulation program. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a h...
Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): inference under a Bayesian spatially explicit framework.
Molecular Ecology 17(3):757 (2008)
The present distribution of freshwater fish in the Alpine region has been strongly affected by colonization events occurring after the last glacial maximum (LGM), some 20,000 years ago. We use here a spatially explicit simulation framework to model and better understand their colonization dynami...
Statistical evaluation of alternative models of human evolution.
PNAS 104(45):17614 (2007)
An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is st...