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Scleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers, by hybridization, and by morphological plasticity. Here we applied RAD sequencing to the study of species delimitation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia with the objectives to test primary species hypotheses based on mitochondrial DNA sequencing, and to study the genetic structure among sampling sites inside species. Regarding the varying levels of missing data observed among samples we tested different filtering strategy. The main genetic differentiation was observed between samples from Oman and French Polynesia, which also corresponded to different mitochondrial lineages and species hypotheses. In Oman, we did not observe any clear differentiation according to the main mitochondrial lineages considered here, nor between sampling sites. In French Polynesia where a single mitochondrial lineage was studied, we did not evidence any differentiation according to sampling sites. These results provide an additional example of the importance of using independent nuclear markers for the study of species delimitation. Our analyses also allowed the identification of clonal lineages in our samples, and to take them into account in our interpretations. We used simulations to study the impact of clonal reproduction on the distribution of statistics of genetic diversity and genetic structure among loci.

Understanding how new species arise through the progressive establishment of reproductive isolation barriers between diverging populations is a major goal in Evolutionary Biology. One important result of speciation genomics studies is that the genomic regions involved in reproductive isolation frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain highly debated, since they relate to contrasted mechanisms of speciation that are not fully understood yet. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in reproductive isolation between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype-resolved whole-genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in reproductive isolation between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably participated to the establishment of reproductive isolation between the two D. labrax lineages.Author summarySpeciation is often viewed as a progressive accumulation of reproductive isolation barriers between two diverging lineages through the time. When initiated, the speciation process may however take different routes, sometimes leading to the erosion of an established species barrier or to the acquisition of new speciation genes transferred from another species boundary. Here, we describe such a case in the European sea bass. This marine fish species has split 300,000 years ago into an Atlantic and a Mediterranean lineage, which remained partially reproductively isolated after experiencing postglacial secondary contact. For unknown reasons, genomic regions involved in reproductive isolation between lineages have started to diverge well before the split. We here show that diverged alleles were acquired by the Atlantic lineage from an ancient event of admixture with a parapatric sister species about 80,000 years ago. Introgressed foreign alleles that were locally driven to high frequencies in the Atlantic have subsequently resisted to introgression within the Mediterranean during the postglacial secondary contact, thus contributing to increased reproductive isolation between two sea bass lineages. These results support the view that reproductive isolation barriers can evolve via reticulate gene flow across multiple species boundaries.

The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks — 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe — which in turn may have driven the first human mediated dispersal of cats in Europe.

Understanding the genetic underpinnings of fitness trade-offs across spatially variable environments remains a major challenge in evolutionary biology. In Mediterranean gilthead sea bream, first-year juveniles use various marine and brackish lagoon nursery habitats characterized by a trade-off between food availability and environmental disturbance. Phenotypic differences among juveniles foraging in different habitats rapidly appear after larval settlement, but the relative role of local selection and plasticity in phenotypic variation remains unclear. Here, we combine phenotypic and genetic data to address this question. We first report correlations of opposite signs between growth and condition depending on juvenile habitat type. Then, we use single nucleotide polymorphism (SNP) data obtained by Restriction Associated DNA (RAD) sequencing to search for allele frequency changes caused by a single generation of spatially varying selection between habitats. We found evidence for moderate selection operating at multiple loci showing subtle allele frequency shifts between groups of marine and brackish juveniles. We identified subsets of candidate outlier SNPs that, in interaction with habitat type, additively explain up to 3.8% of the variance in juvenile growth and 8.7% in juvenile condition, these SNPs also explained significant fraction of growth rate in an independent larval sample. Our results indicate that selective mortality across environments during early-life stages involves complex trade-offs between alternative growth strategies.

International audience; Seven microsatellite markers were used to investigate the population structure of the offshore ecotype of the European anchovy (Engraulis encrasicolus) by comparing 12 marine samples collected off the Moroccan coast with an inshore sample taken as a reference for the lagoonal ecotype. F-statistics, correspondence analysis and Bayesian assignment all concurred to cluster the European anchovy in this region into three groups: (i) one reference lagoonal sample, (ii) samples north of the 25°N latitude and (iii) samples south of it. Moreover, the Bayesian cluster analysis pointed toward the existence of an admixture between the group north of 25°N and the lagoonal ecotype, while this was not detectable with the group south of 25°N. Differential introgression between the two ecotypes could be one of the plausible explanations for the observed genetic structure and reveals the possible existence of a phylogeographic break around the 25th parallel North. Our study illustrates the fact that, for those species that encompass several incompletely isolated ecotypes, the level of gene flow among them may vary in space and serve as a tool for stock identification. This information may be useful to improve fishery management of this important harvested species along the Moroccan coast.

Evaluating species dispersal across the landscape is essential to design appropriate management and conservation actions. However, technical difficulties often preclude direct measures of individual movement, while indirect genetic approaches rely on assumptions that sometimes limit their application. Here, we show that the temporal decay of admixture tracts lengths can be used to assess genetic connectivity within a population introgressed by foreign haplotypes. We present a proof‐of‐concept approach based on local ancestry inference in a high gene flow marine fish species, the European sea bass (Dicentrarchus labrax). Genetic admixture in the contact zone between Atlantic and Mediterranean sea bass lineages allows the introgression of Atlantic haplotype tracts within the Mediterranean Sea. Once introgressed, blocks of foreign ancestry are progressively eroded by recombination as they diffuse from the western to the eastern Mediterranean basin, providing a means to estimate dispersal. By comparing the length distributions of Atlantic tracts between two Mediterranean populations located at different distances from the contact zone, we estimated the average per‐generation dispersal distance within the Mediterranean lineage to less than 50 km. Using simulations, we showed that this approach is robust to a range of demographic histories and sample sizes. Our results thus support that the length of admixture tracts can be used together with a recombination clock to estimate genetic connectivity in species for which the neutral migration‐drift balance is not informative or simply does not exist.

International audience; North Africa is now recognized as a major area for the emergence and dispersal of anatomically modern humans from at least 315 kya. The Mediterranean Basin is thus particularly suited to study the role of climate versus human-mediated changes on the evolutionary history of species. The Algerian mouse (Mus spretus Lataste) is an endemic species from this basin, with its distribution restricted to North Africa (from Libya to Morocco), Iberian Peninsula and South of France. A rich paleontological record of M. spretus exists in North Africa, suggesting hypotheses concerning colonization pathways, and the demographic and morphologic history of this species. Here we combined genetic (3 mitochondrial DNA loci and 18 microsatellites) and climatic niche modeling data to infer the evolutionary history of the Algerian mouse. We collected 646 new individuals in 51 localities. Our results are consistent with an anthropogenic translocation of the Algerian mouse from North Africa to the Iberian Peninsula via Neolithic navigators, probably from the Tingitane Peninsula. Once arrived in Spain, suitable climatic conditions would then have favored the dispersion of the Algerian mice to France. The morphological differentiation observed between Spanish, French and North African populations could be explained by a founder effect and possibly local adaptation. This article helps to better understand the role of climate versus human-mediated changes on the evolutionary history of mammal species in the Mediterranean Basin.

International audience

Ecosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effectively to environmental changes, and would be favored in variable environments. In this study, we investigated the thermal stress response in Pocillopora coral colonies from two contrasting environments by exposing them to heat stress. We compared the physiological state, bacterial and Symbionaceae communities (using 16S and ITS2 metabarcoding), and gene expression levels (using RNA-Seq) between control conditions and heat stress (the temperature just below the first signs of compromised health). Colonies from both thermal regimes remained apparently normal and presented open and colored polyps during heat stress, with no change in bacterial and Symbionaceae community composition. In contrast, they differed in their transcriptomic responses. The colonies from Oman displayed a more plastic transcriptome, but some genes had a higher basal expression level (frontloading) compared to the less thermotolerant colonies from New Caledonia. In terms of biological functions, we observed an increase in the expression of stress response genes (including induction of tumor necrosis factor receptors, heat shock proteins, and detoxification of reactive oxygen species), together with a decrease in the expression of genes involved in morpho-anatomical functions. Gene regulation (transcription factors, mobile elements, histone modifications and DNA methylation) appeared to be overrepresented in the Oman colonies, indicating possible epigenetic regulation. These results show that transcriptomic plasticity and frontloading can be co-occurring processes in corals confronted to highly variable thermal regimes.

Speciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unlinked to speciation can interfere. Here, we used haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. We show that genomic islands first emerged in allopatry through the effect of linked selection acting on a heterogeneous recombination landscape. Upon secondary contact, preexisting islands were strongly remolded by differential introgression, revealing variable fitness effects among regions involved in reproductive isolation. Interestingly, we found that divergent regions containing ancient polymorphisms conferred the strongest resistance to introgression.

International audience; Hybrid zones provide natural experiments where new combinations of genotypes and phenotypes are produced. Studying the reshuffling of genotypes and remodeling of phenotypes in these zones is of particular interest to document the building of reproductive isolation and the possible emergence of transgressive phenotypes that can be a source of evolutionary novelties. Here, we specifically investigate the morphological variation patterns associated with introgressive hybridization between two species of sole, Solea senegalensis and Solea aegyptiaca. The relationship between genetic composition at nuclear loci and individual body shape variation was studied in four populations sampled across the hybrid zone located in northern Tunisia. A strong correlation between genetic and phenotypic variation was observed among all individuals but not within populations, including the two most admixed ones. Morphological convergence between parental species was observed close to the contact zone. Nevertheless, the samples taken closest to the hybrid zone also displayed deviant segregation of genotypes and phenotypes, as well as transgressive phenotypes. In these samples, deviant body shape variation could be partly attributed to a reduced condition index, and the distorted genetic composition was most likely due to missing allelic combinations. These results were interpreted as an indication of hybrid breakdown, which likely contributes to postmating reproductive isolation between the two species.

The life cycle of most marine species is characterized by high fecundity, dispersal during a planktonic larval phase and a sessile or sedentary adult phase with large census population size (Figure 1). Many articles on marine population genetics start by recalling these main characteristics and ensuing expectations, namely: high genetic diversity within population, low genetic differentiation between populations, high influx of effectively selected advantageous and deleterious mutations, and a high migration load opposing local adaptation. Most of the time, this reminder serves to better emphasize the paradox that observations deviate from these expectations, the most popular being genetic differentiation despite larval dispersal, challenging the idea that marine populations are open and well connected, just followed by pervasive local adaptation, challenging the idea that high migration rates prevent the establishment of locally adapted alleles in the sea, and finally low effective population size ( N e) despite large census size ( N ). The list of such counterexamples became so long that what was initially thought paradoxical finally became a shift to a new paradigm (Hauser and Carvalho 2008): (1) larval dispersal would be less effective than expected to homogenize allele frequencies between populations with high rates of self-recruitment, as, for example, in coral reef fishes (Palumbi and Warner 2003; Jones et al. 2005), (2) selection would be rampant in genomes and easy to identify with genome scans, as, for example, adaptation to brackish waters of the Baltic Sea that would target nothing less than ∼500 loci homogeneously distributed in the herring genome (Lamichhaney et al. 2012; Martinez Barrio et al. 2016), and (3) genetic drift would be stronger than thought owing to a very low proportion of individuals effectively contributing to the following generation, as, for example, in exploited fish and shellfish stocks (Hauser et al. 2002; Ovenden et al. …

Transcaucasia comprises a key region for understanding the history of both the hybrid zone between house mouse lineages and the dispersal of the Neolithic way of life outside its Near Eastern cradle. The opportunity to document the colonization history of both men and mice in Transcaucasia was made possible by the discovery of mouse remains accumulated in pits from a 6000-year-old farming village in the Nakhchivan (Autonomous Republic of Nakhchivan, Azerbaijan). The present study investigated their taxonomy and most likely dispersal path through the identification of the Mus lineage to which they might belong using a geometric morphometric approach of dental traits distances between archaeological and modern populations of the different Mus lineages of South-West Asia. We demonstrate that the mouse remains trapped in the deep storage pits of the dwelling belong to the Mus musculus domesticus from the Near East, with dental shapes similar to current populations in Northern Syria. These results strongly suggest that the domesticus lineage was dispersed into Transcaucasia from the upper Euphrates valley by Neolithic migration, some time between the 7th and 5th millennium BC, providing substantial evidence to back up the scenario featuring near-eastern stimuli in the emergence of agriculture in the South Caucasus. The domesticus mitochondrial DNA signature of the current house mouse in the same location 5000 years later, as well as their turnover towards a subspecies musculus/castaneus phenotype, suggests that early domesticus colonizers hybridized with a later musculus (and maybe castaneus) dispersal originating from south of the Caspian Sea and/or Northern Caucasia. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 108, 917-928.

Accurate knowledge of the biogeographic history and precise characterization of the genetic make-up of a taxon are essential to investigate speciation processes and achieve sound evolutionary comparisons. A case in point is the house mouse Mus musculus and its three parapatric subspecies, which have become a model for such studies. However, although Mus musculus domesticus and Mus musculus musculus constitute genetically well-characterized homogeneous entities, the case of Mus musculus castaneus remains poorly documented. Using mtDNA control region variation in a sample of 402 individuals, covering much of the distribution range of this subspecies, we identify four haplogroups that show largely non-overlapping geographic distributions. They appear to have undergone post-Neolithic expansions, presumably through commensalism with humans, but exhibit a much more ancient divergence. These results point towards a strong past subdivision and a vicariant origin of the different haplogroups, with each retaining a subfraction of the total variability. The genomic consequences of this spatial heterogeneity on the present taxonomic partition will have to be appraised, and may challenge the use of this subspecies as a single entity in evolutionary studies. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.

Chantier qualité GA; International audience; The meagre Argyrosomus regius is a large Sciaenid fish known to reproduce in the eastern Atlantic and Mediterranean Sea in just five distinct and restricted geographic areas: along the Mauritanian coast and at estuary openings (Gironde, Tagus, Guadalquivir and Nile). The biological traits of A. regius (high dispersal capabilities, high fecundity, long larval phase, overlapping generations, reproduction until 40 years of age) are, in principle, favourable to high gene flow, which should lead to genetic homogeneity over large geographic scales. Nevertheless, the high geographic distances between the few reproductive areas leads one ask whether there is genetic differentiation in this species. In the present study, the genetic differentiation of the wild A. regius was investigated across most of its natural range from the Atlantic Ocean (France, Portugal, Spain, Mauritania) to the Mediterranean Sea (Egypt, Turkey), using 11 microsatellite markers previously identified in another Sciaenid, the red drum Sciaenops ocellatus. At least two very distinct groups could be identified, separated by the Gibraltar Strait. Genetic divergences (FST values) were intermediate between the Atlantic samples (0.012–0.041), high between Egypt and the Atlantic (0.06–0.107) or Aegean Sea (0.081) and extremely high between the Aegean Sea and the Atlantic (0.098–0.168). A. regius exhibited a very high level of genetic differentiation rarely reported in marine fishes. These results also demonstrate the existence of a sixth independent spawning area in the Menderes delta (Turkey). Factors potentially involved in this very high genetic fragmentation are discussed, including physical barriers, glaciation pulses and biological traits.

The completion of genomic sequences of physiologically important genes frequently reveals non-coding genetic elements such as tandem repeats (micro- and minisatellites) that are often more polymorphic than nearby coding sequences. We obtained the complete genomic sequences of three hormone genes in sea bass Dicentrarchus labrax : growth hormone (dlGH ), somatolactin (dlSL ) and insulin-like growth factor-1 (dlIGF-1 ), including 5′- and 3′-untranslated regions. Mini- and microsatellites were discovered in both flanking and intron regions. Some were partially conserved across Perciformes. To assess the usefulness and relevance of these gene-associated markers for understanding population structure, an investigation was made on genetic diversity and differentiation at four of them in (i ) five wild populations from the North Sea, the Bay of Biscay and the Western Mediterranean, and (ii ) two samples of hatchery-bred individuals from a freshwater-acclimation experiment. Gene and allelic diversities were lower in cultured individuals than in wild ones. Significant genetic differentiation was demonstrated between Bay of Biscay + North Sea and Mediterranean populations (F st > 0.06, p -associated markers. Significant genetic differentiation was also detected among the Atlantic and North Sea samples, but restricted to the locus associated with dlSL . Significant genetic differentiation was also found among experimental individuals before and after a salinity challenge (F st ≈ 0.05, p and dlIGF-1 loci. Gene-associated markers proved to be more efficient than formerly used anonymous microsatellite markers in providing a clear picture of genetic differentiation.

International audience; A physical sublimation process, generally used for the metals, has been applied to an amino acid, glycine. When this molecule is submitted by this physical process, it could acquire new chemical and physical properties so new therapeutic activities. We have studied the differences of the two glycine forms in solid state and in aqueous solution using the physical and chemical analysis. This study has been carried out with the following techniques: differential scanning calorimeter (DSC), thermogravimetric analyses (TG), thermostimulated current (TSC) and electrochemical impedance.

Coastal and estuarine areas in the Bay of Biscay are essential nursery habitats for sole (Solea solea). Using three intronic markers, we investigated patterns of genetic differentiation among cohorts of juveniles (0+, 1+, sub-adults) inhabiting four major nurseries in the Vilaine and Loire river estuaries, the Pertuis d' Antioche strait, and the Gironde estuary. Genetic differentiation was not significant for the age 0- and 1-groups, but was among sub-adult samples (theta(WC) = 0.017; P = 0.031). Hierarchical analyses of genotypic frequencies by nested multivariate ANOVA using redundancy analysis indicated that northern nurseries of Loire and Vilaine rivers had different patterns of genotypic variation with age than southern nurseries of the Pertuis d' Antioche and Gironde estuaries (F = 1.36; P = 0.007). Bay of Biscay nurseries appeared to be spatially structured between a southern and a northern group that exhibit different genotypic distributions. Genetic drift and gene flow explains this pattern poorly, but a statistical test (P < 0.035) suggested that the metallothionein (MT) locus may be significantly impacted by selection in southern estuaries. As metallothionein is involved in heavy-metal detoxification, and southern nurseries are known to be affected by cadmium, this indicates a possible correlation between observed genotypic distributions and some nursery habitat features in sole. Some selective patterns might also be proposed to explain patterns of linkage disequilibrium observed at amylase loci in three of the four nurseries. (C) 2008 Elsevier Ltd. All rights reserved.

Few genetic data document the postglacial history of the western house mouse, Mus musculus domesticus. We address this by studying a sample from the southeastern tip of the Fertile Crescent in the Iranian province of Ahvaz. Including other published and unpublished data from France, Germany, Italy, Bulgaria, Turkey and other places in Iran, altogether 321 mitochondrial D-loop sequences are simultaneously analysed. The patterns of coalescence obtained corroborate the classical proposal according to which the Fertile Crescent is where commensalism with humans has started in the Western Hemisphere, and from where the subspecies has expanded further west. Our data also clearly show that despite multiple colonisations and long-range transportation, there is still a rather high PhiST of 0.39. The original expansion signal is still recognisable, with two well-separated derived clades, allowing us to propose a hypothetical scenario in which expansion toward Europe and Asia Minor took at least two routes, tentatively termed the Mediterranean and the Bosphorus/Black Sea routes. This scenario resembles that of another domesticated species, the goat, and fits with the known progression of Neolithic culture. Given the concomitance of both phenomena around 12,000 years ago, we propose a recalibration of the D-loop mutation rate to a much faster tick of approximately 40% per site per million years (Myr). This value should be used for intrasubspecific polymorphism, while the interspecific rate in Mus is presently estimated at 6-10%/site/Myr. This is in keeping with the now well recognised fact that only a subfraction of segregating mutations go to fixation.

International audience; A multilocus analysis was initiated in order to infer the general effect of demography and the indirect effect of positive selection on some chromosome segments in Bathymodiolus. Mussels of the genus Bathymodiolus inhabit the very hostile, fragmented and variable environment of deep-sea hydrothermal vents which is thought to cause recurrent population bottlenecks via extinction/colonisation processes and adaptation to new environmental conditions. In the course of this work we discovered that the assumption of neutrality of non-coding polymorphisms usually made in genome scan experiments was likely to be violated at one of the loci we analysed. The direct effect of slight purifying selection on non-coding polymorphisms shares many resemblances with the indirect effect of positive selection through genetic hitchhiking. Combining polymorphism with divergence data for several closely related species allowed us to obtain different expectations for the direct effect of negative selection and the indirect effect of positive selection. We observed a strong excess of rare non-coding polymorphisms at the second intron of the EF1α gene in the two species Bathymodiolus azoricus and Bathymodiolus thermophilus, while two other loci, the mitochondrial COI gene and an intron of the Lysozyme gene, did not exhibit such a deviation. In addition, the divergence rate of the EF1α intron was estimated to be unexpectedly low when calibrated using the closure of the Panama Isthmus that interrupted gene flow between the two species. The polymorphism to divergence ratio was similar to the one observed for the other two loci, in accordance to the hypothesis of purifying selection. We conclude that slight purifying selection is likely to act on polymorphic intronic mutations of the EF1α second intron and discuss the possible relationship with the specific biology of Bathymodiolus mussels.

This work presents a study of the distribution and pattern of variation throughout the ranges of three free-living mouse species of the genus Mus-M. macedonicus, M. spicilegus, and a M. cypriacus - based on sequencing of two segments of the mitochondrial DNA (mtDNA) control region. The study shows a similar level of variability in the three species and suggests their recent population expansion. The highest proportion of variation is found within populations indicating low genetic structuring. Phylogenetic analysis confirms the significant divergence of a mitochondrial lineage of M. macedonicus from Israel, recently described as a new subspecies, M. macedonicus spretoides. Conversely, no genetic hiatus is revealed between European and Asian populations of M. macedonicus macedonicus. Although phylogenetic relationships among M. spicilegus populations could not be unravelled precisely, the results suggest a recent westward expansion of the species. The mtDNA divergence between M. macedonicus and M. spicilegus is 7.3%, suggesting their split between c. 700,000 and 1 million years ago. These dates correspond with a coalescent estimate about 720,000 years ago. On the other hand, M. cypriacus appeared almost twice as divergent from the former species (4.5%) as from the latter (8.8%) suggesting a divergence of c. 430,000-610,000 years ago (coalescent approximately 490,000 years ago) and 830,000-1.2 million years ago (coalescent approximately 780,000 years ago), respectively. Approximate times of population expansion have also been estimated for all taxa and groups of populations. Existence of several glacial refuges and various colonization scenarios are discussed; since all estimated divergence times fall within interglacial periods it seems that climatic oscillations did not play a crucial role in the evolution of the three species.

International audience; Convincing evidence reporting adaptive variation for physiologically and/or ecologically important traits in marine taxa is often derived from studies comparing field and laboratory observations and based on candidate-gene markers, mainly allozymes, responding to habitat selection. Likewise, patterns of genetic differentiation between sea and lagoon populations of the euryhaline European sea bass (Dicentrarchus labrax) were shown to correlate with changes in allele frequencies recorded during experimental salinity challenges, suggesting potential role for local adaptation. However, there has been criticism of these past approaches, causing a need for further investigation. We reinvestigated this correlation in European sea bass using a set of 20 micro- and one minisatellite markers, some of which are associated with candidate genes. We used rigorous experimental settings to demonstrate that only one single gene-associated marker consistently reported significant genetic differentiation between fish raised in seawater compared to fish acclimated to freshwater (locus EIF3E; F ST = 0.060; p = 0.007, n = 268). A few other loci were shown to be false positive and did not respond to selection. Furthermore, a field study of sea–lagoon differentiation in wild European sea bass (n = 144) using the same loci reported marginally significant genetic differentiation at locus EIF3E (F ST = 0.0114, p = 0.068). This locus was identified as putatively under selection. Two other microsatellite loci associated with genes (DLA0070 and DLA0060, respectively) were found to significantly participate to sea–lagoon differentiation and deviate from neutral expectation. The evidence for sea–lagoon local adaptation in sea bass remains faint if not highly elusive.

Background The phylogeography of the house mouse (Mus musculus L.), an emblematic species for genetic and biomedical studies, is only partly understood, essentially because of a sampling bias towards its most peripheral populations in Europe, Asia and the Americas. Moreover, the present-day phylogeographic hypotheses stem mostly from the study of mitochondrial lineages. In this article, we complement the mtDNA studies with a comprehensive survey of nuclear markers (19 microsatellite loci) typed in 963 individuals from 47 population samples, with an emphasis on the putative Middle-Eastern centre of dispersal of the species. Results Based on correspondence analysis, distance and allele-sharing trees, we find a good coherence between geographical origin and genetic make-up of the populations. We thus confirm the clear distinction of the three best described peripheral subspecies, M. m. musculus, M. m. domesticus and M. m. castaneus. A large diversity was found in the Iranian populations, which have had an unclear taxonomic status to date. In addition to samples with clear affiliation to M. m. musculus and M. m. domesticus, we find two genetic groups in Central and South East Iran, which are as distinct from each other as they are from the south-east Asian M. m. castaneus. These groups were previously also found to harbor distinct mitochondrial haplotypes. Conclusion We propose that the Iranian plateau is home to two more taxonomic units displaying complex primary and secondary relationships with their long recognized neighbours. This central region emerges as the area with the highest known diversity of mouse lineages within a restricted geographical area, designating it as the focal place to study the mechanisms of speciation and diversification of this species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0306-4) contains supplementary material, which is available to authorized users.

International audience; Rarefaction methods have been introduced into population generics (from ecology) for predicting and comparing the allelic richness of future samples (or sometimes populations) on the basis of currently available samples, possibly of different sizes. Here, we focus our attention on one such problem: Predicting which population is most likely to yield the future sample having the highest allelic richness. (This problem can arise when we want to construct a core collection from a larger germplasm collection.) We use extensive simulations to compare the performance of the Monte Carlo rarefaction (repeated random subsampling) method with a simple Bayesian approach we have developed-which is based on the Ewens sampling distribution. We found that neither this Bavesian method nor the (Monte Carlo) rarefaction method performed uniformly better than the other. We also examine briefly some of the other motivations offered for these methods and try to make sense of them from a Bayesian point of view.

Euryhaline teleosts possess the capacity to osmoregulate under various environmental conditions (freshwater to hypersaline water). This physiological capacity is generally monitored using enzyme activity assays (Na+/K+-ATPase...), hormones quantification (prolactine, growth hormone) or their mRNAs expression. To date, few studies addressed the genetic correlates of adaptation to varying salinity at a molecular level in such fish. In the sea bass Dicentrarchus labrax, genetic differentiation was observed at specific allozyme loci between lagoon- and open-sea populations. In the present study, we investigated transcriptomic response of D. labrax to salt- and freshwater acclimation in two organs involved in osmoregulation, gill and intestine. By using suppression subtractive hybridisation, we characterised 586 partial cDNA sequences encoding proteins potentially involved in the metabolism of sea bass acclimated to salt- or freshwater under experimental conditions. Using these results, we first characterised complete genomic sequence of a carbonic anhydrase and then analysed mRNA expression of genes potentially involved in osmoregulation mechanisms (Na+/K+-ATPase, carbonic anhydrase, angiotensin-converting enzyme and claudin-3), cell-cycle regulation (secretagogin) and immune system (nephrosin) in gill and intestine of wild fish from open sea and lagoons. Our analyses indicate a strong tissue- and environmental-dependant expression pattern for all the genes studied. A transcriptomic approach such as described in the present paper provides thus a first description of genes involved in metabolic or structural functions important for coping with environmental salinity variations in a euryhaline fish like the common sea bass D. labrax. It should be supplemented by proteomics to check the direct involvement of the gene products at the protein level, and by polymorphism analyses if one is to understand population or individual fluctuations in acclimation to salinity variation. (c) 2006 Elsevier B.V. All rights reserved.

We studied the genetic basis of post-zygotic isolation in the marine musselsMytilus edulisandMytilus galloprovincialis. Evidence was obtained for a high number of recessive Dobzhansky–Muller substitutions in the genome of these two mussel taxa. We analysed the segregation of unlinked diagnostic markers in the progeny of two backcrosses and an F2cross, 36 h and 200 days after fertilization. Directional selection favouringM. galloprovincialisgenotypes was observed in both kinds of cross. In the F2, epistatic interactions between each pair of chromosome fragments mapped by the markers were identified in addition. Our results imply that homozygous–homozygous interactions are required for breakdown of coadaptation, in accordance with the dominance theory of post-zygotic isolation. Endogenous post-zygotic selection distributed over many loci throughout the genome provides the missing factor explaining the astonishing persistence and strength of barriers to neutral introgression in such a dispersive taxon asMytilus.

Tine, Mbaye ... et. al.-- 10 pages, 5 figures, supplementary information https://doi.org/10.1038/ncomms6770, The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation, This work was initiated during the MARINE GENOMICS EUROPE project EU-FP6 505403 and was supported by grants from the Max Planck Society (MPG for genome sequencing, assembly and annotation), LIFECYCLE EU-FP7 222719 and BMBF-01GS0805 to R.R., and the French ANR grants LABRAD-SEQ 11-PDOC-009-01 to P.-A.G. and REGULBASS 09-GENM-003 to B.G. M.T. received a fellowship from the MPG, H.K. was partly financed by LIFECYCLE EU-FP7 222719 and F.K. by the BMBF-01GS0805 grant. L.B. was supported by the grant Progetto 12/MI/2004 from the Veneto Region. R.S.T.M. and B.L. were in receipt of fellowships SFRH/BPD/66742/2009 and SFRH/BPD/89889/2012 from the Foundation for Science and Technology of Portugal

We analysed the patterns of allele frequency change for ten diagnostic autosomal allozyme loci in the hybrid zone between the house mouse subspecies Mus musculus domesticus and M. m. musculus in central Jutland. After determining the general orientation of the clines of allele frequencies, we analysed the dine shapes along the direction of maximum gradient. Eight of the ten clines are best described by steep central steps with coincident positions and an average width of 8.9 km (support limits 7.6-12.4) flanked by tails of introgression, indicating the existence of a barrier to gene flow and only weak selection on the loci studied. We derived estimates of migration from linkage disequilibrium in the centre of the zone, and by applying isolation by distance methods to microsatellite data from some of these populations. These give concordant estimates of σ = 0.5-0.8 km generation -1/2 . The barrier to gene flow is of the order of 20 km (support limits 14-28), and could be explained by selection of a few per cent at 43-120 under-dominant loci that reduces the mean fitness in the central populations to 0.45. Some of the clines appear symmetrical, whereas others are strongly asymmetrical, and two loci appear to have escaped the central barrier to gene flow, reflecting the differential action of selection on different parts of the genome. Asymmetry is always in the direction of more introgression into musculus, indicating either a general progression of domesticus into the musculus territory, possibly mediated by differential behaviour, or past movement of the hybrid zone in the opposite direction, impeded by potential geographical barriers to migration in domesticus territory.

Recu le 8 avril 2004 ; Accepte le 7 octobre 2004 Resume – Une analyse phylogeographique de quinze echantillons de Dicentrarchus labrax dont cinq sont originaires de Mediterranee occidentale, sept de Mediterranee orientale et trois echantillons d’elevage en provenance de trois piscicultures francaises a ete effectuee a partir du polymorphisme de six locus microsatellites. Parmi les echantillons orientaux, trois ne se regroupent pas en fonction de leur origine geographique, mais plutot avec le groupe occidental. Ces echantillons presentent egalement une diversite allelique legerement reduite, indiquant qu’ils proviennent d’un nombre limite de geniteurs d’origine occidentale. Parmi les stocks d’elevage, un seul montre une reduction significative de la variabilite genetique, ce qui indique que ces cheptels sont ouverts et font largement appel a des geniteurs sauvages. L’utilisation d’alevins d’origine occidentale pour ensemencer les premieres fermes d’elevage du bassin oriental remonte au plus tard au debut des annees 80. Ceci souleve la question des mecanismes biologiques expliquant le maintien de poissons d’origine occidentale dans un contexte oriental pendant au moins deux ou trois generations.

To investigate the origin and maintenance of the genetic discontinuity between Atlantic and Mediterranean populations of the common sea bass (Dicentrarchus labrax) we analysed the genetic variation at a fragment of mitochondrial cytochrome b sequence for 18 population samples. The result were also compared with new or previously published microsatellite data. Seven mitochondrial haplotypes and an average nucleotidic divergence of 0.02 between Atlantic and Mediterranean populations that matches a Pleistocene allopatric isolation were found. The frequency variation at the cytochrome b locus was many times greater between Atlantic and Mediterranean populations ((θ) over cap (C) = 0.67) than at microsatellite loci ((θ) over cap (N) = 0.02). The examination of the different evolutionary forces at play suggests that a sex-biased hybrid breakdown is a likely explanation for part of the observed discrepancy between mitochondrial and nuclear loci. In addition, an analysis is made of the correlation between microsatellite loci points towards the possible existence of a hybrid zone in samples from the Alboran Sea.

Populations of marine organisms are potentially affected by numerous selective pressures such as temperature and salinity, or anthropogenic pressures such as xenobiotics that may preclude adaptation to particular habitats. Such selective pressures may also affect their demography. Examples include modifications of the population dynamics through shifts in growth rate, and in life history traits affecting fitness such as size or age of first reproduction. However, the documentation of variation in phenotypically plastic traits specific to distinct environments cannot be taken as the ultimate proof that natural selection has occurred. Measurement of the impact of selection and subsequent local adaptation of fish populations based exclusively on morphological or physiological characters is one of the most difficult things to achieve because it depends on the use of phenotypic characters that closely match the genotype. Molecular markers can help to overcome this problem and, under some circumstances, can record the footprints of selection. A combination of polymorphisms that are under selection and those that are not can provide complementary information. In this paper, we review how and why selection can be detected at the molecular level, using genetic markers analysed in a population genetic framework. We then report and discuss case studies in fish.

A mitochondrial and nuclear gene analysis allowed us to precise the taxonomical position of the two sympatric species of mice known to be present on Cyprus. One of them is the commensal house mouse M. m. domesticus, and the other revealed to be a new taxon that is a sister species of M. spicilegus and M. macedonicus. The new species is equidistant from each of these, the divergence dating around 0.5-1 Myr. Its origin either results from an ancient accidental colonisation of the island or from a recent transportation by the first epipalaeolithic settlers. In this last eventuality, the new species would also exist somewhere else in Asia Minor.

International audience; Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations.

In the present study the genetic structure of Dicentrarchus labrax (14 samples from the Mediterranean) was analysed at six microsatellite loci, in order to test the hypothesis that some enzymatic loci undergo selection between marine and lagoon habitat. Eight of the 14 samples were analysed at both microsatellite and allozyme markers. The analysis of the genetic variation among the Mediterranean samples showed that (i)Fcirc;ST values obtained with the six microsatellite loci were much smaller than those obtained with the 28 allozymes and (ii) microsatellite loci seemed to reflect more the geographical proximity than an ecological one. Thirteen enzymatic loci exhibited moderate to high values compared with microsatellites. This was interpreted as evidence that these allozymes are non-neutral. However, only six loci seemed to be implicated in differentiation between marine and lagoon samples, the causes of selection being unknown for the others. A possible scenario of population dynamics of the sea bass between marine and lagoon habitat is suggested.

A comparative study of disturbed (downstream) and undisturbed (upstream) populations in a French Mediterranean river (the Sorgue) was conducted to assess the fate of introgressing hatchery-genes in the aboriginal gene pool. Variation was assessed at 27 protein-coding loci, three microsatellite loci and two mtDNA restriction sites. The results were compared to those from another Mediterranean drainage basin (that of the river Orb). The genetic pattern observed among markers and drainage basins was found to be noticeably different. A reduction in population size is hypothesized to explain the lower variability observed in the upper part of the river Sorgue. Estimations of hatchery gene flow were different between loci but in the same range of values between markers.

International audience; The genetic impact of restocking Mediterranean brown trout populations with hatchery stocks was investigated in the Orb River drainage (France), using genetic data from three microsatellite loci. We sampled two wild populations, the main river which is restocked each year and one of its tributaries which has not been restocked for 6 years. Each sample was divided into two age groups (juveniles/ adults). Introgression of each native population by hatchery stocks was previously estimated using allele frequencies from two diagnostic protein-coding loci and one mtDNA haplotype. The genetic structure and allelic frequency at three microsatellite loci in native populations were compared with two hatchery samples belonging to stocks usually used for restocking this drainage. High levels of polymorphism (23±27 alleles per locus) were detected for two loci, whereas the third was less polymorphic. Polymorphism was signi®cantly higher in the restocked population than in the now undisturbed population. Signi®cant dierences between age groups were observed in the main river, but not in its tributary. The introgression estimates using microsatellites were compared to those obtained from proteins and mtDNA. The dierent possible origins of alleles common to hatcheries and wild populations (homoplasy, ancestral polymorphism or introgression) are discussed.

The genetic basis and evolutionary implications of local adaptation in high gene flow marine organisms are still poorly understood. In several Mediterranean fish species, alternative migration patterns exist between individuals entering coastal lagoons that offer favourable conditions for growth and those staying in the sea where environmental conditions are less subject to rapid and stressful change. Whether these coexisting strategies are phenotypically plastic or include a role for local adaptation through differential survival needs to be determined. Here, we explore the genetic basis of alternate habitat use in western Mediterranean populations of the gilthead sea bream (Sparus aurata). Samples from lagoonal and open-sea habitats were typed for three candidate gene microsatellite loci, seven anonymous microsatellites and 44 amplified fragment length polymorphism markers to test for genotype-environment associations. While anonymous markers globally indicated high levels of gene flow across geographic locations and habitats, non-neutral differentiation patterns correlated with habitat type were found at two candidate microsatellite loci located in the promoter region of the growth hormone and prolactin genes. Further analysis of these two genes revealed that a mechanism based on habitat choice alone could not explain the distribution of genotype frequencies at a regional scale, thus implying a role for differential survival between habitats. We also found an association between allele size and habitat type, which, in the light of previous studies, suggests that polymorphisms in the proximal promoter region could influence gene expression by modulating transcription factor binding, thus providing a potential explanatory link between genotype and growth phenotype in nature.

International audience; The population genetic structure of sea bass (Dicentrarchus labrax) along a transect from the Atlantic Ocean (AO) to the Eastern Mediterranean (EM) Sea differs from that of most other marine taxa in this area. Three populations (AO, Western Mediterranean [WM], EM) are recognized today, which were originally two allopatric populations. How two ancestral genetic units have evolved into three distinct units has not been addressed yet. Therefore, to investigate mechanisms that lead to the emergence of the central WM population, its current status, and its connectivity with the two parental populations, we applied 20 nuclear loci that were either gene associated or gene independent. Results confirmed the existence of three distinct gene pools, with higher differentiation at two transitional areas, the Almeria-Oran Front (AOF) and of the Siculo-Tunisian Strait (STS), than within any population. Significant linkage disequilibrium and heterozygote excess indicated that the STS is probably another tension zone, as already described for the AOF. Neutrality tests fail to reveal marker loci that could be driven by selection within or among metapopulations, except for locus DLA0068. Collectively, results support that the central WM population arose by trapping two tensions zones at distinct geographic locations of limited connectivity. Population assignment further revealed that WM individuals were more introgressed than individuals from the other two metapopulations. This suggests that this population might result from hybrid swarming, and was or is still seeded by genes received through the filter of each tension zone.

International audience; Estimates of the proportion of amino acid substitutions that have been fixed by selection (a) vary widely among taxa, ranging from zero in humans to over 50% in Drosophila. This wide range may reflect differences in the efficacy of selection due to differences in the effective population size (N e). However, most comparisons have been made among distantly related organisms that differ not only in N e but also in many other aspects of their biology. Here, we estimate a in three closely related lineages of house mice that have a similar ecology but differ widely in N e : Mus musculus musculus (N e ; 25,000-120,000), M. m. domesticus (N e ; 58,000-200,000), and M. m. castaneus (N e ; 200,000-733,000). Mice were genotyped using a high-density single nucleotide polymorphism array, and the proportions of replacement and silent mutations within subspecies were compared with those fixed between each subspecies and an outgroup, Mus spretus. There was significant evidence of positive selection in M. m. castaneus, the lineage with the largest N e , with a estimated to be approximately 40%. In contrast, estimates of a for M. m. domesticus (a 5 13%) and for M. m. musculus (a 5 12 %) were much smaller. Interestingly, the higher estimate of a for M. m. castaneus appears to reflect not only more adaptive fixations but also more effective purifying selection. These results support the hypothesis that differences in N e contribute to differences among species in the efficacy of selection.

Pearl oysters belonging to the genus Pinctada (Bivalvia: Pteriidae) are widely distributed between the Indo-Pacific and western Atlantic. The existence of both widely distributed and more restricted species makes this group a suitable model to study diversification patterns and prevailing modes of speciation. Phylogenies of eight out of the 11 currently recognised Pinctada species using mitochondrial (cox1) and nuclear (18S rRNA) data yielded two monophyletic groups that correspond to shell size and presence/absence of hinge teeth. Character trace of these morphological characters onto the molecular phylogeny revealed a strong correlation. Pinctada margaritifera appears polyphyletic with specimens from Mauritius grouping in a different clade from others of the French Polynesia and Japan. Hence, P. margaritifera might represent a species complex, and specimens from Mauritius could represent a different species. Regarding the putative species complex Pinctada fucata/Pinctada martensii/Pinctada radiata/Pinctada imbricata, our molecular analyses question the taxonomic validity of the morphological characters used to discriminate P. fucata and P. martensii that exhibited the lowest genetic divergence and are most likely conspecific as they clustered together. P. radiata and P. imbricata were recovered as monophyletic. The absence of overlapping distributions between sister lineages and the observed isolation by distance suggests that allopatry is the prevailing speciation mode in Pinctada. Bayesian dating analysis indicated a Miocene origin for the genus, which is consistent with the fossil record. The northward movement of the Australian plate throughout the Miocene played an important role in the diversification process within Pinctada.

International audience; The electron densities in three crystal forms of piracetam (triclinic form II, monoclinic form III, and triclinic piracetam monohydrate) were derived from high resolution X-ray diffraction experiments carried out at 100 K. For comparison, quantum mechanics calculations were also performed for the three compounds. The experimental electron density was refined using the Hansen-Coppens multipole model. The electron deformation density and the electrostatic potential were carefully analyzed in the three forms of piracetam. The atomic charges obtained by the flux of the electric field were found in excellent agreement with those obtained by the conventional volume integration method. The charge values compare qualitatively well with those obtained by theoretical calculations. The total electrostatic force exerted on each atom of the molecule has been investigated by using the Maxwell stress tensor as well as the interatomic forces. The experimental electrostatic interaction energies between dimers in the three crystal forms of piracetam were also estimated. Monoclinic form III exhibits the strongest piracetam-piracetam dimer electrostatic interaction energy (-131.9 kJ/mol) compared to -116.0 and -103.3 kJ/mol found in triclinic form II and the monohydrate form, respectively. The experimental interaction electrostatic energy of the piracetam-water contact was estimated as -175.0 kJ/mol in the monohydrate form. © 2011 American Chemical Society.

The molecular signatures of the recent expansion of the western house mouse,Mus musculus domesticus, around the Mediterranean basin are investigated through the study of mitochondrial D-loop polymorphism on a 1313 individual dataset. When reducing the complexity of the matrilineal network to a series of haplogroups (HGs), our main results indicate that: (i) several HGs are recognized which seem to have almost simultaneously diverged from each other, confirming a recent expansion for the whole subspecies; (ii) some HGs are geographically delimited while others are widespread, indicative of multiple introductions or secondary exchanges; (iii) mice from the western and the eastern coasts of Africa harbour largely different sets of HGs; and (iv) HGs from the two shores of the Mediterranean are more similar in the west than in the east. This pattern is in keeping with the two-step westward expansion proposed by zooarchaeological data, an early one coincident with the Neolithic progression and limited to the eastern Mediterranean and a later one, particularly evident in the western Mediterranean, related to the generalization of maritime trade during the first millennium BC and onwards. The dispersal of mice along with humans, which continues until today, has for instance left complex footprints on the long ago colonized Cyprus or more simple ones on the much more recently populated Canary Islands.

We assessed genetic polymorphism of a bi-allelic anonymous DNA locus in otherwise highly homogeneous Turbinaria ornata populations in French Polynesia, Hawaii, Solomon, Wallis and La Réunion Islands. Large heterozygote deficiencies occurred in almost all populations, which may be related to possible self-fertilisation and short dispersal distance of zygotes. There was a high genetic differentiation among samples (Fst=0.5269***) and this was correlated with a gradient of hydrodynamic conditions prevailing on French Polynesian coral reefs. This correlation is tentatively associated with balancing selection acting on, or on the vicinity of, this anonymous DNA locus.

Contact: berville@supagro.inra.fr Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; The present diversity of the olive (crop) and oleaster (wild) tree was investigated with nuclear and cytoplasm markers. Patterns of diversity of the wild form inferred eleven ancestral populations in the East and the West of the Mediterranean basin. Patterns of diversity for cultivars are less clear, but we showed that cultivars admixed to nine groups that corresponded to oleaster ancestral populations. We inferred that nine domestication events took place in the olive, but these origins were blurred by gene flow from oleaster and by human displacements. These origins of domestication probably reflected different reasons and uses to domesticate the oleaster. To cite this article: C Breton et al., C R. Biologies 332 (2009). (C) 2009 Academie des sciences; La diversité actuelle de l’olivier (cultivé) et de l’oléastre (sauvage) a été étudiée avec des marqueurs nucléaires et cytoplasmiques. Les patrons de diversité de la forme sauvage conduisent onze populations ancestrales à l’Est et l’Ouest du bassin méditerranéen. Pour les cultivars, les patrons de diversité sont moins tranchés, mais nous avons montré qu’ils se rattachent à neuf groupes qui correspondent à neuf des onze populations ancestrales d’oléastre. Nous en avons déduit que neuf évènements de domestication différents se sont produits pour conduire à l’olivier actuel, mais les origines sont rendues diffuses du fait de flux de gènes avec l’oléastre et des déplacements des cultivars par l’homme. Ces origines de domestication reflètent probablement diverses motivations et utilisations de l’olivier et de ses produits. Pour citer cet article : C. Breton et al., C. R. Biologies 332 (2009)

The GM2 ganglioside represents an important target for specific anticancer immunotherapy. We designed and synthesized a neoglycopeptide immunogen displaying one or two copies of the GM2 tetrasaccharidic moiety. These glycopeptides were prepared using the Huisgen cycloaddition, which enables the efficient ligation of the alkyne-functionalized biosynthesized GM2 with an azido CD4 + Tcell epitope peptide. It is worth noting that the GM2 can be produced on a gram scale in bacteria, which can be advantageous for a scale-up of the process. We show here for the first time that a fully synthetic glycopeptide, which is based on a ganglioside carbohydrate moiety, can induce human tumor cell-specific antibodies after immunization in mice. Interestingly, the monovalent, but not the divalent, form of GM2 peptide construct induced antimelanoma antibodies. Unlike traditional vaccines, this vaccine is a pure chemically-defined entity, a key quality for consistent studies and safe clinical evaluation. Therefore, such carbohydrate-peptide conjugate represents a promising cancer vaccine strategy for active immunotherapy targeting gangliosides.

International audience; Background: Reconstructing the history of divergence and gene flow between closely-related organisms has long been a difficult task of evolutionary genetics. Recently, new approaches based on the coalescence theory have been developed to test the existence of gene flow during the process of divergence. The deep sea is a motivating place to apply these new approaches. Differentiation by adaptation can be driven by the heterogeneity of the hydrothermal environment while populations should not have been strongly perturbed by climatic oscillations, the main cause of geographic isolation at the surface. Methodology/Principal Finding: Samples of DNA sequences were obtained for seven nuclear loci and a mitochondrial locus in order to conduct a multi-locus analysis of divergence and gene flow between two closely related and hybridizing species of hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis. The analysis revealed that (i) the two species have started to diverge approximately 0.760 million years ago, (ii) the B. azoricus population size was 2 to 5 time greater than the B. puteoserpentis and the ancestral population and (iii) gene flow between the two species occurred over the complete species range and was mainly asymmetric, at least for the chromosomal regions studied. Conclusions/Significance: A long history of gene flow has been detected between the two Bathymodiolus species. However, it proved very difficult to conclusively distinguish secondary introgression from ongoing parapatric differentiation. As powerful as coalescence approaches could be, we are left by the fact that natural populations often deviates from standard assumptions of the underlying model. A more direct observation of the history of recombination at one of the seven loci studied suggests an initial period of allopatric differentiation during which recombination was blocked between lineages. Even in the deep sea, geographic isolation may well be a crucial promoter of speciation.

International audience; The electron density of monoclinic paracetamol was derived from high-resolution X-ray diffraction at 100 K. The Hansen– Coppens multipole model was used to refine the experimental electron density. The topologies of the electron density and the electrostatic potential were carefully analyzed. Numerical and analytical procedures were used to derive the charges integrated over the atomic basins. The highest charge magnitude (À1.2 e) was found for the N atom of the paracetamol molecule, which is in agreement with the observed nucleophilic attack occurring in the biological media. The electric field generated by the paracetamol molecule was used to calculate the atomic charges using the divergence theorem. This was simultaneously applied to estimate the total electrostatic force exerted on each atom of the molecule by using the Maxwell stress tensor. The interaction electrostatic energy of dimers of paracetamol in the crystal lattice was also estimated.

International audience; In order to study further the genetic structure of the pearl oyster Pinctada margaritifera in French Polynesia with a special consideration for the sampling scale, we analyzed or re-analyzed sets of data based on nuclear DNA markers obtained at different spatial scales. At a large scale (several 1,000 km), the remote Marquesas Islands were confirmed to be significantly differentiated from Tuamotu-Gambier and Society archipelagos, with a marked difference however for the two main islands that are different from each other. At a medium scale (several 10 to several 100 km), overall homogeneity was observed within and between these two archipelagos, with some exceptions. This could be attributed both to large-scale larval dispersal and to human-driven spat translocations due to pearl oyster cultivation. These results contrast with those observed (1) at a small scale (less than 10 km) in a lagoon heavily impacted by translocation and cultural practices, where significant genetic differentiation was detected among three laying beds, and (2) at a micro scale where we detected an important variability of the genetic composition of young spat recruited on artificial collectors. Such patterns could result from a high variance in the number of genitors at the origin of each cohort, or from pre- or post-settlement selection on linked loci. Altogether, our data support the hypothesis that under certain conditions populations of bivalves may exhibit patterns of chaotic genetic patchiness at local scale, in line with the increasing report of such patchiness in marine benthic organisms. This underlines the importance of sampling scale that should be rigorously defined depending on the questions to be answered. Nevertheless, a survey of about 80 articles dealing with population genetics of marine invertebrates showed that only 35% of those studies disclosed details about the sampling strategy (particularly the area explored). These results emphasize the need for cautious interpretation of patterns of genetic structure at medium scale when rigorous sampling strategies are not deployed.

Background Few models of genetic hitchhiking in subdivided populations have been developed and the rarity of empirical examples is even more striking. We here provide evidences of genetic hitchhiking in a subdivided population of the marine mussel Mytilus edulis. In the Bay of Biscay (France), a patch of M. edulis populations happens to be separated from its North Sea conspecifics by a wide region occupied only by the sister species M. galloprovincialis. Although genetic differentiation between the two M. edulis regions is largely non-significant at ten marker loci (average FST~0.007), a strong genetic differentiation is observed at a single locus (FST = 0.25). We validated the outlier status of this locus, and analysed DNA sequence polymorphism in order to identify the nature of the selection responsible for the unusual differentiation. Results We first showed that introgression of M. galloprovincialis alleles was very weak in both populations and did not significantly affect their differentiation. Secondly, we observed the genetic signature of a selective sweep within both M. edulis populations in the form of a star-shaped clade of alleles. This clade was nearly fixed in the North Sea and was segregating at a moderate frequency in the Bay of Biscay, explaining their genetic differentiation. Incomplete fixation reveals that selection was not direct on the locus but that the studied sequence recombined with a positively selected allele at a linked locus while it was on its way to fixation. Finally, using a deterministic model we showed that the wave of advance of a favourable allele at a linked locus, when crossing a strong enough barrier to gene flow, generates a step in neutral allele frequencies comparable to the step observed between the two M. edulis populations at the outlier locus. In our case, the position of the barrier is now materialised by a large patch of heterospecific M. galloprovincialis populations. Conclusion High FST outlier loci are usually interpreted as being the consequence of ongoing divergent local adaptation. Combining models and data we show that among-population differentiation can also dramatically increase following a selective sweep in a structured population. Our study illustrates how a striking geographical pattern of neutral diversity can emerge from past indirect hitchhiking selection in a structured population. Note Nucleotide sequences reported in this paper are available in the GenBank™ database under the accession numbers EU684165 – EU684228.

Sarotherodon melanotheron is one of the most euryhaline teleosts able to withstand variations in environmental salinity ranging from freshwater (FW) to 130%0 hyper-saline waters (HSW). Although significant progress has been made in exploring the cellular and molecular changes that accompany salinity adaptation in teleosts, little is known about the effects of long-term acclimation to HSW. We sought to identify in this tilapia species the genes whose transcription is induced by long-term acclimation either to HSW or FW. Two subtractive cDNA libraries were made from gills of fish acclimated for 45 days to either condition, with 320 partial cDNA sequences encoding proteins potentially involved in the response to the two salinity extremes. The ESTs comparisons with genomic databases allowed putative functions to be attributed to 197 of these genes. The suppression subtractive hybridisation (SSH) results were validated by Real-time PCR for 13 candidate genes having presumably a role in osmoregulation, supplemented by Na+, K+- ATPase a-subunit and carbonic anhydrase, two genes known to be implicated in this function. In fish acclimated to both salinity extremes, the functional category of cellular process was the predominant one, which may indicate high cellular turnover rates in FW and HSW-adapted fish. The acclimation to FW and HSW also appeared to trigger the expression of genes involved in transport activity, biological regulation and metabolic processes, at a higher level in fish acclimated to HSW, suggesting higher metabolic activity in this situation. These results are a first step towards the identification of key molecular processes involved in the fish acclimation to extreme salinities. (Resume d'auteur)