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F Bonhomme

Publications and source records attributed to F Bonhomme.

At least 19 recordsLinked to original sources
PubMed2006

A transcriptomic approach of salinity response in the euryhaline teleost, Dicentrarchus labrax.

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.

Adaptation, Physiological↗
PubMed2006

A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus musculus domesticus.

Changes in gene expression are known to occur between closely related species, but it is not yet clear how many of these are due to random fixation of allelic variants or due to adaptive events. In a microarray survey between subspecies of the Mus musculus complex, we identified the mitogen-activated protein-kinase-kinase MKK7 as a candidate for change in gene expression. Quantitative PCR experiments with multiple individuals from each subspecies confirmed a specific and significant up-regulation in the testis of M. m. domesticus. Northern blot analysis shows that this is due to a new transcript that is not found in other tissues, nor in M. m. musculus. A cis-trans test via allele specific expression analysis of the MKK7 gene in F1 hybrids between domesticus and musculus shows that the expression change is mainly caused by a mutation located in cis. Nucleotide diversity was found to be significantly reduced in a window of at least 20 kb around the MKK7 locus in domesticus, indicative of a selective sweep. Because the MKK7 gene is involved in modulating a kinase signalling cascade in a stress response pathway, it seems a plausible target for adaptive differences between subspecies, although the functional role of the new testis-specific transcripts will need to be further studied.

Animals↗
PubMed2005

Maintenance of genetic differentiation across a transition zone in the sea: discordance between nuclear and cytoplasmic markers.

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 (theta(C) = 0.67) than at microsatellite loci (theta(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.

Animals↗
PubMed2004

Spatio-temporal variation in the genetic composition of wild populations of pearl oyster (Pinctada margaritifera cumingii) in French Polynesia following 10 years of juvenile translocation.

Abstract The genetic impact of the cultural practice of spat collection and translocation between genetically distinct stocks of black-lipped pearl oyster, Pinctada margaritifera cumingii, was studied by comparing samples collected in the 1980s and 2000s from seven atolls in French Polynesia. An amova revealed homogenization of the previously genetically distinct wild stocks of Tuamotu-Gambier and Society archipelagos (the indices of genetic differentiation among archipelagos and among populations within archipelagos, respectively, Phi(CT) and Phi(ST), decreased from 0.032* and 0.025*, respectively, to 0.006(NS) and 0.007(NS)). These results suggest high success of spontaneous reproduction in farms, probably due to the very high density of cultivated pearl oysters, and underline the importance of genetic monitoring of future hatchery produced stocks.

Analysis of Variance↗
PubMed2004

Mouse biodiversity in the genomic era.

Comparative genomics has developed by comparison of distantly related genomes, for which the link between the reported evolutionary changes and species development/physiology/ecology is not obvious. It is argued that the mouse (genus Mus) is an optimal model for microevolutionary genomics in vertebrates. This is because the mouse genome sequence, physical and genetic map have been completed, because mouse genetics, morpho-anatomy, pathology, behavior and ecology are well-studied, and because the Mus genus is a diverse, well- documented taxon, allowing comparative studies at the level of individual, population, subspecies, and species. The potential of the interaction between mouse genome and mouse biodiversity is illustrated by recent studies of speciation in the house mouse Mus musculus, and studies about the evolution of isochores, the peculiar pattern of GC-content variation across mammalian genomes.

Animals↗
PubMed2003

Introgression patterns in the mosaic hybrid zone between Mytilus edulis and M. galloprovincialis.

Hybrid zones are fascinating systems to investigate the structure of genetic barriers. Marine hybrid zones deserve more investigation because of the generally high dispersion potential of planktonic larvae which allows migration on scales unrivalled by terrestrial species. Here we analyse the genetic structure of the mosaic hybrid zone between the marine mussels Mytilus edulis and M. galloprovincialis, using three length-polymorphic PCR loci as neutral and diagnostic markers on 32 samples along the Atlantic coast of Europe. Instead of a single genetic gradient from M. galloprovincialis on the Iberian Peninsula to M. edulis populations in the North Sea, three successive transitions were observed in France. From South to North, the frequency of alleles typical of M. galloprovincialis first decreases in the southern Bay of Biscay, remains low in Charente, then increases in South Brittany, remains high in most of Brittany, and finally decreases again in South Normandy. The two enclosed patches observed in the midst of the mosaic hybrid zone in Charente and Brittany, although predominantly M. edulis-like and M. galloprovincialis-like, respectively, are genetically original in two respects. First, considering only the various alleles typical of one species, the patches show differentiated frequencies compared to the reference external populations. Second, each patch is partly introgressed by alleles of the other species. When introgression is taken into account, linkage disequilibria appear close to their maximum possible values, indicating a strong genetic barrier within all transition zones. Some pre- or postzygotic isolation mechanisms (habitat specialization, spawning asynchrony, assortative fertilization and hybrid depression) have been documented in previous studies, although their relative importance remains to be evaluated. We also provided evidence for a recent migratory 'short-cut' connecting M. edulis-like populations of the Charente patch to an external M. edulis population in Normandy and thought to reflect artificial transfer of spat for aquaculture.

Alleles↗
PubMed2003

Direct selection on allozymes is not required to explain heterogeneity among marker loci across a Mytilus hybrid zone.

Unequal differentiation between two types of loci (allozyme and DNA markers) across a Mytilus hybrid zone has recently been claimed as evidence for direct selection on some allozyme loci. We provide here a counter-example: a noncoding DNA locus that exhibits as much differentiation as the incriminated allozymes do. The levels of genetic differentiation varied widely among both allozymes and noncoding DNA markers and no clear difference emerged between the two types of markers. This suggests that the strong interlocus variance in genetic differentiation has been confounded with a discrepancy between marker types as a result of an insufficient and unbalanced locus sampling. Heterogeneity in differentiation among neutral loci can be created by stochastic variance during the allopatric divergence preceding a secondary contact. In hybrid zones, a further source of variance is differential introgression among chromosomal regions after the secondary contact owing to the local influence of selected genes on more or less distant markers. However, the degree of differentiation alone gives no way to distinguish indirect pseudo-selection (a regular and ubiquitous feature of hybrid zones) from direct selection. More generally, we suggest that comparative neutrality tests based on discrepancies among marker types have to be applied with caution when the presence of semi-permeable genetic barriers to gene exchange is suspected.

Animals↗
PubMed2003

Large discrepancies in differentiation of allozymes, nuclear and mitochondrial DNA loci in recently founded Pacific populations of the pearl oyster Pinctada margaritifera.

This study presents a comparative analysis of population structure applied to the pearl oyster (Pinctada margaritifera) from the Central Pacific islands using three classes of molecular markers: two mitochondrial genes (mtDNA), five anonymous nuclear loci (anDNA), and eight polymorphic allozymes. Very low levels of haplotype diversity and nucleotidic divergence detected for mtDNA validate the hypothesis of a recent (re)colonization of Polynesian lagoons after their exondation during the last glaciations. Some nuclear loci, however, showed highly significant FST values, indicating a reduced amount of larval exchange between archipelagos at present. A large interlocus variance of FST was nevertheless observed. We discuss whether this pattern is inherent to the stochasticity of the drift process since recolonization, or if it could result from balancing selection acting on certain loci. This study illustrates once more the need to combine the analysis of several kinds of loci when unrelated phenomena are likely to leave their footprints on genetic structure.

Animals↗
PubMed2003

Evidence for male-biased effective sex ratio and recent step-by-step colonization in the bivalve Pinctada mazatlanica.

This paper presents a comparison of the geographical distribution of genetic variability at mitochondrial and nuclear loci among pearl oyster populations from the tropical American Pacific coast (Pinctada mazatlanica). Surprisingly, both mitochondrial and nuclear gene variability decreased regularly from north to south of the studied area, which, altogether with a significant correlation between genetic and geographical distances for mtDNA, suggests a recent colonization or re-colonization of the southern areas. However, the loss of diversity between north and south was much more important for mitochondrial than for nuclear DNA, and this did not translate into measurable fixation index at nuclear loci (theta = 0.03, n.s.), contrary to the mitochondrial data (theta = 0.18*). Smaller effective size of mtDNA accentuated by a strong male-biased effective sex ratio and step-by-step colonization from northern areas can explain this discrepancy among natural populations of this protandric species.

Animals↗
PubMed2002

Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus Fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses.

Empirical studies of natural populations have commonly reported departures from Hardy-Weinberg expected proportions of heterozygote individuals. Recent advances in statistical population genetics now offer the potential to exploit individual multilocus genotypic information to test more rigorously for possible sources of heterozygote deficiencies. In a previous study in lacustrine brook charr (Salvelinus fontinalis), we reported stronger deficits in small than in large lakes. In the present paper, we propose a methodology for empirically testing alternative hypotheses to identify the cause of the deficits observed in three of the smallest lakes (85, 109 and 182 ha) analysed. First, as in several salmonid species, brook charr may exhibit a trophic polymorphism in north temperate lakes. If morphs are genetically divergent, indiscriminate sampling of both forms would result in less heterozygote individuals than expected in a randomly mating population (Wahlund effect). Using an individual-based method aiming at detecting cryptic population structure, we can reject this explanation as the sole source of deficits for all three lakes. Secondly, mating among relatives could also be frequent in small lakes and lead to heterozygote deficiencies. Significantly more fish than expected at random had low individual multilocus heterozygosity in two of the lakes, suggesting that inbred fish may have been present. Thirdly, sampling of genetically related fish would also lead to departures from Hardy-Weinberg proportions. In the same two lakes, the distribution of pairwise relatedness coefficients departed from its random expectation, suggesting that non-random sampling of kin may have occurred.

Animals↗
PubMed2002

Evidence for a mitochondrial lineage originating from the Arabian peninsula in the Madagascar house mouse (Mus musculus).

Various subspecies of the house mouse (Mus musculus sensu lato) are known to have contributed to its worldwide expansion. However, the origin of mice on some larger islands such as Madagascar has remained unknown, with several sources being possible. In order to classify the Malagasy house mouse, individuals were trapped in 13 different localities distributed throughout the island. For 33 individuals the control region (D-Loop) of the mitochondrial DNA was partially sequenced and 21 males were typed for a Zfy-2 polymorphism of the Y chromosome. Malagasy mt DNA lineages constitute a narrow monophyletic group which suggests a recent and probably single origin, and are very close to the gentilulus mitochondrial lineages from Yemen. This was supported by the fact that all the males have the domesticus type Y chromosome, like gentilulus. From these results, it can be inferred that the Malagasy house mice originate probably from the Arabian peninsula in a single colonisation wave, unlike its human population. Our results provide a better molecular description of the Yemeni-Malagasy mitochondrial clade which clearly belongs to the Mus musculus radiation.

Animals↗
PubMed2002

Two deeply divergent mitochondrial clades in the wild mouse Mus macedonicus reveal multiple glacial refuges south of Caucasus.

A survey of 77 individuals covering the range of Mus macedonicus from Georgia in the East to Greece and Bulgaria in the West and Israel in the South has shown the existence of two deeply divergent mitochondrial clades. The southern clade was until now undetected and characterises mice from Israel. Nuclear genes also show some amount of regional differentiation tending to separate the southern M. macedonicus from the northern ones. These results point towards the fact that the eastern Mediterranean short-tailed mouse, which was seen as a fairly homogeneous monotypic species, has in fact a more complex phylogeographic history than has been suspected, and that it warrants the existence of two subspecies. The reasons for this non-uniformity probably ought to be looked for in the history of faunal movements linked to glacial periods, underlining the possible existence of at least two refugia south of the Caucasus.

Animals↗
PubMed2002

Polymerase chain reaction-single strand conformation polymorphism analyses of nuclear and chloroplast DNA provide evidence for recombination, multiple introductions and nascent speciation in the Caulerpa taxifolia complex.

Independent lines of evidence support an Australian origin for the Mediterranean populations of the tropical alga Caulerpa taxifolia. To complement previous biogeographical studies based on nuclear rDNA internal transcribed spacer (ITS), a new chloroplast marker was developed--the cp 16S rDNA intron-2. Sequence variability for both nuclear and chloroplast markers were assessed in 110 individuals using single strand conformation polymorphism. Comparison of intrapopulation genetic diversity between invasive Mediterranean and 'native' Australian populations revealed the occurrence of two divergent and widespread clades. The first clade grouped nontropical invasive populations with inshore-mainland populations from Australia, while the second clustered all offshore-island populations studied so far. Despite our finding of nine distinct nuclear and five distinct chloroplast profiles, a single nucleocytoplasmic combination was characteristic of the invasive populations and sexual reproduction was found to be very rare. C. taxifolia is clearly a complex of genetically and ecologically differentiated sibling species or subspecies.

Australia↗
PubMed2001

The zone of sympatry and hybridization of Mytilus edulis and M. galloprovincialis, as described by intron length polymorphism at locus mac-1.

Intron-size variation at the actin gene locus mac-1 was used to characterize mussel, Mytilus spp., populations in the approximately 2000-km wide zone of contact and hybridization ('hybrid zone') between M. edulis and M. galloprovincialis in western Europe. Twenty-five samples were collected in 1995-99 in locations within the hybrid zone and from reference populations of each species. We used correspondence analysis on the matrix of allelic frequencies to determine which alleles are characteristic of each species, and to characterize samples along the genetic gradient between M. edulis and M. galloprovincialis. In the hybrid zone, some samples exhibited mac-1 allele frequencies that were typical of M. edulis; other samples were distributed along the M. edulis/M. galloprovincialis gradient and displayed variable levels of intergradation that were not correlated with geography. Some of the latter samples exhibited significant heterozygote deficiencies. The simple admixture hypothesis (Wahlund effect) could not be rejected for two-fifths of the samples. The hybrid zone thus appeared as a mosaic of populations which are either pure M. edulis, or hybrid between M. galloprovincialis and M. edulis, or a mixture of the foregoing with M. galloprovincialis individuals. These results were consistent with published allozyme data, suggesting that they can be extended to the entire nuclear genome. M. edulis mac-1 alleles were present at moderate frequency in Atlantic M. galloprovincialis, and at significantly lower frequency in some Mediterranean samples. This pattern was homogeneous over a broad geographical range within each basin. It was not evident that introgression of M. edulis into M. galloprovincialis presently occurs south of the zone of contact. We propose that the distinctness of the Atlantic M. galloprovincialis population results from past introgression by M. edulis alleles.

Actins↗
PubMed2000

Fragmentation of sea bass populations in the western and eastern Mediterranean as revealed by microsatellite polymorphism.

We studied the genetic structure at six microsatellite loci of the Mediterranean sea bass (Dicentrarchus labrax) on 19 samples collected from different localities in the western and eastern Mediterranean basins. Significant divergence was found between the two basins. The distance tree showed two separate clusters of populations which matched well with geography, with the noticeable exception of one Egyptian sample which grouped within the western clade, a fact attributable to the introduction of aquaculture broodstock. No heterogeneity was observed within the western basin (theta = 0.0014 and n.s.). However, a significant level of differentiation was found among samples of the eastern Mediterranean (theta = 0.026 and p < 0.001). These results match with water currents but probably not with the dispersal abilities of this fish species. We thus hypothesize that selective forces are at play which limit long-range dispersal, a fact to be taken into account in the debate about speciation processes in the marine environment.

Animals↗
PubMed2000

Properties of bias and variance of two multiallelic estimators of F(ST).

This study compares theoretical and simulated properties of two estimators of fixation indices F(ST) for multiallelic data from a single locus. The estimators are due to Weir and Cockerham (straight theta(WC)) and to Robertson and Hill (;straight theta(RH)), respectively. Both estimators are linear combinations of biallelic estimators which differ in the way frequent and rare alleles are weighted. Consequently, their sampling properties differ as far as bias and variance are concerned. In the infinite island model at migration-drift equilibrium, in the case of one multiallelic locus, we analytically approximate the bias of the two estimators and show that;straight theta(WC) is nearly unbiased, whereas;straight theta(RH) is negatively biased. Hence, we propose a correction of bias of the latter. Moreover, we reexamine the properties of variance of the initial estimators: due to their construction, their variances are minimal, each over different parameter ranges,;straight theta(RH) performing better for low differentiation and;straight theta(WC) for high differentiation. These theoretical properties are confirmed by simulations, which show that our correction of bias of;straight theta(RH) performs well and does not affect its property of minimal variance for low differentiation. Hence, we advocate the use of;straight theta(WC) for high values of differentiation, and the use of;straight theta(RH), with our correction of bias, for low or moderate differentiation.

Alleles↗
PubMed2000

Do discrepancies between microsatellite and allozyme variation reveal differential selection between sea and lagoon in the sea bass (Dicentrarchus labrax)?

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.

Adaptation, Physiological↗