Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Key message Molecular markers were used for paternity recovery in a maritime pine (Pinus pinasterAit.) polycross trial, facilitating forward selection. Different breeding strategies for seed orchard establishment were evaluated by comparing genetic gains and diversity. This work opens up new perspectives in maritime pine breeding.Context Polycross mating designs are widely used in forest tree breeding to evaluate parental breeding values for backward selection. Alternatively, polycross progeny trials may be used to select the best trees on the basis of individual breeding values and molecular pedigree analysis.Aims This study aimed to test such a forward selection strategy for the maritime pine breeding program.Methods In a maritime pine polycross trial, progeny with higher breeding values for growth and stem straightness was first preselected with or without relatedness constraints. After paternity recovery, the preselected trees were ranked on the basis of their breeding values, estimated from the recovered full pedigree. Finally, the best candidates were selected with three different strategies (forward, backward, mixed) and three levels of coancestry constraints to establish a virtual clonal seed orchard.Results Complete pedigrees were successfully recovered for most of the preselected trees. There was no major difference in expected genetic gains between the two preselection strategies which differed for relatedness constraints. Genetic gains were slightly higher for forward selection than for classical backward selection.Conclusion This seminal study opens up new perspectives for using forward selection within the French maritime pine breeding program.
ISSN: 1932-6203

hal-01601804
https://hal.archives-ouvertes.fr/hal-01601804
DOI : 10.1371/journal.pone.0049990
PRODINRA : 391860

Éditeur(s) : HAL CCSD
Résumé :   Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
As part of a programme of degraded soils rehabilitation, and in order to follow the biological processes connected with the soils reconstitution, it is a requisite to determine indicators able to account for the evolution of the soil. These indicators can he found on structural and/or functional characteristics of the bacterial communities, such as soil respiration, denitrification or genetic diversity. Theses descriptors are able to characterize the global community or targeted communities chosen for their importance in the ecosystem functioning. In this work, we tried to know whether soil bacteria genetic diversity was able to be a relevant indicator of the soil evolution in a rehabilitated sequence. This diversity is apprehended via a molecular technique: ARISA. A chronosequence situated on a gold mine, already experimented as part of a programme of degraded zones rehabilitation, was at our disposal. Results show that ARISA is a very sensitive technique, able to account for the bacterial community heterogeneity in a soil but unable, at the parcel scale, to discriminate the treatments nor to account for the evolution in lime of planted treatments. Lastly, the advantage of this indicator of genetic diversity may arise from its confrontation to other indicators (functional, for example).
Dans le cadre de la revégétalisation d'un sol dégradé et afin de pouvoir suivre les processus biologiques liés à la reconstitution des sols, il est nécessaire de déterminer des indicateurs pouvant rendre compte de l'évolution de l'état du sol. Ces indicateurs peuvent être fondés sur des caractéristiques fonctionnelles et/ou structurales des communautés bactériennes telles que la respiration, la dénitrification ou la diversité génétique. Ces descripteurs peuvent analyser la communauté globale ou des communautés cibles choisies pour leur importance dans le fonctionnement de l'écosystème. L'objectif de ce stage était de savoir si la diversité génétique des bactéries du sol pouvait être un indicateur de l'évolution des sols au sein d'une séquence de revégétalisation. Cette diversité est appréhendée par une technique de biologie moléculaire : l'ARISA. On dispose d'une chronoséquence située sur une mine d'or étudiée dans le cadre d'un programme de réhabilitation des zones dégradées. Les résultats montrent que l'ARISA est une technique très sensible, qui rend bien compte de l’hétérogénéité des communautés bactériennes présentes dans un sol mais est incapable, à l’échelle de la parcelle, de discriminer ni les traitements ni de rendre compte de l'évolution dans le temps de ces parcelles. Enfin, l'intérêt de cet indicateur de diversité génétique pourra résulter de sa confrontation avec d'autres indicateurs (fonctionnels par exemple).
https://hal.archives-ouvertes.fr/hal-01189155

hal-01189155
https://hal.archives-ouvertes.fr/hal-01189155
PRODINRA : 9464

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The formation of ovarian follicles is a finely tuned process that takes place within a narrow time-window in rodents. Multiple factors and pathways have been proposed to contribute to the mechanisms triggering this process but the role of endocrine factors, especially estrogens, remains elusive. It is currently hypothesized that removal from the maternal hormonal environment permits follicle formation at birth. However, experimentally-induced maintenance of high 17β-estradiol (E2) levels leads to subtle, distinct, immediate effects on follicle formation and oocyte survival depending on the species and dose. In this study, we examined the immediate effects of neonatal E2 exposure from post-natal day (PND) 0 to PND2 on the whole organism and on ovarian follicle formation in rats. Measurements of plasma E2, estrone and their sulfate conjugates after E2 exposure showed that neonatal female rats rapidly acquire the capability to metabolize and clear excessive E2 levels. Concomitant modifications to the mRNA content of genes encoding selected E2 metabolism enzymes in the liver and the ovary in response to E2 exposure indicate that E2 may modify the neonatal maturation of these organs. In the liver, E2 treatment was associated with lower acquisition of the capability to metabolize E2. In the ovary, E2 depleted the oocyte pool in a dose dependent manner by PND3. In 10 µg/day E2-treated ovaries, apoptotic oocytes were observed in newly formed follicles in addition to areas of ovarian cord remodeling. At PND6, follicles without any visible oocyte were present and multi-oocyte follicles were not observed. Our study reveals a major species-difference. Indeed, neonatal exposure to E2 depletes the oocyte pool in the rat ovary, whereas in the mouse it is well known to increase oocyte survival.
ISSN: 1932-6203

hal-00936582
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00936582
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00936582/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00936582/file/Systemic_Compensatory_Response-accepted.pdf
DOI : 10.1371/journal.pone.0082175

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the USA. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of twenty V. cholerae and four V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as four clinical V. metoecus strains were sequenced and compared to reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. V. metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin co-regulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. V. metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01264332
http://hal.upmc.fr/hal-01264332
http://hal.upmc.fr/hal-01264332/document
http://hal.upmc.fr/hal-01264332/file/Genome%20Biol%20Evol-2015-Orata-gbe_evv193.pdf
DOI : 10.1093/gbe/evv193

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The scleractinian coral Pocillopora damicornis type β is known to present a mixed reproduction mode: through sexual reproduction, new genotypes are created, while asexual reproduction insures their propagation. In order to investigate the relative proportion of each reproduction mode in P. damicornis type β populations from Reunion Island, Indian Ocean, clonal propagation along the west coast was assessed through four sampling sites with increasing geographical distance between sites. Coral colonies were sampled either exhaustively, randomly or haphazardly within each site, and genotypic diversity was assessed using 13 microsatellite loci over a total of 510 P. damicornis type β determined a posteriori from their mtDNA haplotype (a 840 bp sequenced fragment of the Open Reading Frame). Overall, 47% of all the sampled colonies presented the same multi-locus genotype (MLG), a superclone, suggesting that asexual propagation is extremely important in Reunion Island. Within each site, numerous MLGs were shared by several colonies, suggesting local clonal propagation through fragmentation. Moreover, some of these MLGs were found to be shared among several sites located 40 km apart. While asexual reproduction by fragmentation seems unlikely over long distances, our results suggest a production of parthenogenetic larvae. Despite shared MLGs, two differentiated clusters were enclosed among populations of the west coast of Reunion Island, revealing the necessity to set up appropriate managing strategies at a local scale.
ISSN: 1932-6203

hal-01450078
http://hal.univ-reunion.fr/hal-01450078
DOI : 10.1371/journal.pone.0169692

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND:Sickle cell anaemia (SCA) is a severe hereditary haemoglobinopathy characterised by haemorheological abnormalities, which play a role in the occurrence of several acute and chronic clinical complications. While βS -haplotypes and alpha-thalassaemia modulate SCA clinical severity, their effects on blood rheology have been incompletely described. The aim of this study was to test the effects of these genetic modifiers on the haemorheological properties and clinical complication of children with SCA.PROCEDURE:Steady-state haemorheological profile, biological parameters, βS -haplotypes, alpha-globin status, vaso-occlusive crisis (VOC) and acute chest syndrome frequencies were analysed in 128 children (aged 5 to 18 years) with SCA.RESULTS:Patients with alpha-thalassaemia showed increased red blood cell (RBC) deformability and aggregation compared to those without. Median VOC rate was higher in patients with homozygous alpha-thalassaemia compared to those with a normal alpha genotype. Conversely, the haemorheological profile and clinical complications were not influenced by the βS -haplotypes in our study.CONCLUSION:Our results demonstrate that alpha-thalassaemia is associated with higher risk for VOC events in children with SCA, which may be due in part to its effects on RBC deformability and aggregation.
ISSN: 1545-5009

hal-01668317
https://hal.univ-antilles.fr/hal-01668317
DOI : 10.1002/pbc.26455
PUBMED : 28097791

Éditeur(s) : Colloque IMBC - International Marine Biotechnology Conference
Résumé : Since 1997, a new pathology seasonally occurs in new caledonian shrimp farms during the warm season. Diseased Litopenaeus stylirostris shrimp suffer from a systemic vibriosis which was attributed to highly pathogenic Vibrio nigripulchritudo. At the present time, only two farms among 17 are affected by the so called "summer syndrome". In such a context it appears urgent to develop reliable diagnostic tools to detect V. nigripulchritudo strains and to differentiate highly virulent strains from non virulent ones in order to understand the mechanisms of infection and overcome disease spreading. Multilocus Sequencing Typing (MLST) analysis on 24 bacterial strains isolated in geographically distinct shrimp farms highlighted the existence of a cluster A containing only strains displaying moderate to high virulence. Since experimental infection procedure for virulence status determination is material intensive and time consuming, and MLST method not accurate enough to inform on the virulence status of strains, it appeared of great interest to develop other diagnostic tools. Two phylogenetically closed strains, one highly virulent SFn1 and the other non-virulent SFn118 were selected in order to characterize genes specific of the virulent strain by Substractive Suppression Hybridization (SSH). Firstly, a total of 622 DNA fragments specific of SFn1 were sequenced, characterized and further used as probes in a DNA macroarray. Testing 24 strains, hybridization profiles were found to be strongly correlated with both MLST genotypes and bacterial virulence status. A total of 96 representative probes were secondly selected to validate macroarray results on 34 more additionnal strains, allowing identification of genetic markers of virulence. Most of DNA fragments specific of highly virulent strains associated to summer syndrome were found to be bore by a plasmid successfully isolated in the laboratory. In next future, these results would permit the development of relevant diagnostic tools useful for accurate epidemiological survey of the summer syndrome.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/acte-3398.pdf
http://archimer.ifremer.fr/doc/00000/3398/

Éditeur(s) : Springer
Résumé : The great fecundity and very high larval mortality of most marine invertebrates and fish make possible substantial variance in the number of offspring contributed by adults to subsequent generations. The reproductive success of such organisms may thus resemble a sweepstakes lottery, in which a minority of progenitors succeeds in replacing an entire population, while the majority fails to procreate. One specific prediction of this hypothesis, that genetic diversity of newly settled cohorts should be less than that of the adult population, is tested in the present study. Microsatellite DNA markers were examined in naturally spawned juvenile European flat oysters Ostrea edulis (L.), collected over a 12-day period in 1993 from the western Mediterranean Sea, near Sete, France (43 degrees 32'N, 3 degrees 56'E) and grown out for a period of up to 10 months. Variation in these juveniles was compared to that in a pooled sample of adults collected in 1994 from two locations (Thau Lagoon and Port St. Louis) that had statistically homogeneous allelic frequencies. Though nearly twice as large as the pooled adult sample, the juvenile sample had only 60% of the adult allelic diversity. Analyses of linkage disequilibrium and kinship, as well as estimation of the effective number of parents, suggested that 10-20 adults produced this juvenile cohort. This observation supports the hypothesis of sweepstakes reproductive success and suggests that partial inbreeding may occur even in species with large populations and dispersing planktonic larvae.
Marine Biology (0025-3162) (Springer), 2007-03 , Vol. 150 , N. 6 , P. 1173-1182

Droits : 2007 Springer
http://archimer.ifremer.fr/doc/2007/publication-2616.pdf
DOI:10.1007/s00227-006-0441-y
http://archimer.ifremer.fr/doc/00000/2616/

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : The Mediterranean Sea is one of the most oligotrophic marine areas on earth where nitrogen fixation has formally believed to play an important role in carbon and nitrogen fluxes. Although this view is under debate, the diazotrophs responsible for this activity have still not been investigated in the open sea. In this study, we characterised the surface distribution and species richness of unicellular and filamentous diazotrophs across the Mediterranean Sea by combining microscopic counts with size fractionated in situ hybridization (TSA-FISH), and 16S rDNA and nifH genes phylogenies. These genetic analyses were possible owing to the development of a new PCR protocol adapted to scarce microorganisms that can detect as few as 1 cell ml(-1) in cultures. Low concentrations of diazotrophic cyanobacteria were detected and this community was dominated at 99.9% by picoplankton hybridized to the Nitro821 probe, specific for unicellular diazotrophic cyanobacteria (UCYN). Among filamentous cyanobacteria only 0.02 filament ml(-1) of Richelia were detected in the eastern basin, while small (0.7-1.5 mu m) and large (2.5-3.2 mu m) Nitro821-targeted cells were recovered at all stations with a mean concentration of 3.5 cell ml(-1). The affiliation of the small Nitro821-targeted cells to UCYN-A was confirmed by 16S and nifH phylogenies in the western Mediterranean Sea. In the central and the eastern Mediterranean Sea no 16S rDNA and nifH sequence from UCYN was obtained as cells concentration were close to, or below PCR detection limit. Bradyrhizobium sequences dominated nifH clone libraries from picoplanktonic size fractions. A few sequences of gamma-proteobacteria were also detected in the central Mediterranean Sea. While low phosphate and iron concentrations could explain the absence of Trichodesmium sp., the factors that prevent the development of UCYN-B and C remain unknown. We also propose that the dominating picoplankters probably developed specific strategies, such as associations with protists or particles, and/or photosynthetic activity, to acquire carbon for sustaining diazotrophy.
Biogeosciences (1726-4170) (Copernicus Gesellschaft Mbh), 2011 , Vol. 8 , N. 3 , P. 827-840

Droits : Author(s) 2011. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00133/24392/22416.pdf
DOI:10.5194/bg-8-827-2011
http://archimer.ifremer.fr/doc/00133/24392/

Éditeur(s) : HAL CCSD Wiley
Résumé : Rainforest tree species can be difficult to identify outside of their period of reproduction. Vascular tissues from Carapa spp. individuals were collected during a short field trip in French Guiana and analysed in the laboratory with nuclear and chloroplast markers. Using a Bayesian approach, > 90% of the samples could be assigned to one of two distinct clusters corresponding to previously described species, making it possible to estimate the genetic structure of each species and to identify cases of introgression. We argue that this blind procedure represents a first-choice rather than a fallback option whenever related taxa are investigated.
ISSN: 0962-1083

hal-01031226
https://hal.archives-ouvertes.fr/hal-01031226
DOI : 10.1111/j.1365-294X.2006.03040.x

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Epigenetics, as a DNA signature that affects gene expression and enables rapid reaction of an organism to environmental changes, is likely involved in the process of biological invasions. DNA methylation is an epigenetic mechanism common to plants and animals for regulating gene expression. In this study we show, for the first time in any marine species, significant reduction of global methylation levels during the expansive phase of a pygmy mussel (Xenostrobus securis) recent invasion in Europe (twoyear old), while in older introductions such epigenetic signature of invasion was progressively reduced. Decreased methylation was interpreted as a rapid way of increasing phenotypic plasticity that would help invasive populations to thrive. This epigenetic signature of early invasion was stronger than the expected environmental signature of environmental stress in younger populations sampled from ports, otherwise detected in a much older population (>90 year old) of the also invasive tubewormFicopomatus enigmaticus established in similar locations. Higher epigenetic than genetic diversity found in X. securis was confirmed from F. enigmaticus samples. As reported for introduced plants and vertebrates, epigenetic variation could compensate for relatively lower genetic variation caused by founder effects. These phenomena were compared with epigenetic mechanisms involved in metastasis, as parallel processes of community (biological invasion) and organism (cancer) invasions.
ISSN: 2045-2322

hal-01488962
https://hal-univ-perp.archives-ouvertes.fr/hal-01488962
https://hal-univ-perp.archives-ouvertes.fr/hal-01488962/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01488962/file/Epigenetic.pdf
DOI : 10.1038/srep42193

Éditeur(s) : Wiley-blackwell
Résumé : In bird species that have a high movement capacity, dispersal may connect subpopulations over vast geographical regions, with important consequences for the design of conservation management strategies. Here we used a molecular approach to infer the patterns and rates of dispersal among eight Mediterranean subpopulations of the endangered Bonelli's Eagle, based on 245 individuals screened at 17 microsatellite loci. There was moderate genetic differentiation between subpopulations sampled in the western (Iberia and Morocco) and eastern (Cyprus) Mediterranean, whereas differentiation among subpopulations in the former region was weak to moderate and followed a pattern of isolation by distance. Within the western Mediterranean, the small, peripheral and ecologically unique population of southwest Portugal had the lowest genetic diversity and the highest differentiation. The remaining subpopulations formed two loose clusters, one including Morocco and southwest and eastern Spain, and the other northeast Portugal and western and central Spain. Few recent migrants were detected, and they originated primarily from adjacent subpopulations. Our findings suggest that western Mediterranean Bonelli's Eagles may have a large-scale metapopulation structure, with subpopulations connected to some extent by distance-dependent dispersal, probably influenced by natal philopatry and the geographical configuration of subpopulations. The combination of marked ecological and genetic divergence suggests that the peripheral subpopulation of southwest Portugal may be regarded as a distinct management unit.
Ibis (0019-1019) (Wiley-blackwell), 2013-07 , Vol. 155 , N. 3 , P. 485-498

Droits : 2013 British Ornithologists’ Union
http://archimer.ifremer.fr/doc/00148/25924/24018.pdf
DOI:10.1111/ibi.12065
http://archimer.ifremer.fr/doc/00148/25924/

Éditeur(s) : HAL CCSD Elsevier
Résumé : High-precision Ni isotopic variations are reported for the metal phase of equilibrated and unequilibrated ordinary chondrites, carbonaceous chondrites, iron meteorites, mesosiderites, and pallasites. We also report new Zn and Cu isotopic data for some of these samples and combine them with literature Fe, Cu, and Zn isotope data to constrain the fractionation history of metals during nebular (vapor/solid) and planetary (metal/sulfide/silicate) phase changes. The observed variations of the Ni-62/Ni-58, Ni-61/Ni-58, and Ni-60/Ni-58 ratios vary linearly with mass difference and define isotope fractionation lines in common with terrestrial samples. This implies that Ni was derived from a single homogeneous reservoir. While no Ni-60 anomaly is detected within the analytical uncertainties, Ni isotopic fractionation up to 0.45 parts per thousand per mass-difference unit is observed. The isotope compositions of Ni and Zn in chondrites are positively correlated. We suggest that, in ordinary chondrites, exchange between solid phases, in particular metal and silicates, and vapor followed by mineral sorting during accretion are the main processes controlling these isotopic variations. The positive correlation between Ni and Zn isotope compositions contrasts with a negative correlation between Ni (and Zn) and Cu isotope compositions, which, when taken together, do not favor a simple kinetic interpretation. The observed transition element similarities between different groups of chondrites and iron meteorites are consistent with the genetic relationships inferred from oxygen isotopes (IIIA/pallasites and IVA/L chondrites). Copper is an exception, which we suggest may be related to separate processing of sulfides either in the vapor or during core formation. (C) 2007 Elsevier Ltd. All rights reserved.
ISSN: 0016-7037

hal-00408304
https://hal.archives-ouvertes.fr/hal-00408304
DOI : 10.1016/j.gca.2007.06.049

Éditeur(s) : Society for General Microbiology
Résumé : A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16:1 omega7c, 15: 0 iso, 16: 0 and 13: 0 iso. The G + C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98%), Shewanella oneidensis (97%) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were < 20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella, Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (= DSM 15900(T)-JCM 12080(T)) as the type strain.
International journal of systematic and evolutionary microbiology (1466-5026) (Society for General Microbiology), 2004-11 , Vol. 54 , N. 6 , P. 1943-1949

Droits : 2004 International Union of Microbiological Societies
http://archimer.ifremer.fr/doc/2004/publication-590.pdf
DOI:10.1099/ijs.0.03007-0
http://archimer.ifremer.fr/doc/00000/590/

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : En Amérique centrale, l’élevage des abeilles sans dard est une pratique vieille d’au moins deux millénaires, qui a connu son apogée à la fin de l’ère maya. Les Méliponinés, sous-famille à laquelle appartiennent ces abeilles, rassemblent près de 500 espèces distribuées pour l’essentiel en zone intertropicale. La plupart d’entre elles nichent dans des cavités d’arbres secs ou sous terre, et affectionnent les forêts ombrophiles où elles assurent un rôle actif dans la pollinisation des plantes sauvages. Sur l’île de Cuba, une seule espèce de méliponinés (Melipona beecheii) est présente, elle a probablement été introduite durant l’époque précolombienne à partir de souches génétiques originaires de la péninsule du Yucatán. Dans les campagnes autour de La Havane, les abeilles mélipones continuent d’être un vecteur de socialisation, car leur domestication correspond souvent à une tradition familiale et parce que les bénéficiaires des produits de la ruche sont des familiers du méliponiculteur. En forêt, en revanche, le miel donne davantage lieu à des pratiques de cueillette. Depuis une vingtaine d’années, la prise de conscience du rôle de l’abeille dans le fonctionnement des écosystèmes et la valeur des services qu’elles seraient susceptibles de rendre à l’agriculture sont à l’origine d’une évolution rapide des représentations sociales associées à l’insecte. Cette évolution contribue à diversifier les profils des éleveurs, à détacher les pratiques du poids des traditions d’élevage ou de cueillette, et à concevoir la méliponiculture comme une activité de loisir voire à envisager son intégration dans une logique marchande.
In central America, stingless beekeeping is a practice older than two thousand years which reached its peak at the end of the Maya era. The melipona sub-family which these bees belong to gather more than 500 species mainly in the intertropical area. Most of them nest in cavities, in dead wood or underground, and have a liking for ombrophile forests where they provide the pollinisation of wild plantes in Cuba. There is only are single species (Melipona beecheii) probably introduced during the pre-colombian era, from genetic strains deriving from the Yucatan peninsula. In the countryside surrounding Havana, the melipona bees are still a vector of socialization, knowing their domestication often results from a familial tradition and is profitable to the beekeeper’s relatives. On the other hand, in the forest, honey is the fruit of gathering. For twenty years now people have been aware of the essential function of bees in the ecosystem and of the valuable services they are able to provide agriculture. This awareness has launched a quick evolution in the social representation of the insect. Thanks to this evolution the beekeepers’ profiles are becoming more diverse, traditions in beekeeping or gathering, weigh less heavily on practices, and the meliponiculture can be regarded as a space-time activity or even a trade one.
Cuba

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.6967
http://journals.openedition.org/etudescaribeennes/6967

Éditeur(s) : HAL CCSD
Résumé : Transposable elements play a major role in the evolution of eukaryotic genomes. Knowing the distribution of transposable elements between different species within the same taxon is essential to study their dynamics and to better understand their role in the evolution of species. Given their abundance, species diversity and living environment, crustaceans are an excellent model for studying comparative genomics of retrotransposons. It is notably in the squat lobsters that the GalEa clade of Superfamily Copia was defined. We studied the distribution of two well-known LTR retrotransposons superfamilies: Gypsy and Copia, in crustaceans. By combining PCRs with degenerate primers and in silico analysis, we identified 35 families of Copia retrotransposons and 46 families of Gypsy retrotransposons in 15 and 18 species of crustaceans (mainly Malacostraca: crabs, shrimp, krill ...). These elements have different distribution and diversity in crustaceans. Gypsy elements appear relatively commonly and diverse in all species. Conversely, the Copia elements seem rare, and consequently more difficult to detect, and are largely dominated by the elements of the clade GalEa. These results suggest two different dynamic strategies for retrotransposons Gypsy (the Red Queen theory) and retrotransposons GalEa (‘domino days spreading’ branching process). In addition, GalEa elements present a great evolutionary success being widely distributed in many branches of metazoans. They are also present in certain red algae and we have also detected them in Fungi. Taking advantage of the large amount of available genomic data, we have studied the distribution of GalEa elements of Fungi, in order to compare it with the results obtained in crustaceans. In fact, they appear only in a large phylum of Ascomycetes, in Pezizomycotina, and they form a monophyletic group within the GalEa. Finally, in the Fungi, the GalEa elements are not majority among Copia retrotransposons. We have therefore initiated a new study in molluscs, to define if the results obtained in crustaceans are a feature of GalEa elements, Malacostraca or metazoans.
Les éléments transposables jouent un rôle majeur dans l’évolution des génomes eucaryotes. La connaissance de la distribution des éléments transposables entre différentes espèces au sein d’un même taxon est une condition essentielle pour étudier leur dynamique et mieux comprendre leur rôle dans l'évolution des espèces. Compte tenu de leur abondance, de leur diversité spécifique et de milieu de vie, les crustacés sont un excellent modèle pour étudier la génomique comparative des rétrotransposons. C’est notamment chez les Galathées qu’a été défini le clade GalEa des éléments de la superfamille des Copia. Nous avons étudié la distribution de deux superfamilles de rétrotransposons à LTR bien connus: les Gypsy et les Copia, au sein des crustacés. En combinant des PCRs avec amorces dégénérées et des analyses in silico, nous avons identifié 35 familles de rétrotransposons Copia et 46 familles de rétrotransposons Gypsy dans respectivement 15 et 18 espèces de crustacés (principalement des malacostracés : crabes, crevettes, krill...). Ces éléments présentent une distribution et une diversité différentes au sein des crustacés. Les éléments Gypsy apparaissent relativement fréquents et diversifiés dans toutes les espèces. A l’inverse, les éléments Copia semblent rares, donc difficilement détectables, et sont largement dominés par les éléments du clade GalEa. Ces résultats suggèrent deux stratégies différentes de dynamique pour les rétrotransposons Gypsy (théorie de la Reine Rouge) et les rétrotransposons GalEa (‘domino days spreading’ branching process). De plus, les éléments GalEa présentent un grand succès évolutif en étant largement distribués dans de nombreuses branches de métazoaires. Ils sont aussi présents chez quelques algues rouges et nous en avons également détecté chez des Fungi. Profitant des nombreuses données génomiques disponibles, nous avons donc étudié la distribution des éléments GalEa de Fungi, dans le but de comparer celle-ci aux résultats obtenus chez les crustacés. En fait, ils n’apparaissent qu’au sein d’un grand embranchement d’ascomycètes, les Pezizomycotina, et ils forment un groupe monophylétique au sein des GalEa. Enfin, chez les Fungi, les éléments GalEa ne sont pas majoritaire parmi les rétrotransposons Copia. Nous avons donc initié une nouvelle étude chez les mollusques, afin de définir si les résultats obtenus chez les crustacés sont une caractéristique des éléments GalEa, des malacostracés ou des métazoaires.
https://tel.archives-ouvertes.fr/tel-01132413

NNT : 2015PA066017
tel-01132413
https://tel.archives-ouvertes.fr/tel-01132413
https://tel.archives-ouvertes.fr/tel-01132413/document
https://tel.archives-ouvertes.fr/tel-01132413/file/these_archivage_2600252o.pdf

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : Xylem density is a physical property of wood that varies between individuals, species and environments. It reflects the physiological strategies of trees that lead to growth, survival and reproduction. Measurements of branch xylem density, ρx, were made for 1653 trees representing 598 species, sampled from 87 sites across the Amazon basin. Measured values ranged from 218 kg m−3 for a Cordia sagotii (Boraginaceae) from Mountagne de Tortue, French Guiana to 1130 kg m−3 for an Aiouea sp. (Lauraceae) from Caxiuana, Central Pará, Brazil. Analysis of variance showed significant differences in average ρx across regions and sampled plots as well as significant differences between families, genera and species. A partitioning of the total variance in the dataset showed that species identity (family, genera and species) accounted for 33% with environment (geographic location and plot) accounting for an additional 26%; the remaining "residual" variance accounted for 41% of the total variance. Variations in plot means, were, however, not only accountable by differences in species composition because xylem density of the most widely distributed species in our dataset varied systematically from plot to plot. Thus, as well as having a genetic component, branch xylem density is a plastic trait that, for any given species, varies according to where the tree is growing in a predictable manner. Within the analysed taxa, exceptions to this general rule seem to be pioneer species belonging for example to the Urticaceae whose branch xylem density is more constrained than most species sampled in this study. These patterns of variation of branch xylem density across Amazonia suggest a large functional diversity amongst Amazonian trees which is not well understood.
ISSN: 1726-4170

hal-01032137
https://hal.archives-ouvertes.fr/hal-01032137

Éditeur(s) : Actes de colloques Ifremer, Tahiti, French Polynesia, 20 Feb - 4 Mar 1989, n°9, chap. 54, pp.563-568
Résumé : Leporinus friderici is a South American promising species for fish culture. In French Guiana the "morphological species", L. friderici, L. granti, L. lebaili and L. affinis steyermarki are found. Their identification is sometimes difficult on usual criterion. To constitute an initial broodstock of L. friderici from local wild populations, the genetic structure of these species was studied. Fifteen enzyme systems, representing twenty loci, were screened.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1989/acte-1441.pdf
http://archimer.ifremer.fr/doc/00000/1441/

Éditeur(s) : HAL CCSD AGU and the Geochemical Society
Résumé : International audience
In the Wadi Haymiliyah of the Oman ophiolite (Haylayn block), discordant wehrlite bodies ranging in size from tens to hundreds of meters intrude the lower crust at different levels. We combined investigations on natural wehrlites from the Wadi Haymiliyah section with an experimental study on the phase relations in a wehrlitic system in order to constrain the petrogenesis of the crustal wehrlites of the Oman ophiolite. Secondary ion mass spectrometry analyses of clinopyroxenes from different wehrlite bodies imply that the clinopyroxenes were crystallized from tholeiitic, mid-ocean ridge (MORB)-type melts. The presence of primary magmatic amphiboles in some wehrlites suggests a formation under hydrous conditions. Significantly enhanced Sr-87/Sr-86 isotope ratios of separates from these amphiboles imply that the source of the corresponding magmatic fluids was either seawater or subduction zone-related. The experiments revealed that under wet conditions at relatively low temperatures, a MORB magma has the potential to produce wehrlite in the ocean crust by accumulation of early olivine and clinopyroxene. These show typically high Mg# which is a consequence of the oxidizing effect of the prevailing high aH(2)O. First plagioclases crystallizing after clinopyroxene under wet conditions are high in An content, in contrast to the corresponding dry system. Trace element compositions of clinopyroxenes of those wehrlites from the Moho transition zone are too depleted in HREE to be in equilibrium with present-day MORB, implying a genetic relation to the V2 lavas of the Oman ophiolite, which are interpreted to be the result of fluid-enhanced melting of previously depleted mantle. We present a model on the petrogenesis of the crustal wehrlites in an upper mantle wedge above an initial, shallow subduction zone at the beginning of the intraoceanic thrusting.
ISSN: 1525-2027

hal-00429373
https://hal.archives-ouvertes.fr/hal-00429373
DOI : 10.1029/2009GC002488

Éditeur(s) : HAL CCSD NRC Research Press
Résumé : Molecular, cytological, and morphological data support the existence of a hybrid population between Schoenus nigricans and Schoenus ferrugineus. This population was found in northeastern Italy, where S. nigricans is central with respect to its natural range and S. ferrugineus is marginal, being most common in the Alps and in central and northern Europe. Molecular marker data show that the putative hybrid population is genetically intermediate between nearby populations of the parent species. Cytological evidence confirmed the hybrid nature of this population, as does the almost complete sterility of plants within the population. Although no seeds were produced by the hybrid population, some possibly fertile pollen grains were produced; this suggests that the possibility of introgression between the two species through the hybrids cannot completely be excluded.
ISSN: 0831-2796

hal-01032047
https://hal.archives-ouvertes.fr/hal-01032047
DOI : 10.1139/G01-138