Éditeur(s) : Université de Paris 6 – Pierre et Marie Curie
Résumé : Since 1997, a new pathology seasonally occurs in new caledonian shrimp farms during the warm season and was named Summer Syndrome. Diseased Litopenaeus stylirostris shrimp suffer from a septicemic vibriosis which was attributed to V. nigripulchritudo. Preliminary studies based on a collection of V. nigripulchritudo strains have brought to light different virulence levels according to experimental infections results; three virulence statuses were defined: highly (HP), moderately (MP) and non pathogenic (NP). The aim of this work was to genetically characterize virulent V. nigripulchritudo strains. In a first step the genetic diversity of 58 V. nigripulchritudo strains was analyzed by MLST and AP-PCR, revealing a cluster of HP and MP strains, characterized by a low genetic variability and that includes all Summer Syndrome-associated isolates. This confirms the emergence of one cluster of pathogenic V. nigripulchritudo simultaneously with the emergence of the Summer Syndrome ; in a second step, 368 genetic markers of virulence were identified by a Suppressive Subtractive Hybridization performed between the genomes of a HP strain and a genetically close, NP isolate; the distribution of the screened SSH fragments was studied in 58 V. nigripulchritudo isolates by macro-array: 78 DNA fragments were selected, allowing to characterize clusters identified and pathogenic statuses; 13 are specific of the HP strains involved in Summer Syndrome. Interestingly, 10 of these markers are carried by a plasmid pSFn1 that contains sequences highly similar to those of a plasmid pAK1, detected in Vibrio shilonii, a coral pathogen. The origin and consequences of this plasmid acquisition are discussed.
Depuis 1997, les élevages de crevettes en Nouvelle-Calédonie sont confrontés à une nouvelle maladie, le Syndrome d'été, une vibriose septicémique dont l'agent étiologique est Vibrio nigripulchritudo. Les résultats d'infection expérimentale sur une collection de souches, ont montré l'existence de trois pathotypes distincts : hautement (HP), moyennement (MP) et non pathogène (NP). L'étude du polymorphisme génétique de 58 souches par typage moléculaire en MLST et AP-PCR, a mis en évidence un groupe phylogénétique particulier caractérisé par un très faible degré de variabilité génétique (confirmant l'émergence de ce groupe en parallèle à l'émergence du Syndrome d'été) et constitué uniquement de souches HP (dont toutes celles associées au Syndromed'été) et de souches MP. Afin d'identifier des marqueurs génétiques de la virulence des souches responsables du Syndrome d'été, et parmi ces marqueurs des gènes codant potentiellement pour des effecteurs de la virulence, une approche soustractive par SSH a été développée entre une souche HP de type Syndrome d'été et une souche NP : 368 marqueurs génétiques ont ainsi été mis en évidence ; la distribution de ces marqueurs a été étudiée chez les 58 souches de la collection par une approche en macroarray : 78 marqueurs ont été sélectionnés, qui permettent de caractériser les différents groupes phylogénétiques et les différents pathotypes, dont 13 fragments spécifiques des souches HP type Syndrome d'été. Parmi ces 13 fragments, 10 ont été localisés sur le plasmide pSFn1 qui a été entièrement séquencé. Ce même plasmide a été purifié uniquement des souches HP de type Syndrome d'été. Par ailleurs, une très forte homologie a été mise en évidence entre pSFn1 et pAK1, un autre plasmide également séquencé et retrouvé chez la souche V. shilonii AK1, responsable du blanchiment du corail Oculina patagonica en Méditerranée. Ces résultats ont ouvert la discussion sur le rôle de pSFn1 dans la virulence de V. nigripulchritudo.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-3906.pdf
http://archimer.ifremer.fr/doc/00000/3906/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.
ISSN: 0962-1083

hal-01681650
https://hal.archives-ouvertes.fr/hal-01681650
DOI : 10.1111/mec.14389

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been described, the interpenetration of both environments leads to hybridization between strains that may be at risk for human health.
ISSN: 1567-1348

pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/document
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/file/Mercier_et_al_IGE2011.pdf
DOI : 10.1016/j.meegid.2011.05.003

Éditeur(s) : Elsevier
Résumé : Two populations of the Latin American shrimp Penaeus (Litopenaeus)stylirostris domesticated in Hawaii and in New Caledonia were previously shown to be genetically differentiated and proven highly inbred. In New Caledonia, where different Vibriosis affect shrimp production and antibiotic use is banned in growing ponds, the Hawaiian population was introduced to increase the allelic variability available for local shrimp farmers and start a genetic improvement program. Growth and survival rates of the two pure populations and the two-way F-1-hybrids obtained by breeding Hawaiian animals with New Caledonian animals were assessed in several simple experiments (earthen ponds, floating cages and experimental infection challenges) during two years on two successive generations. Results were very consistent: F-1-hybrids growth rates in earthen ponds were 37% (+/-7% SD) higher than for pure populations. Cage experiments demonstrated no competition between the different populations when reared together or separately in a common environment. The F-1-hybrids also showed better survival rates in all experiments. Combining the results on growth and survival rates leads to the conclusion that biomass production is much higher with F-1-hybrid populations than with pure populations using the same quantity of juveniles stocked: biomass production in ponds was increased 1.4 and 2.3 times on year I and year 2 respectively, and 1.9 times in floating cages. The advantage of growing F-1-hybrids appeared proportionally higher when environmental and sanitary conditions led to poorer survival (34% in year 2 vs. 56% in year 1). These results are a good example of performance improvement by heterosis effect and/or of performance loss due to inbreeding in the pure populations. This study demonstrates that aquaculture industries which cannot afford large selection programs may benefit from using two different inbred parental stocks to produce F-1-hybrids for each commercial growout. This is notably true when only inbred populations are available, or when introduction of genetic variability from the wild or from other genetic resources represents a zoo-sanitary risk. In our case, the expected increase in L stylirostris production could be around 85% (according to our average results) if producers keep stocking their ponds at their current densities using F-1-hybrids. However, for sustainability reasons, it is advisable to stock F-1-hybrid animals at lower densities, the gain in performance allowing producing the same amount of biomass with less input. (C) 2008 Elsevier B.V. All rights reserved.
Aquaculture (0044-8486) (Elsevier), 2008-06 , Vol. 278 , N. 1-4 , P. 43-50

Droits : 2008 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2008/publication-4316.pdf
DOI:10.1016/j.aquaculture.2008.03.018
http://archimer.ifremer.fr/doc/00000/4316/

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : International audience
Key message: Genetic diversity appears to be unaffected by disturbance in a stand of the light-demanding Neotropical treeV. michelii. Although spatial genetic structure is modified in post-disturbance cohorts, mixing of seeds from different mother trees in canopy gaps appears to efficiently maintain genetic admixture. Context: The interplay between genetic and demographic processes has major consequences on population viability. Population size affects demographic trends, while genetic diversity insures viability by reducing risks of inbreeding depression and by maintaining adaptive potential. Yet, the consequences of increases in census size (as opposed to effective size) on genetic diversity of forest populations are poorly known. Aims: We have studied the structure of genetic diversity in populations of saplings of the light-responsive tree, Virola michelii (Myristicaceae, the nutmeg family), in two plots having undergone different levels of canopy-gap opening disturbance. This allowed us to test the “intermediate disturbance” hypothesis, which generally applies to species diversity, at the intra-specific scale. Methods: Levels and distribution of genetic diversity were compared between plots and between life stages. Sapling parentage was analysed to infer each adult tree’s contribution to regeneration. Results: Genetic diversity was higher, and spatial genetic structure was stronger in the post-disturbance than in the control seedling population. Parentage analysis suggested that a limited number of parents contributed to most of the regeneration, but that efficient mixing of their progeny may have enhanced the diversity of saplings occupying canopy gaps. Conclusion: A mixture of demo-genetic processes may contribute to maintain genetic diversity in spite of, or possibly due to, ecosystem disturbance in V. michelii.
ISSN: 1286-4560

hal-01502942
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942/file/art_10.1007_s13595-015-0508-3-1_%7B869D58F4-272C-491F-A903-DAD6CDBDC042%7D.pdf
DOI : 10.1007/s13595-015-0508-3

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Meiotic recombination predominantly occurs at discrete genomic loci called recombination hotspots, but the features defining these areas are still largely unknown (reviewed in refs 1-5). To allow a comprehensive analysis of hotspot-associated DNA and chromatin characteristics, we developed a direct molecular approach for mapping meiotic DNA double-strand breaks that initiate recombination. Here we present the genome-wide distribution of recombination initiation sites in the mouse genome. Hotspot centres are mapped with approximately 200-nucleotide precision, which allows analysis of the fine structural details of the preferred recombination sites. We determine that hotspots share a centrally distributed consensus motif, possess a nucleotide skew that changes polarity at the centres of hotspots and have an intrinsic preference to be occupied by a nucleosome. Furthermore, we find that the vast majority of recombination initiation sites in mouse males are associated with testis-specific trimethylation of lysine 4 on histone H3 that is distinct from histone H3 lysine 4 trimethylation marks associated with transcription. The recombination map presented here has been derived from a homogeneous mouse population with a defined genetic background and therefore lends itself to extensive future experimental exploration. We note that the mapping technique developed here does not depend on the availability of genetic markers and hence can be easily adapted to other species with complex genomes. Our findings uncover several fundamental features of mammalian recombination hotspots and underline the power of the new recombination map for future studies of genetic recombination, genome stability and evolution.
ISSN: 0028-0836

hal-00877681
https://hal.archives-ouvertes.fr/hal-00877681
DOI : 10.1038/nature09869
PUBMED : 21460839

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS: Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes. The results of expression quantitative trait locus (eQTL) analyses were also replicated with a Gene Expression Omnibus (GEO) data set. The effects of eQTLs on overall survival (OS) and disease-free survival (DFS) were evaluated. RESULTS: Five ancestry-related SNPs were identified as cis-eQTLs in the DNA polymerase beta (POLB) gene (false discovery rate [FDR]<0.01). The homozygous/heterozygous genotypes containing the African allele showed higher POLB expression than the homozygous white allele genotype (P<.001). A replication study using a GEO data set validated all 5 eQTLs and also showed a statistically significant difference in POLB expression based on genetic ancestry (P=.002). An association was observed between these eQTLs and OS (P<.037; FDR<0.0363) as well as DFS (P=.018 to.0629; FDR<0.079) for oral cavity and laryngeal cancer patients treated with platinum-based chemotherapy and/or radiotherapy. Genotypes containing the African allele were associated with poor OS/DFS in comparison with homozygous genotypes harboring the white allele. CONCLUSIONS: Analyses show that ancestry-related alleles could act as eQTLs in HNSCC and support the association of ancestry-related genetic factors with survival disparities in patients diagnosed with oral cavity and laryngeal cancer. (C) 2016 American Cancer Society.
ISSN: 0008-543X

hal-01519253
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01519253
DOI : 10.1002/cncr.30457
PUBMED : 27906459

Éditeur(s) : Elsevier
Résumé : The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1–D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity.
Harmful Algae (1568-9883) (Elsevier), 2014-12 , Vol. 40 , P. 75-91

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00225/33611/32310.pdf
DOI:10.1016/j.hal.2014.10.006
http://archimer.ifremer.fr/doc/00225/33611/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Predicting the impact of underground engineering on the environment requires the knowledge of natural media at different scales. In particular, understanding basic phenomena controlling the properties of rocks in the presence of complex fluids necessitates a detailed atomic description of the solid/fluid/solid contacts, the subject of Part I of the present study. First, building the solid interspace between two different crystals in a non-periodic situation is achieved using the ab initio and molecular mechanics code GenMol (TM). A description of the fluid confined within the interspace is then derived from the original genetic iterative multi-species (GIMS) algorithm implemented in the same code. This approach consists of equilibrating chemical potentials, cycle after cycle and species after species, between the confined fluid and the free natural fluid. An elementary iteration for a species k consists of different steps incrementing the number N-k of particles k, with other numbers N-k remaining constant. At each step, an optimum fluid composition is obtained by a genetic process distributing the fluid particles on a grid by stochastic shots, followed in fine by a refining process. The effectiveness of the GIMS approach is demonstrated in the case study of a fluid confined between two (0 0 1) kaolinite faces, with apertures h varying between 4 and 10 A. connected to a 9-species external solution [H2O, Cl-, Na+ CO2(aq), NaCl(aq), Ca2+, Mg2+, HCO3-, H3O+] where concentrations are ranging from 55 to 10(-4) mol/L. The results show a drastic variation in the solute/solvent and cations/ions ratios in the confined fluid when aperture h is lowered to less than 1 nm. These results obtained with a very rapid convergence of the iterative algorithm combined with a very competitive genetic optimizer are validated with high precision on a free solution. This description of contacts between crystals is original and unattainable by standard crystal interface approaches. It opens the way to understanding and/or predicting phenomena between crystals in a complex natural environment, such as adhesion or repulsion investigated in the Part II of this study.
ISSN: 0022-0248

hal-00544569
https://hal.archives-ouvertes.fr/hal-00544569
DOI : 10.1016/j.jcrysgro.2010.08.009

Éditeur(s) : HAL CCSD
Résumé :  
For a comprehensive evaluation of human influences on the genetic system, the simulation model EGO-GENE was developed. The model combines population genetic and population dynamic processes with forest growth models. The dynamics of genetic structures (single locus and multilocus genotypes up to 200 loci) can be simulated. Spatial and temporal genetic dynamics are included in the model. Overlapping or separated generations can be created and different modes of mating systems can be implemented. The model can be run with empirical and fictitious input data. The simulated genetic structures can be directly analysed with established genetic analysis programmes. An example demonstrates the use of the model far validation of interactions among components of the mating system. Another example demonstrates the applicability of the model in decision-making for seed sampling strategies. The genetic differences between the adult trees and the harvested seeds and the danger of genetic drift regarding to different seed sampling strategies are investigated by use of the genetic distance and the reproductively effective population size.
Silvae genetica

hal-01032083
https://hal.archives-ouvertes.fr/hal-01032083

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
Biological Journal of the Linnean Society

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711/document

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Holoprosencephaly (HPE) is the most common congenital cerebral malformation, characterized by impaired forebrain cleavage and midline facial anomalies. Heterozygous mutations in 14 genes have been associated with HPE, and are often inherited from an unaffected parent underlying complex genetic bases. It is now emerging that HPE may result from a combination of multiple genetic events, rather than from a single heterozygous mutation. To explore this hypothesis, we undertook whole exome sequencing (WES) and targeted high-throughput sequencing approaches to identify mutations in HPE subjects. We report here two HPE families in which two mutations are implicated in the disease. In the first family presenting two fetuses with alobar and semi-lobar HPE, we found mutations in two genes involved in HPE, SHH and DISP1, inherited respectively from the father and the mother. The second reported case is a family with a 9-year old girl presenting lobar HPE, harbouring two compound heterozygous mutations in DISP1. Together, these cases of digenic inheritance SHH/DISP1 and autosomal recessive HPE suggest that in some families, several genetic events are necessary to cause HPE. This study highlights the complexity of HPE inheritance and has to be taken into account by clinicians to improve HPE genetic counseling.
ISSN: 0009-9163

hal-01259228
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259228
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259228/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259228/file/Complex%20mode%20of%20inheritance%20in%20holoprosencephaly_accepted.pdf
DOI : 10.1111/cge.12722

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé :  
In this paper, we report a study of the mating system and gene flow of Symphonia globulifera, a hermaphroditic, mainly bird-pollinated tree species with a large geographic distribution in the tropical Americas and Africa.Using three microsatellites, we analysed 534 seeds of 28 open pollinated families and 164 adults at the experimental site 'Paracou' in French Guiana. We observed, compared to other tropical tree species, relatively high values for the effective number of alleles. Significant spatial genetic structure was detected, with trees at distances up to 150 m more genetically similar than expected at random. We estimated parameters of the mating system and gene flow by using the mixed mating model and the TwoGener approach. The estimated multilocus outcrossing rate, tm, was 0.920. A significant level of biparental inbreeding and a high proportion of full-sibs were estimated for the 28 seed arrays. We estimated mean pollen dispersal distances between 27 and 53 m according to the dispersal models used. Although the adult population density of S. globulifera in Paracou was relatively high, the joint estimation of pollen dispersal and density of reproductive trees gave effective density estimates of 1.6 and 1.3trees/ha. The parameters of the mating system and gene flow are discussed in the context of spatial genetic and demographic structures, flowering phenology and pollinator composition and behaviour.
ISSN: 0018-067X

hal-01032178
https://hal.archives-ouvertes.fr/hal-01032178
DOI : 10.1038/sj.hdy.6800560

Éditeur(s) : HAL CCSD Springer Verlag
Résumé :  
Quantitative genetic diversity is a fundamental component of the interaction between natural populations and their environment. In breeding programmes, quantitative genetic studies on tropical trees have so far focused on fast-growing, light-demanding species, but no information exists on shade-tolerant, slow-growing species. For this study, 27 3-year-old open-pollinated families of the Neotropical shade-tolerant rainforest tree Sextonia rubra were measured in semicontrolled conditions for 20 morphological, growth, and photosynthesis traits; the effect of genetic relatedness, habitat of provenance, and mother tree status on seedling traits was analysed. Nine traits displayed significant genetic effects, while mother tree status and habitat effects were not significant (P>0.05) for an y trait. Estimated heritability varied between 0.14 and 0.28, with growth-related traits having the highest values. Additive genetic variation correlated positively with nonheritable variation, suggesting that ecological-evolutionary factors increasing or decreasing additive genetic variance may also affect nonheritable variation in the same direction. Our results suggest that quantitative genetic variability should be taken into account in ecological studies on, and in the management of, natural tropical rainforests; further research is needed to investigate genetic × environment interactions, in particular from the point of view of the genetic response of shade-tolerant plant species to variations in light availability.
ISSN: 1614-2942

hal-01032145
https://hal.archives-ouvertes.fr/hal-01032145
DOI : 10.1007/s11295-009-0251-8

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
ISSN: 0024-4066

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711v2/document
http://hal.ird.fr/ird-00759711/file/FauvelotBorsa_Scomberomorus%20commerson%20p%20HAL.pdf

Éditeur(s) : Université des Antilles. Service commun de la documentation INCA 5Instituto Nacional de Ciencias Agrícolas), Cuba
Extrait de : 52e congrès annuel de la Société caribéenne des plantes alimentaires / 52nd annual meeting of the Caribbean food crops society (CFCS), du 10 au 16 juillet 2016. INRA, CFCS
Description : The methodology is supported on the basis of the experience acquired by a group of researchers, farmers and technicians from Cuba in the implementation of Participatory Plant Breeding. The proposal presents a number of methodological considerations with the necessary flexibility to allow proper application of the method and follows a logical sequence of activities to be executed in a manner that facilitates their implementation in various contexts in which it is of interest to apply. Its implementation, as such, is a learning process in action for all actors involved in it; also enables participants to understand the scale of the needs of the producers and breeding programs and dissemination of varieties in terms of the real interest of these. The methodology has 4 main phases: 1) diagnosis, 2) Collection of plant genetic resources, 3) Establishment of demonstration plots and development diversity fairs and 4) farmer experimentation. Besides the four basic stages of Participatory Plant Breeding in Cuba other tools that allowed the PPB constitute a successful process were used, these tools are: action learning as interest Schools Farmers Festivals innovation, exchange visits and retreats, capacity building of students on stage in local innovation and creation of local seed banks.
Siècle(s) traité(s) : 21
Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V16317
V16317

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
IntroductionLeishmania RNA virus type 1 (LRV1) is an endosymbiont of some Leishmania (Vianna) species in South America. Presence of LRV1 in parasites exacerbates disease severity in animal models and humans, related to a disproportioned innate immune response, and is correlated with drug treatment failures in humans. Although the virus was identified decades ago, its genomic diversity has been overlooked until now.Methodology/Principles findingsWe subjected LRV1 strains from 19 L. (V.) guyanensis and one L. (V.) braziliensis isolates obtained from cutaneous leishmaniasis samples identified throughout French Guiana with next-generation sequencing and de novo sequence assembly. We generated and analyzed 24 unique LRV1 sequences over their full-length coding regions. Multiple alignment of these new sequences revealed variability (0.5%±23.5%) across the entire sequence except for highly conserved motifs within the 5' untranslated region. Phylogenetic analyses showed that viral genomes of L. (V.) guyanensis grouped into five distinct clusters. They further showed a species-dependent clustering between viral genomes of L. (V.) guyanensis and L. (V.) braziliensis, confirming a long-term co-evolutionary history. Noteworthy, we identified cases of multiple LRV1 infections in three of the 20 Leishmania isolates.Conclusions/SignificanceHere, we present the first-ever estimate of LRV1 genomic diversity that exists in Leishmania (V.) guyanensis parasites. Genetic characterization and phylogenetic analyses of these viruses has shed light on their evolutionary relationships. To our knowledge, this study is also the first to report cases of multiple LRV1 infections in some parasites. Finally, this work has made it possible to develop molecular tools for adequate identification and genotyping of LRV1 strains for diagnostic purposes. Given the suspected worsening role of LRV1 infection in the pathogenesis of human leishmaniasis, these data have a major impact from a clinical viewpoint and for the management of Leishmania-infected patients.
ISSN: 1935-2727

pasteur-01583523
https://hal-riip.archives-ouvertes.fr/pasteur-01583523
DOI : 10.1371/journal.pntd.0005764
PUBMED : 28715422

Éditeur(s) : HAL CCSD
Résumé : Understanding of the mechanisms driving diversification of species is a significant way to improve the management of ecosystems, predict the impacts of climate change and understand the actual and past biodiversity level. The aim of this thesis is to understand and comprehend genetic mechanisms behind the diversification of species in the presence of gene flow. This thesis is focused on the biological model Symphonia globulifera, which presents two ecotypes: the S.globulifera, specialist of seasonally flooded lowlands and S.sp1, specialist of terra firme. These two ecotypes show low genetic differentiation, despite the presence of two apparent phenotypes. A first part of this thesis was to test the presence of local adaptation of this using reciprocal transplant experiment gardens, allowing the understanding of the ecotypes distributions in their natural habitats. Then, this local adaptation in the presence of gene flow, directed me to the regulation of gene methylation in order to see the role this brand of epigenetics can have in the divergence of the ecotypes. In a third part of the thesis, new generation sequencing of the transcriptome ecotypes in reciprocal gardens transplantations allowed me to show the evidence of gene regulation to differentiate the ecotypes. This work thesis is based on phenotype records data, AFLP genotyping and high-throughput sequencing of the transcriptome, in order to show the important value of gene regulation in the divergence of the locally adapted ecotypes, and a weak role of DNA methylation in the establishment of local adaptation.
Connaitre et appréhender les mécanismes de la diversification des espèces est important pour la gestion des écosystèmes, la prévision des impacts des changements climatiques et la compréhension de la biodiversité actuelle et passée. Le but de cette thèse est de comprendre et de déceler les mécanismes génétiques à l’origine de la diversification des espèces en présence de flux de gènes. Cette thèse se focalise sur le modèle biologique Symphonia globulifera, qui compte deux écotypes : le S.globulifera spécialiste de la terra firme et le S.sp1, spécialiste des bas-fonds. Ces deux écotypes montrent une faible différenciation génétique, malgré la présence de deux phénotypes différents.Une première étape a été de mettre en évidence la présence d’une adaptation locale au sein de cette espèce, par le biais d’une expérimentation de jardins de transplantation réciproques, permettant d’expliquer la répartition des écotypes dans leur habitat naturel. Ensuite, dans le but d’identifier les mécanismes sous-jacent à cette adaptation locale, j’ai testé l’hypothèse que la méthylation des gènes pourrait être une marque de l’épigénétique contribuant à la divergence des écotypes, par l’utilisation d’enzyme sensibles à la méthylation dans un protocole de génotypage AFLP. Enfin, un séquençage haut-débit du transcriptome des écotypes en jardins de transplantation réciproques m’a permis de mettre en évidence une expression différentielle des gènes entre les écotypes, qui pourrait expliquer les différences phénotypiques observées entre les écotypes malgré une faible différentiation génétique. Ces travaux de thèse s’appuie, ainsi, sur des données de traits phénotypiques, de génotypage AFLP et de séquençage à haut débit du transcriptome pour montrer la valeur importante de la régulation des gènes dans la divergence des écotypes adaptés localement, et un faible rôle de la méthylation de l’ADN dans l’établissement cette adaptation locale.
https://tel.archives-ouvertes.fr/tel-01405400

NNT : 2015YANE0005
tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400/document
https://tel.archives-ouvertes.fr/tel-01405400/file/these_-_tinaut.pdf

Éditeur(s) : HAL CCSD
Résumé :  
The spatial genetic differentiation among European beech stands in western Germany was analysed by a new method. The genetic structure at 8 enzyme gene loci of 100 sampled populations was used as data base. The data represent authors' own results and published data from 8 different studies. For 10 geographic distance classes [h] from 0 to 500 km, the average genetic distance between the populations for each single gene locus, a gene-pool distance and the semivariances of genetic diversity gam were computed. Significant deviation from random spatial genetic structure was tested by permutation analysis. In many cases (Lap-B, Mdh-B, Mdh-C and 6Pgdh-C) the mean genetic distance between stands with spatial distance up to 200 km was significantly smaller and the genetic distance between stands with geographic distances of 200 and 400 km was significantly greater than expected for random spatial genetic structure. Similar tendencies were found for the gene-pool distance and the semivariances of diversity. Kriging, as a method for spatial interpolation, was used to draw synthetic maps of the spatial patterns of allelic frequencies and genetic diversity. The influence of postglacial recolonisation and regeneration with foreign seed material on the spatial genetic patterns are discussed
Forest genetics

hal-01032093
https://hal.archives-ouvertes.fr/hal-01032093

Éditeur(s) : HAL CCSD Elsevier
Résumé : Over-exploitation and fragmentation are serious problems for tropical forests. Most sustainable forest management practices avoid clear-cuts and apply selective logging systems focused on a few commercial species. We applied a simulation model to estimate the impact of such selective logging scenarios on the genetic diversity and demography of four tropical tree species from French Guiana. The simulations used data on genetic and demographic composition, growth, phenology and pollen and seed dispersal obtained for Dicorynia guianensis, Sextonia rubra, Symphonia globulifera and Vouacapoua americana at the experimental site in Paracou. Whereas Symphonia globulifera serves as a model for a species with low logging pressure, the other three species represent the most exploited tree species in French Guiana. In simulations with moderate logging, typical for French Guiana, with large cutting diameter (>60 cm diameter) and long cutting cycles (65 years), the two species V. americana and Sextonia rubra were not able to recover their initial stock at the end of the rotation period, with a large decrease in the number of individuals and in basal area. Under a more intensive logging system (cutting diameter >45 cm diameter, cutting cycles of 30 years) that is common practice in the Brazilian Amazon, only Symphonia globulifera showed no negative impact. Generally, the differences between the genetic parameters in the control scenarios without logging and the logging scenarios were surprisingly small. The main reasons for this were the overlapping of generations and the effective dispersal ability of gene vectors in all species, which guarantee relative homogeneity of the genetic structure in different age classes. Nevertheless, decreasing the population size by logging reduced the number of genotypes and caused higher genetic distances between the original population and the population at the end of the logging cycles. Sensitivity analysis showed that genetic changes in the logging scenarios were principally determined by the growth, densities and cutting diameter of each species, and only to a very small extent by the reproductive system including factors such as pollen and seed dispersal and flowering phenology
ISSN: 0006-3207

hal-01032050
https://hal.archives-ouvertes.fr/hal-01032050
DOI : 10.1016/j.biocon.2006.02.014