Résumé : The tropical seabass Lates calcarifer was introduced in Tahiti in 1984 and then was domesticated without other introduction. Three successive generations have been obtained in captivity. Tissue samples of the 38 animaIs which represent the total Tahitian broodstock were preserved in alcohol to be genotyped with four microsatellite markers (Yue et al., 2001). Three of four described markers were successfully transferred to the laboratory of genetics of Tahiti (marker LcaM01, LcaM02, LcaM03), as the revelation technology available locally did not allow the use of LcaM04 in routine. The results show that the genetic diversity of the tahitian broodstock is not equivalent of the one of the species, which could be explained by the small size of the founder population, which is consistant with the history of the Tahitian population. The structuration of the 4th generation into several batches obtained from different parents appears to be the minimum management procedure to limit inbreeding.
Le loup tropical Lates calcarifer a été introduit à Tahiti en 1984 puis domestiqué sans apport d'animaux extérieurs. Trois générations successives ont été obtenues en captivité. Des prélèvements de tissus sur les 38 géniteurs qui constituent l'intégralité du stock de reproducteurs tahitiens sont conservés dans l'alcool pour être génotypés à l'aide de quatre marqueurs microsatellites (Yue et al., 2001). Trois des quatre marqueurs décrits ont pu être transférés avec succès au laboratoire de génétique de Tahiti (marqueurs LcaM01, LcaM02, LcaM03), la technique de révélation disponible localement ne permettant pas d'utiliser LcaM04 en routine. Les résultats montrent qu'on ne dispose pas à Tahiti de toute la variabilité génétique de l'espèce, ce qui pourrait s'expliquer, compte tenu de l'histoire de cette population, par un faible nombre de géniteurs fondateurs. La structuration de la 4ème génération en plusieurs lots issus de parents différents apparaît comme la mesure de gestion minimale pour limiter la consanguinité au sein de cette population.

Droits : 2003 Ifremer
http://archimer.ifremer.fr/doc/00142/25300/23372.pdf
http://archimer.ifremer.fr/doc/00142/25300/

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
The within-population spatial structure of genetic diversity is shaped by demographic processes, including historical accidents such as forest perturbations. Information drawn from the analysis of the spatial distribution of genetic diversity is therefore inherently linked to demographic-historical processes that ultimately determine the fate of populations. All adult trees and saplings in a 1.4-ha plot within a mixed Norway spruce (Picea abies [L.] Karst) stand were characterised by means of chloroplast (paternally inherited) markers, and a large sub-sample of these were genotyped at mitochondrial (maternally inherited) molecular markers. These data were used to analyse the spatial distribution of genetic variation and to compare the patterns corresponding to the two marker types. The plot presented non-homogeneous local stem density in the younger cohorts, and the indirect effect of this source of variation on the spatial genetic structure was investigated. Results suggest that (i) spatially limited seed dispersal induced patchiness in genotype distribution, while pollen flow had a homogenising effect; (ii) deviations from random spatial structure were stronger in the demographically most stable portions of the stand, while they were weaker where sudden bursts of regeneration occurred; (iii) spatially overlapping adult and sapling cohorts displayed the same spatial genetic structure (stronger on stable areas, weaker in portions of the stand undergoing events of intense regeneration), which was substantiated by the influence of local demographic processes. Regeneration dynamics as modulated by demography thus influences the distribution of genetic diversity within the stand both in the younger life stages and in the adult population.
ISSN: 0378-1127

hal-01032063
https://hal.archives-ouvertes.fr/hal-01032063
DOI : 10.1016/j.foreco.2008.03.023

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
Childhood absence epilepsy is a prototypic form of generalized nonconvulsive epilepsy characterized by short impairments of consciousness concomitant with synchronous and bilateral spike-and-wave discharges in the electroencephalogram. For scientists in this field, the BS/Orl and BR/Orl mouse lines, derived from a genetic selection, constitute an original mouse model "in mirror" of absence epilepsy. The potential of MALDI imaging mass spectrometry (IMS) for the discovery of potential biomarkers is increasingly recognized. Interestingly, statistical analysis tools specifically adapted to IMS data sets and methods for the identification of detected proteins play an essential role. In this study, a new cross-classification comparative design using a combined discrete wavelet transformation-support vector machine classification was developed to discriminate spectra of brain sections of BS/Orl and BR/Orl mice. Nineteen m/z ratios were thus highlighted as potential markers with very high recognition rates (87-99%). Seven of these potential markers were identified using a top-down approach, in particular a fragment of Synapsin-I. This protein is yet suspected to be involved in epilepsy. Immunohistochemistry and Western Blot experiments confirmed the differential expression of Synapsin-I observed by IMS, thus tending to validate our approach. Functional assays are being performed to confirm the involvement of Synapsin-I in the mechanisms underlying childhood absence epilepsy.
ISSN: 1535-3893

hal-00877728
https://hal.archives-ouvertes.fr/hal-00877728
DOI : 10.1021/pr3006974
PUBMED : 22994238

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species.[br/] [br/] [b]Location[/b][br/] Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America.[br/] [br/] [b]Methods[/b][br/] Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times.[br/] [br/] [b]Results[/b][br/] Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal.[br/] [br/] [b]Main conclusions[/b][br/] The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.
ISSN: 0305-0270

hal-01032395
https://hal.archives-ouvertes.fr/hal-01032395
DOI : 10.1111/j.1365-2699.2011.02678.x

Éditeur(s) : Wiley-blackwell
Résumé : The reef fauna connectivity of the West Indian Ocean (WIO) is one of the least studied globally. Here we use genetic analyses of the grouper Epinephelus merra (Bloch 1793) to determine patterns of connectivity and to identify barriers to dispersal in this WIO marine area. Phylogeographic and population-level analyses were conducted on cytochrome b sequences and microsatellites (13 loci) from 557 individuals sampled in 15 localities distributed across the West Indian Ocean. Additional samples from the Pacific Ocean were used to benchmark the WIO population structure. The high level of divergence revealed between Indian and Pacific localities (of about 4.5% in sequences) might be the signature of the major tectonic and climatic changes operating at the Plio-Pleistocene transition, congruently with numerous examples of Indo-Pacific speciation. In comparison, the E. merra sequences from the Indian Ocean constitute a monophyletic clade with a low average genetic distance (d < 0.5%). However both genetic markers indicated some structure within this ocean. The main structure revealed was the isolation of the Maldives from the WIO localities (a different group signature identified by clustering analysis, great values of differentiation). Both marker types reveal further significant structure within the WIO, mainly the isolation of the Mascarene Islands (significant AMOVA and isolation-by-distance patterns) and some patchy structure between the northernmost localities and within the Mozambique Channel. The WIO genetic structure of E. merra appeared congruent with main biogeographic boundaries and oceanographic currents.
Marine Ecology-an Evolutionary Perspective (0173-9565) (Wiley-blackwell), 2015-09 , Vol. 36 , N. 3 , P. 447-461

Droits : 2014 Blackwell Verlag GmbH
http://archimer.ifremer.fr/doc/00189/30046/28566.pdf
DOI:10.1111/maec.12153
http://archimer.ifremer.fr/doc/00189/30046/

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) : Elsevier
Résumé : Correlation between DNA microsatellite heterozygosity and growth rate was investigated in two hatchery-propagated stocks of the shrimp Penaeus stylirostris, which had been genetically isolated from wild founders for 17 generations, and from each other for five more generations. presumed demographic history of these populations suggested that they were maintained at small effective population sizes. and this was confirmed by significant changes in allelic frequencies between the two stocks. Despite a small sample size (n = 60) and a small number of loci screened, a significant positive correlation was detected between microsatellite tri-locus heterozygosity and growth rate in one of the two stocks (r = 0.3, P = 0.02). In the other stock (n = 48), the positive correlation was not significant, but the combined test of single locus heterozygote advantage over the three loci was significant (P = 0.005).Use of DNA microsatellite markers, whose selectively neutral status is generally accepted, allowed us to reject the hypothesis of direct overdominance at marker loci as an explanation for an association of growth rate with heterozygosity. The average depression associated with one locus in our case is above or equivalent to the amount observed for a 10% increase of inbreeding in other species. These results suggest that heterozygosity at neutral marker loci is sufficiently well correlated with individual inbreeding coefficients to reveal a significant residual inbreeding load for growth rate in Tahitian P. stylirostris stocks. Inbreeding during hatchery propagation was, thus, insufficient to purge the ancestral load.
Aquaculture (0044-8486) (Elsevier), 2000-04 , Vol. 184 , N. 3-4 , P. 203-219

Droits : 2000 Elsevier Science B.V. All rights reserved
http://archimer.ifremer.fr/doc/2000/publication-753.pdf
DOI:10.1016/S0044-8486(99)00331-2
http://archimer.ifremer.fr/doc/00000/753/

Éditeur(s) : Natl Marine Fisheries Service Scientific Publ Office
Résumé : Twenty homologous microsatellite markers, or simple sequence repeats (SSRs), were developed for blackfin tuna (Thunnus atlanticus) through the use of a direct Seq-to-SSR approach. The number of alleles per locus ranged between 5 and 26, and the expected heterozygosity ranged between 0.640 and 0.969. Three loci displayed significant departure from Hardy-Weinberg equilibrium expectations, likely reflecting occurrence of null alleles. Another locus showed consecutive alleles that differed by one base pair only. Consequently, this locus may be prone to elevated rates of scoring errors. The remaining 16 loci will be valuable for studies in conservation genetics of blackfin tuna.
Fishery Bulletin (0090-0656) (Natl Marine Fisheries Service Scientific Publ Office), 2014-10 , Vol. 112 , N. 4 , P. 322-325

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00239/34999/33529.pdf
DOI:10.7755/FB.112.4.8
http://archimer.ifremer.fr/doc/00239/34999/

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. We developed a method to compare genome-wide diversity estimates while taking into account-and factoring out-variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels. An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers. RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots. RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).
ISSN: 1286-4560

hal-01032413
https://hal.archives-ouvertes.fr/hal-01032413
DOI : 10.1007/s13595-013-0302-z

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Background. In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied.[br/]Methods. We assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree [i]Eperua falcate Aubl[/i]. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers.[br/]Results. Despite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of differentiation for these outliers are compatible with scenarios of strong divergent selection
ISSN: 1932-6203

hal-01204220
https://hal.archives-ouvertes.fr/hal-01204220
https://hal.archives-ouvertes.fr/hal-01204220/document
https://hal.archives-ouvertes.fr/hal-01204220/file/journal.pone.0121394.PDF
PRODINRA : 287494

Éditeur(s) : HAL CCSD Wiley
Résumé : The routes through which Norway spruce recolonized the Alps after the last ice age were investigated at the genetic level. Seven populations along the Alpine range plus one Apennine population were characterized for seven sequence-characterized amplified region (SCAR) loci, detecting an overall FST = 0.118. This rather high value for forest species reflects an uneven distribution of genetic variability, and was analysed through different statistical methods. Alternative hypotheses were tested under the isolation-by-distance model and using the analysis of molecular variance (amova) frame. We conclude that the hypothesis of the existence of a glacial refugium in the Apennines should be rejected, while a putative relict population is identified in the Maritime Alps. The Alpine range of Norway spruce appears to be split in two parts across a north-south line. The results are discussed in comparison with data based on morphological markers, isozymes, chloroplast microsatellites and mitochondrial markers.
ISSN: 0962-1083

hal-01031243
https://hal.archives-ouvertes.fr/hal-01031243
DOI : 10.1046/j.1365-294x.2000.00911.x

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The Western Indian Ocean harbors one of theworld’s most diverse marine biota yet is threatened byexploitation with few conservation measures in place.Primary candidates for conservation in the region are theScattered Islands (Iles Eparses), a group of relativelypristine and uninhabited islands in the MozambiqueChannel. However, while optimal conservation strategiesdepend on the degree of population connectivity amongspatially isolated habitats, very few studies have beenconducted in the area. Here, we use highly variablemicrosatellite markers from two damselfishes (Amphiprionakallopisos and Dascyllus trimaculatus) with differing lifehistory traits [pelagic larval duration (PLD), adult habitat]to compare genetic structure and connectivity among theseislands using classic population structure indices as well asBayesian clustering methods. All classical fixation indexesFST, RST, G0ST, and Jost’s D show stronger genetic differentiationamong islands for A. akallopisos compared to D.trimaculatus, consistent with the former species’ shorterPLD and stronger adult site attachment, which may restrictlarval dispersal potential. In agreement with these results,the Bayesian analysis revealed clear genetic differentiationamong the islands in A. akallopisos, separating the southerngroup (Bassas da India and Europa) from the center(Juan de Nova) and northern (Iles Glorieuses) islands, butnot for D. trimaculatus. Local oceanographic patterns suchas eddies that occur along the Mozambique Channel appearto parallel the results reported for A. akallopisos, but suchfeatures seem to have little effect on the genetic differentiationof D. trimaculatus. The contrasting patterns ofgenetic differentiation between species within the samefamily highlight the importance of accounting for diverselife history traits when assessing community-wide connectivity,an increasingly common consideration in conservationplanning.
ISSN: 0722-4028

hal-01561992
https://hal-univ-perp.archives-ouvertes.fr/hal-01561992
DOI : 10.1007/s00338-016-1495-z

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : Isozyme markers were used to characterize levels of diversity, genotypic structure and spatial genetic structure for the low-density tree species, Carapa procera (five adults per ha), within 300 ha of a continuous tropical rain forest stand. Both seed and adult stages were investigated, a high level of genetic diversity being found in both. Fixation indices showed excess homozygosity in seeds, and excess heterozygosity in adults, which might be caused by selection in favour of heterozygotes. Autocorrelation analysis of the spatial distribution of genotypes revealed no significant pattern in adults or in seeds before dispersal, and there was a high variability in correlogram shapes among alleles. This suggests that gene flow is extensive in C. procera, probably mainly through long-distance pollen dispersal, as seed dispersal is expected to be rather limited in this species (maximum distances of about 50 m). No clear-cut spatial pattern was observed in pollen allele frequencies, which supports the hypothesis of extensive pollen flow. This overall lack of structure is consistent with the data already available on the mating system of this predominantly outcroissing species.
ISSN: 0018-067X

hal-01032057
https://hal.archives-ouvertes.fr/hal-01032057
DOI : 10.1038/hdy.1997.124

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Microbial genetic diversity is often investigated via the comparison of relatively similar 16S molecules through multiple alignments between reference sequences and novel environmental samples using phylogenetic trees, direct BLAST matches, or phylotypes counts. However, are we missing novel lineages in the microbial dark universe by relying on standard phylogenetic and BLAST methods? If so, how can we probe that universe using alternative approaches? We performed a novel type of multi-marker analysis of genetic diversity exploiting the topology of inclusive sequence similarity networks. Results: Our protocol identified 86 ancient gene families, well distributed and rarely transferred across the 3 domains of life, and retrieved their environmental homologs among 10 million predicted ORFs from human gut samples and other metagenomic projects. Numerous highly divergent environmental homologs were observed in gut samples, although the most divergent genes were over-represented in non-gut environments. In our networks, most divergent environmental genes grouped exclusively with uncultured relatives, in maximal cliques. Sequences within these groups were under strong purifying selection and presented a range of genetic variation comparable to that of a prokaryotic domain. Conclusions: Many genes families included environmental homologs that were highly divergent from cultured homologs: in 79 gene families (including 18 ribosomal proteins), Bacteria and Archaea were less divergent than some groups of environmental sequences were to any cultured or viral homologs. Moreover, some groups of environmental homologs branched very deeply in phylogenetic trees of life, when they were not too divergent to be aligned. These results underline how limited our understanding of the most diverse elements of the microbial world remains, and encourage a deeper exploration of natural communities and their genetic resources, hinting at the possibility that still unknown yet major divisions of life have yet to be discovered.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01257771
http://hal.upmc.fr/hal-01257771
http://hal.upmc.fr/hal-01257771/document
http://hal.upmc.fr/hal-01257771/file/s13062-015-0092-3.pdf
DOI : 10.1186/s13062-015-0092-3

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : 4 pages
International audience
This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba.
ISSN: 1755-098X

hal-00823716
https://hal.archives-ouvertes.fr/hal-00823716
DOI : 10.1111/1755-0998.12095
PUBMED : 23521844

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
Microsatellite markers were developed for the coral reef fish Chaetodon vagabundus using shotgun pyrosequencing. As threats to coral reefs intensify, information on larval connectivity is of increasing value for efficient conservation planning. Here, 11 novel microsatellites were characterized for 192 individuals from Papua New Guinea. The number of alleles per locus ranged from 7 to 32, while observed and expected heterozygosity values varied from 0.214 to 0.903. These markers will be used to study population structure and larval connectivity of this iconic coral reef fish in coral reefs across the Indo-Pacific.
ISSN: 1877-7252

hal-01136139
https://hal.archives-ouvertes.fr/hal-01136139
DOI : 10.1007/s12686-015-0440-8

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé :  
South American leaf blight caused by the ascomycete Microcyclus ulei is the most harmful disease of the rubber tree in Latin America and a potential threat to Asiatic and African natural rubber production. Until now, the variability of this fungus was assessed through observation of pathogenicity of isolates on a range of rubber tree clones with known resistance reactions. The present study describes the process used to design 11 microsatellite markers and evaluates their usefulness in detecting genetic polymorphism. Nine of these markers were polymorphic among six isolates from Brazil (with two to three alleles per locus) and five markers were polymorphic among four isolates from French Guiana (with two to four alleles per locus).
ISSN: 1471-8278

hal-01032087
https://hal.archives-ouvertes.fr/hal-01032087
DOI : 10.1111/j.1471-8286.2004.00589.x

Résumé : Le maintien de ressources génétiques suffisamment larges est nécessaire pour assurer la viabilité et le potentiel évolutif des populations naturelles. Cette thèse a le principal objectif de caractériser la diversité et la variabilité génétique chez le genre Virola (Myristicaceae) pour décrire les processus évolutifs qui en sont à l'origine. Premièrement,une étude de la régénération d'un échantillonnage exhaustif de V. michelii a été menée dans une parcelle du dispositif expérimental de Paracou ayant subi une exploitation forestière de faible intensité et comparée à une parcelle témoin. La diversité génétique mesurée à partir de marqueurs AFLP (Amplified Fragment-Length Polymorphism, N=229) en zones perturbées s'est révélée être plis grande qu'en zone non-perturbées. Puis, l'adaptation locale a été étudiée à travers ces mêmes individus et certains loci (AFLP) montrent une sélection divergente pour des environnements contrastés, indiquant un signe d'adaptation. Enfin, l'étude des niveaux de divergence génétique chez trois espèces de Virola du bouclier guyanais (V. michelii, V. surinamensis et V. kwatae) montrent que deux d'entre elles (V. surinamensis et V. kwatae) montrent de fortes similarités génétiques malgré leur distribution sur des environnements contrastés. des Flux de gènes intersécifiques ont été mis en évidence chez ces deux espèces-soeurs et l'hypothèse d'une spéciation écologique est avancée. Ce travail a permis d'aborder différents processus évolutifs à l'origine de la diversité génétique actuelle chez ces espèces forestières tropicales et peut fournir une contribution pour appréhender le devenir des populations.
Genetic diversity is an essential component of biodiversity. The maintenance of sufficient genetic resources is needed to ensure the adaptive potential and the viability of natural populations. In the current context of global changes, the study of adaptation in living organisms is a key task, particularly for tropical forest trees that are dominant components (in terms of biomass and as ecological drivers) of some of the most diverse ecosystems on Earth. The main objective of this thesis is to characterize genetic diversity and genetic variability to understand the evolutionary processes that act on them. This ecological-genetic study was carried out at the interspecific and intraspecific level in the Virola genus.If overall high levels of genetic diversity are a guarantee of prosperity for the future of the species, it seems essential to perform studies on the impact of environmental disturbance on genetic diversity. In the first section, the genetic consequences of regeneration dynamics were studied in an exhaustive sample of V. michelii in a low-intensity logging plot and in a control plot at the Paracou experimental site. A greater genetic diversity, measured from AFLP markers (Amplified Fragment Length Polymorphism, N = 229), was found in perturbed areas. Because studying genetic diversity within species may be useful for understanding species adaptation to environmental changes, in the second section. I studied local adaptation in a population of V. michelii on the Paracou experimental site. A genome scan approach with AFLPs (N = 229) was conducted on 77 adult individuals and 401 juveniles to identify genetic differences between populations associated to contrasting conditions for an array of environmental variables. Some loci (N = 2) were found to be subject to divergent selection, indicating adaptation to contrasting habitats.In the third section, the study of levels of genetic divergence in three Virola species of the Guiana Shield (V. michelii, V. surinamensis and V. kwatae) was investigated for nuclear and chloroplast molecular markers. V. surinamensis and V. kwatae showed strong genetic similarities despite their contrasting habitats preferences. Coalescent analyses have revealed, on one hand, a recent divergence between these two species suggesting an ecological speciation, and one the other hand that interspecific gene flow occurs between these sister-species.This work focuses on understanding evolutionary processes shaping genetic diversity and provides a useful contribution for biodiversity conservation programs.

http://www.theses.fr/2011AGUY0480/document

Éditeur(s) : HAL CCSD Wiley
Résumé : Genetic variation is generally considered a prerequisite for adaptation to new environmental conditions. Thus the discovery of genetically depauperate but geographically widespread species is unexpected. We used 12 paternally inherited chloroplast microsatellites to estimate population genetic variation across the full range of an emblematic circum-Mediterranean conifer, stone pine (Pinus pinea L.). The same chloroplast DNA haplotype is fixed in nearly all of the 34 investigated populations. Such a low level of variation is consistent with a previous report of very low levels of diversity at nuclear loci in this species. Stone pine appears to have passed through a severe and prolonged demographic bottleneck, followed by subsequent natural- and human-mediated dispersal across the Mediterranean Basin. No other abundant and widespread plant species has as little genetic diversity as P. pinea at both chloroplast and nuclear markers. However, the species harbors a nonnegligible amount of variation at adaptive traits. Thus a causal relationship between genetic diversity, as measured by marker loci, and the evolutionary precariousness of a species, cannot be taken for granted
ISSN: 0014-3820

hal-01032062
https://hal.archives-ouvertes.fr/hal-01032062
DOI : 10.1111/j.1558-5646.2007.00294.x

Éditeur(s) : Elsevier
Résumé : The Latin American shrimp Litopenaeus stylirostris was introduced in three different Pacific islands (Tahiti, New Caledonia via Tahiti, and Hawaii) and hatchery-propagated for 7-25 generations to develop shrimp farming based on these domesticated stocks. Three microsatellite markers have been used in an attempt to assess the genetic bases of the populations available to start a selective breeding program. The comparison of eight hatchery stocks (five New Caledonian, two Hawaiian and one Tahitian stocks) and one wild Ecuadorian population showed a much lower variability in the domesticated stocks than in the wild population, especially in New Caledonia and Tahiti (2-3.7 vs. 14-27 alleles per locus; 20-60% vs. 90% expected heterozygosity). The Tahitian and the New Caledonian stocks share the same alleles, suggesting that the loss of alleles occurred during the common past of these populations. On the contrary, New Caledonian and Hawaiian populations share only one common allele at the three loci studied. Although the low genetic variability and the resulting inbreeding of the New Caledonian stocks do not seem to affect their present performance, the results of this study demonstrate the usefulness of the introduction of new stocks in order to increase the potential responses to new controlled or uncontrolled selective pressures. The introduction in New Caledonia of the Hawaiian domesticated stocks, which would provide the local shrimp industry with 40% of the allelic diversity of the species, is advised and preferred to the one of wild animals in order to take advantage (i) of the spontaneous selection which occurred during domestication and (ii) of their favourable sanitary "specific pathogen free" status (no presence of four viruses: WSV, YHV, IHHNV, TSV) which limits the risk of introduction of pathogens.
La crevette d'Amérique latine Litopaenus stylirostris a été introduite dans trois îles du Pacifique (à Tahiti, en Nouvelle-Calédonie via Tahiti, et à Hawaii), et a été ensuite reproduite en écloserie pendant 7 à 25 générations à des fins d'aquaculture. Trois marqueurs microsatellites ont été utilisés pour évaluer les bases génétiques des populations disponibles pour le démarrage d'un programme d'amélioration génétique. L'étude comparative de 8 populations domestiquées (cinq néo-calédoniennes, deux hawaiiennes et une tahitienne) et d'une population sauvage d'Equateur révèle une variabilité très réduite dans les populations d'élevage, en particulier en Nouvelle-Calédonie et à Tahiti (2 à 3.7 allèles par locus au lieu de 14 à 27 en population sauvage ; 20% à 60% d'hétérozygotie au lieu de 90%). Les souches tahitiennes et calédoniennes disposent des mêmes allèles, ce qui suggère que la perte d'allèles a eu lieu lors de l'histoire commune des ces populations. A l'inverse, les populations néo-calédoniennes et hawaiiennes n'ont en commun qu'un seul allèle sur les 3 locus étudiés. Bien que la très faible variabilité génétique du cheptel calédonien ne semble pas affecter ses performances actuelles, les résultats de cette étude démontrent l'utilité de l'introduction de variabilité afin d'augmenter la capacité de réponse à de nouvelles pressions de sélection (contrôlées ou non). L'introduction des souches hawaiiennes en Nouvelle-Calédonie qui permettrait à la filière locale de disposer de 40% de la diversité allélique de l'espèce) est préconisée de préférence à celle d'animaux sauvages afin de bénéficier (i) de la sélection spontanée qu'elles ont subi lors de leur domestication et (ii) de leur statut sanitaire « specific pathogen free, SPF » (absence de 4 virus : WSV, YHV, IHHNV, TSV) qui limite les risques de transferts de pathogènes.
Aquatic Living Resources (0990-7440) (Elsevier), 2003-12 , Vol. 16 , N. 6 , P. 501-508

Droits : 2003 Published by Elsevier, Paris.
http://archimer.ifremer.fr/doc/2003/publication-596.pdf
DOI:10.1016/j.aquliv.2003.07.001
http://archimer.ifremer.fr/doc/00000/596/