Éditeur(s) : HAL CCSD SpringerLink
Résumé : Trinucleotide microsatellites have proven to be the markers of choice in human genetic analysis because they are easier to genotype than dinucleotides. Their development can be more time-consuming due to their lower abundance in the genome. We isolated trinucleotide microsatellites in Norway spruce (Picea abies K.) using an enrichment procedure for the genomic-library construction. Here we report on the characterisation of 85 ATC microsatellite-containing clones, from which 39 markers were developed. Many of the clones showed the occurrence of tandem repeats of higher order than the trinucleotide ones, often resembling minisatellite repeats. The sequencing of a sample of the alleles at one of the loci revealed size homoplasy due to base substitutions within the microsatellite region. The presence of ATC motifs within repetitive sequence families was observed. We found a significant relationship between the level of polymorphism and the length of the microsatellite. The levels of variability for ATC trinucleotide markers were lower than those for dinucleotides, both when tested on all loci in a set of six individuals and on a subset of loci in four natural populations. This difference is most likely attributable to lower mutation rates for trinucleotide than for dinucleotide loci. The availability of markers with different mutation rates allows one to select the proper marker set to investigate population processes on different time scales.
Theoretical and Applied Genetics

hal-01032029
https://hal.archives-ouvertes.fr/hal-01032029
DOI : 10.1007/s00122-002-0986-1

Éditeur(s) : Université de la Réunion
Résumé : The green turtle (Chelonia mydas) is an emblematic species of marine life. However, nowadays it is subject to many threats (poaching, by-catch). Even if there is deep growing measures for its protection, the green turtle still is an endangered species and it is listed in Appendix I of Washington Convention (CITES). In order to elaborate efficient conservation and management plans, perfect knowledge of green turtle biology, but also of its population structure and their characteristics, are needed. In this thesis, we have assessed genetic structure of green turtle populations in the South-Western Indian Ocean by using genetic tools. In all, 1551 tissue samples have been collected from our study zone and from our control site French Polynesia (37 samples). All kinds if individuals were sampled (except males in reproductive phase) from 15 sampling sites including nesting, foraging, and immature development site. We used both control region of mitochondrial DNA and 6 microsatellite loci to better infer maternal and paternal lineages. We identified 29 haplotypes in the South-Western Indian Ocean. They are distributed in 3 independent and highly divergent clades, including one composed with haplotypes from Atlantic Ocean. For 7 of these haplotypes, it was the first time they were detected in the study zone. Fifteen haplotypes were previously undescribed, distributed in all the 3 clades. These new haplotypes seem to be specific to the South-Western Indian Ocean, which is then an original zone. Besides, we found a high allelic richness. These results show the South-western Indian Ocean is rich and very diversified. This region plays an important role in the global diversity of the species. The South-Western Indian Ocean is one of the two contact zones presently known between the two metapopulations of green turtles (Atlantic-Mediterranean and Indo-Pacific). This contact induces a genetic cline based on CM8 (Atlantic) and C3 (Indo-Pacific) haplotype frequencies. Analysis of the microsatellite differentiation between individuals provides evidence of genetic exchanges between the two metapopulations in the region. The South-Western Indian Ocean participates to green turtle global genetic mixing. Studying the influence of several intrinsic and extrinsic factors on population structuring provides useful information for management plan elaboration. We found no significant difference between genetic structures of foraging females and males, contrary to immature turtles which seem to be organised in 'regional pools'. This organisation could be due to both immature natal homing and influence of oceanic currents. High mitochondrial differentiation of nesting females and low global microsatellite differentiation of our samples indicate male-mediated gene flow among populations of the study zone. The genetic composition of a sampling site presents no significant variation along the year, even if we could notice some trends. Nevertheless, it can be significantly different from a year to an other one. This may result from alternation of distinct populations on the same site. We noticed different evolution in 10 or 20 years of the genetic composition depending on the sampling site. Geographic distance seems not to have significant influence on population structuring concerning microsatellite markers. Nesting females of Saziley Beach (Mayotte Island, Comoros Archipelago) present genetic divergence from females nesting in the two other sampled beaches of this island. The observed population structure shows no contradiction with the organisation of oceanic currents in the South-Western Indian Ocean. Comparing the results from the two genetic markers used, we identified 8 genetic differentiated clusters of turtles in the study zone and at least 6 distinct populations. These clusters constitute 8 potential management units (MUs) which could serve as basis in the elaboration of conservation and management plans.
La tortue verte (Chelonia mydas) constitue l'un des espèces emblématiques de la vie marine, pourtant de nombreuses menaces pèsent de nos jours encore sur sa survie (braconnage, captures accidentelles). Ainsi, malgré l'essor de mesures de protection menées à travers pour sa sauvegarde, la tortue verte constitue une espèce 'en danger d'extinction' et figure dans l'Annexe I de la Convention de Washington (CITES). Afin d'élaborer des plans de gestion et de conservation qui soient efficaces, il est important d'avoir une parfaite connaissance de la biologie de la tortue verte, mais aussi de la structure de ses populations et de leurs caractéristiques. C'est dans ce cadre que s'inscrit la présente étude. L'objectif de cette étude était d'acquérir des connaissances sur la structure des populations de tortues vertes dans le sud-ouest de l'océan Indien grâce à l'utilisation de l'outil génétique. Au total, 1551 échantillons de tissu ont été collectés dans la zone d'étude et dans notre site témoin la Polynésie française (37 échantillons). Toutes les catégories d'individus ont été échantillonnées (excepté les mâles en phase de reproduction) et les 15 sites d'échantillonnage comprennent à la fois des sites de ponte, d'alimentation et de développement pour les immatures. Deux types de marqueurs ont été utilisés : la région contrôle de l'ADN mitochondrial et 6 loci microsatellites, afin d'appréhender au mieux l'apport des lignées maternelles et paternelles. Nous avons pu mettre en évidence la présence dans le sud-ouest de l'océan Indien de 29 haplotypes distincts, appartenant à trois clades fortement divergents dont l'un constitué d'haplotypes originaires de l'océan Atlantique. Parmi ces haplotypes, 7 ont été détectés pour la première fois dans la zone d'étude, et 15 autres n'ont jamais été précédemment décrits chez cette espèce. Ils sont présents dans chacun des 3 clades d'haplotypes. Ces nouveaux haplotypes semblent spécifiques à la région, et en font une zone originale. On observe par ailleurs une grande richesse allélique dans les effectifs analysés. Ces résultats montrent que le sud-ouest de l'océan Indien est une zone riche et très diversifiée. Cette région joue un rôle important dans la diversité génétique globale de l'espèce. Le sud-ouest de l'océan Indien constitue l'une des deux seules zones connues à l'heure actuelle de contact entre les deux métapopulations de tortues vertes (Atlantique-Méditerranée et Indo-Pacifique). Ce contact a entraîné la formation d'un cline génétique portant principalement sur les fréquences relatives des haplotypes CM8 (Atlantique) et C3 (Indo-Pacifique). Les résultats obtenus lors de l'analyse microsatellite de la différenciation entre les individus originaires des deux métapopulations montrent que le sud-ouest de l'océan Indien constitue une zone d'échanges génétiques entre les deux métapopulations, participant au brasage génétique de l'espèce. L'étude de facteurs, intrinsèques et extrinsèques, pouvant influencer la structuration des populations apportent de nombreuses informations qui pourraient s'avérer utiles lors de l'élaboration de plans de gestion. La structure des femelles et des mâles en alimentation ne diffère pas, contrairement à celle des immatures qui semble s'organiser en 'pools régionaux' qui seraient le fruit de l'interaction d'un comportement de philopatrie et d'une influence des courants océaniques. La forte différenciation mitochondriale des femelles en ponte et la très faible différenciation microsatellite observée à l'échelle de la région, indiquent l'existence de flux de gènes via les mâles. La composition génétique d'un site ne varie pas de manière significative au cours de l'année. Par contre, elle peut varier d'une année à l'autre, signifiant l'alternance dans certains sites de ponte de plusieurs populations distinctes. L'évolution de la composition génétique d'un groupe, au cours de 10 ou 20 ans, diffère selon le site considéré. La distance ne semble pas influencer de manière significative la structuration des populations au niveau microsatellite. Les femelles en ponte sur la plage de Saziley (Mayotte) diffèrent génétiquement de celles pondant sur les deux autres plages de l'île. La structure observée des populations est en accord avec l'organisation des courants océanique dans la région. La confrontation des résultats obtenus à partir des deux marqueurs génétiques utilisés, permet la détermination de 8 ensembles génétiquement différenciés dans la zone d'étude et l'identification d'au moins 6 populations distinctes. Ces ensembles constituent autant d'unités de gestion (MUs) potentielles qui pourront servir de base à l'élaboration de plans de gestion et de conservation.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-3532.pdf
http://archimer.ifremer.fr/doc/00000/3532/

Éditeur(s) : HAL CCSD Elsevier
Résumé : We report a preliminary analysis on the relationships between drainage basin structure and genetic structure of populations of the European vector of fasciolosis, Galba truncatula. In the study area, 251 snails belonging to 12 populations were collected along different ditches of a same river network. Each snail was genotyped at six variable microsatellite loci. Our results show that all sample sites are characterized by a low level of polymorphism and a very high and significant heterozygote deficiency. Our data reveal a significant genetic differentiation, even at a small scale, and failed to delimit clear patterns of isolation by euclidian distance. Our study shows that genetic differentiation significantly increases with hydrographic distance along the streams (p < 0.002), in consistence with the hypothesis that dispersion along the stream is dependent on the direction of water flow. This study shows that relationships can exist between the organization of the hydrological network and population biology of a disease vector, which has strong potential applications to drainage network management issues.
ISSN: 1567-1348

hal-00496374
https://hal.archives-ouvertes.fr/hal-00496374
DOI : 10.1016/j.meegid.2010.01.005

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
Centropyge bispinosa is one of the most frequently coral reef fish exported through the aquarium trade. We developed fifteen microsatellite markers to evaluate possible distinct breeding stocks throughout its Indo-Pacific distribution range. Number of alleles varied from 2 to 50 per locus, observed and expected heterozygosities ranged from 0.486 to 0.953 and 0.482 to 0.974 respectively. Significant deviations from HWE were detected in two loci. Cross-amplifications were tested in four congener species: C. loriculus, C. bicolor, C. flavissima and C. vroliki. The 15 new microsatellite loci will be helpful tools for the identification of breeding units, connectivity studies, as well as phylogenetic relationships among pygmy angelfishes.
ISSN: 1877-7252

hal-01341716
https://hal-univ-perp.archives-ouvertes.fr/hal-01341716
DOI : 10.1007/s12686-014-0363-9

Éditeur(s) : Institut national agronomique Paris Grignon
Résumé : The flat oyster Ostrea edulis L. is the indigenous oyster of the Atlantic as well as the Mediterranean coasts of Europe. Its commercial exploitation dates back to Antiquity but its breeding is now threatened by two parasitic protozoa, among which Bonamia ostreae. Various aspects of the genetics of this species' natural and farmed populations have been studied with the aid of microsatellite markers. At first, the implementation and the screening of two partial genomic libraries made it possible to identify 28 new microsatellite loci. Analysis of the segregation of 12 of these loci and of two enzymatic loci shows that most microsatellite loci are transmitted in a Mendelian way, but some loci have significant segregation distortions. Moreover, seven linkage groups, of which four contain at least two markers, were identified in Ostrea edulis. The genetic variability of three populations selected for one or two generations for resistance to Bonamia ostreae was analysed with the aid of 5 microsatellite loci. In spite of the absence of genealogical data, we have shown that these selected populations were descended from a very low number of founding genitors (from 3 to 15 depending on the population) and for two populations, we were able to reconstruct the genealogy and the relationships between the individuals were identified. These selected populations have, in addition to a very low genetic variability, real and at times high levels of consanguinity. These results have a significant implication for the continuation of the selection programme (consanguinity management, augmentation of genetic variability by introducing wild genitors). The geographical structuring of the genetic variability of natural populations of Ostrea edulis has been analysed with the aid of 5 microsatellite loci on a sampling covering almost the entire distribution area of the species (from Norway to the Adriatic Sea). The results are consistent with those published in the literature and using enzymatic markers. The populations show a low level of differentiation that could correspond to a model of isolation by distance. The Atlantic populations, which have a reduced polymorphism, could be descended from post-glacial recolonisation from Mediterranean populations that had survived the glaciations of the Quaternary Period. The current distribution of flat oyster populations is surely also subject to anthropogenic activities. Finally, the genetic bases of the heterozygosis-growth correlation were studied in a natural population with the aid of enzymatic and microsatellite markers. Although leads favouring the direct contribution of enzymatic loci have been found, biases in the sampling design make it impossible to come to a formal conclusion. However, this study has made it possible to show that the capture of individuals over a short period (around ten days) leads to a sampling of a population descended from a very low number of founding genitors, in contradiction with the generally accepted idea that marine bivalve populations are large panmictic populations with significant, efficient numbers. These results confirm in a natural population the observations of a significant reduction of efficient sizes in hatchery populations.
L'huître plate Ostrea edulis L. est l'huître indigène des côtes européennes aussi bien atlantiques que méditerranéennes. Son exploitation commerciale remonte à l'Antiquité mais son élevage est aujourd'hui menacé par deux protozoaires parasites dont Bonamia ostreae. Différents aspects de la génétique des populations naturelles et cultivées de cette espèce ont été étudiés à l'aide de marqueurs microsatellites. Dans un premier temps, la réalisation et le criblage de deux banques génomiques partielles ont permis l'identification de 28 nouveaux locus microsatellites. L'analyse de la ségrégation de 12 de ces locus et de deux locus enzymatiques montre que la plupart des locus microsatellites sont transmis de façon mendélienne, mais certains locus présentent des distorsions de ségrégation importantes. Par ailleurs, sept groupes de liaison dont quatre contiennent au moins deux marqueurs ont été identifiés chez Ostrea edulis. La variabilité génétique de trois populations sélectionnées depuis une ou deux générations pour une résistance à Bonamia ostreae a été analysée à l'aide de 5 locus microsatellites. Malgré l'absence de données généalogiques, nous avons montré que ces populations sélectionnées étaient issues d'un très faible nombre de géniteurs fondateurs (de 3 à 15 selon les populations) et pour deux populations, la généalogie a pu être reconstituée et les liens de parenté entre les individus ont été identifiés. Ces populations sélectionnées présentent, outre une très faible variabilité génétique, des niveaux de consanguinité réels et parfois élevés. Ces résultats ont une implication importante pour la continuation du programme de sélection (gestion de la consanguinité, augmentation de la variabilité génétique par introduction de géniteurs sauvages). La structuration géographique de la variabilité génétique des populations naturelles d'Ostrea edulis a été analysée à l'aide de 5 locus microsatellites sur un échantillonnage couvrant presque toute l'aire de répartition de l'espèce (de la Norvège à la Mer Adriatique). Les résultats sont cohérents avec ceux publiés dans la littérature et utilisant des marqueurs enzymatiques. Les populations montrent un niveau de différenciation faible qui pourrait correspondre à un modèle d'isolement par la distance. Les populations atlantiques, qui présentent un polymorphisme réduit, pourraient être issues de recolonisation post-glaciaire à partir de populations méditerranéennes ayant survécu aux glaciations du Quaternaire. La répartition actuelle des populations d'huître plate est certainement aussi soumise aux actions anthropiques. Enfin, les bases génétiques de la corrélation hétérozygotie-croissance ont été étudiées dans une population naturelle à l'aide de marqueurs enzymatiques et microsatellites. Bien que des pistes en faveur de la contribution directe des locus enzymatiques aient été trouvées, des biais dans le dispositif expérimental ne permettent pas de conclure de façon formelle. Cependant, cette étude a permis de montrer que le captage d'individus sur une faible période (une dizaine de jours) conduit à l'échantillonnage d'une population issue d'un nombre très réduit de géniteurs fondateurs, en contradiction avec l'idée reçue que les populations de bivalves marins sont de larges populations panmictiques à effectif efficace important. Ces résultats confirment dans une population naturelle les observations de réduction importante des tailles efficaces dans des populations d'écloserie.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1998/these-1919.pdf
http://archimer.ifremer.fr/doc/00000/1919/

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) : Elsevier
Résumé : Genetic variation was surveyed at 11 microsatellite loci and at 517 bp of the mitochondrial control region to investigate the presence of genetic stock structure in swordfish (Xiphias gladius) in four proximal localities of the southwest Indian Ocean. One aim of this study was to serve as a preliminary examination for congruency of structure detected by these two genetic markers, prior to conducting a more comprehensive basin-wide survey of the Indian Ocean and nearby surrounding areas. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences both revealed a great homogeneity between samples. Genetic diversity detected at the regional scale was not significantly higher than detected at the local scale. Results suggest that the southwest Indian Ocean globally functions as a unique panmictic population. However, some discrete genetic differences appeared that could possibly indicate influence from a second genetic pool in the northern part of the Indian Ocean. This structure appeared to be sex-dependent with genetic differences higher among female than among male samples. This result may indicate a higher level of spawning area fidelity for females with a subsequent sampling bias tending to homogenise male genotypic distributions. (c) 2009 Elsevier B.V. All rights reserved.
Fisheries Research (0165-7836) (Elsevier), 2009-05 , Vol. 97 , N. 3 , P. 263-269

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6455.pdf
DOI:10.1016/j.fishres.2009.03.004
http://archimer.ifremer.fr/doc/00000/6455/

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) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next-generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.
ISSN: 1755-098X

hal-01544754
https://hal.archives-ouvertes.fr/hal-01544754
DOI : 10.1111/1755-0998.12467

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
With the development of genetics methods, it becomes possible to study the population structure and some aspects of the reproductive behaviour of endangered sharks. Here we describe the isolation of 20 polymorphic microsatellite markers in the bull shark Carcharhinus leucas (Carcharhinidae) and their characteristics. Two to 10 alleles per locus were detected. Observed and expected heterozygosities ranged from 0.00 to 0.78 and from 0.05 to0.80, respectively. Four markers showed deviations from Hardy–Weinberg equilibrium; among them, three showed presence of null alleles. No linkage disequilibrium was detected among any of the loci. Moreover, four, 11 and 19 of these 20 markers successfully cross-amplified in the tiger shark Galeocerdo cuvier, the sandbar shark Carcharhinus plumbeus and the dusky shark Carcharhinus obscurus, respectively.
ISSN: 1877-7252

hal-01253773
https://hal.archives-ouvertes.fr/hal-01253773
https://hal.archives-ouvertes.fr/hal-01253773/document
https://hal.archives-ouvertes.fr/hal-01253773/file/Pirog%20et%20al.%20-%202015%20-%20Isolation%20and%20characterization%20of%2020%20microsatellit_hal.pdf
DOI : 10.1007/s12686-014-0308-3

Éditeur(s) : HAL CCSD
Résumé : Diffusion du document : INRA Antilles-Guyane, UMR ECOFOG, 97387 Kourou, Guyane (France)Diplôme : Master Recherche
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
Cette étude s’inscrit dans le cadre d'un projet intitulé «Impact du degré d'exploitation sur la biodiversité ». Ici, nous avons analysé l'effet de cette perturbation sur les caractéristiques démo-génétiques d’une espèce forestière héliophile Jacaranda copaia. Nous avons travaillé sur quatre parcelles (chacune de 6,25 ha) du dispositif de Paracou, dont une parcelle témoin et trois parcelles à degré d'exploitation croissant. Un échantillonnage exhaustif de tous les arbres appartenant à l'espèce a été réalisé sur les quatre parcelles, La population se répartit en deux groupes : les adultes ayant potentiellement participé à la régénération (DBH > 10 cm ; N = 133) et les juvéniles issus de la régénération (DBH < 10 cm). Ces derniers sont séparés en deux sous-groupes selon leur position : dans les trouées d'exploitation (N = 564) ou hors des trouées d'exploitation (N = 127). A l’aide de quatre marqueurs microsatellites SSR. Nous avons donc comparé la diversité génétique, le coefficient de consanguinité, la différenciation, le déséquilibre génotypique et la proximité génétique des individus en fonction de la distance spatiale (auto corrélation génétique spatiale). Les résultats ainsi obtenus ne montrent pas d'effet de l’exploitation sur la diversité génétique globale. Cependant celle-ci est plus structurée dans l'espace et se traduit par une consanguinité plus forte. La présence de déséquilibres génotypiques et une répartition en agrégats des juvéniles présents dans les trouées d’exploitation. Ceci pourrait s’expliquer par une contribution inégale des adultes à la régénération dans les zones exploitées mais il faudra cependant tenter d’expliquer quels en sont les mécanismes et comment interagissent-ils avec les caractéristiques écologiques de l’espèce.
https://hal.archives-ouvertes.fr/hal-01189281

hal-01189281
https://hal.archives-ouvertes.fr/hal-01189281
PRODINRA : 22898

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a similar to 6-km transect, to evaluate dispersal ability, and between paired bank populations along a similar to 65-km stretch of the Approuague river, to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale, and conclude that the species has a restricted dispersal ability that is probably tied to its life-history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river, and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is the result of restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life-history traits comparable with A. andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 356373.
ISSN: 0024-4066

hal-01032422
https://hal.archives-ouvertes.fr/hal-01032422
DOI : 10.1111/j.1095-8312.2012.01871.x

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) : 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) : 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 Elsevier
Résumé : International audience
A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and tem perate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylo genies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms.
ISSN: 1055-7903

hal-01359407
https://hal.archives-ouvertes.fr/hal-01359407
https://hal.archives-ouvertes.fr/hal-01359407/document
https://hal.archives-ouvertes.fr/hal-01359407/file/Postaire-etal2016MolPhylEvol_sp_delim_hydraires_HAL.pdf
DOI : 10.1016/j.ympev.2016.08.013

Éditeur(s) : HAL CCSD Wiley
Résumé :  
Drier periods from the late Pleistocene and early Holocene have been hypothesized to have caused the disappearance of various rainforest species over large geographical areas in South America and restricted the extant populations to mesic sites. Subsequent improvement in climatic conditions has been associated with recolonization. Changes in population size associated with these extinction-recolonization events should have affected genetic diversity within species. However, these historical hypotheses and their genetic consequences have rarely been tested in South America. Here, we examine the diversity of the chloroplast and nuclear genomes in a Neotropical rainforest tree species, Vouacapoua americana (Leguminosae, Caesalpinioideae) in French Guiana. The chloroplast diversity was analyzed using a polymerase chain reaction-restriction fragment length polymorphism method (six pairs of primers) in 29 populations distributed over most of French Guiana, and a subset of 17 populations was also analyzed at nine polymorphic microsatellite loci. To determine whether this species has experienced extinction-recolonization, we sampled populations in areas supposedly not or only slightly affected by climatic changes, where the populations would not have experienced frequent extinction, and in areas that appear to have been recently recolonized. In the putatively recolonized areas, we found patches of several thousands of hectares homogeneous for chloroplast variation that can be interpreted as the effect of recolonization processes from several geographical origins. In addition, we observed that, for both chloroplast and nuclear genomes, the populations in newly recolonized areas exhibited a significantly smaller allelic richness than others. Controlling for geographic distance, we also detected a significant correlation between chloroplast and nuclear population differentiation. This result indicates a cytonuclear disequilibrium that can be interpreted as a historical signal of a genetic divergence between fragmented populations. In conclusion, the spatial genetic structure of contemporary V. americana populations shows evidence that this species has experienced large extinction-recolonization events, which were possibly caused by past climatic change.
ISSN: 0014-3820

hal-01032194
https://hal.archives-ouvertes.fr/hal-01032194
DOI : 10.1111/j.0014-3820.2003.tb01517.x

Éditeur(s) : HAL CCSD SpringerLink
Résumé : The development of microsatellite markers can be a time-consuming process, especially in species such as conifers where many microsatellites have been shown to be associated with the repetitive fraction of the genome and to produce complex banding patterns following electrophoresis. Therefore, procedures to eliminate this fraction from further processing are sought. In this paper, we report on the development of 53 dinucleotide SSR markers in Norway spruce, 35 of which (66%) produce simple, polymorphic patterns. This high efficiency is obtained by introducing a dot-blot selection against high copy number sequences, performed on the microsatellite-containing clones. The resulting markers turned out to be polymorphic and useful for population genetic studies and for linkage mapping. Seven additional markers that were not subject to the dot-blot selection are also presented.
Theoretical and Applied Genetics

hal-01031865
https://hal.archives-ouvertes.fr/hal-01031865
DOI : 10.1007/s00122-001-0843-7

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

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : Four populations of Norway spruce (Picea abies Karst.) were screened using nine nuclear microsatellite markers (three trinucleotides and six dinucleotides) and four chloroplast markers (all mononucleotides). Marker classes were compared for their variability, mutation rate and ability to detect differentiation between stands. Dinucleotide markers proved to be the most variable group and chloroplast stretches the least variable, with differences in mutation rate between the former and the latter spanning over two orders of magnitude. Variability correlated to the number of repeats but not to the absolute length of the microsatellite region. The different marker classes were combined with two different measures of genetic distance in order to investigate the performance of markers and evolutionary models for the study of genetic variation in natural populations of Norway spruce. Weir and Cockeram's F$_{rm ST}$ generally performed better in this clear-cut, four-population model study. Chloroplast haplotypes turned out to be the most sensitive marker system, being able to differentiate populations and to detect differences in genetic variability between sub-regions.
ISSN: 1286-4560

hal-01032048
https://hal.archives-ouvertes.fr/hal-01032048
DOI : 10.1051/forest:2006029