The aim of this PhD study was to gain new insights into the evolutionary history of the Central African rainforests, which are among the most complex and diverse ecosystems on earth. Even today, many questions regarding the underlying dynamics and evolutionary processes shaping that remarkable diversity remain unanswered, since relatively few studies have focused on the vast tropical forests growing in the Congo Basin. Therefore, we applied various molecular approaches to study the levels of genetic diversity and patterns of differentiation within and between population of the tropical tree species Scorodophloeus zenkeri, Staudtia kamerunensis and Prioria balsamifera. In Chapter 2, we conducted a phylogeographic study on the widespread tropical tree Scorodophloeus zenkeri to assess the impact of past forest fragmentation in Central African lowland forests. By applying Bayesian clustering methods, we revealed six intraspecific genetic clusters within the species. The observed genetic discontinuities most likely result from forest fragmentation during the glacial periods of the Pleistocene. Populations in Lower Guinea appeared differentiated from those in Congolia, and both bioregions harboured distinct genetic clusters.In Chapter 3, we developed 16 highly polymorphic microsatellite primers (SSRs) for Staudtia kamerunensis, a timber species for which species-specific genetic markers were lacking. By validating the developed markers in three populations, we demonstrated their usefulness to study gene flow, population structure and spatial distribution of genetic diversity in S. kamerunensis.In Chapter 4, we applied the newly developed SSRs, two nuclear gene markers and a chloroplast marker to search for evolutionary lineages in Staudtia kamerunensis, a species with a complex taxonomical history. Our analyses reveal multiple genetic discontinuities among populations throughout Central Africa, probably resulting from ancient rainforest fragmentation during cold and dry periods in the Pliocene and/or Pleistocene. However, the clear genetic disjunction observed between northern and southern populations in Lower Guinea could correspond to a genetic break between the kamerunensis and gabonensis varieties described in Staudtia kamerunensis.In Chapter 5, we developed two new sets of microsatellite primers (SSRs); 16 primer pairs for Prioria balsamifera and 15 primer pairs for Prioria oxyphylla. Validation of the primers in two populations of each species, as well as the cross-amplification tests, demonstrated the usefulness of the SSRs to study gene flow and spatial genetic structure in African Prioria species, which is needed to prevent genetic erosion and to set up proper conservation guidelines.In Chapter 6, the 16 newly developed microsatellite loci were amplified in individuals of P. balsamifera from Gabon and the Democratic Republic of the Congo, to assess the levels of genetic diversity and intraspecific differentiation. Our analyses show that the genetic diversity in P. balsamifera populations is relatively low, so efforts should be made to prevent further depletion of the gene pool. Bayesian clustering analyses revealed multiple genetic discontinuities throughout the Congo Basin, probably caused by ancient forest fragmentation. The inferred intraspecific clusters show a parapatric distribution, so they can potentially be used to determine the origin of individuals at a regional scale. Additionally, various genetic assignment methods show that the SSR dataset generated in this study can be used as a reference database for Gabon and DR Congo. The general discussion allows us to show similarities in the genetic structures of species that can be interpreted in terms of forest cover history in Central Africa. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The African buffalo (Syncerus caffer) is a member of one of Africa’s most well known tourist attractions and unique grouping of mammals – the ‘big five’. Historical records indicate that during the 19th century approximately 3 million African buffaloes inhabited almost the whole of sub-Saharan Africa. Several factors such as disease, habitat fragmentation, over-hunting and drought reduced the buffalo population to approximately 400 000 by 1990. The African buffalo is host to a variety of sub-acute diseases, such as bovine tuberculosis (BTB), foot-and-mouth disease (FMD) and corridor disease (CD). Disease is an important factor which influenced African buffalo populations throughout the continent and more specifically the Kruger National Park (KNP) and is largely responsible for the fact that buffaloes are restricted to enclosed areas with strict regulations imposed on their movement. The social organization of animals influences the distribution and spread of a disease - especially in the case of the African buffalo in the KNP. The emergence of BTB in the largest conservation area in South Africa (the KNP), threatens wild and domestic animals and humans who are in close proximity to the Park. The potential economic losses associated with this disease are excessive. The results presented in this thesis provide baseline information into the genetic status of sampled African buffaloes in the KNP, genetic relatedness between sampled individuals as well as BTB associations between sampled African buffaloes in the KNP, based on a limited dataset of 181 animals. Twelve microsatellite markers were used to evaluate 181 samples which were collected from 39 locations dispersed throughout the KNP. Specific population genetic parameters revealed information based on the intra and inter - relationships at the ‘per population’ level as well as at the ‘per prevalence group’ level. Evidence indicates a medium to high level of genetic diversity, a low to medium level of inbreeding (inbreeding coefficient (Fis) for each group ranges between 0.143 and 0.147) and a relatively high level of migration for buffaloes associated with each prevalence group. Pairwise relatedness estimates were determined between individuals, to reveal their level of relatedness (unrelated, full siblings, parent-offspring or half siblings), based on Queller and Goodnight’s (1989) coefficient of relatedness. Relatedness was determined on different levels, intra and interpopulation level, BTB infected and BTB uninfected group level as well as prevalence group levels. Evaluation of data based on these different levels and between different groups, painted an overall picture of the disease condition and genetic relatedness within and between sampled BTB infected and BTB uninfected buffaloes. Evidence indicated that the greater majority of our sampled African buffaloes (BTB infected or uninfected), were genetically unrelated (in terms of sibling and parent-offspring relationships), irrespective of their disease status. M. bovis infected buffaloes sampled and used in our study are not more closely related to each other than to uninfected buffaloes in the same population or prevalence group. / Dissertation (MSc)--University of Pretoria, 2010. / Production Animal Studies / unrestricted

<p>  </p> <p>Tar spot is a new foliar disease of corn in the United States. Tar spot was first detected in 2015 and is now among the most important corn diseases in the Midwest. Tar spot is caused by the obligate biotrophic fungus, <em>Phyllachora maydis</em> Maubl, from the genus, <em>Phyllachora </em>which consist of over 1,200 species of host-specific fungi. Due to the recent emergence, studies relating to <em>P. maydis</em> population dynamics in the U.S. are limited. How much genetic diversity, variation, and level of gene flow are occurring within and among these populations? Knowledge of the population dynamics is imperative for understanding the pathogen’s biology, ecology, epidemiology, and management. Currently, no corn hybrid is fully resistant to tar spot. Foliar fungicides are currently the most effective option for disease management, but best practices for fungicide management remain unknown. Better information is needed on fungicide efficacy and fungicide application timing to reduce tar spot severity, protect yield, and increase profitability for Indiana corn growers. </p> <p>This research dissertation presents four chapters to answers those questions and bridge the gaps between the knowns and unknows of this novel corn-<em>Phyllachora maydis</em> pathosystem. <strong>Chapter 1</strong> presents a literature review on tar spot of corn, its economic impact, the causal pathogen, its host, lifecycle, distribution, and known management strategies as a resource for understanding the pathosystem in the U.S. <strong>Chapter 2</strong> examines the genetic population structure, diversity, geneflow and mode of reproduction in Midwest U.S. by employing microsatellite (SSR) markers. <strong>Chapter 3</strong> presents results from multi-year, multi-location, small-plot field trials on the net return of foliar fungicides and fungicide timing on tar spot management in Indiana. Lastly, <strong>Chapter 4</strong> concludes by evaluating of an integrated management strategy for tar spot by examining the integration of tillage, corn hybrids and fungicide application in reducing tar spot severity while protecting yields.</p> <p>Results provided in this research dissertation will be used to guide future studies and provide stakeholders such as researchers, corn growers, extension personnel in academia and industry with valuable information needed to guide effective disease management decisions. </p>

European hazelnut is a significant crop in the Pacific Northwest, and the US ranks 4th internationally for hazelnut production. Production in the Pacific Northwest is threatened, however, by the disease eastern filbert blight (EFB) caused by the fungus Anisogramma anomala (Peck) E. Müller. To meet the challenges faced by the hazelnut industry in Oregon and Washington, the breeding program at Oregon State University has focused on developing DNA marker technology and producing EFB resistant cultivars. This study focused on developing new microsatellite markers from hazelnut transcriptome sequences and on disease resistance from three accessions ('Culpla,' 'Crvenje,' and OSU 495.072) which showed no disease symptoms following a series of inoculations. DNA markers have been useful in hazelnut breeding for marker-assisted selection, construction of genetic linkage maps, cultivar fingerprinting, and phylogeny studies. Previously developed markers include AFLP, RAPD, ISSR, and microsatellite (SSR) markers developed from enriched libraries and ISSR fragments. This study utilized the transcriptome sequence from 'Jefferson' hazelnut to mine for microsatellites, align with the genomic sequence, design primers, screen for polymorphism, and characterize and map polymorphic markers. A total of 1432 microsatellites were mined from the transcriptome sequence, and the most frequently found motifs were AG (35.8%), AT (13.3%), and AAG (12.7%), and 382 primer pairs were designed. Screening showed that 119 markers were polymorphic, and these were characterized on sets of 50 and 14 accessions. Fifty-three markers that segregated in the mapping population or in three alternate populations were mapped and assigned to linkage groups. A dendrogram showed that accessions clustered mostly according to geographic origin. These results confirm the high level of diversity present in hazelnut, and the markers developed in this study will be useful for further genetics studies in hazelnut. The three EFB resistant parents 'Culpla,' 'Crvenje,' and OSU 495.072 were subjected to two inoculation treatments: greenhouse inoculations and exposure under an inoculation structure. The accessions remained free of disease after both treatments. Progeny segregating for resistance were produced. The progeny were inoculated either in the greenhouse or under the structure, and disease response recorded for each individual. DNA was extracted from seedlings, and sets of 32 seedlings from each resistant parent were screened with previously mapped markers using PCR and capillary electrophoresis. All three resistance sources were correlated with marker A614, allowing the resistance loci to be assigned to linkage group (LG) 6. The progeny were then screened with all known microsatellite markers on LG 6, and linkage maps constructed of the marker loci and resistance loci. Markers KG821, LG628, and LG696 are especially close to the resistance loci and will be useful for marker-assisted selection. Although these resistance loci are located in the same region of LG 6 as the 'Gasaway' resistance gene, they are different from 'Gasaway,' and markers linked to resistance will be useful for introgressing and pyramiding resistance in new cultivars. / Graduation date: 2013

Made available in DSpace on 2014-08-20T13:59:13Z (GMT). No. of bitstreams: 1 dissertacao_luciana_nogueira_machado.pdf: 513011 bytes, checksum: 7c2764a3f1c5001fdbbcf496c8d8702f (MD5) Previous issue date: 2011-04-15 / The peach (Prunus persica (L) Batsch) is the predominant stone fruit around the world, but in Brazil, due to factors such as incidence of pests in orchards, low quality plant propagation material and the lack of suitable rootstocks culture, the productivity is still considered low. In this context, is necessary to develop new rootstocks of Prunus, more adapted to the ecological conditions of the Southern region of Brazil and carrying genes for pests resistance such as nematodes. In this study, microsatellite loci (SSR) were used to verify the hybrid offspring of genotypes and makers segregation in an F2 population of peach rootstocks, obtained from controlled crosses, generating data to marker-assisted selection (MAS) of new genotypes carrying genes for nematode resistance. This work was divided in two articles; the first was a paternity test to verify the paternal and maternal offspring of 13 hybrids from controlled crosses between several rootstocks and scion with desirable agronomic traits. We obtained confirmation of paternity for 11 of the 13 hybrids analyzed. Two genotypes, presumably descendants of Prunus mume as male parent, were confirmed as being generated by selfing of genotipe Aldrighi P1. In the second article, a linkage map was constructed for a population of 50 F2 plants obtained by selfing of F1 hybrid, derived from a cross between the peaches Capdeboscq&#8223; x Flordaguard'. The segregation of 37 SSR loci was evaluated and 11 markers showed a link, allowing us to build a map with two groups. It was found that the markers BPPCT004, CPDCT044, BPPCT034 and BPPCT002 were grouped in a manner similar to that found in the GL2 Prunus reference map. With the data obtained suggests that these SSR loci are associated with genes for resistance to Meloidogyne spp. in different mapping populations, in which case inherited from the rootstock 'Flordaguard', and may be used directly in SAM and improvement genetic peach rootstocks derived from a cross between Capdeboscq&#8223; x Flordaguard&#8223;. / O pessegueiro (Prunus persica (L) Batsch) é a frutífera de caroço mais predominante em todo mundo, porém, no Brasil, devido a fatores como incidência de pragas nos pomares, baixa qualidade fitossanitária do material propagativo e falta de porta-enxertos adequados para a cultura, a produção ainda é considerada baixa. Neste contexto, existe a grande necessidade de desenvolver novos porta-enxertos de Prunus, mais adaptados as condições edafoclimáticas da Região Sul do Brasil e portadores de genes de resistência a pragas, dentre as quais os fitonematóides. No presente trabalho, locos de microssatélites (SSR) foram utilizados com o objetivo de verificar a descendência e a segregação de marcadores em genótipos híbridos da população F2 de porta-enxertos de pessegueiro, obtida a partir de cruzamento controlado, gerando dados para auxiliar na seleção assistida por marcadores (SAM) de novos genótipos portadores de genes de resistência a nematóides das galhas. Esta dissertação foi dividida em dois artigos, no primeiro, foi realizado um teste de paternidade, para verificar a descendência de 13 híbridos provenientes de diversos cruzamentos controlados entre diversos porta-enxertos e copas com características agronômicas desejáveis. Obteve-se confirmação da paternidade para 11 dos 13 híbridos analisados. Dois genótipos, supostamente descendentes de Prunus mume como parental masculino, foram confirmados como sendo gerados por autofecundação da cultivar Aldrighi. No segundo artigo, foi construído um mapa de ligação para uma população de 50 plantas F2 obtidas por autofecundação de um híbrido F1, proveniente do cruzamento entre os pessegueiros cv. Capdeboscq&#8223; x Flordaguard&#8223;, onde a segregação de 37 locos SSR foi avaliada e 11 marcadores apresentaram ligação, permitindo a elaboração de um mapa com dois grupos. Verificou-se que os marcadores BPPCT004, CPDCT044, BPPCT034 e BPPCT002 foram agrupados de forma similar ao encontrado no GL2 do mapa de referência de Prunus. Com os dados obtidos, sugere-se que estes locos SSR, estejam associados a genes de resistência a Meloidogyne spp., em diferentes populações de mapeamento, sendo neste caso herdados do porta-enxerto Flordaguard&#8223; e poderão ser utilizados diretamente em SAM e melhoramento genético de porta-enxertos do cruzamento entre os pessegueiros cv. Capdeboscq&#8223; x Flordaguard&#8223;.

Les changements globaux récents affectent la physiologie, la distribution et la phénologie des espèces, ainsi que la dynamique des populations et les interactions entre espèces. Les interactions plantes-pollinisateurs sont particulièrement menacées par les changements globaux et la perturbation de ces interactions peut avoir des conséquences importantes sur le système de reproduction des espèces végétales. Dans ce contexte des changements globaux, nous avons déterminé les cortèges de visiteurs de Rhododendron ferrugineum le long de gradients environnementaux et étudié comment la variabilité de leur efficacité affectait le système de reproduction de cette espèce. Nous nous sommes également intéressés à l’histoire biogéographique de cette espèce et comment elle a répondu à des changements passés tels que les dernières glaciations. Nous avons mis en évidence que R. ferrugineum est visité par une large diversité d’espèces d’insectes. L’efficacité des cortèges de visiteurs varie le long de gradients environnementaux mais ne semble pas avoir un impact sur le système de R. ferrugineum. Cette espèce présente un système mixte de reproduction, avec une capacité à l’autofécondation mais les taux élevés de dépression de consanguinité limitent le développement des individus issus d’autofécondation. Cette forte dépression de consanguinité a permis un maintien relativement élevé de la diversité génétique dans les Pyrénées. Un tel niveau de dépression de consanguinité ne permet pas l’évolution de l’autofécondation et maintient ainsi le système mixte de reproduction chez R. ferrugineum. La capacité d’autofécondation de R. ferrugineum pourrait lui permettre de coloniser de nouveaux milieux ou de survivre aux changements globaux. Durant les dernières glaciations, R. ferrugineum a survécu dans de grands refuges de basse altitude ainsi que dans des nunataks (refuges de haute altitude). Quelques populations marginales présentent un taux significatifs de consanguinité (FIS> 0) et des niveaux de diversité génétique particulièrement faibles. Ce patron génétique est consistant avec des évènements de fondation accompagnés de perte de diversité génétique et d’hétérozygotie durant les périodes d’expansion de l’aire de répartition de l’espèce. Ces données suggèrent que la dépression de consanguinité dans ces populations devait être faible et que l’assurance reproductive a joué un rôle fondamental dans l’établissement de ces populations. / Recent global changes affect the physiology, distribution and phenology of species, also they impact population dynamic and interactions among species. Plantpollinators interactions are particularly threated by global changes and perturbations of these interactions may lead to important changes in plant mating system. In this context of globalchanges, we determined the pollinator assemblages of Rhododendron ferrugineum and howthe variability of their efficiencies affects the mating system. We also studied thebiogeographic history of R. ferrugineum and how it responds to past climatic changes.We have shown that R. ferrugineum is visited by a large variety of insects. Visitorassemblages efficiency varied along environmental gradients but did not seem to impact themating system of R. ferrugineum. This species presents a mixed mating system, indeed it isable to self-fecundate but high levels of inbreeding depression are limiting the development of self-fecundate descendants. High levels of inbreeding depression maintain high genetic diversity in the Pyrenees. Also, it did not allow the evolution of selfing and maintain a mixed mating system. The ability to self-fecundate may favor the colonization of new habitats.During the last glaciation, R. ferrugineum survived in large lowland refugia and in nunataks at high altitude. Some marginal populations present a high level of selfing (FIS> 0) and low genetic diversity. This genetic pattern is consistent with foundation events and loss of genetic diversity and heterozygosity along colonization rods. Our data suggest that inbreeding depression in these populations should have been low and the reproductive assurance played akey role in the establishment of these populations.

Si les patrons d'expression de la diversité génétique des essences forestières à distribution grégaire des forêts tropicales humides ont fait l'objet de nombreuses études, les connaissances sur les essences forestières disséminées et représentées à très faible densité à l'hectare (dites rares) restent encore embryonnaires. Ces dernières suivent elles les mêmes patrons de distribution de la diversité génétique? Quels facteurs biotiques et abiotiques régissent l'organisation spatiale et l'évolution de la diversité génétique chez ce type d'espèce ? Afin d'améliorer les connaissances sur la biologie des espèces rares, nous nous proposons au travers de marqueurs microsatellites nucléaires(nuc) et chloroplastiques(cp) (i) d'analyser le régime de reproduction chez une espèce rare (ii) d'évaluer sa capacité de dispersion des gènes via les graines et le pollen , et enfin de(iii) décrire l'organisation spatiale de la diversité génétique à fine et à large échelle. Nous avons abordé ces questions avec Baillonella toxisperma (le Moabi), une essence commerciale dite rare (1 adulte/15ha à 20 ha), à multi- usages, représentée à travers les différentes écozones du bassin du Congo. Trois résultats majeurs découlent de nos travaux : (i) En dépit d'un isolement prononcé des adultes, B. toxisperma présente un régime de reproduction allogame prépondérant (tm ≈ 98%) avec des taux réduits d'autofécondation (1 - tm < 3%) probablement favorisé par la protandrie. (ii) Comme attendu dans le cas d'arbres disséminés, l'intensité de sa structure génétique spatiale à fine échelle est faible (Spnuc = 0.003 ; Spcp = 0.015) et reflète bien les flux de gènes à longues distances mesurés via le pollen [σp = 9.8 km à 10.8 km] et les graines [σs = 4.0 km à 6.3 km], probablement dû aux disperseurs efficaces que sont la chauve-souris, l'éléphant et l'homme. A large échelle spatiale, un signal phylogéographique a été détecté entre les individus situés de part et d'autre de l'équateur thermique, notamment entre ceux du massif forestier Camerounais et du Gabon (Rst = 0.313 > Rstp = 0.115, P < 0.001). Deux sous-groupes du massif forestier gabonais qui séparent les individus des forêts côtières de l'Ouest, de ceux des forêts planitaires de l'intérieur des terre, à l'Est, ont également été détectés, et présentent une différenciation génétique modérée (FST = 0.068, P < 0.001). La divergence génétique entre ces trois groupes pourrait s'expliquer par un isolement géographique qui remonterait aux perturbations climatiques du pléistocène et de l'Holocène sur la forêt tropicale humide africaine, et qui serait encore aujourd'hui maintenu par un isolement dans la reproduction du fait d'un asynchronisme dans la période de floraison entre leurs individus. La mise en évidence de ces trois groupes génétiques suggère une répartition biogéographique de B. toxisperma dans le bassin du Congo en partie façonnée par le climat actuel et passé. Nos conclusions peuvent servir d'outils d'aide à la décision pour les programmes de conservation et d'aménagement durable de la biodiversité en Afrique centrale. / If genetic diversity patterns of gregarious rainforest forest trees are well known, few knowledges are available about low density tree species. Does those last one follow the same genetic distribution pattern? Which biotic and abiotic factors underline the spatial structure and evolution of the genetic diversity of such species? In order to improve the knowledge of the biology of such species, we have propose through nuclear microsatellite(nuc) and chlorosplastic (cp) markers to (i) analyse the reproductive system of a low density tree species, (ii) assess its dispersal capacity through seeds and pollen, and finally to (iii) describe the spatial genetic structure at a fine and large scale. We have addressed those questions with Baillonella toxisperma Pierre (commonly named Moabi), a commercial tree of many uses, known to be rare (1 ind/15ha à 20 ha) and distributed through different ecologicals areas of Congo basin. Three main results rise from our study: (i) Despite a strong isolation of the adults, B. toxisperma has a dominant allogamous reproductive system (tm ≈ 98%) with a reduce rate of self-pollination (1- tm< 3%) which is probably due to occurrence of protandry. (ii) As expected in the case of low density trees, the spatial statistic (Sp) of the fine spatial genetic structure is very low [Spnuc = 0.003 ; Spcp = 0.015]. Those reflected a very high gene flow mediated through pollen [σp = 9.8 km à 10.8 km] and seeds [σs = 4.0 km à 6.3 km], that probably mediated by efficient dispersal vectors like bats, human and elephant. At a large scale, a phylogenetic signal has been detected between individuals located in both side of the thermic equator, mainly between those from the block forest of Cameroon and Gabon [RST = 0.313 > RSTp = 0.115, P < 0.001]. Two discretes genetics units from the Gabon block forest which separate individuals of the West coastal forests from the lowland forest ones (in the inland) have also been detected and showed a moderate genetic differentiation [FST = 0.068, P < 0.001]. The genetic differentiation between these three units could be explained by a geographical isolation during past climatic disturbances in the African rainforest, occurred in the Pleistocene and Holocene, and which will be still maintained up to date by a reproductive isolation caused by flowering asynchrony periods among individuals. The occurrence of these three genetic units suggests a biogeographical repartition of B. toxisperma in the Congo basin that is mainly due to the past and current climate. Our conclusions may lead to implement conservation strategies and sustainable management programm for biodiversity in Central Africa.

La dispersion, caractérisée par les mouvements d’individus dans l’espace et dans le temps, conduit à la production d’un flux de gènes et permet la connectivité des populations. Comprendre les facteurs qui façonnent les flux de gènes et la structuration des populations est d’une importance capitale pour améliorer les pratiques de gestion et de conservation des espèces. Celles caractérisées par une anadromie facultative, telles que la truite commune (Salmo trutta L.), sont des modèles de choix pour étudier le rôle de la diversité écotypique et comportementale, sous l’effet des activités anthropiques, sur le fonctionnement des populations. En utilisant la génétique des populations cette thèse se propose donc d’analyser la structuration des populations de la truite commune dans le fond du Golfe de Gascogne mais également de déterminer l’influence combinée de la dispersion de la truite de mer, de son comportement reproducteur et des activités anthropiques (repeuplements, transport de reproducteur) sur leur fonctionnement. Cette thèse aborde également la contribution des populations de truites communes (via leur origine natale) au stock de truites de mer capturées par la pêche professionnelle, sur le même site d’étude, en couplant de la génétique des populations et de la microchimie des otolithes. Nos résultats montrent une structuration génétique forte des populations de truite commune avec la présence de sept populations distinctes dans le bassin de l’Adour. Ceci semble être en partie expliqué par un comportement marqué de fidélité au site de naissance des truites de mer, couplé à un mouvement directionnel de celles-ci du sud (Espagne) vers le nord qui ne semble pas résulter en une dispersion effective (i.e. mouvement suivi d’une reproduction). En outre, les repeuplements récents, semblent impacter faiblement la structuration génétique des populations sauvages. Certains flux de gènes détectés localement semblent être dus à d’autres activités anthropiques, telles que le transport de reproducteurs. Les truites de mer capturées par la pêche professionnelle proviennent majoritairement de la population du gave d’Oloron et peu des populations des Nives et du Gave de Pau. La raison pourrait se trouver en premier lieu dans le fait que le Gave de Pau est fortement impacté par la présence de barrières à la migration et en second lieu dans les différences phénotypiques (taille plus petite) présentées par les truites de mer des Nives, par rapport à celle des gaves. Ceci suggère donc une différenciation de cette population et peut expliquer que la pêche professionnelle les capture dans une moindre proportion. Cette thèse a d’autre part pu démontrer les difficultés dans l’assignation d’une origine natale via la génétique lorsque les signatures génétiques sont relativement proches. Elle confirme l’utilité d’un couplage génétique des populations - microchimie des otolithes pour assigner des individus à leur origine natale à une échelle plus fine que le bassin. Les résultats obtenus au cours des trois années de thèse ont permis la détermination de populations génétiquement distinctes dont l’une contribue très largement à l’activité de pêche professionnelle. Ces populations peuvent être considérées comme de potentielles unités de gestion qui pourront servir de base à l‘élaboration de plans de gestion et de conservation. La meilleure compréhension de la biologie et du fonctionnement de la truite commune, et de l’impact des activités anthropiques sur la structuration des populations, acquise lors de cette thèse, pourra également permettre d’améliorer la prise de décisions des gestionnaires locaux pour la conservation et la gestion des populations de truites communes. / Dispersal, characterized by the movements of individuals in space and time leading to gene flows, allows populations to connect. Understanding factors shaping gene flow and population structure is vital to improve management and conservation practices of species. Those characterized by a partial anadromy, such as brown trout (Salmo trutta L.), are models of choice to study the role of ecotypic and behavioral diversity, under anthropic activities on population functioning. By using population genetics, this theses proposes to analyse population structure of brown trout in the Bay of Biscay, but also to determine the combined influence of sea trout dispersal, its reproductive behavior, and anthropic activities (stocking, transport of spawners) on their functioning. This thesis also addresses the contribution of brown trout populations (natal origin) on sea trout stock captured by professional fisheries, on the same study site, by coupling population genetics and otolith microchemistry. Results show a strong hierarchical structure of Brown trout population with seven distinct population detected in Adour basin. This seems to be explained a high site fidelity movement of sea trout together with a directional movement of sea trout from South (Spain) to North. This directional movement did not result into effective dispersal (i.e. movement followed by reproduction). Furthermore, a limited contemporary impact of stocking on genetic structure of wild population is observed. A few cases of inter-population gene flow detected seems to be explained by wild population management, particularly transport of spawners. The majority of sea trout captured by professional fisheries come from Gave d’Oloron and few from Nives and Gave de Pau. The reason is that Gave de Pau is impacted by migration barriers. And also that sea trout from Nives have phenotypic differences (smaller length) from sea trout originated from gaves. This suggest a differentiation of this population and can explained that professional fisheries capture them in smaller proportion.On the other hand, this thesis have been shown the difficulties to assign natal origin by using genetics when population are closed genetically. This confirm the usefulness to coupling population genetics and otolith microchemistry together to assign individuals to their natal origin at a finer scale than basin.Results obtained during these three years of thesis have made it possible the determination of distinct populations one of which contribute in majority of professional fisheries activities. These populations can be considered like potential management units (MUs) which could serve as basis in the elaboration of conservation and management plans. The better understanding of brown trout biology and functioning, and the impact of anthropic activities on population structure, obtained in this thesis, can also improve the decision-making of local managers for brown trout population conservation and management.

Pentadesma butyracea Sabine est l’une des quatre espèces du genre Pentadesma endémique de l’Afrique. Elle est distribuée de la Sierra Léone au Gabon dans deux grands types d’habitats :les forêts denses humides discontinues du domaine guinéo-congolais (Haute- et Basse-Guinée) et le domaine soudanien du couloir sec du Dahomey (assimilé à une barrière à l’échange de gènes et d’espèces entre les deux blocs guinéo-congolais). Dans ce dernier, l’espèce se retrouve dans des galeries forestières et occupe une place capitale dans le développement socio-économique des communautés locales en raison des multiples biens et services que procurent ses produits (alimentation, médecine et pharmacopée traditionnelle, etc.). Cependant, des pressions d’origines multiples, telles que le ramassage des graines pour fabriquer du beurre, la fragmentation de l’habitat et sa destruction en faveur du maraîchage, les pratiques culturales inadaptées, les incendies, font peser de lourdes menaces sur l’espèce.<p>Le but de ce travail est d’acquérir les connaissances requises pour la conservation et la gestion durable des ressources génétiques de l’espèce. Trois objectifs ont été définis :(i) étudier la phylogéographie de l’espèce, (ii) étudier sa variabilité morphologique et génétique au Bénin et (iii) caractériser sa biologie de reproduction. En amont de ces travaux, nous avons développé onze marqueurs microsatellites nucléaires chez P. butyracea (chapitre 2). Ils ont été utilisés pour l’étude de la phylogéographie et la diversité génétique de P. butyracea (chapitres 3 et 5), ainsi que pour étudier la dépression de consanguinité et les paramètres de son système de reproduction (chapitre 7).<p>La caractérisation de la répartition spatiale des lignées génétiques de régions intergéniques de l’ADN chloroplastique et de l’ADN ribosomal (ITS) a détecté deux lignées génétiques allopatriques entre le Haut et le Bas-Guinéen, indiquant une forte différenciation génétique et un signal phylogéographique. L’analyse des microsatellites détecte trois pools géniques correspondant aux trois régions étudiées (Haute Guinée, Dahomey Gap et Basse Guinée). La diversité génétique est faible dans le Dahomey Gap, modérée dans le Haut-Guinéen et élevée dans le Bas-Guinéen. Ces résultats indiquent une séparation très ancienne des populations d’Afrique centrale et d’Afrique de l’ouest, alors que celles du Dahomey Gap pourraient résulter des forêts denses humides de l’Afrique de l’ouest lors de la période Holocène humide africaine. Dans ce couloir sec, les populations ont subi une forte dérive génétique, potentiellement due à des évènements de fondation. Au Bénin, deux groupes éco-morphologiques ont été détectés suivant un gradient nord-sud, contrastant avec deux pools géniques présentant une distribution est-ouest. <p>P. butyracea est une espèce auto-compatible majoritairement allogame. La corrélation de paternité est plus élevée aux niveaux intra-fruit vs. inter-fruits, et au sein d’une population de petite taille vs. de grande taille. Les principaux pollinisateurs au Bénin sont deux oiseaux (Cyanomitra verticalis, Cinnyris coccinigastrus) et trois abeilles (Apis mellifera, Meliponula togoensis, Hypotrigona sp.). La productivité totale en fruits augmente en fonction de l’âge de l’arbre et varie en fonction de l’année, atteignant un pic pour les arbres ayant un diamètre de 60-80 cm. Les graines sont récalcitrantes et ont une teneur en eau de 42.5 ± 2.9 %. <p>L’analyse des paramètres de reproduction et de diversité génétique, associés aux facteurs écogéographiques, nous a permis de proposer un échantillon de neuf populations représentatives de la diversité à l’échelle du Bénin, dans la perspective d’une conservation in situ. Le succès de celle-ci dépendra des efforts conjugués des communautés locales, de la recherche forestière et de la définition d’un cadre législatif par le politique pour la protection des habitats. La conservation ex situ est envisagée sous forme d’un verger rassemblant diverses origines, présentant l’intérêt supplémentaire de permettre d’étudier les contributions de la diversité génétique et de la plasticité phénotypique à la variation phénotypique. / Pentadesma butyracea Sabine is one of the four species of the endemic genus Pentadesma in Africa. The species is distributed from Sierra Leone to Gabon in two major types of habitats: the discontinuous and dense Guineo-Congolian rainforests (Upper and Lower Guinea) and the Sudanian domain of the dry corridor of Dahomey (considered as a barrier to the exchange of genes and species between Upper and Lower Guinea). In the latter, the species is found in gallery forests and plays a vital role in the socio-economic livelihood of local communities due to the various resources and services that provide its products (food, medicine and traditional, etc.). However, pressure from many sources including the collection of seeds to make butter, habitat fragmentation and its destruction for market gardening, inadequate agricultural practices, fires, are serious threats to the species.<p>The aim of this work was to acquire appropriate knowledge for the conservation and sustainable management of genetic resources of the species. Three objectives were defined (i) study the phylogeography of the species; (ii) evaluate its morphological and genetic variability in Benin; and (iii) characterize its reproductive biology. In a preliminary work, eleven nuclear microsatellite markers of P. butyracea were developed (Chapter 2). They were used for the study of phylogeography and genetic diversity of P. butyracea (chapters 3 and 5), and to study the inbreeding depression and parameters of its breeding system (Chapter 7).<p>The characterization of the genetic lineages and their spatial distribution using intergenic regions from chloroplast DNA and ribosomal DNA (ITS) region detected two allopatric genetic lineages between Upper and Lower Guinea, indicating a high genetic differentiation and a phylogeographic signal. Microsatellite markers allowed us to detect three genepools matching with the three studied regions (Upper Guinea, Dahomey-Gap and Lower Guinea). Genetic diversity was low in the Dahomey Gap, moderate in Upper Guinea and high in Lower Guinea. These results indicate an ancient separation of populations from Central and West Africa, while those from Dahomey Gap could originate West African rainforests (Upper Guinea) during the African humid Holocene period. In this dry corridor, populations experienced high genetic drift, possibly due to founding events. In Benin, two eco-morphological groups were detected following a north-south gradient, contrasting with two gene pools presenting an east-west distribution.<p>Pentadesma butyracea is a self-compatible, mainly allogamous species. The correlation of paternity was higher within-fruit vs. among-fruits, and in population of small size vs. large size. The main pollinators in Benin are two birds (Cyanomitra verticalis, Cinnyris coccinigastrus) and three bees (Apis mellifera, Meliponula togoensis, Hypotrigona sp.). Total productivity in fruit increases with tree age and varies yearly, reaching a peak for trees of 60-80 cm of diameter class. Seeds are recalcitrant (i.e. they cannot be conserved at low temperature), having a water content of 42.5 ± 2.9% at maturity.<p>The analysis of reproduction and genetics parameters, associated with eco-geographic factors, enabled us to select nine populations representative of the diversity in Benin, from the perspective of in situ conservation. The success of the latter will depend on combined efforts of local communities, forest research and an adequate legislative framework for the protection of habitats. Ex situ conservation is envisaged as an orchard assembling various origins, and would have the additional advantage of allowing to study the contribution of genetic diversity and phenotypic plasticity to phenotypic variation. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished