La conservation des zones humides fortement modifiées par les pratiques anthropiques, nécessite l’acquisition de données scientifiques sur leur diversité et leur fonctionnement. Cette thèse vise à relier l’anthropisation des zones humides à la diversité génétique, niveau de base de la biodiversité lié à la capacité adaptative des populations et au maintien des espèces. L’effet de l’anthropisation sur la diversité génétique de végétaux aquatiques est étudié à plusieurs échelles d’espaces (zone humide et bassin versant) et de temps (études synchroniques et diachroniques). La diversité génétique de populations de deux espèces rudérales (Berula erecta et Apium nodiflorum) et une compétitive (Nuphar lutea) est comparée dans deux plaines alluviales contrastées (trophie, connectivité hydrologique et restauration), à l’aide de marqueurs microsatellites adaptés à l’étude d’espèces clonales. La diminution de la connectivité hydrologique augmente la différenciation génétique et diminue la diversité génétique pour les espèces rudérales étudiées alors qu’elle n’a pas d’effet sur l’espèce compétitive. L’impact de la connectivité est donc dépendant de la stratégie de reproduction. La diversité génétique des espèces rudérales diminue également dans les zones humides plus eutrophes. L’augmentation de la diversité génétique post-restauration chez B. erecta est corrélée à la fréquence des perturbations (assecs) qui créent des niches favorisant le recrutement des graines. Cette étude propose des préconisations de gestion pour les zones humides et apporte des connaissances sur la dynamique de la diversité génétique des plantes aquatiques en lien avec leur environnement / The conservation of wetlands which are strongly modified by human practices, requires the acquisition of knowledge about their diversity and functioning. This thesis aimed to link the human pressures and plant genetic diversity in wetlands, which is the basic level of biodiversity linked to the adaptive capacity of populations and species maintenance. The effect of anthropization on the genetic diversity of aquatic plants is studied at several spatial and temporal scales (wetland and watershed; synchronic vs. diachronic studies). The genetic diversity of populations of two ruderal (Berula erecta and Apium nodiflorum) and one competitive species (Nuphar lutea) in two contrasting floodplains (in terms of trophic status, hydrological connectivity and restoration) is compared using microsatellite markers suitable for the study of clonal species. A reduction in hydrological connectivity increases genetic differentiation and decreases genetic diversity for ruderal species studied, while it did not affect the competitive species. The impact of connectivity is related to plant reproductive strategy. The genetic diversity of ruderal species also decreases in most eutrophic wetlands. The increase of genetic diversity of B. erecta after restoration is correlated with the frequency of disturbances (dewatering) that create niches for seed recruitment. This study provides management recommendations for the impacted wetlands and provides knowledge about the dynamics of the genetic diversity of aquatic plants in relation to their environment

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No. of bitstreams: 1 TeseASMCS.pdf: 3312400 bytes, checksum: c898700835e5f7333425c663a26a29d4 (MD5) Previous issue date: 2015-08-14 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / The intense destruction of the environment contributed to the decline and isolation of wild populations, providing an intensification of genetic drift and inbreeding effects. These factors reduce the ability of individuals to adapt to environmental changes, making them more vulnerable to extinction. The two largest predators of the Americas, the cougar (Puma concolor) and jaguar (Panthera onca) are animals which are threatened by the reduction and fragmentation of habitats, especially in the Atlantic Forest, which is one of the most degraded biomes in the world due to human actions. The present study aimed to investigate both demographic parameters and the distribution of the genetic diversity of cougar and jaguar populations within Atlantic Forest remnants. The chosen areas (Serra da Mantiqueira, Serra do Mar continuous and Iguaçu National Park) are among the most important for the conservation of these cats. Mostly non-invasive samples (feces and hair) were collected in protected areas present in those remaining. The depositor species was confirmed by amplification of the ATP6 gene and the samples were individualized using microsatellite loci, which were also employed in population analyses. The sex of the individuals was determined using a small fragment of amelogenin gene. The results suggest that at least seven individuals of jaguars (4F:3M) inhabit the Iguaçu National Park and 12 (5F:7M) are present in the Serra do Mar continuous. These populations seem to be different, with evidence of low gene flow between them (lack of migrant and mixed individuals and pairs of highly related individuals). In Iguaçu is also estimated to exist at least seven cougars (3F:4M), also four (1F:3M) in the Serra da Mantiqueira and 14 (5F:9M) in the Serra do Mar continuous. Genetic structure was detected in this species, but evidencing gene flow maintenance between two detected populations (sign of migrants and mixed individuals and predominantly non related individuals). In both species high genetic diversity could be observed. This study obtained critical information and still unknown, about the demographic and structure of jaguar and cougar populations in the Atlantic Forest remain. These data will provide substantial information that can be used in monitoring, as well as being crucial and decisive in the increase of effective strategies for the conservation of these species. / A intensa devastação no ambiente vem contribuindo significativamente para o declínio e isolamento de populações selvagens, proporcionando uma intensificação dos efeitos da deriva genética e na taxa de endogamia. Estes fatores, por sua vez, reduzem a habilidade dos indivíduos se adaptarem às mudanças ambientais, tornando-os vulneráveis à extinção. Os maiores predadores das Américas, a onça-parda (Puma concolor) e a onça-pintada (Panthera onca) estão entre os animais ameaçados pela redução e fragmentação dos habitats, principalmente na Mata Atlântica, que é um dos biomas mundiais mais antropizados. Assim, o presente trabalho teve como objetivo investigar parâmetros demográficos e a distribuição da diversidade genética de populações de onças presentes em remanescentes de Mata Atlântica. Os fragmentos elegidos (Serra da Mantiqueira, contínuo da Serra do Mar e Parque Nacional do Iguaçu) estão entre os mais importantes para a conservação desses felinos. Amostras predominantemente não invasivas (fezes e pelos) foram coletadas em Unidades de Conservação presentes nesses remanescentes. A espécie depositora das fezes foi confirmada através da amplificação do gene ATP6 e as amostras foram individualizadas por meio de locos de microssatélites, os quais também foram empregados nas análises populacionais. O sexo dos indivíduos foi determinado por meio de um fragmento do gene da amelogenina. Os resultados indicaram que ao menos sete indivíduos de onças-pintadas (4F:3M) habitam o Parque Nacional do Iguaçu e 12 (5F:7M) estão presentes no contínuo da Serra do Mar. Essas populações parecem estar diferenciadas, com evidência de baixo fluxo gênico entre elas (ausência de indivíduos migrantes e misturados, além de pares de indivíduos altamente relacionados). No Iguaçu também foi estimado existir pelo menos sete onças-pardas (3F:4M), além de quatro (1F:3M) na Serra da Mantiqueira e 14 (5F:9M) no contínuo da Serra do Mar. Estruturação genética foi detectada nessa espécie, entretanto, com indícios de fluxo gênico entre as duas populações detectadas (evidência de indivíduos migrantes e misturados, além de pares de indivíduos predominantemente não relacionados). Em ambas as espécies foram exibidos altos níveis de diversidade genética. Este estudo gerou informações primordiais, ainda desconhecidas, sobre a demografia e a estruturação de populações de onças na Mata Atlântica. Tais dados poderão ser utilizados em monitoramentos, além de serem cruciais e decisivos no incremento de estratégias efetivas para a conservação dessas espécies.

La mondialisation et les changements globaux actuels ont un impact considérable sur la distribution des espèces et la composition des communautés. Lorsque ces espèces sont impliquées dans une interaction hôte-parasite les changements dans leur répartition peuvent entraîner la (ré)émergence de maladies infectieuses. La fasciolose, maladie causée par les grandes douves du foie (Fasciola hepatica et Fasciola gigantica) est réémergente dans de nombreux points du globe. Il est difficile de mettre en place des programmes de contrôle parce que (1) les hôtes intermédiaires, des mollusques d’eau douce de la famille des Lymnaeidae, sont composés d’un groupe d’espèces cryptiques difficilement identifiables et (2) plusieurs espèces impliquées dans cette maladie sont invasives. L’objectif de cette thèse était d’étudier les facteurs écologiques et évolutifs à large échelle de l’interaction entre la grande douve du foie et ses hôtes intermédiaires susceptibles de favoriser une (ré)émergence de la fasciolose. J’ai, dans un premier temps, développé des approches moléculaires pour reconnaître les espèces cryptiques tant du côté de la grande douve du foie que du côté des Lymnaeidae. L’utilisation d’une des techniques développées sur Galba schirazensis, Galba cubensis et Galba truncatula, trois espèces de limnées, m’a permis d’identifier leur distribution respective et de modéliser leur niches bioclimatiques grâce à l’utilisation de modèles de niches écologiques. Cette approche de modélisation de niches permet d’inférer la distribution potentielle des trois espèces et nous amène à discuter des avantages potentiels de ces modèles dans la gestion de la fasciolose. Dans un second temps, je me suis intéressée à la structuration de la diversité génétique chez des espèces invasives du système grande douve du foie-limnée, par des approches de génétique des populations et de phylogénie. J’ai pu retracer l’histoire de colonisation, les dynamiques démographiques et le système de reproduction chez P. columella, G. schirazensis et G. cubensis. J’ai montré que ces trois espèces font préférentiellement de l’autofécondation entrainant des pertes drastiques de diversité génétiques sur le front d’invasion. G. cubensis présente cependant une coexistence de plusieurs génotypes dans les aires anciennement colonisées. Les différences génétiques entre ces trois espèces sont discutées à la lumière de ce qu’on sait de leur écologie. Enfin ces résultats m’ont permis de discuter de l’avantage d'être autofécondant en cas d’invasion biologique. Pour conclure l’invasion par ces populations d’hôtes intermédiaires dépourvus de diversité génétique pourrait représenter un risque épidémiologique. En effet un parasite a plus de probabilité de circuler dans une population hôte clonale que dans une population polymorphe. Cette thèse fait le lien entre écologie, interactions hôtes-parasites et génétique de l’invasion afin de mieux comprendre les facteurs d’expansion de la fasciolose à échelle globale. / Globalization and the current global change have significant impacts on species distribution and community composition. When these species are involved in a host-parasite interaction, changes in species range distribution can result in the (re)emergence of infectious diseases. Fasciolosis, a disease caused by the liver flukes (Fasciola hepatica and Fasciola gigantica) is reemerging in many parts of the world. It is difficult to implement control programs because (1) the intermediate hosts, freshwater molluscs of the Lymnaeidae family, are composed by a group of cryptic species (2) several species involved in this system are invasive. The objective of this thesis was to study the ecological and evolutionary factors at a large scale in the interaction between the liver fluke and its intermediate hosts that might drive to fasciolosis (re)emergence. First, I developed molecular approaches to quickly identify cryptic species on the two liver flukes and on three Lymnaeidae species. Using one of these techniques, I identify the respective distribution of Galba schirazensis, Galba cubensis and Galba truncatula and infer their respective climatic envelope by ecological niche modelling. We then modelled and projected the potential species distribution ranges. We discussed the contribution of models to predict the species distribution in space and time giving a considerable advantage to control fasciolosis. I then study the genetic diversity structuration in invasive snails involved in the transmission of F. hepatica, using population genetics and phylogeny. I could infer colonization history, population dynamics and reproductive system of Pseudosuccinea columella, G. schirazensis and G. cubensis. I showed that these three species preferentially make inbreeding causing drastic losses of genetic diversity in the invasion front. However G. cubensis presents a coexistence of several genotypes in formerly colonized areas. Genetic differences between these three species are discussed in the light of what we know about their ecology. Overall, these results illustrate how dramatic the reduction in genetic diversity can be for hermaphrodite animals. Finally, we discuss the epidemiological risk related to the invasion by intermediate hosts depleted in genetic diversity. Indeed, a parasite might circulate easily in a clonal host population than in a polymorphic population. In my thesis I linked ecology, host-parasite interactions with genetics of the invasion to better understand the expansion of fasciolosis at a global scale.

Des approches traditionnelles en combinaison avec des méthodes moléculaires et biochimiques ont été utilisées pour étudier les communautés zooplanctoniques de la saline de Sfax. Une dizaine d'espèces ont été identifiées dans 4 bassins de salinité croissante. Les copépodes étaient la composante la plus représentative du compartiment zooplanctonique dans les bassins A5, A16 et C41. Le bassin M2 est monozoïque avec une présence exclusive d'Artemia salina.Nous avons montré le rôle crucial de la salinité dans la distribution des espèces mais nous avons souligné également l’influence, quoique plus faible, d’autres facteurs comme le ratio N:P qui pourrait être liée au mode de vie des animaux et directement aux phytoplancton. La composition en acides gras des copépodes et des Artemia est liée aux facteurs physico-chimiques et biologiques. Grâce à leur teneur en acides gras hautement insaturés, les copépodes et les Artemia peuvent être utilisés comme source alimentaire pour les poissons d'élevage. La phylogénie des copépodes est controversée puisque la structuration génétique de ce groupe n’est pas nettement identifiable. L’existence d’espèces cryptiques au sein des Paracartia grani est supposée mais reste à confirmer. Les facteurs abiotiques ne sont pas impliqués dans ces processus de divergence génétique. Chez Artemia salina, la forte teneur en sel, est un facteur de ségrégation des populations, l’adaptation des artémies à cette condition aboutit à des populations génétiquement distinctes. Un clivage génétique est repéré, il met en évidence une séparation entre les populations vivant dans de fortes teneurs en sel et celles en pleine mer. / Zooplankton community of solar saltern of Sfax. A dozen of species were identified in four ponds of increasing salinity. Copepods were the most abundant group in A5, A16 and C41. M2 is monozoic with an exclusive presence of Artemia salina. Salinity have a crucial role in species distribution, whereas, other factors such as N:P ratio have smaller influence. Fatty acids composition of copepods and Artemia depends on physico-chemical and biological parameters. Owing to their Highly unsaturated fatty acids (HUFAs) composition, copepods and Artemia of the saltern of Sfax can be used as food source for cultured fishes. Copepods phylogeny is controversial because their genetic structure is not clearly identifiable. The existence of cryptic species within Paracartia grani is assumed but should be confirmed. Abiotic factors are not involved in processes of genetic divergence. For Artemia salina, the high salinity, is a factor of population segregation, the adaptation of Artemia in such condition leads to distinct, genetically, population. A genetic divide was identified, it highlights a separation between population living in high salinity and those in the sea.

Pour de nombreux écologistes, les forêts tropicales sont synonymes de richesse et de diversité spécifique ; aussi l'existence de forêts monodominantes, à savoir de forêt dominée par une seule espèce, reste un formidable énigme. Nous présentons ici la première étude de l'autécologie d'une nouvelle espèce monodominante : Spirotropis longifolia (DC) Baill. (Leguminosae-Papilionoideae) se développant en Guyane française. La monodominance du S. longifolia est très importante, ce dernier pouvant représenter jusqu'à 70% du peuplement. Par ailleurs, le cortège floristique associé à cette espèce diffère largement de celui de la forêt adjacente, très diversifiée. La monodominance du S. longifolia ne peut être expliquée ni par des conditions pédologiques particulières ni par l'absence de compétiteur dans ses peuplements. Nous suggérons en revanche que ses étonnantes capacités à réitérer et à marcotter lui permettent d'installer de maintenir sa monodominance. Nous avons de plus développé un jeu de marqueurs microsatellites et constitué une banque de gènes au cours d'une importante campagne de terrain. Nous proposons une nouvelle classification de la monodominance afin de mieux appréhender les processus écologiques qui lui sont associés, et y replaçons le S. longifolia. Enfin, nous mettons en perspective nos résultats avec la gestion des peuplements naturels. / Large expanses of forest dominated by a single tree species, i.e. monodominant forests, occur through the tropics and remain an long-standing conundrum to most ecologists. In French Guiana, we described a new monodominant tree species: Spirotropis longifolia (DC) Baill. (Leguminosae-Papilionoideae), and studied, for the first time, its autecology. We reported a strong monodominant feature (up to 70 % of stems >10 cm in d.b.h.) and a marked difference between floristic composition of the dominated and adjacent, highly diverse, stands. The monodominance of S. longifolia was supported neither by peculiar soil conditions nor by a lack of competitors but may be owned to its astonishing self-coppicing and layering abilities which induce a sharp spatial structure. We also developed a set of microsatellite markers and conduct a large field survey to built up a gene data base. Facing the variety of ecological processes involved in monodominance, we identified a lack of conceptual framework, set a new classification of monodominance and positioned S. longifolia within. We finally discuss these results in the frame of the forest management.

As alterações que a ação antrópica vem causando nos ambientes costeiros tem provocado impactos sobre as espécies a eles associadas. Larus dominicanus é uma espécie de ave marinha amplamente distribuída ao longo do Hemisfério Sul. Por possuir um hábito alimentar generalista, os resíduos da ação antrópica tem beneficiado a espécie, que, assim como outras gaivotas, vem apresentando um crescimento demográfico acelerado. O presente estudo, através do uso de marcadores de microssatélites, mostra que, apesar disso, a espécie possui uma baixa variabilidade genética, com fraca estruturação populacional, que provavelmente são o reflexo da origem recente da espécie e de uma diferenciação recente entre as populações. Múltiplas forças atuam para determinar a estruturação populacional, sendo elas o isolamento por distância, as barreiras físicas e a filopatria. Os sinais de gargalo populacional encontrados em algumas das colônias levantam a possibilidade de efeitos fundadores por colonização recente nas colônias mais ao norte da costa brasileira e redução populacional nas colônias da Argentina e da Antártica como conseqüência da última glaciação. Estes dados chamam a atenção para a necessidade de considerar as informações genéticas para a implantação de planos de manejo. Uma vez que a diferenciação entre as populações é recente, a variabilidade dentro de cada uma delas deve ser mantida. O controle populacional da espécie através de métodos diretos deve ser também acompanhado por planos de manejo ambiental, visando reduzir ou eliminar as condições que propiciam o crescimento desequilibrado dos gaivotões. / The changes in the coast that has been caused by human action has led to impacts on species associated with this environment. Larus dominicanus is a seabird species widely distributed throughout the Southern Hemisphere. The generalist feeding habits allow this species take advantage from human action, leading to population growth, which is also observed in other species of gulls. This study, through the use of microsatellite markers, shows that, despite of the population growth, Larus dominicanus has a low genetic variability, with low population structure, which probably reflects the recent origin of species and a recent differentiation among populations. Multiple forces act to determine the population structure, among them the isolation by distance, physical barriers and philopatry. Some colonies presents a bottleneck sign, raising the hypothesis of recent founder effects in the colonies to the north of Brazil and population reduction of colonies of Argentine and Antarctic as consequence of the last glaciation. These data show the need to consider genetic information for the implementation of management plans. The variability within populations must be maintained, since the differentiation between them is recent. Furthermore, the species population control by direct methods must also be accompanied by environmental management plans, to reduce or eliminate the conditions that favor the unbalanced growth of the gulls

An important goal of biology is to understand the key mechanisms of evolution underlying the diversity of living organisms on Earth. In that respect, the recent innovations in the field of new generation sequencing technologies (NGS) are bringing new and exciting opportunities. This thesis presents results obtained with these tools in the specific context of the study of two sister species of cold-adapted leaf beetles, Gonioctena intermedia and G. quinquepunctata. More specifically, this work is focused around four research directions: the two first explore methods of statistical inference using a spatially explicit model of coalescence, by (1) evaluating the potential of various summary statistics to discriminate phylogeographic hypotheses, and (2) investigating the dispersal abilities of a montane leaf beetle, G. quinquepunctata, using an original method that avoids using summary statistics. The third research direction focuses on the adaptation to cold conditions in this montane leaf beetle, by testing the association between genetic polymorphism across tens of thousands of genetic markers and altitude in samples collected at various elevation levels in the Vosges (France). Finally, the fourth, and last, research axis presents the discovery of mitochondrial heteroplasmy, i.e. the presence in an individual of multiple copies of the mitochondrial genome, in natural populations of G. intermedia. We illustrate, here, how NGS technologies could help identify this phenomenon, probably underestimated in animals, on a large scale. / 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

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