La perchaude (Perca flavescens) constitue une ressource socioéconomique de grande importance dans le Lac Saint-Pierre (Québec, Canada). Bien que ce lac fluvial soit désigné réserve de la biosphère par l’UNESCO, le statut de la perchaude est préoccupant. Afin de permettre à l’espèce de persister en fonction des diverses pressions anthropiques, il est important de comprendre sa dynamique populationnelle et les mécanismes qui en sont responsables. La perchaude est connue pour sa philopatrie ; le fait de toujours se reproduire à son site de naissance peut entraîner la subdivision d’une espèce en de multiples populations, où chacune pourra être pourvue d’adaptations locales distinctes. Il est possible d’étudier ces processus à l’aide des signaux génétiques associés à la reproduction des individus. Toutefois, une faible différentiation génétique entre les populations du Lac Saint-Pierre est envisagée en raison de la colonisation récente du système (moins de 8000 ans). L’objectif de cette étude est de déterminer s’il existe plusieurs populations de perchaude dans le Lac Saint-Pierre. Les simulations réalisées ont révélé que l’utilisation de marqueurs AFLP (amplified fragment length polymorphism), permettant une analyse globale du génome, affiche une meilleure détection de la différentiation des populations que celle des marqueurs microsatellites. Afin d’associer les individus à leur site de naissance, la méthode d’AFLP et des microsatellites ont été utilisées sur des larves capturées suite à l’éclosion des oeufs. Trois analyses distinctes d’AFLP ont indiqué une corrélation entre la composition génétique des individus et des sites géographiques, confirmant ainsi la présence de plusieurs populations sympatriques dans le Lac Saint-Pierre, découlant vraisemblablement de la philopatrie de l’espèce. L’absence de différentiation génétique relatée par les marqueurs microsatellites vient confirmer l’importance du choix des marqueurs génétiques. Bien que la différentiation génétique observée soit relativement faible, la gestion de la perchaude devrait tenir compte de la dynamique des populations distinctes dans ce système. / Yellow perch (Perca flavescens) is a commercially-exploited freshwater fish species in Lake Saint-Pierre (Quebec, Canada). Even if this fluvial lake is designated as a biosphere reserve by UNESCO, the yellow perch status is of concern. To ensure the persistence of species facing to anthropogenic pressures, understanding dynamics and mechanism that structure populations are of major importance. Because the habitat characteristics are spatially structured and this species is known to display natal site fidelity, a subdivision of the species in multiple populations and local adaptations may occur. It is possible to detect these processes according to genetic signal associated with individuals’ reproduction. However, low genetic differentiation is hypothesised due to the recent colonization of the system (< 8 K years). This study aims at determining if there are multiple populations of yellow perch in Lake Saint-Pierre. Simulations was first performed to confirm that population differentiation is better depicted by amplified fragment length polymorphism (AFLP) than microsatellite markers. In order to associate individuals to their site of birth, larvae captured after hatching were used. A survey of the variation throughout the entire genome was then performed by using the AFLP approach and variations at microsatellite loci were used to further investigate the organization of these populations. Three distinct AFLP analyses indicated a correlation between genetic composition of individuals and spawning sites, and thus confirmed the presence of multiple sympatric populations in Lake Saint-Pierre, resulting likely from natal site fidelity. At the opposite, the lack of genetic differentiation reported by microsatellites markers confirms the importance of the choice of genetic markers. While the genetic differentiation is very low, the management of this species should take into account the existence of distinct population structures in this system.

Les variétés traditionnelles de vigne nécessitent de très nombreux traitements phytosanitaires pour lutter contre les maladies cryptogamiques qui touchent leurs parties herbacées, comme le mildiou et l'oïdium, causés par Plasmopara viticola et Erysiphe necator respectivement. Ces traitements, coûteux et préjudiciables pour l'environnement, pourraient être réduits par l'emploi de variétés résistantes. La vigne cultivée européenne (Vitis vinifera, 2n=38) est très sensible au mildiou et à l'oïdium. En conséquence, la résistance doit être introduite à partir d'autres Vitaceae ayant un niveau de résistance plus élevé à ces maladies. Plusieurs origines de résistance ont déjà été observées et inventoriées, en particulier chez l'espèce d'origine américaine Muscadinia rotundifolia (2n=40). Ces facteurs sont d'un intérêt majeur pour la sélection de variétés résistantes. Cependant, lors du processus d'introgression, des difficultés à obtenir des pépins viables en F1 ainsi que des anomalies phénotypiques dans les descendances en rétrocroisement ont été constatées. Afin d'optimiser la gestion des résistances provenant de cette espèce dans les programmes d'amélioration variétale, il est nécessaire de comprendre l'organisation génétique et génomique de M. rotundifolia, et de compléter la connaissance des facteurs de résistance issus de cette espèce. Dans ce contexte, les objectifs de la thèse sont : (i) de réaliser une analyse comparative des génomes de V. vinifera et M. rotundifolia et (ii) d'identifier de nouveaux facteurs de résistance chez M. rotundifolia utilisables à terme en sélection. Pour cela, une carte génétique de M. rotundifolia a été développée à partir d'une population de 200 individus issue de l'autofécondation de M. rotundifolia cv. Regale. Parallèlement, la même population a été testée pour son niveau de résistance au mildiou et à l'oïdium. Une carte génétique couvrant 950 cM a été réalisée. Elle comprend 191 marqueurs microsatellites répartis sur les 20 chromosomes de M. rotundifolia, et permet de conclure à un niveau de macrosynténie très élevé avec V. vinifera. Le groupe de liaison 20 de M. rotundifolia correspondrait à la partie inférieure du groupe de liaison 7 de V. vinifera. Par ailleurs, un QTL de résistance au mildiou a été détecté sur le groupe de liaison 18 de M. rotundifolia, au niveau d'une région riche en gènes de type NBS-LRR, et un nouveau QTL de résistance majeur à la l'oïdium a été mis en évidence sur le groupe de liaison 14 de M. rotundifolia. Ce QTL, nommé Ren5 pour 'Resistance to Erysiphe necator 5', montre une action précoce dans l'arrêt de la croissance du mycélium du pathogène, dès l'établissement des premiers stades de biotrophie du champignon. De plus, le QTL Ren5 a été confronté à deux souches supplémentaires d'E. necator, appartenant aux deux groupes d'oïdium retrouvés dans vignobles européens, contre lesquelles il reste efficace. Les données de cartographie génétique générées pour M. rotundifolia dans ce travail, ainsi que la mise en évidence de Ren5 et de son mode d'action, permettront d'améliorer la gestion des facteurs de résistance issus de cette espèce pour la sélection de variétés résistantes au mildiou et à l'oïdium.

Black grouse (Tetrao tetrix) is a bird species with a lek mating system found in the Palearctic boreal taiga. It is assumed that it has a continuous distribution along Scandinavia and Siberia, whereas in Central Europe it has declined during the last decades. The primary objective of this thesis was to obtain a deeper understanding of the history, systematic classification and the genetic structure of black grouse on different geographical scales using microsatellites and control region mtDNA sequences (CR). I determined how much the mating system, habitat fragmentation and historical population processes have influenced the partitioning of genetic diversity in this species. Phylogeographical results are consistent with a demographic population expansion, and the patterns of postglacial dispersal suggest that a glacial refugium was located somewhere in central Asia, and from there black grouse spread out to Europe following the retreat of glacial ice sheets. I suggest that the two European black grouse subspecies, T. t. Tetrix and T. t. britannicus correspond to only one subspecies: T. t. tetrix, and that this lineage has diverged from T.t. viridanus, a subspecies found in Kazakhstan. The British population is significantly divergent from the remaining Eurasian samples for microsatellites but it is not for mtDNA. Therefore, they should regard as a separate Management Unit and not as a subspecies. Furthermore, British black grouse occur in three independent genetic units, corresponding to Wales, northern England/southern Scotland and northern Scotland. There was also genetic structure within Sweden. Habitat fragmentation is the main cause of population genetic structure in southern Swedish black grouse. In contrast, low levels of genetic differentiation and high connectivity were found in northern Sweden due to female-biased dispersal. On a finer geographical scale, I found genetic differences between leks due to a mixture of related and unrelated individuals within leks. However, mean relatedness values hardly differed from zero. Some leks were similar to one another and I interpret this as a result of variation in local reproductive success and philopatry. These factors would cause genetic structuring but this by itself would not reveal that kin selection is operating within black grouse leks.

Made available in DSpace on 2014-12-17T15:49:13Z (GMT). No. of bitstreams: 1 PamelaLR_DISSERT.pdf: 3477786 bytes, checksum: e908a438292b6fd69e56fc50da98d37c (MD5) Previous issue date: 2013-03-11 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Vriesea minarum is a rupiculous bromeliad species, with naturally fragmented populations, restricted to the Iron Quadrangle, Minas Gerais, Brazil. It is a threatened species, which is suffering from habitat loss due to the growth of cities and mining activities. The knowledge of genetic variability in plant populations is one of the main branches of conservation genetics, linking genetic data to conservation strategies while the knowledge about plant reproductive biology can aid in understanding key aspects of their life story, as well as in the comprehension of their distribution and survival strategies. Thus, the study of diversity, richness, and genetic structure, as well as the reproductive biology of populations of V. minarum can contribute to the development of conservation actions. Chapter 1 presents the transferability of 14 microsatellite loci for V. minarum. Among the results of this chapter, we highlight the successful transferability of 10 microsatellite loci described for other species of Bromeliaceae, all of which are polymorphic. In Chapter 2, we present the genetic analyses of 12 populations of V. minarum that are distributed throughout the Iron Quadrangle. We used the 10 microsatellite loci tested in Chapter 1. The results show a low population structuring (Fst = 0.088), but with different values of genetic richness (mean = 2.566) and gene diversity (mean = 0.635) for all populations; and a high inbreeding coefficient (Gis = 0.376). These may be the result of pollinators action and/or efficient seed dispersal, thus allowing a high connectivity among populations of naturally fragmented outcrops. The reproductive biology and floral morphology of a population of V. minarum, located in the Parque Estadual da Serra do Rola-Mo?a, are studied in Chapter 3. This reserve is the only public environmental protection area where the species occurs. As a result of field experiments and observations, we found that the species has its flowering period from January to March, with flowers that last for two days and that it has a mixed pollination syndrome. It is primarily alogamous, but also has the capacity to be self-ferilized. It is expected that data obtained in chapters 1, 2 and 3 serve as basis for other studies with species from the ferruginous rocky fields, since until now, to our knowledge, there are no other survey of endemic species from the Iron Quadrangle, seeking to merge the genetic knowledge, with the data of the reproductive biology, with the ultimate aim of biodiversity conservation. Considering the great habitat loss for the species by mining, it becomes crucial to analyze the creation of new protected areas for its conservation / Vriesea minarum ? uma esp?cie de brom?lias rup?cola, com popula??es naturalmente fragmentadas, restrita a regi?o do Quadril?tero Ferr?fero, em Minas Gerais, Brasil. ? uma esp?cie amea?ada, que est? sofrendo com a perda de habitat devido ao crescimento das cidades e ?s atividades de minera??o. O conhecimento da variabilidade gen?tica em popula??es de plantas ? um dos principais ramos de gen?tica da conserva??o, associando dados gen?ticos para as estrat?gias de conserva??o, enquanto que o conhecimento sobre a biologia reprodutiva pode ajudar na compreens?o de aspectos fundamentais da hist?ria de vida, distribui??o e estrat?gias de sobreviv?ncia das plantas. Assim, o estudo da diversidade, riqueza, estrutura gen?tica e biologia reprodutiva das popula??es de V. minarum podem contribuir para o desenvolvimento de a??es de conserva??o. O cap?tulo 1 apresenta a transferabilidade de 14 loci de microssat?lites para V. minarum. Entre os resultados desse cap?tulo, destaca-se o sucesso da transferabilidade de 10 loci de microssat?lites descritos para outras esp?cies de Bromeliaceae, sendo todos eles polim?rficos. No cap?tulo 2, ? apresentada a gen?tica de 12 popula??es de V. minarum que se distribuem por todo o Quadril?tero Ferr?fero. Os resultados obtidos mostram pouca estrutura??o entre as popula??es (Fst = 0,088), mas com diferentes valores de riqueza (m?dia = 2.566) e diversidade gen?tica (m?dia = 0.635) para todas as popula??es; o coeficiente de endogamia foi alto (Gis = 0.376). Estes dados podem ser resultado da a??o de polinizadores e/ou dispers?o de sementes eficientes, j? que as popula??es s?o naturalmente fragmentadas. No cap?tulo 3, ? estudada a biologia reprodutiva e morfologia floral de uma popula??o de V. minarum, situada no Parque Estadual da Serra do Rola-Mo?a, Minas Gerais. Como resultado, foi poss?vel identificar que a esp?cie possui flora??o de janeiro a mar?o; com flores que duram dois dias; s?ndrome mista de poliniza??o; sendo primariamente al?gama, mas tamb?m tem capacidade para ser auto fecundada. Espera-se que dados obtidos nos cap?tulos 1, 2 e 3 sirvam como base para outros estudos com esp?cies de campos rupestres ferruginosos, j? que at? o presente momento, n?o ? de nosso conhecimento a exist?ncia de registros de outras pesquisas feitas com esp?cies end?micas do Quadril?tero Ferr?fero, que busquem conciliar o entendimento da gen?tica, com os dados da biologia reprodutiva, tendo como alvo a conserva??o da biodiversidade neste h?bitat altamente amea?ado pela minera??o. Torna-se crucial uma an?lise cuidadosa para a cria??o de novas ?reas de prote??o, para conserva??o das popula??es da esp?cie

Made available in DSpace on 2014-07-29T15:16:37Z (GMT). No. of bitstreams: 1 AnaClaraferraz.pdf: 1870286 bytes, checksum: d17e1fe96ee32ca1852c51743beff160 (MD5) Previous issue date: 2010-01-12 / The progress of Molecular Biology and Genetics provided the appearance of several molecular markers that detect the genetic polymorphism directly at DNA. Among these markers are the microsatellites (SSR), which are distinguished by their high degree of polymorphism. The use of these markers for individual genotyping has evolved into multiplex systems, which allow many SSR fragments to be detected and analyzed simultaneously. Currently there are several articles in literature discussing the criteria to be used in the primer design for use in PCR, as well as various softwares are available for this end. However, there are few studies and tools for the analysis of compatibility between pairs of primers for use in multiplex systems, where multiple fragments are simultaneously amplified using PCR. This paper evaluated different criteria for compatibility between pairs of primers. A set of 74 combinations of pairs of primers, involving the amplification of 94 SSR loci were evaluated in duplex systems. The same combinations were evaluated according to different criteria, including the degree of complementarity between primers, the magnitude of differences of denaturation temperatures (Tm) and the tendency to annealing between pairs of primers based on the Gibbs free energy resulting from the association between them. The comparison between the different criteria allowed the identification of a set of criteria with positive predictive value equal to 94%. These criteria were implemented for use in a software called Multiplexer, which from the analysis in sequence of pairs of primers, suggests compatible combinations for use in multiplex genotyping systems. Using this tool can significantly reduce the costs related to laboratory activities for genotyping using PCR. / Os avanços da Biologia Molecular e da Genética proporcionaram o surgimento de diversos marcadores moleculares que detectam o polimorfismo genético diretamente no DNA. Entre estes marcadores se encontram os microssatélites (SSR), que se destacam pelo seu elevado grau de polimorfismo. O uso desses marcadores para fins de genotipagem individual tem evoluído para sistemas multiplex, os quais permitem que vários fragmentos SSR sejam detectados e analisados simultaneamente. Atualmente são abundantes na literatura artigos que discutem os critérios a serem utilizados no desenho de pares de primers para aplicação em PCR, bem como estão disponíveis diversos softwares para este fim. No entanto, ainda são escassos os estudos e ferramentas destinados à análise de compatibilidade entre pares de primers para aplicação em sistemas multiplex, onde vários fragmentos são amplificados simultaneamente por PCR. Neste trabalho são avaliados diferentes critérios de compatibilidade entre pares de primers. Um conjunto de 74 combinações de pares de primers, envolvendo a amplificação de 94 locos SSR foram avaliados em sistemas duplex. As mesmas combinações foram avaliadas segundo diferentes critérios, incluindo o grau de complementariedade entre primers, magnitude das diferenças de temperaturas de desnaturação (Tm) e a tendência ao anelamento entre pares de primers com base na energia livre de Gibbs resultante da associação entre eles. A comparação entre os diferentes critérios permitiu a identificação de um conjunto de critérios com valor preditivo positivo igual a 94%. Estes critérios foram implementados para utilização em um software denominado Multiplexer, que a partir da análise de sequências de pares de primers, sugere combinações compatíveis para a utilização em sistemas de genotipagem multiplex. O uso dessa ferramenta pode reduzir consideravelmente os custos laboratoriais relativos às atividades de genotipagem utilizando PCR.

A Mata Atlântica é considerada uma das grandes prioridades para a conservação de biodiversidade em todo o continente americano. Este bioma é um dos oito hotspots do planeta e caracteriza-se pelo alto grau de endemismo e pela alta diversidade de espécies que encerra. As abelhas Euglossini estão restritas à região Neotropical, com uma faixa de distribuição que se estende desde o Norte do México até a província de Córdoba, na Argentina. As espécies dessa tribo são abundantes em florestas tropicais úmidas/chuvosas e florestas subtropicais da América Central e América do Sul onde ocorrem em maior diversidade. Em virtude do alto impacto causado pelas ações humanas em áreas de Mata Atlântica e o pouco que se conhece sobre sua diversidade, este trabalho propõe um estudo geral sobre a estrutura das comunidades de espécies de Euglossini presentes em uma área de planície litorânea continental, Parque Estadual da Serra do Mar - Núcleo Picinguaba (PESM), e uma área insular, Parque Estadual da Ilha Anchieta (PEIA), no município de Ubatuba, norte de São Paulo, Brasil. O PESM abrange uma área de aproximadamente 47.500 hectares e quase todos os ecossitemas da Mata Atlântica são encontrados em seus domínios. O PEIA cobre toda a extensão da Ilha Anchieta (828 hectares), distante cerca de 600 m do continente. As coletas foram realizadas mensalmente, de Agosto/2007 a Julho/2009, com o uso de 14 compostos aromáticos utilizados como iscas artificiais para a atração de machos, além de indivíduos coletados em flores. Mil quinhentos e setenta e seis espécimes (73 fêmeas e 1503 machos), pertencentes a 24 espécies, foram registrados no presente trabalho. A espécie mais abundante foi Euglossa cordata (36,4%), seguida por Euglossa iopoecila (13,9%) e Euglossa sapphirina (13,3%). Dezoito espécies foram amostradas na Ilha Anchieta, sendo que quatro delas foram exclusivas desta área, ao passo que 20 espécies foram amostradas no PESM e seis delas foram registradas apenas neste local. Na Ilha Anchieta, Eg. cordata representou 63,2%, quase dois terços do total de espécies coletadas. Já em Picinguaba, Eg. iopoecila (23,0%) e Eg. sapphirina (21,0%) foram as duas espécies dominantes. A espécie Eg. iopoecila, a mais abundante na área continental, não foi registrada na llha e Eg. sapphirina, a segunda espécie mais frequente no PESM, foi representada apenas por nove indivíduos na Ilha Anchieta e por 200 em Picinguaba. Estes dados sugerem que essas duas espécies podem atuar como bioindicadores de ambientes preservados, como sugerido para outras espécies de Euglossini. Por outro lado, alguns autores evidenciaram que Eg. cordata é uma espécie favorecida por ambientes perturbados, o que pode estar associado à sua alta abundância na Ilha Anchieta. Dados de literatura mostram que há um sinal evidente de perturbação ambiental, além da perda de espécies, é a dominância de algumas espécies. A Ilha Anchieta apresenta um longo histórico de ocupação humana e diversas espécies de plantas e animais foram introduzidos em seus domínios. / The Atlantic Forest is considered as one of the highest priorities for the conservation of biodiversity in the American continent. This biome is one of the eight biodiversity hotspots in the world and is characterized by high species diversity and endemism. Euglossini bees are restricted to the Neotropics, with a geographic range that extends from northern Mexico to the Córdoba Province in Argentine. Species from this tribe are abundant in humid and rainy tropical forests and in sub-tropical forests of Central and South America, where their diversity is high. Due to the high impact caused by human activities in the Atlantic Forest and the poor knowledge on its biodiversity, in the present study we assessed the community structure of the Euglossini in a coastal lowland area: Parque Estadual da Serra do Mar - Núcleo Picinguaba (PESM); and in an insular area: Parque Estadual da Ilha Anchieta (PEIA), Ubatuba, both located in northern São Paulo State, Brazil. PESM has an area of approximately 47.500 ha and almost all ecosystems of the Atlantic Forest are found within its domains. PEIA covers all the extension of the Anchieta Island (828 ha), about 600 m away from the continent. Sampling was carried out monthly, from August 2007 to July 2009, using artificial baits with 14 aromatic compounds to attract males, as well as by collecting individuals on flowers. One thousand five hundred and seventy-six specimens (73 females and 1,503 males), represented by 24 species were recorded. The most abundant species was Euglossa cordata (36.4%), followed by Euglossa iopoecila (13.9%) and Euglossa sapphirina (13.3%). Eighteen species were sampled on Anchieta Island and four of them were exclusive to this area; whereas 20 species were sampled in PESM and six of them were only recorded there. On Anchieta Island, E. cordata represented almost two thirds of the total species collected (63.2%). In Picinguaba, E. iopoecila (23.0%) and E. sapphirina (21.0%) were the dominant species. E. iopoecila, the most abundant species in the continental area, was not recorded on the island, and E. sapphirina, the second most frequent species in PESM, was represented only by nine individuals on Anchieta Island and by 200 in Picinguaba. Results suggest that these two species may act as bioindicators of preserved environments, as suggested for other Euglossini species. However, some authors evidenced that E. cordata is favored by disturbed environments, which may be associated with its high abundance on Anchieta Island. Other studies show that an evident sign of environmental perturbation, besides species loss, is the dominance of some species. Anchieta Island exhibits a long history of human occupation and several plant and animal species were introduced there.

La stratégie de reproduction est l’un des principaux facteurs responsables du maintien de l’eusocialité et du succès écologique des fourmis. Chez les fourmis monogynes, la fondation solitaire induit de forts degrés d’apparentement entre les membres de la colonie, ce qui garantit la fitness indirecte des ouvrières. Par ailleurs, la territorialité assure le maintien de l’intégrité de la colonie. Par contre, chez les fourmis polygynes, l’ouverture sociale est plus importante, les reines ont perdu la capacité à fonder de manière indépendante et la présence de plusieurs lignées maternelle peut faire chuter les degrés d’apparentement, ce qui à terme, pourrait pousser les membres de la colonie au népotisme. Crematogaster pygmaea est une fourmi hautement polygyne dont la biologie la rapproche paradoxalement des fourmis monogynes. Dès lors, elle représente un modèle intéressant pour tester ces différentes prédictions, qui dans un cadre plus large, contribuent à une meilleure compréhension de l’évolution et de la maintenance de la coopération des reines chez les fourmis.<p>A l’aide de confrontations en milieu naturel, nous avons montré que C. pygmaea est clairement une espèce multicoloniale. Les confrontations traditionnelles en boîte de Pétri se sont avérées insuffisantes pour déterminer le degré d’ouverture des colonies de C. pygmaea. Le profil d’hydrocarbures cuticulaires des ouvrières est simple mais présente quelques alcanes branchés et quelques alcènes qui pourraient suffire au codage de l’odeur coloniale. Les colonies de C. pygmaea sont formées de plusieurs calies qui s’échangent des ouvrières. Ces échanges contribueraient à l’homogénéité et à l’intégrité génétique et chimique des colonies au sein des populations. <p>Contrairement à ce qui est observé chez d’autres fourmis, la forte polygynie de C. pygmaea n’est pas associée à l’incapacité d’une fondation solitaire. En effet, le dimorphisme reines-ouvrières est très marqué, l’haplométrose et la pléométrose sont possibles en laboratoire et des essaimages et tentatives de fondations solitaires ont été observés dans la nature. La dissémination des colonies par essaimage pourrait avoir lieu sur de courtes distances, comme le suggère la corrélation positive entre les distances génétique et géographique qui séparent les colonies. <p>Les reines sont capables de suivre des pistes, ce qui pourrait favoriser leur pénétration dans une colonie existante. Néanmoins, les ouvrières sont capables de reconnaître une reine étrangère et les degrés d’apparentements au sein des colonies sont élevés. Les analyses génétiques ont montré que les colonies forment des unités familiales dont les reines sont recrutées au sein d’une même génération. Ces reines sont à l’origine des ouvrières présentes dans la colonie. Chez les colonies pérennes, la présence d’un bottleneck royal pendant la saison sèche, associée à des accouplements intranidaux, devraient atténuer l’érosion des degrés d’apparentement liée au chevauchement entre les générations. Par ailleurs, nos résultats montrent aussi que les ouvrières peuvent produire des mâles fertiles. Le maintien de forts degrés d’apparentement et la présence de worker policing devraient garantir la fitness indirecte des ouvrières. <p>Enfin, nous montrons dans cette étude que les profils cuticulaires des individus pondeurs et non pondeurs diffèrent par la présence de quatre alcènes. L’accouplement ne modifie par le profil cuticulaire. Le profil des reines matures, très attractives vis-à-vis des ouvrières, est paradoxalement plus proche des individus non pondeurs. Néanmoins, le pentacosene présent uniquement chez les individus fertiles, pourrait être interprété comme un signal de fertilité par les ouvrières.<p>Dans cette étude, nous montrons que C. pygmaea bien que hautement polygyne possède plusieurs caractéristiques typiques des espèces monogynes. Sa stratégie de reproduction différenciée (la philopatrie des sexués et les essaimages) permet vraisemblablement à la fois la production massive d’ouvrières lors de la dilatation des colonies à la saison des pluies et la colonisation de territoires plus éloignés. La flexibilité de la gynie et de la polydomie de C. pygmaea contribueraient à une meilleure adaptation des colonies face aux saisons marquées du Nordeste brésilien/<p><p>Reproductive strategy is one of the main factors explaining eusociality and the ecological success of ants. In monogynous ants, independent foundation lead to high levels of relatedness between workers, ensuring their indiret fitness. Territoriality helps to maintain the social cohesion of the colony. In polygynous ants, nestmate recognition is generally less efficient, queens have lost the capability of solitary foundation and several maternal lineages lead to lower degrees of relatedness. Although highly polygynous, Crematogaster Pygmaea seems to share several biological traits with monogynous ants. These characteristics make this species a particularly interesting model to test several of the assumptions proposed to explain the origin and maintenance of polygyny in ants.<p><p>In the field, our results reveal that workers of this species are clearly aggressive towards non-nestmates. Populations of C. pygmaea are therefore multicolonial. Traditional Petri dish confrontations were insufficient to determine colonies’ degree of openness. Despite a simple cuticular hydrocarbon profile, alkenes and branched alkanes could be sufficient to support the colonial odor. Colonies of C. pygmaea consist of thousands of workers exchanged between different calies. Genetic and chemical data show that these exchanges contribute to the homogeneity and integrity of the colonies within populations.<p><p>Queen-worker dimorphism is pronounced in C. pygmaea and, in the laboratory, young mated queens are able to initiate a new colony by claustral foundation (in haplometrosis and pleometrosis). In the field, nuptial flights were noted at the beginning of the rain season and several young mated queens were observed digging the wet soil actively, confirming that solitary foundation is likely in this species. Swarming may occur over short distances, as suggested by the positive correlation between genetic and geographic distances among colonies.<p>Queens are able to follow chemical trails. Therefore, they could enter in established colonies. Nevertheless, since (i) workers are able to discriminate and kill foreign queens and (ii) relatedness is strong within colonies, adoption of foreign queens is probably rare. Genetic analysis rather suggest that colonies form family units in which the queens are recruited within a single generation and produce the workers of this generation. <p>Our results also show that workers are able to produce fertile males in the absence of queens. Despite this ability to reproduce, reproductive altruism in workers is probably maintain by high degree of relatedness between colony members and worker policing behaviours.<p><p>Our data show that cuticular lipid of non-fertile individuals (workers and winged virgin queens) differ from those of fertile ones by the presence of four alkenes. Mating does not alter the cuticular profile. Surprisingly, the cuticular lipid profile of mature queens is more similar to those of infertile individuals than to those of young egg-laying queens, although mature laying queens are twice as attractive as young laying queens. However, the relative proportion of one alkene (pentacosene) is clearly higher in mature queens than in their non-laying nestmates. It is therefore suggested that alkenes, and more particularly pentacosene, could be involved in fertility signalling but that queen attractiveness to workers could be released by other, non-cuticular compounds. <p><p>The biological traits of C. pygmaea have been interpreted in terms of adaptation to its environment characterized by sharply contrasting seasons. It is suggested that high number of related queens and polydomy ensure a rapid expansion of the colonies during the rainy season, allowing this species to exploit available resources with efficiency.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Abstract Many waders are in decline, and the number of endangered species and populations is increasing. Their protection and management requires knowledge of both ecological and genetic state of the populations. In this thesis, I studied the distribution-wide genetic variation, structure and phylogeography of the Temminck’s Stint (Calidris temminckii) and Terek Sandpiper (Xenus cinereus) using microsatellites and sequence data from the mitochondrial control region and cytochrome oxidase I gene. I compared these regionally endangered species to other waders with varying evolutionary histories, breeding systems and habitat preferences to examine the levels of genetic variation and structure at different spatial scales. In addition, I studied the genetic structure of the endangered Baltic population of the Southern Dunlin (Calidris alpina schinzii) with microsatellites. I used genetic information in all three study species to determine units for conservation. The Temminck’s Stint and Terek Sandpiper, both not restricted to the Arctic, had low distribution-wide structuring. They also had quite low levels of variation when compared to other species breeding at similar latitudes, indicating reductions in population sizes during past climate changes. Especially the peripheral breeding populations were differentiated and showed signs of inbreeding and genetic drift when compared to the main range. The Temminck’s Stint populations at the Bothnian Bay and Yakutia, and Terek Sandpiper populations in Finland and Belarus, should be treated as separate management units. The broader interspecific comparison of waders suggests that habitat availability, mating system and the extent of philopatry may affect the genetic composition of species. The genetic analyses of the Southern Dunlin indicated strong effects of philopatry and inbreeding throughout the range. Local subpopulations at the Bothnian Bay and in Sweden need to be considered as separate management units. Management efforts at the Baltic should be focused on increasing connectivity and providing large enough breeding habitats for potential immigrants and recruits. / Tiivistelmä Useat kahlaajapopulaatiot ovat pienentyneet ja uhanalaistuneet maailmanlaajuisesti. Lajien ja populaatioiden ekologiaa ja genetiikkaa on tunnettava, jotta suojelutoimia voidaan kohdistaa oikein. Tutkin väitöskirjassani lapinsirrin (Calidris temminckii) ja rantakurvin (Xenus cinereus) geneettistä rakennetta, muuntelua ja fylogeografiaa levinneisyysalueen laajuisesti mikrosatelliittien ja mitokondrion kontrollialueen ja sytokromioksidaasi I -geenin sekvenssien avulla. Tutkin, mitkä tekijät vaikuttavat geneettisen rakenteeseen ja muunteluun vertaamalla näitä lajeja muihin kahlaajiin, joilla on erilaisia lisääntymisstrategioita, jotka pesivät vaihtelevissa ympäristöissä ja joista monet eroavat toisistaan myös fylogeografialtaan. Lisäksi tutkin Itämeren rannalla pesivän etelänsuosirrin (Calidris alpina schinzii) geneettistä populaatiorakennetta mikrosatelliittien avulla. Käytin geneettistä tietoa hyväksi luonnonsuojeluyksikköjen määrittämisessä kaikille kolmelle tutkimuslajilleni. Lapinsirrin ja rantakurvin fylogeografinen historia oli samankaltainen. Geneettisen muuntelun määrä oli vähäisempää verrattuna muihin, samankaltaisissa ympäristöissä pesiviin kahlaajiin. Molemmat lajit ovat todennäköisesti kärsineet historiallisten ilmaston-muutosten aiheuttamasta populaatioiden pienenemisestä. Erityisesti levinneisyysalueen reunoilla pesivät populaatiot olivat erilaistuneita, ja niissä näkyi sukusiitoksen ja geneettisen satunnaisajautumisen merkkejä. Perämeren ja Jakutian lapinsirri- sekä Valko-Venäjän ja Suomen rantakurvipopulaatioita tulee kohdella erillisinä suojeluyksiköinään. Vertailu muihin kahlaajiin osoitti, että niin pesimä- ja talvehtimisalueiden laajuus kuin lisääntymisstrategiat ja paikkauskollisuus voivat vaikuttaa lajien geneettiseen koostumukseen. Etelänsuosirrin geneettiset analyysit paljastivat merkkejä sukusiitoksesta, joita paikkauskollisuus ja populaatioiden pienuus ovat voimistaneet. Perämeren ja Ruotsin populaatioita tulee kohdella erillisinä suojeluyksiköinään. Suojelutoimet on kohdistettava tarpeeksi suurien, hyvälaatuisten pesimäpaikkaverkostojen ylläpitämiseen.

Magister Scientiae - MSc / In many forensic cases, such as mass disasters reconstruction cases, the recovered DNA is highly degraded. In such incidences, typing of STR loci has become one of the most powerful tools for retrieving information from the degraded DNA. However, as DNA degradation proceeds, three phenomena occur consecutively: loci imbalance, allele dropout and no amplification. To solve the problem of degraded DNA, redesigned primer sets have been developed in which the primers were positioned as close as possible to the STR repeat region. These reduced primer sets were called Miniplexes. Unfortunately, a few of the CODIS STR loci cannot be made into smaller amplicons. For this reason non-CODIS miniSTRs have been developed. The present study was undertaken for the population genetic analysis of microsatellite variation in four South African populations; Afrikaner, Xhosa, Mixed Ancestry and Asian Indian using eight non-CODIS miniSTR loci. These miniSTRs loci were characterized within the populations by estimating the levels of diversity of the markers, estimating the population genetic parameters, and studying the inter-population relationships. All of the miniSTRs were amplified successfully and the genetic variability parameters across all loci in Afrikaner, Mixed Ancestry, Asian Indian and Xhosa were estimated to be in the range of 3 (D4S2364) to 12 (D9S2157) alleles, the total number of alleles over all loci ranged from 100 to 204, the allelic richness ranged from 3.612 to 10.307 and the heterozygosity ranged from 0.4360 to 0.8073. Genetic distance was least between Afrikaner and Asian Indian and highest between Xhosa and Mixed Ancestry. Deviations from Hardy-Weinberg equilibrium were not observed for most of the loci. The low mean FIS (-0.027) and FIT (-0.010) and FST (0.017) values across the populations indicated low level of inbreeding within (FIS) and among (FST) the populations. The Asian Indian population showed higher levels of the inbreeding coefficient, indicating less gene exchange between it and other populations. These 8 markers can be used for genetic investigations and assessing population structure. The study contributed to the knowledge and genetic characterization of four South African populations. In addition, these MiniSTRs prove to be useful in cases where more genetic information is needed. / South Africa

During the past century the Swedish otter (Lutra lutra) population showed a rapid decline in abundance and genetic diversity. Among the most affected areas was the southern province of Skåne. After prohibiting hunting of otters and banning harmful pollutants like PCB, Swedish populations slowly recovered. To some areas the otter returned late, like Kristianstad in north-eastern Skåne. Here, the River Helge å enters Kristianstad’s Vattenrike, Biosphere Reserve and forms a biodiverse wetland. By 2011, otters had established once more along the river. In recent years, a female otter with cubs have appeared outside Vattenriket visitor’s centre “naturum”, to the joy of inhabitants and visitors. In Kristianstad, otters have become a recurring winter attraction. However, not much is known about this new population. For assessment of abundance and genetic diversity, microsatellite variation was investigated among now-living individuals from eleven sites in the Biosphere reserve, and stored museum samples from ten otters with origins in North-eastern Skåne. Using a non-invasive methodology, investigated DNA was extracted from faeces and muscle tissue from dead individuals. Multiple replicate screening was performed to detect errors in genotyping procedures. Results show the presence of three now-living individuals (two males and one female). Now-living otters and museum specimens from north-eastern Skåne were not closely related. Sampled individuals show Hardy-Weinberg Equilibrium, but their heterozygosity is very low. Results suggest that, even though some individuals may remain undetected, low admixture of new genes may be a cause for concern. For long-term protection and management in Kristianstad’s Vattenrike, Biosphere Reserve, further knowledge is needed about our new and precious otter population. / Den svenska utterstammen (Lutra lutra) genomgick drastiska populationsminskningar under mitten av 1900-talet. Minskningen ledde till en förlust av genetisk diversitet i många områden, och bland de värst drabbade var Skåne. Uttern blev fredad från jakt och ett förbud mot det skadliga miljögiftet PCB infördes, vilket skapade förutsättningar för utterpopulationen i Sverige att långsamt återhämta sig i antal. Men uttern återvände sent till vissa områden, som Kristianstad i Nordöstra Skåne. Genom staden Kristianstad rinner Helge å, som formar vidsträckta, artrika våtmarker i Biosfärområde Kristianstads Vattenrike. Uttern visade inga tecken på återkomst till området förrän 2011. De senaste åren har en utterhona med ungar regelbundet visat sig vid besökscentret ”naturum”, till glädje för stadens invånare och besökare. Uttrarna har blivit en återkommande vinterattraktion i Kristianstad. Men kunskapen om den nya populationen är begränsad. För uppskattning av antal och genetisk diversitet, undersöktes mikrosatellitvariationer hos nu levande individer från elva lokaler i Vattenriket. För jämförelse inkluderades arkiverade prover från Naturhistoriska Riksmuseets ”Miljöprovbank”, från tio döda uttrar med ursprung i Nordöstra Skåne. Med icke-invasiva metoder undersöktes DNA som extraherats från avföring- och muskelvävnad. Multipel replikatanalys gjordes för detektering av eventuella fel i genotypningsproceduren. Resultaten visar förekomsten av tre nu levande individer i Vattenriket (två hanar och en hona). Det är dock troligt att en- eller flera nu levande individer kan ha undkommit identifiering. Individerna var inte nära släkt med museiexemplaren från Nordöstra Skåne. Studerade individer är i Hardy-Weinberg jämvikt, men heterozygositeten är låg. Låg heterozygositet kan bero på en låg genomblandning i populationen, vilket kan vara en anledning till oro och bör undersökas närmre. Det behövs ytterligare kunskap och studier för att långsiktigt skydda och förvalta den nya, värdefulla utterpopulationen i Kristianstads Vattenrike.