Genetically structured populations arise when gene flow between groups of individuals is hindered by geographical, behavioural or temporal barriers. The identification of such groups is important for understanding evolution and has large implications for conservation concern. The field of population subdivision has received a lot of interest throughout the years and gained empirical support from a number of species. However, very little is known about population structure at small spatial scales, especially in a highly mobile species such as fish. The main object for my thesis was to further investigate population differentiation, explicitly at small spatial scales in the Eurasian perch. My results show that in this species, genetic differentiation occurs, even at very small spatial scales, both within lakes and in the Baltic Sea. Additionally, the differentiation can be stable over years and thus have a large impact in the evolution of adaptation to different environments. I also found barriers to gene flow that overlapped with the largest change in spring temperature, suggesting a temporal difference in spawning. Morphological differences were found at these small scales as well which indicates that a difference in food resources might be an underlying cause of change. My thesis work shows that the aquatic environment might not be as homogenous as widely thought and that there could be barriers or adaptations to different environments that hinder the fish from genetic panmixia. Slight patterns of isolation by distance (IBD) were found in the Baltic Sea, implying that the distance (i.e. currents) effect the level of differentiation via drifting of larvae and/or small fish. However, I have also theoretically investigated the IBD model of and seen that it is no longer correct when differences in population sizes are introduced. The pattern of IBD can mean high levels of gene flow or no gene flow at all, solely dependent on population size differences and fluctuations. My thesis has resulted in new and important findings regarding the existence and cause of genetic differentiation at very small spatial scales and thus added new knowledge into the field of evolution and speciation. In addition, my results also give insights into the contemporary state of the Eurasian perch and future evolutionary potential.

Les mécanismes à l'origine de la mise en place de l'isolement reproducteur sont relativement peu étudiés dans les radiations adaptatives insulaires. Selon la théorie de la spéciation écologique, l'isolement reproducteur résulte de la sélection divergente agissant sur des populations écologiquement différentes. Par leurs caractéristiques uniques, les îles océaniques constituent des systèmes idéals pour étudier le rôle des facteurs écologiques dans la diversification des lignées endémiques. Le rôle de l'habitat et des pollinisateurs dans la restriction des flux géniques inter et intraspécifique est examiné chez le faham (Jumellea rossii et J. fragrans), une orchidée endémique des Mascareignes. Pour ce faire, les patrons de différenciation phénotypique (traits floraux morphologiques et chimiques), environnementale (habitat, altitude, climat) et génétique (microsatellites nucléaires) ont été confrontés. À l'échelle intraspécifique, les résultats montrent que les flux de gènes sont principalement limités par les différences environnementales entre habitats sans rôle évident des pollinisateurs. A l'échelle interspécifique, outre les variations d'habitat, le changement de pollinisateur semble expliquer l'absence de flux de gènes. Dans le cadre du continuum de spéciation chez le faham, l'isolement reproducteur évoluerait en premier lieu en réponse à l'adaptation aux différents habitats, puis serait renforcé par l'adaptation à différents pollinisateurs. La révision de la taxinomie du clade et les priorités en terme de conservation sont également discutées. / Mechanisms responsible for the establishment of reproductive isolation are little studied in island adaptive radiations. According to the theory of ecological speciation, reproductive isolation results from the ecologically-based divergent selection. By their unique characteristics, oceanic islands are ideal systems to study the role of ecological factors in the diversification of endemic lineages. This study focuses on the role of habitat and pollinators in restricting inter and intraspecific gene flow between populations of faham (Jumellea spp.), an orchid endemic to Mascarene Islands. To do this, patterns of phenotypic differentiation (floral traits), environmental differentiation (habitat, altitude, climate) and genetic differentiation (nuclear microsatellites) were compared. At the intraspecific level, the results show that gene flow restriction is mainly due to the colonization of different habitat types with no obvious role of pollinators. At the interspecific level, in addition to the role of habitat, pollinator shift seems to explain effective complete reproductive isolation. By placing these results into the continuum of speciation, it appears that reproductive isolation evolve initially in response to adaptation to different habitats and, in a second phase, would be enhanced by pollinator-driven divergent selection. Operationally, this study reviews the taxonomy of faham and proposes to define management units and priorities in terms of conservation.

Habitat fragmentation can adversely affect species populations due to reduced genetic diversity and increased population differentiation due to habitat isolation, reduced population size, and disruption of gene flow. Many species suffer from habitat fragmentation and isolation, and Campanula glomerata is a good example of a species that is noticeably declining in many places due to changes in landscape management. The question is how the model species responds to these changes and whether is the change are reflected in genetic diversity and population structure. The aim of this work is to determine the degree of genetic diversity and to reveal the genetic structure of populations of the model species C. glomerata on a small regional scale in the White Carpathians. This system will allow us to compare populations from two different regions that have been affected to varying degrees by agricultural intensification and fragmentation in the last century. It is a southwestern and northeastern part of the region, which differs from each other in the history of management in the landscape, but also in the continuity of meadows, species composition and environmental conditions. For this purpose, I developed and optimized a total of 16 usable microsatellite markers, 4 of which come from related species of...

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

Understanding how migration, genetic drift, and natural selection interact to maintain the genetic and phenotypic variation we observe in natural populations is a central goal of population genetics. Amphibians provide excellent model organisms for investigating the interplay between these evolutionary forces because amphibians are generally characterized by limited dispersal abilities, high philopatry, and are obligately associated with the areas around suitable habitats (e.g. breeding ponds). Thus, on relatively small geographic scales, the relative effects of all of these evolutionary forces can be studied together. Here, we study the interaction of migration, genetic drift, natural selection, and historical process in the ornate chorus frog (Pseudacris ornata). We report the development and characterization of 10 polymorphic microsatellite genetic markers. Number of alleles per locus ranged from 2 to 21 averaging 9.2 and expected heterozygosities ranged from 0.10 to 0.97 averaging 0.52. However, in an analysis of two populations, three locus-by-population comparisons exhibited significant heterozygote deficiencies and indicated that null alleles may be present some loci. Furthermore, we characterized genetic structure and historical biogeographic patterns in P. ornata using these microsatellite markers along with mitochondrial DNA sequence data. Our data indicate that in these frogs, migration may play a large role in determining population structure as pairwise estimates of FST were relatively small ranging from 0.04 to 0.12 (global FST = 0.083). Additionally, we observed an overall pattern of isolation-by-distance in neutral genetic markers across the species range. Moreover, our data suggest that the Apalachicola River basin does not impede gene flow in P. ornata as it does in many vertebrate taxa. Interestingly, we identified significant genetic structure between populations separated by only 6 km. However, this fine scale genetic structure was only present in the more urbanized of two widespread sampling localities. Finally, in this study, we demonstrated that there was a significant correlation between the frequency of green frogs and latitude. There was a higher frequency of green frogs in southern samples and a lower frequency of green frogs in northern samples. However, when we interpreted this phenotypic cline in light of the overall pattern of isolation-by-distance, it was apparent that the neutral evolutionary forces of genetic drift and migration could explain the cline, and the invocation of natural selection was not necessary.

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