Members of the family Placobranchidae have been the focus of numerous studies because of their interesting physiological adaptations (kleptochemistry and kleptoplasty) and ecological associations with marine algae. More than 100 species have been described since the 1800's, but no determination of phylogenetic relationships in the family has occurred. DNA sequences from two mitochondrial genes (large subunit ribosomal and cytochrome c oxidase subunit I) and one nuclear gene (Histone 3) were used to reconstruct relationships among 34 nominal species within the Placobranchidae. Strong support for terminal nodes was found using Bayesian phylogenetic methods; however, a "soft" polytomy was detected at internal nodes. In general, the results confirm the paraphyly of Elysia. Proposals for the designation of the genera, Thallepus Swainson, 1840 and Tridachia Deshayes, 1857 and delineation of species are presented. How intrinsic factors affect speciation rates in groups of animals has been a central focus in evolutionary biology. Adaptive radiation associated with food choice has been postulated for the opisthobranch order Sacoglossa. An increase in the rate of cladogenesis was detected within the family Placobranchidae and intrinsic factors such as larval development, kleptoplasty and food choice were investigated as potential key innovations. Ancestral state reconstruction of characters suggests that food choice played a dominant role in influencing speciation rate within the family Placobranchidae. Life history strategy may play an important role in structuring genetic variation throughout the geographic range of a species. Members of the sacoglossan family Placobranchidae Gray, 1840, exhibit variation in life history strategies such as feeding preference and degree of kleptoplasty that could be influential in population structuring. Three species, Elysia subornata Verrill, 1901, Elysia tuca Marcus and Marcus, 1967, and Elysia crispata Mörch, 1863 were sampled from several locations in an attempt to quantify genetic variation as indicated by cytochrome c oxidase subunit I gene sequencing. Elysia crispata exhibited the highest degree of population subdivision followed by Elysia tuca and Elysia subornata. Nucleotide and haplotype diversity also revealed the same general ranking of species. Preliminary conclusions suggest that diversity in feeding preference and degree of kleptoplasty play significant roles in population subdivision of these species.

The island of Sri Lanka’s exceptional biodiversity and enigmatic biogeography begs investigation, as the island is key in understanding the evolution of the Asian tropical flora. Since the Jurassic, Sri Lanka has been subjected to remarkable tectonic changes, thus its flora could have been influenced by that of a number of nearby landmasses, as well giving Sri Lanka the potential to have played a wider role in the assemblage of floras elsewhere. Firstly, as Sri Lanka originated as a fragment of the supercontinent Gondwana, part of its flora may contain Gondwanan relict lineages. There is also the potential for immigration from Laurasia after the Deccan Plate collided with it 45-50 Mya. Further, Sri Lanka may harbour floristic elements from nearby land masses such as Africa and Southeast Asia as a result of long distance dispersals, and in situ speciation has the potential to have played an important role in enhancing the endemic Sri Lankan flora. I tested the relative contributions of the above hypotheses for the possible origins of the Sri Lankan flora using three representative families, Begoniaceae, Sapotaceae and Zingiberaceae. These families represent both herbaceous and woody elements, and have high diversity across the tropics. Dated molecular phylogenies were constructed for each family. I used recent analytical developments in geographic range evolution modelling and ancestral area reconstruction, incorporating a parameter J to test for founder event speciation. A fine scale area coding was used in order to obtain a better picture of the biogeography of continental Asia. Amongst all the models compared, a dispersal-extinction cladogenesis model incorporating founder event speciation proved to be the best fit for the data for all three families. The dates of origin for Sri Lankan lineages considerably post-date the Gondwanan break up, instead suggesting a geologically more recent entry followed by diversification of endemics within the island. The majority of Sri Lankan lineages have an origin in the Sunda Shelf (53%). Persistence of warm temperate and perhumid climate conditions in southwestern Sri Lanka resembling those of Peninsular Malaysia and Sumatra could have facilitated suitable habitats for these massive dispersals from the Sunda Shelf region. Some trans-oceanic long distance dispersals from Africa (11%) are also evidenced, again these are too young to accept a hypothesis of dispersal during the Deccan Plate’s migration close to the African coast during the late Cretaceous, but occurred later during the Miocene. Further, some lineages of Laurasian origin (20%) are evidenced in the Zingiberaceae with ancestral areas of China and Indochina, which is congruent with a post collision invasion. Among the families tested, dispersals have occurred stochastically, one during the Eocene, six during the Oligocene, seven during the Miocene, two during the Pliocene and one during the Pleistocene. The highest number of dispersals occurred during the Miocene when a warm climate was prevailing during the Miocene thermal maximum. My results confirm that in situ speciation is an important contributor to the Sri Lankan flora. More rapid radiation of endemics has occurred during Pliocene-Pleistocene; two endemics in Begoniaceae, ten endemics in Sapotaceae and ten endemics in Zingiberaceae have evolved in situ during this period. Sri Lanka will have been subjected to expansion and contraction of climatic and vegetation zones within the island during glacial and interglacial periods, potentially resulting in allopatric speciation. As a conclusion, long distance dispersals have played a prominent role in the evolution of the Sri Lankan flora. The young ages challenge the vicariant paradigm for the origin and current disjunct distributions of the world’s tropical lineages and provide strong evidence for a youthful tropics at the species level. The thesis contains six chapters; first two are introductory chapters, then there are three analytical chapters, one for each family, and finally a summary chapter is provided. Each analytical chapter is written as a stand-alone scientific publication, thus there is some repetition of relevant content in each.

Dans les génomes bactériens, les fréquents transferts horizontaux de gènes (HGT) introduisent des innovations génomiques qui peuvent entraîner la diversification des populations bactériennes. À l'inverse, la recombinaison homologue (RH) au sein des populations homogénéise leurs génotypes, et ainsi renforce leur cohésion. Ces processus d'échange génétique, et la fréquence à laquelle ils interviennent au sein et entre les populations, doivent avoir un grand impact sur la cladogénèse bactérienne. Au-delà de la configuration des échanges qui se sont réellement produits entre les bactéries, les traces de RH et de HGT que nous observons dans leurs génomes reflètent les événements qui ont été fixés tout au long de leur histoire. Ce processus de fixation peut être biaisé en ce qui concerne la nature des gènes ou allèles qui ont été introduits. La sélection naturelle peut notamment conduire à la fixation des gènes transférés qui apportent de nouvelles adaptations écologiques. En outre, des biais mécaniques dans le processus de recombinaison lui-même peuvent conduire à la fixation d'allèles non-adaptatifs. Nous avons cherché à caractériser certains de ces processus adaptatifs et non-adaptatifs qui façonnent les génomes bactériens. À cette fin, plusieurs aspects de l'évolution des génomes, comme les variations de leurs répertoires de gènes, de leur architecture et de leur composition en nucléotides ont été examinés à la lumière de leur histoire de transfert et de recombinaison / In bacterial genomes, the frequent horizontal gene transfers (HGT) introduce genomic novelties that can promote the diversification of bacterial populations. In opposition, homologous recombination (HR) within populations homogenizes their genotypes, enforcing their cohesion. These processes of genetic exchange, and their patterns of occurrence among and within lineages, must have a great impact on bacterial cladogenesis. Beyond the pattern of exchanges actually occurring between bacteria, the traces of HR and HGT we observe in their genomes reflect what events were fixed throughout their history. This fixation process can be biased regarding the nature of genes or alleles that were introduced. Notably, natural selection can drive the fixation of transferred genes that bring new ecological adaptations. In addition, some mechanical biases in the recombination process itself may lead to the fixation of non-adaptive alleles. We aimed to characterize such adaptive and non-adaptive processes that are shaping bacterial genomes. To this end, several aspects of genome evolution, such as variations of their gene repertoires, of their architecture and of their nucleotide composition were examined in the light of their history of transfer and recombination