The first metazoan to be sequenced was a nematode (Caenorhabditis elegans), and understanding the genome of this model organism has led to many insights about all animals. Although eleven nematode genomes have been published so far and approximately twenty more are under way, the vast majority of the genomes of this incredibly diverse phylum remain unexplored. Next-generation sequencing has made it possible to generate large amounts of genome sequence data in a few days at a fraction of the cost of traditional Sanger-sequencing. However, assembling and annotating these data into genomic resources remains a challenge because of the short reads, the quality issues in these kinds of data, and the presence of contaminants and co-bionts in uncultured samples. In this thesis, I describe the process of creating high quality draft genomes and annotation resources for four nematode species representing three of the five major nematode clades: Caenorhabditis sp. 5, Meloidogyne floridensis, Dirofilaria immitis, and Litomosoides sigmodontis. I describe the new approaches I developed for visualising contamination and co-bionts, and I present the details of the robust workflow I devised to deal with the problems of generating low-cost genomic resources from Illumina short-read sequencing. Results: The draft genome assemblies created using the workflow described in this thesis are comparable to the draft nematode genomes created using Sanger sequencing. Armed with these genomes, I was able to answer two evolutionary genomics questions at very different scales. The first question was whether any non-coding elements were deeply conserved at the level of the whole phylum. Such elements had previously been hypothesised to be responsible for the phylum body plan in vertebrates, insects, and nematodes. I used twenty nematode genomes in several whole-genome alignments and concluded that no such elements were conserved across the whole phylum. The second question addressed the origins of the highly destructive plant-parasitic root-knot nematode Meloidogyne incognita. Comparisons with the newly sequenced Meloidogyne floridensis genome revealed the complex hybrid origins of both species, undermining previous assumptions about the rarity of hybrid speciation in animals. Conclusions: This thesis demonstrates the role of next-generation sequencing in democratising genome sequencing projects. Using the sequencing strategies, workflows, and tools described here, one can rapidly create genomic resources at a very low cost, even for unculturable metazoans. These genomes can be used to understand the evolutionary history of a genus or a phylum, as shown.

This thesis describes the results of an investigation into the population genetic structure of the blue swimmer crab, Portunus pelagicus, in Australian waters. P. pelagicus is an Indo-West Pacific species, with adults and juveniles that inhabit sheltered benthic coastal environments and a planktonic phase (of modest duration) in its life cycle. The investigation was done by examining the patterns of variation at six microsatellite loci and in a 342 bp portion of the cytochrome oxidase subunit I (COI) gene in the mitochondrial DNA in samples of Portunus pelagicus from a total of 16 different assemblages/waterbodies. Overall, the samples were collected from throughout the geographical range of this species in Australian waters, i.e. from the western seaboard, from the eastern seaboard, from Darwin on the north coast and from South Australia on the south coast. The samples sizes ranged from 4 to 57 individuals, depending on the sample and the genetic assay. The population genetic structure of P. pelagicus was analysed from both a traditional population structure perspective and from a phylogeographical and historical demography perspective. The traditional assessment of the population genetic structure of Portunus pelagicus indicates that this species exhibits a significant amount of genetic heterogeneity in Australian waters (e.g. FST for microsatellite data = 0.098; ¥èST for COI data = 0.375 and ¥ÕST for COI data = 0.492). This assessment also indicates that P. pelagicus exhibits varying degrees of genetic heterogeneity within and between geographical regions in Australian waters, as follows. (1) The genetic compositions of the samples from the different coastlines (i.e. north, south, east and west) invariably showed statistically significant differences for at least two microsatellite loci, although the differences between the samples from the eastern seaboard, Darwin and those from the western seaboard to the north of Port Denison were not as great as those within the western seaboard samples or within South Australian samples. (2) The genetic compositions of the samples from the assemblages on the eastern seaboard of Australia, which ranged from Mackay (21¨¬06¡ÇS) to Port Stephens (32¡Æ40¡ÇS), were essentially homogeneous. (3) The samples from the assemblages on the western seaboard of Australia, which ranged from Broome (17¡Æ58¡ÇS) to Geographe Bay (33¡Æ35¡ÇS), exhibited significant levels of genetic heterogeneity. Furthermore, those from south of Port Denison formed a highly distinctive (but not invariant) group compared to those from elsewhere. (4) The samples from South Australia were also highly genetically distinctive compared to those from elsewhere, although they also showed significant heterogeneity amongst themselves. The above findings were more or less suggested by both the microsatellite and COI markers, although the former generally provided a higher resolution picture of the population structure of P. pelagicus than did the latter. The main findings of the investigation into the phylogeography and recent demographic history of Portunus pelagicus in Australian waters were as follows. (1) A phylogeny constructed from COI sequence variation was shallow, with the lineages showing varied geographical distributions. (2) The results of a nested clade analysis of this variation indicate that range expansion has been a predominant influence on the historical demography of P. pelagicus in Australian waters. (3) The samples from the assemblages on the western seaboard to the south of Port Denison contained low levels of genetic diversity, a sub-set of the diversity present in the samples from lower latitude sites on the western seaboard, and microsatellite-based evidence of having coming from assemblages that have undergone a bottleneck (or founder effect) followed by an expansion in size. (4) The samples from the assemblages in South Australia contained low levels of genetic diversity, phylogenetic affinities with samples from the eastern seaboard, and microsatellite-based evidence of having coming from assemblages that have undergone a bottleneck (or founder effect) followed by an expansion in size. The two major interpretations to stem from the results of this investigation are as follows. (1) Overall, Portunus pelagicus has undergone a recent (in an evolutionary sense) range expansion, from a single source, within Australian waters. At a finer-scale, this species appears to have colonised south-western Australia from a lower latitude site(s) on the western seaboard and probably colonised South Australia from the southern margins of its range on the eastern seaboard. Regardless, there has been limited penetrance of genetic variation into temperate waters on the western seaboard and into South Australia, presumably due one or more of the barriers to gene flow listed below. (2) P. pelagicus experiences significant restrictions to gene flow within its present-day geographical range in Australian waters due to (i) geographic distance per se; (ii) discontinuities in the distribution of the sheltered coastal environments; (iii) hydrological barriers to dispersal and (iv) possibly low temperatures in the temperature margins of the range.

Ostracods are microcrustaceans distinguished by some very particular characteristics. They have a great diversity, occupy different environments - freshwater, marine or semi-terrestrial -, can be adapted to challenging environments as temporary or very restricted water bodies and have an extensive fossil record. All these traits make these animals great models to a variety of biological studies such as ecological, evolutionary or paleoenvironmental ones, just to name a few. In spite of this, studies with the group are not as representative when compared with other crustacean groups. When one dedicates its attention to ostracods living in small, restricted and temporary water bodies, this negligence becomes even more evident. One example of it are the ostracods that inhabit environments such as bamboos, tree holes or bromeliads - together called pythotelmata - and of which we know very little. Actually, solely 14 ostracods are known for phytotelmata from the whole world. From these, eight belong to Elpidium, a genus described in 1880 by Fritz Müller and that is still incredibly poorly understood due to the inconstancy on studies involving the genus. In recent years, however, an effort has been made to fill this gap and improve our knowledge about the genus. In this sense, studies are being made in order to have a clear panorama of what it is the real Elpidium diversity and also to go beyond and think in evolutionary and pluridisciplinary terms. In this work, we aim to continue this effort in understanding this neglected group. To that we planned a broad and pluridisciplinary work that could integrate different aspects of our genus of interest. We dedicate then to (1) ontogeny - clarifying poorly comprehended and/or misunderstood ontogenetic aspects of the type species Elpidium bromeliarum; (2) taxonomy - describing four new species and re-describing Elpidium laesslei; and (3) evolutionary history - proposing the first phylogenetic reconstruction for the genus. Ontogenetic developmental aspects of E. bromeliarum are discussed in chapter 1. In it, we analyzed the possibility - previously proposed on the literature - of an additional moult after the adult stage for this species. Such possibility was not corroborated: the species development is not an exception to the nine developmental stages of the three most important freshwater ostracods superfamilies and it is also in conformity with the well-established fact that ostracods do not moult after mature stage. Taxonomy and diversity are studied in chapters 2 and 3. Such chapters are dedicated to the descriptions of four new species - three from Jamaica and one from Rio de Janeiro, Brazil - and the re-description of E. laesslei from Jamaica. Beyond it, these chapters also discuss about the hypothesis of high degree of diversity and endemism for the genus due to allopatric speciation favored by the relative bromeliad isolation. Chapter 3 is also dedicated to the genus evolutionary history, presenting a hypothesis to the evolutionary relationships between its species. Such phylogenetic reconstruction puts Elpidium as a monophyletic group and its species divided into two major clades. Finally, the need of a pluridisciplinary study to the complete comprehension of the genus and our expectations are discussed / Ostracódes são microcrustáceos acentuadamente diversos que habitam diferentes habitats dulciaquícolas, marinhos e semi-terrestres, evidenciando adaptações a ambientes desafiadores, tais como corpos d\'água temporários ou muito restritos quanto à quantidade de água acumulada. Ademais, têm um extenso registro fóssil. Tais características tornam esses animais bons modelos para estudos biológicos com abordagens ecológicas, evolutivas ou paleoambientais, somente para citar algumas. Apesar disso, investigações científicas envolvendo o grupo não são tão representativas se comparadas a outros grupos de crustáceos. Quando se observa ostrácodes que habitam corpos d\'água pequenos, restritos e temporários, essa negligência se torna ainda mais evidente. Um exemplo disso são ostrácodes que vivem em água acumulada em ocos de colmos de bambu e de árvores ou em tanques de bromélias - ambientes que em conjunto recebem o nome de fitotelmata - e sobre os quais se produziu pouco conhecimento até então. Em termos globais, somente 14 espécies de ostrácodes de fitotelmata foram descritas, das quais oito pertencem a Elpidium, um gênero descrito em 1880 por Fritz Müller e que continua muito pouco compreendido quanto a sua biologia e sistemática, devido à inconstância nos estudos envolvendo o gênero. Recentemente, entretanto, esforços estão sendo feitos para preencher essa lacuna e aprimorar o conhecimento sobre o gênero. Para tanto, estudos estão sendo feitos para verificação da diversidade de Elpidium. Neste trabalho, são apresentados dados inéditos tratando da (1) ontogenia - esclarecendo aspectos ontogenéticos pouco e/ou mal compreendidos da espécie-tipo Elpidium bromeliarum; (2) taxonomia - quatro novas espécies são descritas e Elpidium laesslei, redescrita; e (3) história evolutiva, com a proposição da primeira reconstrução filogenética para o gênero. Aspectos do desenvolvimento ontogenéticos de E. bromeliarum são abordados no capítulo 1. Neste, a possibilidade - proposta anteriormente na literatura - de uma muda adicional após o estágio adulto para a espécie é analisada. Tal possibilidade não foi corroborada e o desenvolvimento da espécie não configura uma exceção ao padrão de nove estágios de desenvolvimento das três principais superfamílias de ostrácodes de água doce e está também em conformidade com o já bem estabelecido fato de que ostrácodes não mudam após atingir a maturidade. Taxonomia e diversidade são abordadas nos capítulos 2 e 3. Tais capítulos são dedicados às descrições de quatro novas espécies - três provenientes da Jamaica e uma do Rio de Janeiro, Brasil - e redescrição de Elpidium laesslei, da Jamaica, além de discorrer sobre a hipótese de que o gênero apresentaria um alto grau de diversidade e endemismo devido à especiação alopátrica favorecida pelo relativo isolamento das bromélias. O capítulo 3 é ainda dedicado à história evolutiva do gênero, apresentando uma hipótese para as relações evolutivas entre suas espécies. Tal reconstrução filogenética coloca Elpidium como um grupo monofilético e suas espécies divididas em dois grandes clados. Finalmente, a necessidade de um estudo pluridisciplinar para o completo entendimento do gênero e nossas expectativas são discutidas

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第19086号 / 人博第739号 / 新制||人||177(附属図書館) / 26||人博||739(吉田南総合図書館) / 32037 / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 瀬戸口 浩彰, 教授 加藤 眞, 教授 市岡 孝朗 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DGAM

Biogeography provides a window into the evolutionary history of populations, and helps explain the diversity and distribution of life through time. Viewed from a systematic perspective, biogeographic studies generate convincing arguments to explain the relationships among organisms and categorize them into useful taxonomies. When taxonomies do not reflect evolutionary histories, inaccurate representations of biodiversity confound future studies and conservation efforts. Two thamnophiine snakes, Nerodia clarkii and Nerodia fasciata, harbor unique morphological and ecological adaptations that obscured natural groupings, leading to controversial taxonomic delimitations. Additionally, population declines documented in N. clarkii compressicauda and N. clarkii taeniata led managers to list N. clarkii taeniata as threatened in 1977. I generated a baseline for continued biogeographic and systematic study of the Nerodia clarkii/fasciata clade. I used mitochondrial DNA to build a parsimony-based haplotype network, infer the phylogenetic relationships between the two species and their thamnophiine relatives, and estimate the divergence times of major N. clarkii/fasciata clades. With these data, I tested biogeographic and systematic hypotheses about the origin and distribution of diversity in this clade. I used principal components analyses to summarize morphological data and discuss ecological observations in search of characters that may unite genetic or taxonomic units. The analyses revealed a peninsular and a panhandle clade in Florida that appeared to iv diverge as a result of Pleistocene glacial fluctuations. I found no support genetically, morphologically, or ecologically for the current taxonomy, indicating a need for range-wide research to generate revised nomenclature. My results do not support the protection status of N. clarkii taeniata

A filogeografia é o campo de estudo que pode revelar a história evolutiva das espécies, sua diversidade e a estrutura genética atual das populações. Neste estudo, foi avaliada a diversidade genética de 13 populações de Epidendrum orchidiflorum (Orchidaceae) utilizando uma abordagem filogeográfica, na tentativa de reconstruir a história evolutiva desta espécie ao longo da Chapada Diamantina e suas serras próximas, do litoral de Bahia e litoral do Rio de Janeiro.Foram usados como marcadores moleculares regiões de DNA de cloroplasto - cpDNA, as quais por serem de herança materna, natureza não recombinante e se encontrarem abundantemente nas plantas, são ideais para este tipo de estudos. Com os dados obtidos do seqüenciamento de duas regiões de cpDNA (rps16-trnK e rpl32-trnL), foram calculados os índices de diversidade para as 13 localidades amostradas, sendo que o número total de haplótipos foi 12. A diversidade haplotípica (Hd) variou de 0 para a população do Litoral da Bahia, Restinga (RE) a 0,889 para a população de Seabra (SE), próxima da Chapada Diamantina. O haplótipo mais freqüente foi o H2 apresentando-se em nove populações. A população RE só apresentou um haplótipo (H2), enquanto que a população de maior diversidade (SE) apresentou seis haplótipos. Além disso, em três populações (SE, Morro do Chapéu e Arraial do Cabo) foram encontrados haplótipos únicos. A análise de variância molecular (AMOVA) indicou que a diferenciação genética encontrada entre populações (FST = 47,5%) é elevada, mostrando que existem diferenças entre populações para esta espécie. No entanto, a proporção de variabilidade de haplótipos encontrados dentro das populações (52,5%, P<0,001) foi maior do que entre as populações.As análises geradas para diferentes agrupamentos testados nas AMOVAS e no programa Migrate-n, sugerem que o melhor modelo que explicaria a conectividade entre as populações seria o modelo de uma grande população panmítica que reúne as populações das serras (JA, PD, RU, MC, CD, SA, LE, CF, MU, PI e SE) com migração para as populações do litoral da Bahia (RE) e a população do Rio de Janeiro (AC). Estas análises são suportadas pelas análises geradas da Modelagem de Nicho Ecológico (EEM), indicando que as populações próximas a Chapada Diamantina se encontram conectadas desde a interglaciação e a última glaciação, porém a população do Rio de Janeiro foi separada durante a ultima glaciação, permanecendo isolada, divergindo ao longo do tempo devido à deriva genética e à mutação. / Phylogeography is the field of study that may reveal the evolutionary history of the species, their diversity and the current genetic structure of populations. In this study, we evaluated the genetic diversity of 13 populations of Epidendrum orchidiflorum (Orchidaceae ) using a phylogeographic approach in an attempt to reconstruct the evolutionary history of this species along the Chapada Diamantina and its nearby sierras, the Bahia coastline and the Rio de Janeiro coastline. We used as molecular markers chloroplast DNA regions - cpDNA, which are maternally inherited, non-recombinant and found abundantly in plants, and for these reasons are ideal for this type of studies. With the data obtained from the sequencing of two regions of cpDNA(rps16-trnK and rpl32-trnL), the diversity index for the 13 sampled locations were calculated, and the total number of haplotypes was 12.The haplotype diversity (Hd) ranged from 0.0 for the Coastal population of Bahia, Restinga (RE) to 0.889 for the population of Seabra (SE), near the Chapada Diamantina. The most common haplotype was the H2 found in nine populations. The RE population showed only one haplotype (H2), while the population of greater diversity (SE) showed six haplotypes. Moreover, in three populations (SE, Morro do Chapéu and Arraial do Cabo) unique haplotypes were found. The analysis of molecular variance (AMOVA) showed that the genetic difference found between populations (FST = 47.5%) is high, showing that there are differences between populations for this species. However, the proportion of haplotypes variability found within populations (52.5%, P <0.001) was higher than among populations. The analyses generated for different groups tested in AMOVAS and in the Migrate-n program suggest that the best model to explain the connectivity between populations would be the model of a large panmitic population that brings together the populations of the Sierras (JA, PD, RU, MC, CD, SA, LE, CF, MU, PI and SE) with migration towards the populations of the coast of Bahia (RE) and the population of Rio de Janeiro (AC). These analyses are supported by the analyses generated by the Ecological Niche Modeling (EEM), indicating that the populations near the Chapada Diamantina are connected since the interglacial and the last glaciation, but the population of Rio de Janeiro was separated during the last glaciation, remaining isolated and diverged over time due to genetic drift and mutations.

Les interactions plantes-pollinisateurs constituent une composante clé de la dynamique de la plupart des écosystèmes terrestres. Les interactions entre espèces jouant un rôle central dans de nombreux évènements de spéciation, l'étude de l'histoire évolutive des caractères étroitement liés à ce type d'interaction contribue à améliorer notre connaissance des mécanismes impliqués. Les insectes représentent le groupe majeur des espèces animales visitant les fleurs pour collecter généralement pollen et/ou nectar, mais certains d'entre eux recherchent d'autres ressources polliniques. Les relations entre les fleurs produisant des lipides et les abeilles spécialisées collectant cette ressource constituent un exemple d'interaction étroite et inhabituelle. Ce type de fleur ne s'observe qu'au sein de 11 familles non apparentées d'angiospermes. L'apparition des structures florales productrices de lipides (élaiophores) résulte d'un seul évènement évolutif dans la plupart de ces familles, à l'exception des Orchidaceae et des Iridaceae où des transitions multiples se sont produites. De plus, même si le nombre de transitions et la manière dont ces structures florales ont évolué à l'intérieur des Iridaceae sont encore inconnus, le nombre et la distribution géographique des espèces sécrétrices de lipides floraux suggèrent que les transitions vers la production de ce type de ressource pourraient avoir joué un rôle clef dans la diversification de la sous-famille des Iridoideae sur le continent américain.L'objectif de cette thèse était d'améliorer la connaissance de l’histoire évolutive de ce système de pollinisation particulier au sein des Iridaceae et d'évaluer son importance en tant que facteur de diversification. Un large échantillonnage de terrain a été réalisé au sein des genres américains de la sous-famille des Iridoideae afin de disposer de phylogénies moléculaires robustes à deux échelles taxonomiques différentes. Le rôle joué par l'évolution des stratégies de pollinisation en relation avec la sécrétion de lipides floraux a été évalué dans le contexte global de la sous-famille mais aussi à une échelle plus réduite. Le genre Sisyrinchium, comprenant à la fois de nombreuses espèces produisant des lipides floraux mais aussi des espèces dont la seule ressource fournie aux pollinisateurs semble être le pollen, et dont la diversification est de loin la plus importante sur le continent américain, a été choisi pour ce deuxième volet de l'étude. Une double démarche a été mise en œuvre, couplant une approche phylogénétique avec la caractérisation micro-morphologique et fonctionnelle des structures susceptibles d'être impliquées dans la relation plante-pollinisateur au sein du genre.Les résultats ont permis de montrer l'apparition répétée des élaiophores aux deux échelles taxonomiques de l'étude et de mettre en évidence le rôle majeur joué par l'apparition de ce caractère homoplasique dans la diversification de la famille sur le continent américain. La poursuite de ce travail nécessitera d'étudier de manière approfondie non seulement la biologie de la reproduction mais aussi la biologie de la pollinisation afin de mieux cerner l'impact de ces interactions sur la dynamique des écosystèmes où elles existent. / Plant-pollinator interactions are key components of the dynamics of most terrestrial ecosystems. Since species interactions are considered to play a central role in many speciation events, studying the evolutionary history of traits closely linked to this kind of interaction contributes to improve our knowledge of the mechanisms involved. Insects are the largest group of animals visiting flowers to collect mostly pollen and/or nectar, but some insects seek other resources. Relationships between oil-secreting flowers and specialized oil-collecting bees constitute an example of a close and uncommon interaction. Flowers offering oil as a resource are found in only 11 families distributed across the angiosperms among unrelated orders. In most of these families floral oil-producing structures (elaiophores) evolved only once, except in Orchidaceae and Iridaceae where oil rewards evolved multiple times. Furthermore, even if our phylogenetic knowledge is too incomplete to infer how many times and how elaiophores have evolved within the Iridaceae, the number and the geographical distribution of oil-flower species suggest that transitions to floral oil-producing structures may well have played a key role in the diversification of the Iridoideae subfamily on the American continent.The goal of this study was to improve our knowledge of the evolutionary history of this uncommon pollination system and to test whether the evolution of elaiophores is a causal factor of diversification within the Iridaceae. Species of the American genera of Iridoideae were widely sampled in the field to produce robust phylogenetic frameworks at two different taxonomic levels. This work aimed at better understanding the evolution of the pollination strategies related to floral oil-secretion not only in the general context of the subfamily but also at a lower taxonomic level. Sisyrinchium, the largest genus in the New World Iridoideae, including species with oil-producing flowers and species with only pollen flowers, was selected for the second part of this study. Phylogenetic analyses were combined with micro-morphological and functional characterizations of the floral structures potentially involved in plant-pollinator interactions within the genus.The results showed that elaiophores evolved several times at both taxonomic levels and that this homoplastic character has played a key role in the diversification of the family on the American continent. For future prospects, thorough studies of the reproductive and pollination biology are required to elucidate how these interactions impact the dynamics of the ecosystems in which they occur.

La biodiversité est définie comme la variété et la variabilité du monde vivant sous toutes ses formes. Elle est souvent appréhendée par la richesse en espèces. Pourtant il existe d'autres « facettes » de la biodiversité (telles que la diversité phylogénétique et fonctionnelle) qui sont à considérer pour comprendre la plupart des processus évolutifs et écologiques. Aujourd'hui, la prise en compte de ces différentes facettes ainsi que les services des écosystèmes –bénéfices que les humains retirent directement des écosystèmes – sont au cœur de l'agenda européen de la conservation. Cependant pour mettre en place de nouvelles actions, une meilleure compréhension des variations spatiales de ces différentes facettes et de leurs relations avec les services des écosystèmes est nécessaire. Ce travail visait à quantifier, décrire et comprendre la distribution de la richesse spécifique et de la diversité phylogénétique et fonctionnelle des tétrapodes d'Europe et leurs liens avec les services écosystémiques. L'étude des patrons spatiaux de la diversité phylogénétique pour différents groupes taxonomiques a montré une absence de recouvrement, une protection inégale et a permis d'identifier des zones particulières d'histoire évolutive indétectables par le prisme unique de la richesse spécifique. Alors que les facteurs environnementaux liés au climat (comme la température ou la productivité primaire) semblent être prépondérant pour expliquer la distribution de chaque facette de diversité, leurs influences respectives varient selon la facette considérée. Enfin, la comparaison de différents scénarios de conservation dans lesquels plus d'importance est donnée soit à la protection de la biodiversité soit à celle des services écosystémiques a mis en avant des relations complexes (synergies et compromis) et non prédictibles mettant en évidence les enjeux liés à la protection simultanée de plusieurs groupes d'espèces, plusieurs facettes de diversité et d'un éventail de services écosystémiques. / Biodiversity is defined as the variety and variability of living organisms on Earth and is often measured through species richness. However, biodiversity is composed of other facets (e.g. phylogenetic and functional diversity) that need to be considered to account for evolutionary and ecological processes. Considering these multiple facets of biodiversity together with ecosystem services – direct benefit human obtain from nature – is central in the European conservation agenda. However, to propose new planning strategies, a better understanding of the spatial variation of these different facets and their relationships to ecosystem services is crucial. The objective of this Ph. D. project was to better quantify, describe and understand the spatial variation of different biodiversity facets and analyse their links to ecosystem services. The study of spatial pattern of phylogenetic diversity showed a low overlap between the different taxonomic groups and an unequal protection within the current European protected areas system. This analysis allowed identifying areas of particular evolutionary history, which would be undetectable through the unique lens of species richness. Although environmental factors related to climate (e.g. temperature, primary productivity) seemed to best explain each facet, their relative importance varied across biodiversity facets. Finally a comparison of conservation scenarios where priority was given either to protecting biodiversity protection or to protecting ecosystem services highlighted complex and unpredictable relationships (synergies and trade-offs) and stressed out the stakes linked to the simultaneous protection of different facets of diversity of multiple taxonomic groups and a set of ecosystem services.

A filogeografia é o campo de estudo que pode revelar a história evolutiva das espécies, sua diversidade e a estrutura genética atual das populações. Neste estudo, foi avaliada a diversidade genética de 13 populações de Epidendrum orchidiflorum (Orchidaceae) utilizando uma abordagem filogeográfica, na tentativa de reconstruir a história evolutiva desta espécie ao longo da Chapada Diamantina e suas serras próximas, do litoral de Bahia e litoral do Rio de Janeiro.Foram usados como marcadores moleculares regiões de DNA de cloroplasto - cpDNA, as quais por serem de herança materna, natureza não recombinante e se encontrarem abundantemente nas plantas, são ideais para este tipo de estudos. Com os dados obtidos do seqüenciamento de duas regiões de cpDNA (rps16-trnK e rpl32-trnL), foram calculados os índices de diversidade para as 13 localidades amostradas, sendo que o número total de haplótipos foi 12. A diversidade haplotípica (Hd) variou de 0 para a população do Litoral da Bahia, Restinga (RE) a 0,889 para a população de Seabra (SE), próxima da Chapada Diamantina. O haplótipo mais freqüente foi o H2 apresentando-se em nove populações. A população RE só apresentou um haplótipo (H2), enquanto que a população de maior diversidade (SE) apresentou seis haplótipos. Além disso, em três populações (SE, Morro do Chapéu e Arraial do Cabo) foram encontrados haplótipos únicos. A análise de variância molecular (AMOVA) indicou que a diferenciação genética encontrada entre populações (FST = 47,5%) é elevada, mostrando que existem diferenças entre populações para esta espécie. No entanto, a proporção de variabilidade de haplótipos encontrados dentro das populações (52,5%, P<0,001) foi maior do que entre as populações.As análises geradas para diferentes agrupamentos testados nas AMOVAS e no programa Migrate-n, sugerem que o melhor modelo que explicaria a conectividade entre as populações seria o modelo de uma grande população panmítica que reúne as populações das serras (JA, PD, RU, MC, CD, SA, LE, CF, MU, PI e SE) com migração para as populações do litoral da Bahia (RE) e a população do Rio de Janeiro (AC). Estas análises são suportadas pelas análises geradas da Modelagem de Nicho Ecológico (EEM), indicando que as populações próximas a Chapada Diamantina se encontram conectadas desde a interglaciação e a última glaciação, porém a população do Rio de Janeiro foi separada durante a ultima glaciação, permanecendo isolada, divergindo ao longo do tempo devido à deriva genética e à mutação. / Phylogeography is the field of study that may reveal the evolutionary history of the species, their diversity and the current genetic structure of populations. In this study, we evaluated the genetic diversity of 13 populations of Epidendrum orchidiflorum (Orchidaceae ) using a phylogeographic approach in an attempt to reconstruct the evolutionary history of this species along the Chapada Diamantina and its nearby sierras, the Bahia coastline and the Rio de Janeiro coastline. We used as molecular markers chloroplast DNA regions - cpDNA, which are maternally inherited, non-recombinant and found abundantly in plants, and for these reasons are ideal for this type of studies. With the data obtained from the sequencing of two regions of cpDNA(rps16-trnK and rpl32-trnL), the diversity index for the 13 sampled locations were calculated, and the total number of haplotypes was 12.The haplotype diversity (Hd) ranged from 0.0 for the Coastal population of Bahia, Restinga (RE) to 0.889 for the population of Seabra (SE), near the Chapada Diamantina. The most common haplotype was the H2 found in nine populations. The RE population showed only one haplotype (H2), while the population of greater diversity (SE) showed six haplotypes. Moreover, in three populations (SE, Morro do Chapéu and Arraial do Cabo) unique haplotypes were found. The analysis of molecular variance (AMOVA) showed that the genetic difference found between populations (FST = 47.5%) is high, showing that there are differences between populations for this species. However, the proportion of haplotypes variability found within populations (52.5%, P <0.001) was higher than among populations. The analyses generated for different groups tested in AMOVAS and in the Migrate-n program suggest that the best model to explain the connectivity between populations would be the model of a large panmitic population that brings together the populations of the Sierras (JA, PD, RU, MC, CD, SA, LE, CF, MU, PI and SE) with migration towards the populations of the coast of Bahia (RE) and the population of Rio de Janeiro (AC). These analyses are supported by the analyses generated by the Ecological Niche Modeling (EEM), indicating that the populations near the Chapada Diamantina are connected since the interglacial and the last glaciation, but the population of Rio de Janeiro was separated during the last glaciation, remaining isolated and diverged over time due to genetic drift and mutations.

Cette thèse étudie le processus de spéciation entre la lamproie fluviatile (Lampetra fluviatilis) et la lamproie de Planer (L. planeri). Les deux espèces présentent des stratégies d'histoire de vie extrêmement différentes : L. fluviatilis est parasite et anadrome alors que L. planeri n'est pas parasite et reste strictement dulcicole. Toutefois, leur degré d'isolement reproducteur et leur histoire de divergence demeurent méconnus. Ces questions ont été abordées par des approches expérimentales, de génomique de populations et de simulations démographiques. Des croisements expérimentaux ont révélé un faible isolement reproducteur, confirmé par des degrés variables de flux géniques dans les populations naturelles. Les analyses génétiques ont montré que les deux taxons représentaient probablement des écotypes avec un isolement reproducteur partiel suggérant que les barrières reproductives endogènes ne réduisaient que partiellement la migration efficace entre écotypes. L'importance du contexte géographique actuel et passé dans l'étude de la spéciation a aussi été mise en évidence par des analyses à l'échelle du génome. Ainsi, les populations isolées de L. planeri évoluent principalement sous l'effet de la dérive génétique et ont une diversité réduite. Les inférences démographiques ont suggéré que la divergence a été initiée en allopatrie puis suivie de contacts secondaires résultant en un parallélisme génomique partiel entre réplicas de paires de populations. Une hétérogénéité de la divergence génomique a démontré que les ilots génomiques de différenciation ne résultaient pas de l'action récente de la divergence écologique. En outre, nos résultats suggèrent un impact faible de la fragmentation anthropique des cours d'eau sur la diversité génétique des populations de L. planeri. Les populations résidentes possèdent une diversité génétique plus grande lorsque le flux de gènes avec L. fluviatilis dans les parties aval des cours d'eau. Globalement cette thèse a démontré que les paires d'écotypes parasites et non-parasites de lamproies représentent un excellent modèle d'étude de la spéciation et notamment de l'architecture génomique de la divergence. / This thesis investigates the process of speciation between the European lampreys Lampetra fluviatilis and L. planeri. The two species have drastically different life history strategies: L. fluviatilis is parasitic and anadromous while L. planeri is non-parasitic and strictly freshwater resident. Yet their level of reproductive isolation and history of divergence remain poorly understood. A multidisciplinary approach including experiments, population genomics analyses and historical reconstruction was undertaken to address these issues. Experimental crosses revealed a very low level of reproductive isolation, partially mirrored by variable levels of gene flow in wild populations. Genetic analyses revealed that the two taxa were best described as partially reproductively isolated ecotypes suggesting that endogenous genetic barriers partially reduced effective migration between ecotypes. Genome wide analyses showed the importance of the current and ancient geographical context of speciation. In particular, parapatric L. planeri populations diverged mostly through drift and displayed a reduced genetic diversity . Demographic inferences suggested that divergence have likely emerged in allopatry and then secondary contacts resulted in partial parallelism between replicate population pairs. A strong heterogeneity of divergence across the genome was revealed by sympatric populations suggesting that genomic islands of differentiation were not linked to ongoing ecological divergence. Further investigations showed that the genetic diversity of L. planeri populations was weakly affected by human-induced river fragmentation. Resident populations displayed a higher diversity when gene flow was possible with L. fluviatilis populations in downstream sections of rivers. Overall this thesis showed that parasitic and non-parasitic lamprey ecotypes represent a promising model for studying speciation and notably the genomic architecture of divergence.