Dissertations / Theses on the topic 'Frontiers in Ecology and Evolution'

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.

All organisms must interact with and adapt to their surrounding environment. There are myriad ways in which species accomplish this; ultimately resulting in the vast diversity of life on earth today. Changes in the environment can have profound impacts on an organisms' ability to compete and utilize their surroundings. Plants are particularly impacted by local environmental differences because of the fact that they are immobile. This environmental variation exists at both large and small spatial scales. For example, on larger scales, forces such as fire and grazers can remove dominant plant competitors. on smaller scales, variation in resource availability (e.g. light, nutrients, water) may benefit more phenotypically plastic species. to better understand how changes in the environment, on both large and small spatial scales, I established a two part study using milkweed (Asclepias spp.) as a model system. in the first chapter, I ask how fire, large grazers, and nutrients have affected milkweed abundance over relatively long time and large spatial scales. Here I found that most milkweed species increase in abundance with burning alone but expressed species-specific responses to other treatment combinations. This indicates that milkweed species have likely experienced unique fluctuations in abundance as fire and large herbivores moved across the landscape. The second aspect of this research focuses in on a single year and relatively small spatial scales. Here, using common milkweed (A. syriaca), I ask how environmental variation shapes spatial structuring of phenotypes within fine-scale physical distance and how genotypes impact phenotypes. I found that environment, not genotype, had a relatively larger role on fine-scale phenotypic variation. Combined, these results have implications for understanding the role of large and small scale environmental variations in plant phenotypes and plant abundance.

Theoretical models in microbiology have a relative short but successful history. Research presented in this thesis explores the evolutionary origin of aging and the methods used to quantify syntrophic cooperation between microbial species that are distantly related. The mathematical and computational tools used in doing so are developed and discussed in detail. Microorganisms were long thought to be capable of immortality until recent evidence demonstrated otherwise. Theoretical models suggest that aging strategies sacrificing repair for segregation of damage have highest evolutionary fitness, but this is not reflected in nature. The model developed here corrects this view of aging through more realistic assumptions regarding repair. Many estimates of the rate of interspecies metabolite transfer are based on spatial point pattern statistics and assumptions regarding cell surface concentrations. These are shown to be very inaccurate, but proposed alternatives required greater parameterisation. The system is sensitive to difficulties in determining consumption affinity constants, an issue also raised by previous authors.

Insects are host to a diverse range of vertically transmitted micro-organisms, but while their bacterial symbionts are well-studied, little is known about their vertically transmitted viruses. The sigma virus (DMelSV) is currently the only natural hostspecific pathogen to be described in Drosophila melanogaster. In this thesis I have examined; the diversity and evolution of sigma viruses in Drosophila, their transmission and population dynamics, and their ability to host shift. I have described six new rhabdoviruses in five Drosophila species — D. affinis, D. obscura, D. tristis, D. immigrans and D. ananassae — and one in a member of the Muscidae, Muscina stabulans (Chapters two and four). These viruses have been tentatively named as DAffSV, DObsSV, DTriSV, DImmSV, DAnaSV and MStaSV respectively. I sequenced the complete genomes of DObsSV and DMelSV, the L gene from DAffSV and partial L gene sequences from the other viruses. Using this new sequence data I created a phylogeny of the rhabdoviruses (Chapter two). The sigma viruses form a distinct clade which is closely related to the Dimarhabdovirus supergroup, and the high levels of divergence between these viruses suggest that they may deserve to be recognised as a new genus. Furthermore, this analysis produced the most robustly supported phylogeny of the Rhabdoviridae to date, allowing me to reconstruct the major transitions that have occurred during the evolution of the family. This data suggests that the bias towards research into plants and vertebrates means that much of the diversity of rhabdoviruses has been missed, and rhabdoviruses may be common pathogens of insects. In Chapter three I examined whether the new sigma viruses in Drosophila affinis and Drosophila obscura are both vertically transmitted. As is the case for DMelSV, both males and females can transmit these viruses to their offspring. Males transmit lower viral titres through sperm than females transmit through eggs, and a lower proportion of their offspring become infected. I then examined natural populations of D. obscura in the UK; 39% of flies were infected and the viral population shows clear evidence of a recent expansion, with extremely low genetic diversity and a large excess of rare polymorphisms. Using sequence data I estimate that the virus has swept across the UK within the last ~11 years, during which time the viral population size doubled approximately every 9 months. Using simulations based on lab estimates of transmission rates, I show that the biparental mode of transmission allows the virus to invade and rapidly spread through populations, at rates consistent with those measured in the field. Therefore, as predicted by the simulations, the virus has undergone an extremely rapid and recent increase in population size. In Chapter four I investigated for the first time whether vertically transmitted viruses undergo host shifts or cospeciate with their hosts. Using a phylogenetic approach I show that sigma viruses have switched between hosts during their evolutionary history. These results suggest that sigma virus infections may be short-lived in a given host lineage, so that their long-term persistence relies on rare horizontal transmission events between hosts. In Chapter five I examined the ability of three Drosophila sigma viruses to persist and replicate in 51 hosts sampled across the Drosophilidae phylogeny. I used a phylogenetic mixed model to account for the non-independence of host taxa due to common ancestry, which additionally allows integration over the uncertainty in the host phylogeny. In two out of the three viruses there was a negative correlation between viral titre and genetic distance from the natural host. Additionally the host phylogeny explains an extremely high proportion of the variation (after considering genetic distance from the natural host) in the ability of these viruses to replicate in novel hosts (>0.8 for all viruses). There were strong phylogenetic correlations between all the viruses (>0.65 for all pairs), suggesting a given species’ level of resistance to one virus is strongly correlated with its resistance to other viruses. This suggests the host phylogeny, and genetic distance from the natural host, may be important in determining viruses ability to host switch. This work has aimed to address fundamental questions relating to host-parasite coevolution and pathogen emergence. The data presented suggests that sigma viruses are likely to be widespread vertically transmitted insect viruses, which have dynamic interactions with their hosts. These viruses appear to have switched between hosts during their evolutionary history and it is likely the host phylogeny is a determinant of such host shifts.

The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Title from PDF of title page (University of Missouri--Columbia, viewed on September 24, 2009). Thesis advisor: Dr. James Spain. Vita. Includes bibliographical references.

Les changements globaux provoquent une augmentation des infections associées aux Vibrio. Les vibrioses affectent les humains, mais aussi des animaux marins. Un problème majeur est le manque de connaissances sur les vibrios présents dans l’environnement. Pour mieux comprendre et gérer ces maladies, nous nous sommes intéressés à l’écologie, l’évolution et la virulence de ces agents infectieux. Tout d’abord, nous avons montré que dans la nature, certains génotypes de Vibrio sont virulents pour les huîtres et que leurs mécanismes de virulence sont impliqués dans la différentiation écologique de ces souches. En France, les parcs ostréicoles font face à des évènements de mortalités massives associés à la présence d’un virus et de bactéries du genre Vibrio. Nous avons montré que le virus n’est ni essentiel, ni suffisant pour induire de fortes mortalités, contrairement aux vibrios qui jouent un rôle majeur. Les huîtres juvéniles malades sont toujours infectées par plusieurs populations, mais une seule, Vibrio crassostreae, est détectée en abondance. La virulence de cette population dépend d’un système de sécrétion de type IV codé par un plasmide conjugatif. Nos résultats suggèrent que V. crassostreae était un colonisateur peu virulent et que l’invasion du plasmide l’a rendu hautement pathogène. La distribution restreinte du plasmide de virulence suggère qu’il a été sélectionné par les hautes densités d’élevages. Enfin, nous avons montré que le transfert ou la sélection du plasmide était favorisé dans l’huître, suggérant que l’huître représente une niche propice aux transfert latéraux de gènes. Ce travail pourra permettre le développement d’outils de diagnostic et le suivi épidémiologique des vibrios pathogènes<br>Global change, including anthropogenic activities, have resulted in an increase in the incidence of Vibrio-associated illnesses. These diseases not only affect humans but also marine animals. Despite strong ecological and economic consequences, little is known about population structure and virulence mechanisms of vibrios in the environment. To better understand and manage those diseases, we explored the ecology, the evolution and the virulence of these infectious agents. First, we found that some environmental strains were virulent towards oyster and we identified original virulence mechanisms related to their ecology and evolution. In France, oyster-farms are facing massive mortality events associated with the presence of a virus and bacteria of the genus Vibrio. We showed that the virus appears neither essential nor sufficient to cause high mortality rates contrary to the vibrios that play a major role. Juvenile diseased oysters were always co-infected by several populations, but only one, Vibrio crassostreae, was detected systematically and in abundance. Its virulence is dependent on a type VI secretion system that is carried by a conjugative plasmid. Our results suggest that V. crassostreae first differentiated into a low-virulent oyster colonizer and turned into a pathogen after acquisition of the virulence plasmid. The narrow distribution of the plasmid suggests that it has been selected by high density farming areas. Finally, we showed that the plasmid transfer or selection was enhanced in oysters, which suggests that oysters represent a niche for horizontal gene transfer. Overall, this work can lead to the development of diagnostic tools and epidemiological monitoring of pathogenic vibrios

L'aqüicultura és el subsector productiu agroalimentari amb més creixement des dels anys setanta. El seu percentatge en la producció alimentària marina ha crescut de manera ininterrompuda. En un context de captures decreixents i estocs pesquers en risc, l'aqüicultura ha estat proposada com la solució a la creixent demanda de productes pesquers. Aquesta tendència ha transformat les pràctiques de producció marina, passant de la pesca a la granja, alhora que ha ofert noves fronteres per a l’entrada del capital a través del desenvolupament d'inversions i d’innovacions sociotecnològiques. Aquesta tesi tracta de contribuir a la millor comprensió d'aquesta transformació i de les relacions socials i ecològiques desiguals produïdes. Es centra en el cas europeu, i planteja la pregunta de com i per què l'aqüicultura transforma les relacions de producció en l'àmbit marí i la seva governança. S'han fet servir diverses metodologies qualitatives, en el marc de l'ecologia política, i s'han abordat tres objectius: (i) analitzar els discursos europeus aqüícoles i identificar de quina manera es relacionen amb els processos de confinament i mercantilització del medi marí; (ii) identificar els conflictes socioambientals relacionats amb les granges aqüícoles a Europa des de la perspectiva de la justícia ambiental; i (iii) explorar l'expansió geogràfica, espacial i taxonòmica de les fronteres extractives associades a l'aqüicultura marina intensiva. Els resultats de la investigació suggereixen que l'aqüicultura de peixos marins condiciona i transforma els espais i les relacions productives marines a través de l'expansió contínua del capital, l'extensió a noves fronteres extractives i el confinament de béns comuns. Un procés que és facilitat pels discursos dominants com ara l'imperatiu del creixement. A través de la recerca de vies per a una major acumulació de capital, la transformació de la pesca cap a l'aqüicultura intensiva marina canvia les relacions socials i ambientals en l'àmbit marí. La reconfiguració resultant de l'accés i el control sobre els comuns marins exclou diversos actors, i això al seu torn genera conflictes socioambientals i demandes de justícia ambiental relacionats amb les granges aqüícoles. La investigació assenyala que aquesta expansió produeix nous règims naturals, espacials i socioeconòmics amb la intenció de superar les crisis d'acumulació del capital vinculades al decreixement dels estocs i captures pesqueres, i es produeix mitjançant el confinament i la mercantilització del medi marí. A través de la investigació realitzada, aquesta tesi contribueix a la literatura d'ecologia política vinculada a l'aqüicultura així com als debats teòrics més amplis associats als confinaments, el canvi agrari i socioambiental i la governança ambiental neoliberal.<br>La acuicultura es el subsector productivo agroalimentario con mayor crecimiento desde los años setenta. Su porcentaje en la producción alimentaria marina ha crecido de manera ininterrumpida. En un contexto de capturas decrecientes y stocks pesqueros en riesgo, la acuicultura ha sido propuesta como la solución a la creciente demanda de productos pesqueros. Esta tendencia ha transformado las prácticas de producción marina, pasando de la pesca a la granja, al tiempo que ha ofrecido nuevas fronteras para la entrada del capital a través del desarrollo de inversiones e innovaciones socio-tecnológicas. Esta tesis trata de contribuir a una mejor comprensión de esta transformación y de las relaciones sociales y ecológicas desiguales producidas por ella. Se centra en el caso europeo, y plantea la pregunta de cómo y por qué la acuicultura transforma las relaciones de producción en el ámbito marino y su gobernanza. Se han usado diversas metodologías cualitativas, en el marco de la ecología política, y se han abordado tres objetivos: (i) analizar los discursos europeos acuícolas e identificar de qué manera se relacionan con los procesos de confinamiento y mercantilización del medio marino; (ii) identificar los conflictos socioambientales relacionados con las granjas acuícolas en Europa desde la perspectiva de la justicia ambiental; y (iii) explorar la expansión geográfica, espacial y taxonómica de las fronteras extractivas asociadas a la acuicultura marina intensiva. Los resultados de la investigación sugieren que la acuicultura de peces marinos condiciona y transforma los espacios y relaciones productivas marinas a través de la expansión continua del capital, la extensión a nuevas fronteras extractivas y el confinamiento de bienes comunes. Un proceso que es facilitado por los discursos dominantes como por ejemplo el imperativo al crecimiento. A través de la búsqueda de vías para una mayor acumulación del capital, la transformación de la pesca a la acuicultura intensiva marina cambia las relaciones sociales y ambientales en el medio marino. La reconfiguración resultante del acceso y el control sobre los comunes marinos excluye a diversos actores, y esto a su vez genera conflictos socioambientales y demandas de justicia ambiental relacionados con las granjas acuícolas. La investigación señala que esta expansión produce nuevos regímenes naturales, espaciales y socioeconómicos con la intención de superar las crisis de acumulación del capital vinculadas al decrecimiento de los stocks y capturas pesqueras, y se produce por medio del confinamiento y la mercantilización del medio marino. A través de la investigación realizada, esta tesis contribuye a la literatura de ecología política vinculada a la acuicultura así como a los debates teóricos más amplios asociados a los confinamientos, el cambio agrario y socioambiental y la gobernanza ambiental neoliberal.<br>Aquaculture is the fastest-growing food-production sector globally—since the 1970s, its share in total seafood production has increased uninterruptedly. In the context of falling captures and endangered fish stocks, aquaculture has been proposed as the solution for supplying the rising global seafood demand. This trend has transformed the practices of seafood production from capture to farming, while opening new frontiers for capital with new types of investments and socio-technical innovations. In this thesis, I contribute to understanding this transformation and the resulting uneven social and ecological production relations. By focusing on the case of Europe, I address the question of how and why marine finfish aquaculture transforms the relations of seafood production and marine governance. Adopting a range of qualitative methodological approaches informed by political ecology, my analysis has three objectives: (i) to analyze discourses on European aquaculture and uncover the way they relate to processes of enclosure and commodification of marine areas; (ii) to identify socio-environmental conflicts related to fish farms in Europe and examine them through the lens of environmental justice; and (iii) to explore the geographic, spatial, and taxonomic expansion of commodity frontiers associated with intensive marine aquaculture. The research findings presented in this thesis suggest that marine finfish aquaculture shapes and transforms marine spaces and production relations through the continuous expansion of capital into new commodity frontiers and the enclosure of marine commons, enabled by dominant discourses like growth imperative. By seeking further capital accumulation, the transformation from capture fisheries to intensive marine aquaculture changes social and ecological relations within marine area. The resulting reconfiguration of access to and control over marine commons excludes a variety of social actors, and leads in turn to socio-environmental conflicts related to fish farms informed by environmental justice demands. I claim that such a continuous expansion underpins how capital produces nature, space, and socio-ecological regimes with the intention of overcoming accumulation crises related to declining stocks and capture fisheries through further enclosing and commodifying marine areas. Through these findings, this thesis contributes to literatures on the political ecology of aquaculture as well as to broader theoretical debates on enclosures, agrarian and socio-environmental change and on neoliberal environmental governance.

Gas obtained from previously unexploited shale rock strata has emerged as an economically viable way of sourcing additional fossil fuel energy resources after the so-called ‘shale gas revolution’ in the United States. In the United Kingdom, the incumbent government has committed to the development of its own shale gas resources. A highly polarised public debate has erupted on the risks and rewards of extracting the shale gas deposits that presently lie underneath large swathes of the country using the controversial method of hydraulic fracturing, or ‘fracking’. This thesis examines how different groups in North West England – the major frontier of fracking in the UK – are contesting, resisting and negotiating the current government’s decision to sanction and push ahead towards the development a domestic shale gas industry. Employing a theoretical framework drawn from political ecology as its core mode of examination, this thesis utilises qualitative methods including in-depth interviews and participant observation techniques. It documents a range of social groupings that are contesting shale gas in the UK in a number of ways, and argues that landscapes and risk are fundamental hinges in this ongoing environmental conflict.

Present-day patterns of species diversity and their ecological characteristics in the tropics result from more than 100 million years of evolution. The environmental conditions in which species evolved have left a fingerprint on their functional traits, so investigating this legacy may improve our understanding of current patterns of ecosystem function and potentially guide us in managing our resources more wisely as the climate changes. Amazonian forests are ideal for such a study as they play a major role in the global carbon cycle and harbour a remarkable diversity of angiosperm lineages and species with a broad range of ecologies. Here, I linked data from long-term forest inventory plots, environmental conditions, and a newly constructed phylogeny in order to investigate the legacy of evolution on modern-day patterns of ecosystem function and diversity. I show first that evolutionarily related taxa are more similar in their demography and carbon storage and processing ability (i.e. wood density, potential size, growth and mortality-rates) than expected by chance. Thus, the degree of evolutionary history shared between lineages is a good proxy for their carbon traits. Next, using the evolutionary relationships among lineages I find a legacy of evolutionary history on current patterns of whole ecosystem productivity across the Amazon, such that communities with more evolutionarily distinct lineages have greater wood productivity. Finally, I compare the role of heritability versus selection on shaping lineages preferences for certain environments (i.e. soils and climate). I show that there is a tendency for evolutionarily related taxa to have more similar environmental preferences than expected by chance, but that certain kinds of habitat specialisation have also occurred repeatedly and independently in many lineages. These findings are important for understanding the future of Amazonian forests under global change and support an evolutionary perspective as an important component of conservation strategies.

Davant el canvi climàtic antropogènic i l'imperatiu per descarbonitzar l'economia mundial, s'observa un creixent interès per part d'organitzacions internacionals, bancs de desenvolupament i inversors privats per promoure la implementació de megaprojectes d'energia renovable al llarg de el Sud Global. L'ímpetu per "desaccelerar" el canvi climàtic "accelerant" el desenvolupament verd troba, però, una creixent resistència a escala local. El progressiu augment de conflictes al voltant de megaprojectes d'energia renovable suggereix noves preguntes per a l'Ecologia Política i la Justícia Ambiental - Com s'està concebent la transició energètica i sota quins supòsits? Com es desenvolupen aquests projectes: a on, per qui, per a qui? Quin tipus de transformacions causen aquestes infraestructures i quin és el paper de les comunitats locals en definir aquests canvis? Aquesta tesi estudia els fenòmens apuntats anteriorment enfocant-se en el cas de l'energia eòlica i solar. El treball parteix d'una perspectiva biofísica, emfatitzant que la necessària sortida de les energies fòssils i cap a les energies renovables implicarà reconfiguracions espai-territorials a diferents escales. Aquests processos, qüestionen el com les energies renovables podrien revertir o, per contra, reforçar, les desiguals estructures de poder existents. Al posicionar l'estudi dels conflictes com a tema central d'anàlisi, la tesi posa llum a les veus que desafien els enfocaments dominants per a la implementació de les energies renovables que es deriven de les fórmules de desenvolupament basades en el creixement. El treball es basa en l'Atles de Justícia Ambiental i altres exercicis de cartografia, proporcionant un anàlisi multi-escalar sobre les inversions i els conflictes. Es presenten estudis de cas sobre Mèxic, les Amèriques, Àsia, Àfrica i Europa, identificant patrons comuns i diferències en les veus que reclamen més reconeixement, participació democràtica i redistribució en la transició energètica. L'anàlisi conjunta llança sis resultats transversals per a l'anàlisi, la planificació i la imaginació de transicions energètiques més justes i sostenibles: 1. La naturalesa intrínseca de les energies renovables -més disperses i menys productives que les fòssils- combinada amb l'imperatiu per mantenir l'expansió del metabolisme industrial, es tradueix en noves formes de canvi i conflicte ambiental. 2.-Sota l'imperatiu del "creixement com a desenvolupament", l'expansió d'energies renovables empeny la creació de noves fronteres energètiques. Aquestes fronteres es caracteritzen per la seva naturalesa "horitzontal": es requereixen grans extensions de terra per aprofitar, a escala industrial, els fluxos de radiació solar i els corrents de vent. 3. Les polítiques neoliberals estan jugant un paper central en "trencar les barreres" per a l'expansió d'aquestes fronteres (incloent la liberalització de terres rurals i el sector elèctric). Es facilita, així, la implementació d'infraestructures corporatives, centralitzades i a gran escala; subministrant electricitat per a diferents activitats extractives, indústries i ciutats. 4. Els canvis en la tinença i usos de la terra, així com en la cobertura vegetal que promouen aquestes infraestructures afecten de manera desproporcionada a les comunitats camperoles, indígenes i altres grups rurals de el Sud Global. En aquest procés, els enfocaments públics i comunitaris per a una transició energètica semblen quedar eliminats. 5. La terra i el territori es converteixen en el tema polític central dels conflictes. A escales més àmplies, els conflictes revelen com els megaprojectes renovables estan reforçant la dinàmica centre-perifèria, rural-urbana, nord-sud que ha caracteritzat a el sistema d'energia fòssil. 6.- En lloc de només negociar els beneficis d'un "desenvolupament baix en carboni", les lluites ambientals populars estan obrint espais cada vegada més amplis per configurar enfocaments alternatius a la transició, considerant transformacions socials que apunten a la configuració de metabolismes basats en la suficiència, l'equitat i els béns comuns.<br>Ante el cambio climático antropogénico y el imperativo por descarbonizar la economía mundial, se observa un creciente interés por parte de organizaciones internacionales, bancos de desarrollo e inversores privados para promover la implementación de megaproyectos de energía renovable a lo largo del Sur Global. El ímpetu por “desacelerar” el cambio climático “acelerando” el desarrollo verde encuentra, sin embargo, una creciente resistencia a escala local. El paulatino aumento de conflictos en torno a megaproyectos de energía renovable sugiere nuevas preguntas para la Ecología Política y la Justicia Ambiental ¿Cómo se está concibiendo la transición energética y bajo qué supuestos? Cómo se desarrollan estos proyectos: ¿en dónde, por quién, para quién? ¿Qué tipo de transformaciones desatan estas infraestructuras y cuál es el rol de las comunidades locales en definir tales cambios? Esta tesis estudia los fenómenos arriba apuntados enfocándose en el caso de la energía eólica y solar. El trabajo parte de una perspectiva biofísica, enfatizando que la necesaria salida de las energías fósiles y hacia las energías renovables implicará reconfiguraciones espacio-territoriales en distintas escalas. Estos procesos, cuestionan el cómo las energías renovables podrían revertir o, por el contrario, reforzar, las desiguales estructuras de poder existentes. Al posicionar el estudio de los conflictos como tema central de análisis, la tesis arroja luz sobre las voces que desafían los enfoques dominantes para la implementación de las energías renovables que se derivan del paradigma de Modernización Ecológica y las fórmulas de desarrollo basadas en el crecimiento. El trabajo se basa en el Atlas de Justicia Ambiental y otros ejercicios de cartografía crítica, proporcionando un análisis multi-escalar sobre las inversiones y los conflictos. Se presentan estudios de caso sobre México, las Américas, Asia, África y Europa, identificando patrones comunes y diferencias en las voces que reclaman mayor reconocimiento, participación democrática y redistribución en la transición energética. El análisis conjunto arroja seis resultados transversales para el análisis, la planificación y la imaginación de transiciones energéticas más justas y sustentables: 1. La naturaleza intrínseca de las energías renovables -más dispersas y menos productivas que las fósiles- combinada con el imperativo por mantener la expansión del metabolismo industrial, se traduce en nuevas formas de cambio y conflicto ambiental. 2.-Bajo el imperativo del “crecimiento como desarrollo”, la expansión de energías renovables empuja a la creación de nuevas fronteras energéticas. Estas fronteras se caracterizan por su naturaleza “”horizontal””: se requieren grandes extensiones de tierra para aprovechar, a escala industrial, los flujos de radiación solar y las corrientes de viento. 3. Las políticas neoliberales están jugando un papel central en ”romper las barreras” para la expansión de estas fronteras, incluyendo la “liberalización” de tierras rurales y el sector eléctrico. Se facilita, así, la implementación de grandes infraestructuras corporativas y centralizadas; suministrando electricidad para distintas actividades extractivas, industrias y ciudades. 4. Los cambios en la tenencia, usos y cobertura de la tierra, están afectando de manera desproporcionada a las comunidades campesinas, indígenas y otros grupos rurales del Sur Global. En este proceso, los enfoques públicos y comunitarios para una transición energética parecen quedar eliminados. 5. La tierra y el territorio se convierten en el tema político central de los conflictos. A escalas más amplias, los conflictos revelan cómo los megaproyectos renovables están reforzando la dinámica centro-periferia, rural-urbana, norte-sur que ha caracterizado al sistema de energía fósil. 6.- En lugar de solo negociar los beneficios de un “desarrollo bajo en carbono”, las luchas ambientales populares están abriendo espacios cada vez más amplios para configurar enfoques alternativos a la transición, considerando transformaciones sociales que apuntan a la configuración de metabolismos basados en la suficiencia, la equidad y los bienes comunes.<br>Renewable energies are expanding globally due to the increasing concerns over anthropogenic climate change and concomitant calls to decarbonize the world economy. In this process, international agencies, developing banks, and private investors are progressively shifting attention towards the “developing world,” promoting a rapid deployment of large-scale projects. This momentum, however, brings a paradox to the fore. The idea of “slowing-down” climate change while “speeding-up” green development encounters increasing resistance at local scales. These processes bring new questions for Political Ecology and Environmental Justice studies: How is the expansion of renewable energies envisioned? Under which assumptions? How is this process taking place (where, by whom, and for whom)? How are local territories being rearranged for such purposes, and how are communities involved, actively or passively, in such processes? This dissertation studies the ongoing expansion of mega wind and solar power projects across the Global South and the local contestations emerging in response. The work starts from a biophysical perspective, highlighting that the required phase out from fossil fuels and towards renewable energies implies spatial reconfigurations at different scales. This process, it shows, involves deep social rearrangements, shifting attention to how renewable energies might reinforce or revert existing power structures. In positioning the study of environmental conflicts as the central subject of analysis, the dissertation sheds light on the emerging voices of dissent that challenge dominant approaches to renewable energy implementation stemming from the Ecological Modernization Paradigm and its growth-based development formulas. The work rests on the Environmental Justice Atlas and other critical-cartography exercises, providing a multi-scalar analysis of renewable energy investments and conflicts. It presents different case-studies from Mexico and other contexts of the Americas, Asia, Africa, and Europe. The thesis provides insights on common patterns and diverse narratives of communities claiming their rights for recognition, democratic participation, and redistribution in envisioning a low-carbon future. Six transversal findings shed light on how space, justice, and politics intersect in the study, planning, and imagination of (just) energy transitions: 1. Renewable energies’ biophysical nature, more dispersed and less productive than fossil ones, combined with the imperative of sustaining the growing industrial metabolism, translates into new forms of environmental change and conflict. 2.-The expansion of renewables under a growth-based development paradigm produces new energy frontiers. These frontiers shift attention to its &#8220;horizontal&#8221; character: vast tracts of land are required to harness the flows of solar radiation and wind currents at an industrial scale. 3. Neoliberal policies are playing a central role in &#8220;breaking the barriers” for these frontiers to expand. The deregulation of land transactions and the “liberalization” of electricity markets facilitate the implementation of large-scale, centralized, and corporate facilities, commonly supplying electricity to extractive activities, industries, and cities. 4. Shifts in land tenure, land uses, and land cover are favoring private energy corporations while disproportionally affecting peasant, indigenous, and other rural communities across the Global South. In this process, public and communal approaches for an energy transition seem to be foreclosed. 5. Land becomes the central political subject of emerging conflicts. Local communities mobilize concerns, claims, and discourses around the lack of recognition, participation, and distribution in changes over access, control, and valuation of their territories. At larger scales, conflicts unveil how mega-renewable projects reinforce the center-periphery, rural-urban, north-south dynamics that have characterized the fossil energy system. 6.-As a framework for analysis and as a discourse of political action, Environmental Justice reveals new insights and sets important political questions in the energy transition. Rather than only negotiating the benefits of low-carbon development, popular environmental struggles are increasingly opening spaces to configure alternative approaches to more sufficient, egalitarian, and commons-based metabolic transformations.<br>Universitat Autònoma de Barcelona. Programa de Doctorat en Ciència i Tecnologia Ambientals

Biological N2 fixation, the reduction of dinitrogen (N2) gas to biologically available nitrogen, is a fundamental process since it represents a source of new nitrogen for marine life in areas where this important element can be limiting, supporting primary productivity and thus biological carbon export to the deep ocean. This process is performed by the nitrogen-fixing prokaryotic microorganisms (the so-called diazotrophs). However, very little is still known about the identity and ecology of diazotrophs, which largely limits our capacity to understand the global significance of this process, and to predict potential variations in nitrogen fixation upon changes in environmental conditions. In this thesis, we aimed at improving the knowledge on the diversity, ecology and evolution of the marine nitrogen-fixing microorganisms in the open ocean. Most current knowledge on diazotrophic diversity has been obtained using the nifH marker gene, which encodes for a structural protein of the enzymatic complex that performs the N2 fixation reaction. Thus, in Chapter 1 we first conducted a global exploration of the nifH gene extracted from metagenomic data derived from 68 globally distributed stations collected during the Tara Oceans expedition. This approach differs from previous studies in that it does not rely on primers to detect the nifH genes, and thus allows a more quantitative estimation of the contribution of these microorganisms and a more realistic view of their diversity. This study provides a first `primer-free¿ global map of the distribution of open ocean diazotrophic communities across ocean basins and throughout the water column, showing that diazotrophs often occurred at very low abundances, and that in general they were significantly more abundant in the mesopelagic than in photic waters. Likewise, we uncovered novel diversity that had remained unnoticed in all previous primer-based studies, since we demonstrate that more than half of the detected nifH variants cannot be captured by the primers used. This suggests that most diazotroph diversity studies may be disregarding an important fraction of the nitrogen-fixing community members. Among the diazotrophs detected in Chapter 1, the most abundant was the unicellular cyanobacterium C. Atelocyanobacterium thalassa (UCYN-A), which lives in symbiosis with a prymnesiophyte alga and has been shown to be a relevant player in nitrogen fixation. Thus, in Chapter 2 and Chapter 3, we explored aspects related to the ecology, diversity and evolution of this remarkable microorganism. We detected UCYN-A in the South Atlantic Ocean using not only metagenomic approaches but also microscopic visualization techniques (CARD-FISH). This allowed us to unveil that different UCYN-A lineages, UCYN-A1 and UCYN-A2, live in symbiosis with two distinct prymnesiophyte partners of different sizes. Both UCYN-A lineages showed a streamlined genome expression towards nitrogen fixation. We estimated that these two lineages diverged almost 100 Mya under a strong purifying selection process. Finally, in Chapter 3 we focused on the study of UCYN-A3, another lineage of which very little was known, to gain insight into its ecology. Using an array of methods (PCR, qPCR, CARD-FISH and metagenomes) we could visualize and identify for the first time UCYN-A3 and its association with an alga of different size, which suggests that different UCYN-A lineages occupy different planktonic compartments that are not always considered when nitrogen fixation of nifH diversity are studied. Finally, we manage to reconstruct a significant fraction of its genome, establishing that this lineage constitutes a new UCYN-A genomic species. Overall, this thesis has significantly contributed to expand the knowledge on marine diazotrophic organisms, unveiling new diversity and new planktonic compartments that could potentially lead to a better understanding of the marine nitrogen cycle.<br>La fijación biológica de nitrógeno, es decir, la reducción del nitrógeno (N2) a amonio, es un proceso fundamental ya que representa una fuente de nitrógeno para la vida marina en áreas donde este elemento es limitante, posibilitando la producción primaria y por tanto la exportación de carbono al océano profundo. Este proceso se lleva a cabo por microorganismos procariotas, los llamados diazotrofos. Sin embargo, aún sabemos muy poco sobre la identidad y la ecología de estos microorganismos, lo que limita enormemente nuestra comprensión de la importancia global de este proceso, y nuestra capacidad de predecir cambios en la fijación de N2 ligados a cambios en el ambiente. El objetivo de esta tesis, por tanto, fue ahondar en el conocimiento de la diversidad, ecología y evolución de los microorganismos diazotrofos en el océano. La mayoría del conocimiento actual sobre la diversidad de diazotrofos se deriva del gen marcador nifH, que codifica una proteína estructural del complejo enzimático responsable de la fijación de nitrógeno. Por tanto, en el Capítulo 1 realizamos una exploración global del gen nifH usando datos metagenómicos de 68 estaciones muestreadas durante la campaña oceanográfica Tara Oceans. Nuestra aproximación se diferencia de los estudios anteriores ya que no se basa en el uso de cebadores para detectar el nifH y posibilita por tanto una cuantificación más precisa de la diversidad real. Este estudio representa el primer mapa global (no basado en cebadores) de la distribución de diazotrofos en el océano desde superficie hasta el mesopelágico. Aunque la abundancia de diazotrofos fue muy baja en general, era significativamente mayor en el océano profundo. Asimismo, descubrimos nuevos diazotrofos que habían pasado desapercibidos en los estudios basados en cebadores: más de la mitad de los diazotrofos detectados no se capturan por los cebadores para el nifH. Esto sugiere que la mayoría de estudios previos pueden haber obviado una fracción importante de las comunidades de fijadores de nitrógeno. Entre los diazotrofos detectados en el Capítulo 1, el más abundante fue la cianobacteria unicelular C. Atelocyanobacterium thalassa (UCYN-A), que vive en simbiosis con un alga primnesiofita y que juega un papel importante en la fijación de nitrógeno. En los capítulos 2 y 3 nos dedicamos a estudiar en detalle los aspectos relacionados con la ecología, diversidad y evolución de este diazotrofo. Mediante el análisis de metagenomas y de técnicas de visualización microscópicas como el CARD-FISH pudimos detectar UCYN-A en el atlántico sur, revelando que UCYN-A1 y UCYN-A2, dos linajes diferentes de UCYN-A, viven en simbiosis con dos hospedadores diferentes, dos primnesiofitas de tamaños distintos. Además, el análisis del perfil de expresión del genoma de ambos linajes mostró una dedicación optimizada a la fijación de nitrógeno. La edad de divergencia de UCYN-A se estimó en unos 100 millones de años, y presumiblemente ocurrió bajo presiones evolutivas de tipo estabilizadora. Por último, en el Capítulo 3, nos centramos en el estudio de UCYN-A3, otro linaje del que se sabe muy poco. Mediante el uso de varios métodos (PCR, qPCR, CARD-FISH y metagenomas) se logró visualizar e identificar por primera vez el linaje UCYN-A3 asociado con una alga de tamaño diferente, lo que sugiere que los distintos linajes de UCYN-A ocupan diferentes compartimentos planctónicos que no siempre se consideran en estudios de diversidad de nifH o de fijación de nitrógeno. Finalmente, pudimos reconstruir una fracción importante del genoma de UCYN-A3, estableciendo que representa una especie genómica diferente a las anteriores. En definitiva, esta tesis ha contribuido significativamente al conocimiento de los diazotrofos en el océano mediante el descubrimiento de nueva diversidad como de nuevos compartimentos del plancton donde puede darse la fijación de nitrógeno y que podrían ayudar a entender mejor el ciclo marino del nitrógeno.

The inclusion of spatial structure in biological models has revealed important phenomenon not observed in “well-mixed” populations. In particular, cooperation may evolve in a network-structured population whereas it cannot in a well-mixed population. However, the success of cooperators is very sensitive to small details of the model architecture. In Chapter 1 I investigate two popular biologically-motivated models of evolution in finite populations: Death-Birth (DB) and Birth-Death (BD) processes. Under DB cooperation may be favoured, while under BD it never is. In both cases reproduction is proportional to fitness and death is random; the only difference is the order of the two events at each time step. Whether structure can promote the evolution of cooperation should not hinge on a somewhat artificial ordering of birth and death. I propose a mixed rule where in each time step DB (BD) is used with probability δ (1 − δ). I then derive the conditions for selection favouring cooperation under the mixed rule for all social dilemmas. The only qualitatively different outcome occurs when using just BD (δ = 0). This case admits a natural interpretation in terms of kin competition counterbalancing the effect of kin selection. Finally I show that, for any mixed BD-DB update and under weak selection, cooperation is never inhibited by population structure for any social dilemma. Chapter 2 addresses the Competitive Exclusion Principle: the maximum number of species that can coexist is the number of habitat types (Hardin, 1960). This idea was borne out in island models, where each island represents a different well-mixed niche, with migration between islands. A specialist dominates each niche. However, these models assumed equal migration between each pair of islands, and their results are not robust to changing that assumption. Débarre and Lenormand (2011) numerically studied a two-niche model with local migration. At the boundary between niches, generalists may stably persist. The number of coexisting species may be much greater than the number of habitat types. Here, I derive the conditions for invasion of a generalist using an asymptotic approach. The prediction performs well (compared with numerical results) even for not asymptotically small parameter values (i.e. epsilon ≈ 1).

I use the fig/fig wasp system to address several questions in the fields of evolutionary and community ecology. I present a general review of speciation and community ecology in insects on plants in general and in fig trees (genus Ficus) and fig wasps (Hymenoptera: Cha1cidoidea) in particular. Following on from this introduction are four experimental chapters. The first experimental chapter investigates the contrasting impact of two genera of parasitic, or non-pollinating fig wasps, on their host Ficus and its pollinating wasps. I present my findings in terms of community ecology and mutualism stability. In the second experimental chapter I describe the community of fig wasps associated with two Ficus species from the Australasian Ficus section Ma/vanthera. Using behavioural, ecological and molecular barcoding data I investigate the host Ficus specificity and trophic role of each genus of wasp. Furthermore I carry out a detailed investigation into the mode of speciation in a key kelptoparasite genus: Sycoscapter (Pteromalidae: Sycoryctinae), highlighting the role of ecological speciation in generating diversity. In the next chapter I present a global multi-gene phylogeny of the subfamily Sycoryctinae before evaluating its age, origins and mode of radiation in relation to other major components of fig wasp communities. The final experimental chapter addresses the assembly of fig wasp communities over evolutionary time. I combine phylogenetic and ecological data from three wasp communities associated with three Ficus species from different continents to investigate the roles of niche stasis and niche lability in shaping community structure. I fmd that overall, general ecological rules appear little constrained by the local pool of insect species in these complex, globally dispersed and multi-trophic communities. A general discussion is presented in the fmal chapter in which I highlight areas for future research and provide closing comments. /.

Mexico is a centre of diversity for cacti. The predominantly Mexican genus Ariocarpus Scheidweiler, comprises geophytic cacti endemic to the Chihuahuan Desert. Recent authors recognise seven species in the genus, and many infraspecific taxa have been recognised by these and other authors. All the species are threatened. Proficient management of the Ariocarpu5 species genetic resource, with respect to conservation programs, requires a good understanding of the phylogenetic relationships of the genus and its evolutionary history as well as the levels of genetic diversity in-situ and ex-situ, and population genetic structure across natural populations. In this conservation paradigm, the aims of this project were focused on evolutionary and ecological questions, combining sequence data in phylogenetic analysis, and microsatellite markers in population analysis. Employing a Bayesian Concordance Analysis (BCA), seven nuclear microsatellite flanking regions (MFRs) and two chloroplast markers provide an estimation of past events in the evolution of the genus. Results are . suggestive of hybridisation early in evolution of the group. Ten microsatellite loci were amplified across 407 individuals collected from 18 populations representing all seven species of Ariocarpus. Genetic parameters and population structures were described per species. Gene flow between populations and correlation between genetic and geographic distances were calculated when all species data were combined. Results suggest vicariance events playa critical role in the speciation process. The same microsatellite loci were characterized in a putative hybrid. Bayesian cluster analysis showed ongoing natural hybridization between two sympatric species. Eleven microsatellite loci were analysed for two populations of the critically endangered A. bravoanus. Selective removal of plants from natural populations is shown to diminish genetic variability and substructure. The use of ex-situ genetic resources might be considered to improve genetic diversity whenever this material can be allocated to its natural source.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.<br>Cataloged from PDF version of thesis. Each chapter with its own abstract. Each appendix with its own summary.<br>Includes bibliographical references.<br>Microbial secondary metabolites are among the most structurally and functionally complex molecules in nature. Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive post-translational modification. Most lanthipeptides are bactericidal but they are also known to act as signaling molecules or morphogenetic peptides, nevertheless the function of many lanthipeptides remains unknown. Prochlorosins are a diverse group of lanthipeptides produced by strains of the ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Unlike other lanthipeptide-producing bacteria, picocyanobacteria utilize an unprecedented mechanism of catalytic promiscuity for the production multiple structurally diverse lanthipeptides using a single biosynthetic enzyme. Also unprecedented is the production of lanthipeptides by single celled, planktonic gram-negative bacteria in a dilute nutrient-limited habitat, which suggests that they may have an unconventional biological function. The overarching goal of this thesis is to further our understanding of the ecology and evolution of the prochlorosins, and provide insights into their biological role in the marine environment. Here, we demonstrate that the prochlorosin genes are widespread in the ocean and that globally distributed populations of marine picocyanobacteria have the genetic potential of producing thousands of different lanthipeptide structures. The diversity of prochlorosin structures provides an interesting model to study the evolutionary forces that drive the creation of new lanthipeptide structures. We present evidence that there is a unique evolutionary interplay between the components of prochlorosin biosynthesis pathway; while the peptide substrates independently expand and diversify within the genome, the catalytically promiscuous biosynthetic enzyme evolves under a strong purifying selection that maintains its substrate tolerant state. This relationship indicates that the lanthipeptide production trait in marine picocyanobacteria might find its evolutionary advantage in the plasticity of the production of multiple cyclic peptides with diverse ring topologies. The remarkable diversity of prochlorosins poses many questions regarding their biological role in the marine environment. In laboratory experiments, we explore of some of the potential bioactivity of the prochlorosins, namely their potential as signaling molecules, antimicrobials and nutrient sources. The results from this exploration open new perspectives for the role of the lanthipeptides in the natural environment - more specifically the oligotrophic ocean.<br>by Andrés Fernando Cubillos-Ruiz.<br>Chapter 1. Chapter 2. Chapter 3. Chapter 4. Chapter 5. Appendix A. Appendix B. Introduction -- Evolutionary radiation of lanthipeptides in natural populations of marine picocyanobacteria / Andres Cubillos-Ruiz ; Jessica W. Berta-Thompson ; Jamie Becker ; Sallie W. Chisholm -- Exploring the biological role of prochlorosins / Andres Cubillos-Ruiz ; Jamie Becker ; Yanxiang Shi ; Wilfred van der Donk ; Sallie W. Chisholm -- Amino acid toxicity and tolerance in prochlorococcus / Andres Cubillos-Ruiz ; Audrey Olshefsky ; Sallie W. Chisholm -- Conclusion and future directions -- Proposed molecular mechanism for the expansion and diversification of prochlorosins - Hawaii Ocean experiment : prochlorosin amendment.<br>Ph. D.

Bacterial infections are an increasing cause for concern as resistance spreads to the majority of our front line antibiotics. To counter antibiotic resistance, new treatment regimens and drug targets are being investigated, including directly targeting bacterial virulence (pathogen-induced harm to the host), and therapies which target resistance mechanisms. The outcome of successful treatment with these compounds is not always killing or halting growth of bacteria, therefore selection for resistance to these types of therapeutics is complex. This complexity is increased by the secretion of many virulence factors, meaning their effects are shared with neighbouring individuals. In addition virulence factors show high phenotypic plasticity due to regulation by processes like quorum sensing (QS), which further complicates treatments targeting virulence, or the regulatory processes themselves. Using the example of quorum sensing inhibitors this study shows the importance of understanding the function and ecology of targeted virulence factors, to predict the selection for resistance to anti-virulence drugs. Later chapters elaborate on this to show how quorum sensing control affects selection on secreted virulence factors. The use of anti-virulence drugs as adjuvants is discussed, with a study showing that the interaction between QS inhibition and translation inhibitors is dependent on the environment. The selection for resistance to combinations of antibiotics and adjuvants is investigated using co-amoxiclav as an example, showing that treatment with high doses of adjuvant are robust to the evolution of resistance.

Microbial communities colonise virtually every habitable environment on earth. They live on us, inside us, and all around us, and are key components of the earth's ecosystem. However, due to the complexity of microbial communities we still understand relatively little about the mechanisms that drive their ecology and evolution. The aim of this thesis is to develop novel experimental and mathematical approaches, in order to investigate complex microbial communities. Specifically, this thesis is split into two parts, focussing in turn on how environmental complexity, and interspecies interactions shape microbial ecology and evolution. In the first part I have studied microbial evolution in porous environments such as one might find in soil or aquifers. Here I have combined microfluidic experiments, mechanistic models, and game theory to study how hydrodynamics mediate competition between bacterial genotypes. With these I have demonstrated how even subtle environmental complexity can fundamentally affect microbial competition, enabling slow growing genotypes to outcompete their faster counterparts. In the second part of this thesis I have investigated how interspecies interactions influence the stability and initial assembly of microbial communities. Here I have developed new tools - from theoretical ecology - in order to study the microbial communities within the mammalian gastro-intestinal tract. With these I have demonstrated how strong, cooperative interactions between species can undermine both the stability, and the assembly of communities. Moreover, I have illustrated how these tools can be applied to real microbiome data, in order to better understand these important communities. In sum, this thesis explores two key drivers of microbial ecology and evolution, and presents a new set of tools for the future investigation of complex microbial communities.

Central to this thesis is the investigation of how several factors (e.g. morphology, ecology, and social conditions) co-vary with consistent individual behavioural variation. Additionally, conceptual work explores the reach of consistent inter-individual behavioural variation in several novel contexts. In doing so, the aim is to contribute novel findings to the quickly growing compendium of knowledge concerning 'animal personality' in various settings. In summary, during this PhD the following research has been performed: • Through the use of lab-reared juvenile three-spined stickleback (Gasterosteus aculeatus) whose parents came from different habitats, I investigated the relative contribution of plasticity and (epi)genetic mechanisms on three behaviours (boldness, activity, and sociality). While these behaviours did not differ between juveniles from both populations, correlations of body length with specific behaviours did. (Chapter 2) • During fieldwork on the Scottish island of North Uist, seven populations of wild three-spined stickleback were surveyed for boldness, exploratory behaviour, and activity. Furthermore, the defensive morphology of these fish was quantified following an armour-staining protocol. Bold fish were found to be less armoured, directly contradicting the phenotypic compensation hypothesis, while more active fish were more armoured, which contradicts the idea that armour is energetically costly. (Chapter 3) • Spurred on by the findings on morphology-behaviour correlations, the ecology of the studied populations was assessed with a focus on parasitism by three common macro-parasites of three-spined stickleback, predation by trout, competition with the nine-spined stickleback, and the availability of resources. I found that all these factors, to some extent, influence individual behavioural variation. Importantly, this study provides the first observational evidence that less-explored factors, such as resource availability and interspecific competition, can be highly relevant influences on individual behaviour. (Chapter 4) • Next, a study on the effect of group behavioural composition on group foraging behaviour was done. With the help of a research visit to Aarhus University, similar experiments were performed on stickleback and social spiders (Stegodyphus dumicola). Group behavioural composition had a strong effect in both study systems, but experience was a more relevant influence on group foraging behaviour in stickleback. By using two different study organisms from quite disparate animal taxa, this allows me to develop hypotheses concerning the evolutionary origin and maintenance of individual behavioural variation and its tentative link with sociality. (Chapter 5) • Lastly, the phenomenon of consistent individual variation in behaviour is explored in novel contexts through conceptual essays (Chapter 6). o Do bacteria offer a suitable system to study ‘personality’? o How can animal personality be leveraged to improve animal welfare? o Are non-antagonistic interspecific interactions an overlooked yet important factor in the study of animal personality?

The evolution of species interactions is a fascinating subject, and one of vital importance if we are to understand how biological communities change over time. This thesis considers the interaction between aphids (Homoptera) and ants (Formicidae). Ants tend aphids for sugary honeydew and in return provide a variety of protective services. A literature review in Chapter 1 introduces the subject and provides background information. Chapter 2 considers ant- aphid interactions in a community setting. Specifically, I consider the fitness effects of the ant- aphid interaction on host plants. Net benefits or costs to plants depend on the densities of ants and aphids; these densities may themselves change depending on context dependent factors. Chapters 3 and 4 consider how semiochemicals can allow species to respectively maintain or avoid synchrony in space and time with mutualists or antagonists. Chapter 3 shows ladybirds avoid prey patches guarded by ants by reducing oviposition in response to ant semiochemicals. Chapter 4 shows that aphid walking dispersal can be limited by ant semiochemicals. This may be adaptive for aphids to remain in areas of enemy- free space. Alternatively, if levels of kin competition are high limited dispersal could be costly to aphids. In Chapter 5 I consider interactions between invasive and native ants. Ecological dominance in ants may be mediated by the ability to monopolise honeydew- producing resources. Chapter 6 explores ants’ decisions whether to tend or prey upon aphids. Predation of aphids depends on colony demand (e.g. through cues from the presence of larvae) as well as the quality or quantity of supply (e.g. increased predation of unproductive aphids). Finally, Chapter 7 deals with macroevolutionary patterns in the interaction between ants and aphids. Specifically, I identify ecological traits that characterise aphid- tending ants. A final discussion chapter summarises how ant-aphid interactions fit into existing mutualism theory.

The Tachinidae is a taxonomically and ecologically diverse clade of parasitoids for which evolutionary and ecological relationships with hosts are largely unknown. Here, I employed a multidisciplinary approach to evaluate the determinants of patterns of host use in the Tachinidae. First, I examined spatio-temporal variation in the tachinid-dominated parasitoid assemblage of one lepidopteran species Grammia geneura . The parasitoid assemblage and parasitism rates varied dramatically among and within sampling sites, seasons, and years. I show that this variability may be a function of habitat-specific parasitism and indirect interactions between this host and other Macrolepidoptera through shared tachinid parasitoids. I then experimentally examined the host selection process in the tachinid Exorista mella. Host movement was an important elicitor of attack behavior. Flies also responded to odors associated with food plants of their host. Experienced flies attacked hosts more readily than did inexperienced flies. Based on these results, I proposed a host selection scenario for this tachinid species. E. mella also teamed to associate colors with hosts and avoided deterrent models that they had experienced. However, I failed to find evidence for odor learning. Learning of host-associated cues by E. mella may allow this parasitoid to take advantage of abundant host populations and maintain host-searching efficiency in an unpredictable environment. To examine how host-associated characteristics evolved in the Tachinidae, I reconstructed the evolutionary relationships within the subfamily Exoristinae using molecular data. Phylogenetic analyses generally supported recent classifications. Analyses of host-related characters indicated that tachinids show great evolutionary lability in behavior, morphology, and host range. Finally, I sampled host species to assess the determinants of tachinid community structure and host range. Several host characteristics were found to affect tachinid species richness. These patterns may be due to the opportunistic use of abundant hosts by polyphagous tachinids, enemy-free space provided by well-defended hosts, and the process of host location. Patterns of tachinid host use varied significantly with sample size, host diet breadth, host gregariousness, plant form, and host morphology. Taken together, these studies indicate high levels of plasticity in tachinid-host associations. This may be responsible for their ecological and evolutionary success.

Family-living has been recognized as a necessary prerequisite for the evolution of advanced cooperative societies, yet the evolutionary and ecological processes that drive the coupling of different forms of cooperation in family-based societies are still poorly understood. In my dissertation, I investigate the correlated evolution of parental care, monogamy, and cooperative breeding in a variety of family-based taxa. I explore the mating and social behavior of family-living beetles with incipient cooperation to better understand the factors driving these social traits. Specifically, I evaluate different causes of extra-pair mating in socially monogamous beetles, the potential benefits that young adult offspring may gain from remaining in the family group, and how these behaviors correspond to different ecological niches. These studies demonstrated that many of the factors predicted to favor family-living in cooperatively breeding animals fail to explain delayed dispersal and family cohesion in this beetle group. In a phylogenetic comparative study of birds, I further evaluate how ecological selective pressures drive the correlated evolution of monogamy, biparental cooperation, and cooperative breeding. Taken together, these studies have implications for our general understanding of the evolution of cooperation, and suggest the action of previously unrecognized processes in shaping and pairing social behaviors.

CCL3LI and CCL4LI are chemokine genes, located on chromosome 17q12. They are copy number variable genes which share 95% sequence identity with their non-copy number variable paralogues CCL3 and CCL4. The copy number of these genes varies between populations and has been reported to be associated with phenotypes such as susceptibility to HIV infection, hepatitis C virus infection, Kawasaki disease and SLE. The aim of this study is to understand the evolutionary history of variation at the CCL3L1/CCL4LI cluster. To accomplish this goal, several approaches including typing microsatellites, single nucleotide polymorphisms (SNPs) and CCL3L 1/CCL4L 1 sequence haplotypes were used to investigate the association with CCL3L 1 and CCL4L 1 copy number. However, the results showed that there is no strong association between a single-copy marker and CCL3L 1 and CCL4LI copy number, but there is evidence of recombination. Therefore, this may suggest that CCL3L 1/CCL4L 1 is a complex region and one plausible hypothesis is that there is a high rate of recombination in this region. This study of the evolution of CCL3L 1/CCL4L 1 haplotypes showed that a major one-copy CCL3L 1/CCL4L I haplotype (about 70% haplotype frequency) identified in humans, represents the ancestral state, as inferred from comparison with chimpanzee.

The rapid pace of anthropogenic global change threatens global biodiversity and the integrity of ecosystems. It is now paramount to understand how organisms can adapt to these changes. Here, I review the literature on the genetic nature of stress responses in Drosophila and bacteria. Then I test how yeast populations adapted to a particular stressor, salt, can resist related stressors which they have not experienced in their recent past, freezing and sorbitol. We found that lines adapted to high salinity did not show increased resistance to sorbitol and freezing. Finally, again with yeast subjected to high salinity, I exposed populations to extremely stressful and continually deteriorating conditions to investigate how adaptation occurs. We found that beneficial mutations started to spread at intermediate stress intensities. We also found that larger populations adapt more rapidly to stress, both because they possess more beneficial mutations and because these mutations have a larger effect on growth. This research will help us understand how population can avoid extinction through adaptation and continues to stress the importance of maintaining large population to allow species survival in a changing environment.<br>Les changements anthropogéniques menacent la biodiversité et l'intégrité des écosystèmes à une échelle globale. Il est donc maintenant essentiel de comprendre comment les êtres vivants peuvent s'adapter à ces changements. Ici, je commence par présenter l'état de la recherche concernant la réponse génétique de la drosophile et des bactéries à l'imposition d'un stress. Je montre ensuite comment j'ai testé la capacité de croitre d'une population adapté à un stress donné, le sel, quand ces populations sont soumis à des stress similaires, la congélation et le sorbitol. J'ai constaté que l'adaptation au sel ne confère pas une plus grande résistance à la congélation ou au sorbitol. Finalement, encore avec la levure soumise à des conditions salées, j'ai exploré comment les populations s'adaptent à un stress important qui augmente continuellement. J'ai découvert que les mutations avec un effet bénéfique prenaient de l'importance dans la population à des niveaux de stress intermédiaires. J'ai aussi découvert que les populations plus nombreuses s'adaptaient plus rapidement parce qu'elles avaient un plus grand nombre de mutations à effet bénéfique et qu'en plus, l'effet de ces mutations était plus grand dans ces grandes populations. Ces recherches nous informent sur le processus d'adaptation et rendent clair une raisons de plus pour laquelle une grande population augmente les chances de survies de l'espèce dans un environnement changeant.

Abstract The environment is now changing much faster than in recent geological time, causing increasing population extinctions. Experiments have shown that extinction can be avoided by adaptation through natural selection leading to evolutionary rescue. I first determined the response of Chlamydomonas to stressful environments by growing populations over a range of salinity. The population growth is halved at 5 g/L salt (NaCl), and 8 g/L is lethal. In this experiment, the genetic correlation between environments increases with environmental similarity. I then manipulated the genotypic diversity in experimental populations and cultured them by serial transfer at 5 g/L salt. The outcome of adaptation is not influenced by initial genetic variation. Instead, populations adapted mainly through the spread of new beneficial mutations. These results suggest that populations have a greater chance of adapting when new environments are similar to current conditions and that adaptation is sometimes dominated by the spread of new mutations, even in the presence of a substantial amount of standing genetic variation.<br>Résumé Notre environnement change maintenant beaucoup plus rapidement que dans le passé géologique récent, précipitant l'extinction de plus en plus d'espèces. Des chercheurs ont démontré que, grâce à l'adaptation par la sélection naturelle, des espèces peuvent éviter l'extinction, un processus nommé sauvetage évolutif. J'ai d'abord étudié la capacité de Chlamydomonas à croitre dans des environnements dont la salinité augmente. J'ai trouvé que 5 g/L de sel diminue la croissance de moitié tandis que 8 g/L est suffisant pour empêcher toute croissance. Ici, la corrélation génétique entre environnement augmente avec la similarité des environnements comparés. J'ai ensuite soumis des populations contenant différentes quantités de diversité génétique initiale à une salinité de 5 g/L. La diversité génétique initiale ne semble pas influencer la capacité d'adaptation. Cependant, les populations semblent plutôt s'adapter en utilisant de nouvelles mutations dont l'effet est bénéfique. Ces résultats suggèrent que les populations s'adapteront plus facilement à des environnements similaires aux conditions présentes. De plus, ce processus sera dominé par la fixation de nouvelles mutations, même dans des populations contenant de la diversité génétique.

This thesis investigates the ecological determinants of chewing louse (Insecta: Phthiraptera) host-specificity on four species of Malaysian swiftlets (Aves: Apodidae). Influences of host coloniality on louse ecology were also demonstrated, illustrating the dependence which these permanent ectoparasites have on their hosts. Louse collections were made to look for incidences of host-specific lice occurring on the "wrong" host ("straggling"). Straggling was observed, implying that lice disperse among host species. Thus, opportunity for louse dispersal (or lack thereof) does not govern the host-specificity of chewing lice on swiftlets. Experimental transfers of lice between hosts were conducted. Louse survival was reduced on foreign host species. This implies adaptation to specific host characters, suggesting that specialisation governs chewing louse host-specificity on swiftlets. There was no evidence for reciprocal adaptation of swiftlets to their normal louse species. Lice had no impact on the fitness of either swiftlets or the related common swift. Furthermore, neither swiftlet nor swift lice were transmitting pathogenic endoparasites. This implies that chewing lice and Malaysian swiftlets have not "coevolved". Survival of transferred lice was determined by the relatedness of donor and recipient hosts. Closer related swiftlet species are more similar in body size and feather dimensions. When the feather dimensions of the microhabitat distributions of the same louse species on different hosts were compared the results suggested that lice keep the dimensions of barb and barbule diameter, at which they occur, "constant" through microhabitat shifts. This suggests that feather dimensions are the host characters which determine the survival (and host-specificity) of chewing lice on birds. The ability of chewing lice to survive on hosts with similar feather morphology implies that "host-switching", between distantly related hosts with similar morphological characters (due to parallel or convergent host evolution), may have been an important factor in the evolution of bird-louse associations.

Understanding the conditions that favour the evolution and maintenance of spiteful bacteriocin production combines two important questions from the fields of social evolution and microbiology. Spiteful behaviours, though, initially thought to be rare represent an important class of interactions between bacteria through the production of bacteriocins. Bacteriocins can be considered spiteful as they are costly to produce (in many cases requiring lysis) and are costly to sensitive bacteria (i.e. they are lethal). However, much about the ecology of spiteful behaviours and bacteriocin production remains unclear. Mathematical models have given us important insights into some conditions that should favour bacteriocin production, but few empirical studies exist supporting these results. In this thesis I use the bacterium Pseudomonas aeruginosa (a prolific producer of bacteriocins), to examine conditions that favour bacteriocin production. I also investigate more specific elements about this system and toxin production in general. I find that bacteriocin production in P. aeruginosa closely follows predictions made from mathematical models under a range of different conditions (e.g. frequency, scale of competition, multiple social traits). I also find that resistance can evolve to bacteriocins and biological mechanisms such as the neutralisation of one’s own toxin can have important consequences. Finally, I consider bacteriocin as a policing trait testing predictions about the role that linkage plays in policing. This work represents a comprehensive study into the importance of bacteriocin production in bacteria.

The marine environment presents fewer absolute geographic barriers to gene flow than its terrestrial and freshwater counterparts. In addition, the prevalence of planktonic larval stages in marine taxa provides potential for gene flow across large geographic distances. These observations raise two fundamental questions. How do new species arise in the marine environment? Considering the potential for gene flow in marine systems, it remains unclear to what extent allopatric speciation alone can account for the high levels of diversity observed in the marine realm, whether marine speciation also operates in the presence of gene flow, and if it does under what specific mechanisms. How far do planktonic larvae travel with marine currents? The generally low levels of genetic structure among marine populations suggests extensive dispersal, yet planktonic larvae are notoriously difficult to track owing to their small size and as a consequence the spatial scale of marine dispersal is still largely eluding ecologists. Here, I consider brightly colored coral reef fishes in the genus Hypop/ectrus (Serranidae) as a model system to address these two questions. I demonstrate the potential for ecological speciation with gene flow to operate in this system through the pleiotropic effect of color pattern, which appears to be involved both in mimicry and mate choice. I show that local processes are operating at the Caribbean scale in this system, suggesting dispersal limitation. I test and confirm this hypothesis by reporting genetic isolation by distance in the barred hamlet (Hypop/ectrus puel/a) at spatial scales ranging from 175 to 3,200 km. In order to estimate mean dispersal distance, I complement genetic data with SCUBA surveys of population densities covering 94,000 m2 of reef and provide dispersal estimates ranging between 2 and 14 km for specific dispersal functions notwithstanding the three-week pelagic larval stage of H. puel/a and very low levels of genetic structure a<br>L'environnement marin présente moins de barrières au flux génétique que ses équivalents terrestres et d'eau douce. De plus, les phases planctoniques larvaires prévalences chez les espèces marines peuvent potentiellement maintenir un flux génétique a travers de grandes distances géographiques. Ces observations soulèvent deux questions fondamentales. Comment se développent de nouvelles espèces dans le milieu marin? Considérant le flux génétique potentiellement important, il demeure incertain dans quelle mesure la spéciation allopatrique peut expliquer la grande diversité observée dans le milieu marin, si la speciation opère également en présence de "flux génétique, et si oui par quels mécanismes. Quelle distance parcourent les phases larvaires planctoniques avec les courants marins? La structure génétique généralement faible parmi les populations marines suggère une dispersion extensive, mais les larves planctoniques sont notoirement difficiles a suivre en raison de leur petite taille et par conséquent I’ échelle spatiale de la dispersion marine échappe encore largement aux écologues.lci, je considère les poissons de récifs coralliens brillamment colores du genre HypopJectrus (Serranidae) comme systeme modèle pour aborder ces deux questions. Je démontre comment la speciation écologique avec flux génétique peut opérer dans ce système par I’ effet plëiotropique du patron de coloration, qui semble être impliquée dans le mimétisme ainsi que dans le choix d'un partenaire sexuel. Je montre que des processus locaux opèrent a I’ échelle des Caraïbes dans ce systeme, ce qui suggère une dispersion limitée. Je teste et confirme cette hypothèse en reportant de I’ isolement génétique par la distance chez HypopJectrus puella des échelles spatiales allant de 175 a3,200 km. Afin d'estimer la distance de dispersion moyenne je complémente les données génétiques avec des relèves de densités de population couvrant

All ecological and epidemiological systems are embedded in space and composed of individuals; these facts often have a profound effect on the dynamics and means many tools and definitions require reformulation. Modelling has always been about taking highly complex dynamical systems, such as the natural environment, and attempting to simplify them to a leve that can be conceptualised, in the process losing all the features that are not understood or not anticipated. The individual based spatial models which form the basis of this work start from the simple rules for individuals and build up to a complex system, allowing new, unexpected phenomenon to arise naturally. The local interactions in spatial models lead to short scale correlations and self-induced spatial heterogeneity as the small fluctuations of environmental noise are amplified into macro-scale patterns. These spatial patterns can lead to ephemeral refuges for hosts from where they can disperse stabilising the dynamics. After discussing the importance and variety of host-parasite interactions several techniques to be used in this work are developed and explained on simple examples. Chapters III and IV introduce a caricature host-pathogen model and how how this deviates from the standard mean field theory approximations. Attention is then turned to host-parasitoid systems and the spatially extended Nicholson-Bailey equations; probems with this coupled map lattice are highlighted and an alternative artificial ecology is formulated. Remaining with the Nicholson-Bailey equations these are forced to be integer based by utilising stochastic events, this greatly stabilises the dynamics hence the method was applied to the persistence of measles epidemics in small populations (=500000). Chapter VII demonstrates how the inclusion of space enhances the effects of parasitism in increasing the evolutionary advantage of sexual hosts over asexual ones. Finally general techniques are developed to implicitly model the effects of spatial correlations and stochastic individual based interactions.