From an ecological perspective, knowledge of demographic history is highly valuable because population size fluctuations can be matched to known climatic events, thereby revealing great insight into a species’ reaction to past climate change. This in turn enables us to predict how they might respond to future climate scenarios. Prominently, with the advent of high-throughput sequencing it is now becoming possible to assemble genomes of non-model organisms thereby providing unprecedented resolution to the study of demographic history and speciation. This thesis utilises four species of grouse (Aves, subfamily Tetraoninae) in order to explore the demographic history and speciation within this lineage; the willow grouse, red grouse, rock ptarmigan and the black grouse. I, and my co-authors, begin by reviewing the plethora of methods used to estimate contemporary effective population size (Ne) and demographic history that are available to animal conservation practitioners. We find that their underlying assumptions and necessary input data can bias in their application, and thus we provide a summary of their applicability. I then use the whole genomes of the black grouse, willow grouse and rock ptarmigan to infer their population dynamics within the last million years. I find three dominant periods that shape their demographic history: early Pleistocene cooling (3-0.9 Mya), the mid-Brunhes event (430 kya) and the last glacial period (110-10 kya). I also find strong signals of local population history – recolonization and subdivision events – affecting their demography. In the subsequent study, I explore the grouse dynamics within the last glacial period in more detail by including more distant samples and using ecological modelling to track habitat distribution changes. I further uncover strong signals of local population history, with multiple fringe populations undergoing severe bottlenecks. I also determine that future climate change is expected to drastically constrict the distribution of the studied grouse. Lastly, I use whole genome sequencing to uncover 6 highly differentiated regions, containing 7 genes, hinting at their role in adaptation and speciation in three grouse taxa. I also locate a region of low differentiation, containing the Agouti pigmentation gene, indicating its role in the grouse plumage coloration.

Approximately 25% of bats globally are threatened, but limited data on African bats, which account for 20% of bat species, hinders our understanding of their conservation status across this ecologically diverse continent. This study combined: modelling techniques, to predict current species distributions for 58 southern African bat species and project past, current and future distributions of 22 endemic and near-endemic species; bat acoustic surveys, to assess landscape features influencing bat activity in arid and semi-arid regions; and conservation planning software to design a large-scale monitoring network for bats across this subcontinent. Species distribution models were employed using a robust and well established presence-only modelling technique (Maximum Entropy – Maxent) to model the current distributions of 58 species in southern Africa. Although the important eco-geographical variables were species- or in some cases family-specific, overall water availability (both temporary and permanent), seasonal precipitation, vegetation and karst (caves/limestone) areas were the most important factors associated with distribution patterns. These species distributions were then used to identify range-restricted and narrow niche breadth species, alongside other life-history strategies considered to put species at risk, such as Old World pteropodids and cave-dwelling bats to identify species most at risk. Nine of the 58 species in this study were identified as ‘at risk’. Considering range-restriction and endemism separately, the results showed that range-restricted species were a higher proportion (50%) of ‘at risk’ species than endemics (41%) but six of the nine identified species were endemic and range restricted (67%). If only areas of high species richness are prioritised, important areas with low species richness but rare, ‘at risk’ or endemic species would be excluded. Species distributions are not fixed but may shift due to changes in environmental conditions. Accurately predicting changes in species’ distributions due to anthropogenic climate change remains a fundamental challenge for conservation biologists, and this is amplified when dealing with taxa such as bats that are inherently difficult to study and in areas, such as Africa, with sparse ecological data. To better understand endemic bat species risk to climate change in southern Africa and to highlight historical and future likely refugia, Maxent was employed to forecast range-shifts for 22 southern African endemic or near-endemic species. Species distributions were projected during the Last Glacial Maximum (LGM ~22,000 BP), present (1950-2000) and future (2070: averaged 2061-2080, using IPCC5 scenarios) climatic conditions. Climate change was predicted to change species composition extensively within a relatively short timescale (within 60 years). By 2070, 86% of species modelled are predicted to have range contractions and six species were highlighted to be most at risk, with range contractions of more than 20%. The majority of southern Africa is composed or arid or semi-arid regions. Generally arid and semi-arid areas are overlooked and understudied due to low species richness, yet these areas are known to have a high proportion of endemic species. As part of this study, driven transects were carried out across arid and semi-arid areas to assess bat activity in these areas. Bat activity was recorded at 94% of the acoustic surveys, demonstrating that driven transects are an effective method of surveying bats in southern Africa. Bat activity increased at lower altitudes and higher latitudes, which characteristically have more rainfall, permanent water and vegetation. Although water has been shown in other studies to be important for bats, temporary water was not shown to influence bat activity and permanent water was positively correlated with bat activity for hipposiderids and rhinolophids and FM bats, which may reflect the fact that water features important for bats at smaller scale. The same two vegetation types that were consistently negatively correlated with bat activity were drier vegetation types (Karoo-Namib shrubland) and high salinity halophytic vegetation. Finally, a systematic conservation planning software tool (Marxan) was used to design multi-species monitoring networks that incorporated all 58 target species across the 11 ecoregions found in southern Africa. To ensure rare, endemic and range-restricted species were monitored at the same level as widespread species, species distributions (mapped using Maxent) were extracted by ecoregion. Monitoring targets (i.e. a percentage of species distribution across ecoregions) were standardised to ensure the same percentage of predicted distribution was included across all species (rare and widespread). To account for different resources and capacity, three optimal monitoring networks (minimum monitoring stations to achieve the monitoring targets) were proposed to survey 1, 5 or 10% of all species distributions within each ecoregion. The optimal solution for monitoring 1% of species distributions within ecoregions was found by monitoring 1,699 stations (survey sites), or for 5% 8,486 stations and finally for 10% 17,867 stations would be needed. In conclusion, the findings presented in this thesis have important conservation implications and have the potential to inform the practical steps required towards the introduction of a bat monitoring programme in southern Africa. While this study has highlighted challenges to African bat conservation, it has also demonstrated that an integrated and multi-disciplinary approach, using emerging techniques and conservation tools (e.g. conservation planning and automated call analysis software) can be used to fill knowledge gaps and inform conservation priorities in the absence of systematically collected data.

Microclimatic gradients may have large influence on individual vital rates and population growth rates of species, and limit their distributions. Therefore, I focused on the influence of microclimate on individual performance and distribution of species. Further, I examined differences in how microclimate affect species with contrasting distributions or different ecophysiological traits, and populations within species. More specifically, I investigated the performance of northern and southern distributed forest bryophytes that were transplanted across microclimatic gradients, and the timing of vegetative and reproductive development among northern, marginal and more southern populations of a forest herb in a common garden. Also, I compared the landscape and continental distributions across forest bryophytes and vascular plants and, thus, their distribution limiting factors at different spatial scales. Lastly, I examined the population dynamics across microclimatic gradients of transplants from northern and southern populations of a forest moss. The effects of microclimatic conditions on performance differed among bryophytes with contrasting distributions. There were no clear differences between northern and southern populations in the timing of development of a forest herb or in the population dynamics of a moss. However, within each region there was a differentiation of the forest herb populations, related to variation in local climatic conditions and in the south also to proportion of deciduous trees. The continental distributions of species were reflected in their landscape distributions and vice versa, in terms of their occurrence optima for climatic variables. The variation in landscape climatic optima was, however, larger than predicted, which limit the precision for predictions of microrefugia. Probably, the distributions of vascular plants were more affected by temperature than the distributions of bryophytes. Bryophytes are sensitive to moisture conditions, which was demonstrated by a correlation between evaporation and the population growth rate of a forest moss. We might be able to predict species’ landscape scale distributions by linking microclimatic conditions to their population growth rates, via their vital rates, and infer larger scale distribution patterns. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p> / EkoKlim

Atualmente estamos presenciando mudanças climáticas ao nível global sem precedentes, as quais se tornarão mais severas no decorrer dos anos, podendo causar danos irreversíveis à biodiversidade. Como as espécies irão reagir a essas mudanças e quais ações de conservações devem ser tomadas estão entre os tópicos mais significantes na ecologia atualmente. As mudanças climáticas têm sido apontadas como uma das principais causas de reduções (e alterações) na distribuição geográfica e abundância de muitas espécies, e até mesmo a extinção. Os modelos de nicho ecológico têm sido uma ferramenta muito utilizada a fim de compreender como a distribuição das espécies pode ser afetada pelas mudanças climáticas. Os modelos fornecem valiosas informações sobre o potencial efeito das mudanças climáticas na distribuição futura das espécies, podendo assim ser usado para a compreensão de como e quais espécies podem ser mais afetadas, além dos locais adequados para sua conservação. Uma vez que informações importantes sobre os organismos não são incorporadas nos modelos, é fundamental o conhecimento sobre a biologia e história natural das espécies para a interpretação dos resultados. No presente estudo é aprestada uma revisão sobre o atual estado de conhecimento das quatro espécies do gênero Eunectes em relação à distribuição geográfica, uso do habitat e microhabitat, atividade diária e sazonal, reprodução, tamanho corporal, dieta e status de conservação. Adicionalmente aspectos da história natural de uma população da sucuri verde, Eunectes murinus, foram estudados em locais florestados, na cidade de Bonito, MS, e aqui são apresentados dados sobre movimentação, uso do microhabitat, reprodução e dieta. Ainda, foram desenvolvidos modelos de nicho climático para cada uma das quatro espécies a fim de entender os possíveis impactos das mudanças climáticas nessas espécies em dois cenários futuros. Foram assumidas duas abordagens de dispersão, com livre dispersão e sem dispersão. A partir dos resultados foi possível reconhecer padrões na biologia das espécies de Eunectes, identificar as principais lacunas de conhecimento e sugerir onde esforços em pesquisa devem ser focados. Além disso, importantes dados sobre a história natural da sucuri verde (E. murinus) foram registrados. Foi observado que, em relação à movimentação, dieta e reprodução, aparentemente a espécie mantém o padrão já registrado em estudos anteriores. Entretanto, o uso do microhabitat diferiu substancialmente, tendo sido encontrado um número muito elevado de indivíduos utilizando árvores. As projeções futuras indicam que, para o intervalo entre os anos de 2061-2080, todas as espécies, menos E. notaeus, perderão grande quantidade de hábitat climaticamente adequado, sendo E. deschauenseei a mais afetada (100% de perda com e sem dispersão no pior cenário). Ainda, as análises apontam que haverá uma mudança de local adequado para a potencial ocorrência de três espécies. Sem dispersão, todas as espécies perderão área, sendo que E. beniensis perderá 100% de habitat adequado em ambos os cenários de alterações climáticas. As informações geradas por este estudo ajudam a melhorar a compreensão da ecologia, história natural e distribuição das espécies do gênero, bem como indica quais as espécies poderão ser mais prejudicadas pelas mudanças climáticas em curso. Finalmente, os resultados fornecem subsídios para a formulação de planos de conservação, indicando importantes áreas que poderão servir de refúgio climático para as espécies / We are currently witnessing unprecedented global climate change, which will become more severe over the years and can cause irreversible damage to biodiversity. How species will react to these changes and what conservation actions should be taken are among the most significant topics in ecology today. Climate change has been identified as a major cause of reductions (and changes) in geographic distribution and abundance of many species, and even extinction. Ecological niche models have been widely used in order to understand how the distribution of species can be affected by climate change. The models provide valuable information on the potential effect of climate change on the future distribution of species and can be used to assess how and which species may be most affected, as well as the appropriate sites for their conservation. Since important information about the species is not incorporated into the models, the knowledge about their biology and natural history is crucial for interpretating the results. In the present study a review is presented on the current state of knowledge about the four species of the genus Eunectes in relation to geographic distribution, habitat and microhabitat use, daily and seasonal activity, reproduction, body size, diet and conservation status. In addition, natural history aspects of a green anaconda (E. murinus) population were studied in forested sites in the Bonito municipality, Mato Grosso do Sul state, Brazil, where data on movement, microhabitat use, reproduction and diet are presented. Furthermore, climate niche models were developed for each of the four species in order to understand the possible impacts of climate change under two future scenarios.Two dispersion approaches were performed, with \"free dispersion\" and \"no dispersion\". It was possible to recognize patterns in the biology of Eunectes species, identify the main knowledge gaps and to suggest where research efforts should be focused. Moreover, important data on the natural history of the green anaconda (E. murinus) were recorded. It was observed that, in relation to movement, diet and reproduction, the species apparently maintains the pattern recorded in previous studies. However, the use of the microhabitat differed substantially, with a very high number of individuals being found on trees. Future projections indicate that, for the interval between the years 2061-2080, all species, but E. notaeus, will lose a large amount of climatically suitable habitat, with E. deschauenseei being the most affected (100% loss with and without dispersion in the worst scenario). Future projections also indicate that there will be a shift in the distribution of suitable habitat for the potential occurrence of three species. Without dispersion, all species will lose area, and E. beniensis will lose 100% of suitable habitat in both climate change scenarios. The information generated by this study helps to improve the knowledge about the ecology, natural history and distribution of the species of Eunectes, as well as indicates which species may be most affected by ongoing climate change. Finally, the results provide subsidies for the formulation of conservation plans, indicating important areas that could serve as a climate refuge for the species

Les grands carnivores recolonisent l’Europe grâce à une augmentation des forêts et des populations d'ongulés sauvages ainsi que des mesures de conservation. Or, les carnivores entrent en interactions avec les activités humaines telles que l’élevage. Quantifier leur distribution peut aider à situer les impacts sur ces activités. Ces espèces sont très mobiles, difficiles à observer et vivent à de faibles densités. La modélisation de leur distribution présente plusieurs défis en raison 1) de leur détectabilité imparfaite, 2) de leur distribution dynamique dans le temps et 3) du suivi à grande échelle basé sur la collecte de données opportunistes sans mesure formelle de l'effort d'échantillonnage. Dans cette thèse, nous nous sommes concentrés sur deux espèces de grands carnivores, le loup et le lynx boréal, pour développer les méthodologies liées à la modélisation de la distribution d’espèces. Nous avons exploré l’application des modèles d’occupancy dans le contexte du suivi des grands carnivores en Europe. Ces modèles établissent le lien entre la présence d’une espèce et l’environnement dans le but d’établir la proportion d'une zone d'étude que l’espèce occupe, tout en prenant en compte une détectabilité imparfaite.Plus précisément, nous avons d'abord évalué la dynamique de la distribution des loups en France de 1994 à 2016, tout en prenant en compte leur détection imparfaite. Nous avons montré l'importance de prendre en compte l’effort d'échantillonnage variant dans le temps et dans l'espace à l’aide de de modèles d’occupancy dynamique.Deuxièmement, comme des faux positifs peuvent être présents lors de la surveillance d'espèces rares, nous avons développé un modèle dynamique d’occupancy qui tenait compte simultanément des faux négatifs et des faux positifs pour analyser conjointement des données qui contenaient à la fois des détections certaines et des détections incertaines. L'analyse des données sur le lynx boréal dans les pays alpins a suggéré que l'incorporation de détections incertaines produisait des estimations des paramètres écologiques plus précises.Troisièmement, nous avons développé un modèle qui prenait en compte l'hétérogénéité de la détection tout en traitant les faux positifs. En appliquant notre nouvelle approche au loup en France, nous avons démontré que l'hétérogénéité de la détection du loup était principalement due à un effort d'échantillonnage hétérogène dans l'espace.Quatrièmement, pour traiter des sources de données multiples, nous avons développé un modèle de processus ponctuel de Poisson qui permettait l'inclusion de différentes sources de données lors de la construction des SDMs. Nous avons montré comment la combinaison des données sur la distribution permettait d’optimiser un suivi en répondant à la question de savoir quelle(s) source(s) d'information apporterait l’essentiel de l’information lors du suivi du lynx en Norvège.Cinquièmement, pour comprendre les mécanismes sous-jacents de la colonisation des loups en France, nous avons développé un cadre statistique pour estimer l'occupation spatio-temporelle et la dynamique des effectifs en utilisant le cadre de diffusion écologique. Nous avons montré le potentiel de notre approche pour prédire la distribution future potentielle du loup à court terme, un élément qui pourrait contribuer à cibler des zones de gestion ou se concentrer sur des zones de conflit potentiel.Dans l'ensemble, nos travaux montrent que les données opportunistes peuvent être analysées à l'aide de modèles de distribution d’espèces qui prennent en compte les contraintes liées au type de suivi utilisé pour produire les données. Nos approches peuvent être utilisées par les gestionnaires pour optimiser la surveillance des grands carnivores, cibler des zones de présence potentielles et contribuer à proposer des mesures destinées à atténuer les conflits. / Large carnivores are recovering in Europe, due to an increasing forest cover, ungulate population and conservation measures. Tthis return poses challenges as carnivores can interact with livestock farming. Assessing their distributions can help to predict and mitigate conflicts with human activities. Because large carnivores are highly mobile, elusive and live at very low density, modeling their distributions presents several challenges due to 1) their imperfect detectability, 2) their dynamic ranges over time and 3) their monitoring at large scales consisting of opportunistic data without a formal measure of the sampling effort. In this thesis, we focused on two carnivore species, wolves (Canis lupus) and Eurasian lynx (Lynx lynx), to develop the methodological aspects related to the modelling of species distributions. We considered the application of occupancy models in the context of monitoring large carnivores in Europe. These models allow the establishment of a link between the species’ presence and environmental covariates while accounting for imperfect detectability, in order to establish the proportion of a study area occupied by the species.We first assessed wolf range dynamics in France from 1994 to 2016, while accounting for species imperfect detection and showed the importance of accounting for time- and space-varying sampling effort using dynamic site-occupancy models.Second, acknowledging that false positives may occur when monitoring rare species, we showcased a dynamic occupancy model that simultaneously accounts for false negatives and positives to jointly analyze data that include both unambiguous detections and ambiguous detections. The analysis of data on the Eurasian lynx in Alpine countries suggested that incorporating ambiguous detections produced more precise estimates of the ecological parameters.Third, we developed a model accounting for heterogeneity in detection while dealing with false positives. Applying our new approach to a case study with grey wolves in France, we demonstrated that heterogeneity in wolf detection was due to a heterogeneous sampling effort across space.Fourth, to deal with multiple data sources, we developed a Poisson point process approach which allows the inclusion of different data sources when building SDMs. By doing so, we also answered the question about which source(s) of information would provide most of the information when monitoring the lynx in Norway.Fifth and finally, to understand the underlying mechanisms of the colonization of wolves in France, we developed a statistical framework for estimating spatiotemporal occupancy and abundance dynamics using the ecological diffusion framework. We demonstrated the potential of our approach to predict the potential future distribution of wolves in the short term, an element that could contribute to target management areas or focus on areas of potential conflict.Overall our work shows that opportunistic data can be analyzed with species distribution models that control for issues linked to the type of monitoring used to produce the data. Our approaches have the potential for being used by decision-makers to optimize the monitoring of large carnivores and to target sites where carnivores are likely to occur and mitigate conflicts.

The aim of this thesis was to create potential distribution models for Dicranum majus (Greater Fork Moss) and Polytrichum alpinum (Alpine Haircap) in Bohemian Switzerland National Park. In the Czech Republic these bryophyte species occur in cold climatic regions typically with higher altitudes. In Bohemian and Saxon Switzerland they can occur in really low altitudes thanks to unique microclimatic conditions of deep inversion ravines. These bryophyte species had low number of occurence records in studied area before the start of my research (4 occurence localities for Dicranum majus, 8 occurence localities for Polytrichum alpinum). Predictive habitat suitability models can be an effective tool for selecting potential new occurence localities, planning field research or management design. During field research I recorded 34 new occurence localities for Dicranum majus and 29 new occurence localities for Polytrichum alpinum in Bohemian Switzerland National Park. I used 8 topographic parameters derived from digital elevation model with 1 m resolution as environmental data. Using these data I created models of potential distribution of the most suitable habitats for both species with algorithms Artificial neural networks (ANN), Generalised linear model (GLM) and Random forest (RF). RF algorithm had the...

L’Afrique centrale atlantique (ACA) englobe l’ensemble du domaine bas-guinéen, les îles du Golfe de Guinée et une partie de l’archipel afromontagnard. Plusieurs centres d’endémisme ont été identifiés en son sein et sont généralement considérés comme liés à la présence de refuges forestiers durant les périodes glaciaires. Cependant, l’origine de cet endémisme, sa localisation et les méthodes permettant d’identifier ces centres restent controversées. La localisation de ces zones d’endémisme et des plantes rares qu’elles abritent, est pourtant un prérequis indispensable pour la mise en place de politiques cohérentes de conservation et demeure une priorité pour les organisations privées, institutionnelles ou gouvernementales actives dans la gestion et le maintien durable de la biodiversité. Cette étude phytogéographique porte sur la famille des Orchidaceae et est basée sur l’analyse de la distribution des taxons endémiques de l’ACA. Elle s’appuie sur un jeu de données original résultant d’un effort d’échantillonnage important au Cameroun et d’un travail d’identification et de localisation de spécimens dans les principaux herbaria européens abritant des collections d’ACA. Durant cette étude, (i) nous avons tout d’abord identifié ces taxons endémiques et documenté leur distribution au travers de plusieurs contributions taxonomiques et floristiques, (ii) nous nous sommes ensuite intéressé aux nouvelles méthodes permettant d’analyser ces données d’herbier de plantes rares et donc pauvrement documentées, testant aussi l’intérêt des Orchidaceae comme marqueurs chorologiques, et finalement, appliquant ces méthodes à notre jeu de données, (iii) nous avons délimité des centres d’endémisme et identifié les territoires phytogéographiques des Orchidaceae en ACA. (i) Une révision taxonomique des genres Chamaeangis Schltr. et Stolzia Schltr. a été réalisée respectivement. Sept nouveaux taxons ont été décrits: Angraecum atlanticum Stévart & Droissart, Chamaeangis spiralis Stévart & Droissart, Chamaeangis lecomtei (Finet) Schltr. var. tenuicalcar Stévart & Droissart, Polystachya engogensis Stévart & Droissart, Polystachya reticulata Stévart & Droissart, Stolzia repens (Rolfe) Summerh var. cleistogama Stévart, Droissart & Simo et Stolzia grandiflora P.J.Cribb subsp. lejolyana Stévart, Droissart & Simo. Plusieurs notes taxonomiques, phytogéographiques et écologiques supplémentaires ont également été redigées. Au total, nous avons identifié 203 taxons d’Orchidaceae endémiques d’ACA parmi lesquels 193 sont pris en compte pour l’étude des patrons d’endémisme. (ii) Au Cameroun, les patrons de distribution des Orchidaceae et des Rubiaceae endémiques d’ACA ont été étudiés conjointement. Des méthodes de rééchantillonnage des données (raréfaction) ont été appliquées pour calculer des indices de diversité et de similarité. Elles ont permis de corriger les biais liés à la variation de l’effort d’échantillonnage. Un gradient de continentalité a été observé, les parties côtières étant les plus riches en taxons endémiques d’ACA. Contrairement à la région du Mont Cameroun et aux massifs de Kupe/Bakossi qui ont connu une attention particulière des politiques et des scientifiques, la partie côtière du sud Cameroun, presque aussi riche, reste mal inventoriée pour plusieurs familles végétales. Cette analyse à l’échelle du Cameroun a également permis de comparer les patrons d’endémisme des Orchidaceae et des Rubiaceae. Les différences observées seraient principalement dues à la présence d’Orchidaceae terrestres dans les végétations basses et les prairies montagnardes de la dorsale camerounaise alors que les Rubiaceae sont généralement peu représentées dans ces habitats. Au sein des habitats forestiers, la concordance entre les patrons d’endémisme des Orchidaceae et des Rubiaceae remet en question l’utilisation des capacités de dispersion des espèces comme critère pour choisir les familles permettant l’identification des refuges forestiers et semble ainsi confirmer la pertinence de l’utilisation des Orchidaceae comme marqueur chorologique. La distribution potentielle a été utilisée pour étudier en détail l’écologie, la distribution et le statut de conservation de Diceratostele gabonensis Summerh., une Orchidaceae endémique de la région guinéo-congolaise uniquement connue d’un faible nombre d’échantillons. Cette méthodologie semble appropriée pour compléter nos connaissances sur la distribution des espèces rares et guider les futurs inventaires en Afrique tropicale. (iii) En ACA, les Orchidaceae permettent d’identifier plusieurs centres d’endémisme qui coïncident généralement avec ceux identifiés précédemment pour d’autres familles végétales. Ces constats supportent aussi l’utilisation des Orchidaceae comme marqueur chorologique. La délimitation des aires d’endémisme des Orchidaceae a ainsi permis de proposer une nouvelle carte phytogéographique de l’ACA. Les éléments phytogéographiques propres à chacune des dix phytochories décrites ont été identifiés et leurs affinités floristiques discutées. Les résultats phytogéographiques obtenus (a) soutiennent l’existence d’une barrière phytogéographique matérialisée par la rivière Sanaga entre les deux principaux centres et aires d’endémisme de l’ACA, (b) étendent l’archipel afromontagnard situé principalement au Cameroun au plateau de Jos (Nigeria) et (c) montrent l’importance de la chaîne montagneuse morcelée Ngovayang-Mayombe pour la distribution de l’endémisme en ACA. Cette chaîne de montagne, qui s’étend le long des côtes de l’océan du sud Cameroun au Congo-Brazzaville et qui correspond à plusieurs refuges forestiers identifiés par de nombreux auteurs, est ici considérée comme une seule aire d’endémisme morcelée./ Atlantic central Africa (ACA) covers the Lower Guinean Domain, the four islands of the Gulf of Guinea and a part of the afromontane archipelago. Different centres of endemism have been identified into this area and are usually considered as related to glacial forest refuges. However, the origin of this endemism, the localization of the centres and the methods employed to identify these centres are subject to debate. Yet, the localization of these centres of endemism and the identification of the rare plants they harbor is an essential prerequisite to setting up rational conservation policies, and remains a priority for private, institutional and governmental organizations which are dealing with the sustainable management of biodiversity. This phytogeographical study focuses on Orchidaceae and analyses the distribution of the taxa endemic to ACA. We use an original dataset resulting from an important sampling efforts and the identification of specimens coming from all the principal herbaria where collections from ACA are housed. During this study, (i) we first identified the taxa endemic to ACA and documented their distribution through several taxonomic and floristic contributions, (ii) we used and developed new methods allowing to correct for sampling bias associated with the use of rare and poorly documented taxa, testing at the same time the use of Orchidaceae as chorological markers, and finally, applying these methods to our dataset, (iii) we delimited the centres of endemism and identified the phytogeographical territories of Orchidaceae in ACA. (i) A taxonomic revision of Chamaeangis Schltr. and Stolzia Schltr. respectively was carried out. Seven new taxa were described: Angraecum atlanticum Stévart & Droissart, Chamaeangis spiralis Stévart & Droissart, Chamaeangis lecomtei (Finet) Schltr. var. tenuicalcar Stévart & Droissart, Polystachya engogensis Stévart & Droissart, Polystachya reticulata Stévart & Droissart, Stolzia repens (Rolfe) Summerh var. cleistogama Stévart, Droissart & Simo and Stolzia grandiflora P.J.Cribb subsp. lejolyana Stévart, Droissart & Simo. Several additional taxonomic, phytogeographical and ecological notes were also published. We finally identified 203 Orchidaceae taxa endemic to ACA, among which 193 were used to study the patterns of endemism. (ii) In Cameroon, the distribution patterns of both Orchidaceae and Rubiaceae endemic to ACA were studied. Subsampling methods (rarefaction) were applied to calculate diversity and similarity indices and to correct potential bias associated with heterogeneous sampling intensity. A gradient of continentality was confirmed in Cameroon, the coastal part being the richest in taxa endemic to ACA. The Cameroon Mountain and the Kupe/Bakossi mountain massifs have received a great consideration of politics and scientists. On the contrary, the Southern coastal part of Cameroon, though almost as rich as the Northern part, remains poorly known for several plant families. This analysis also allowed us to compare patterns of endemism of Orchidaceae and Rubiaceae. The differences observed could be mainly due to the terrestrial habit of some Orchidaceae, which are only found in the grasslands of the highest part of the Cameroonian volcanic line where endemic Rubiaceae are rare. Within forest habitats, the concordance between the patterns of endemism of Orchidaceae and Rubiaceae question the widespread use of dispersal ability as a selection criterion for the families used to identify forest refuges. This also confirms the relevance of Orchidaceae as chorological marker. Species distribution modelling was used of an in depth study of the ecology, the distribution and the conservation status of Diceratostele gabonensis Summerh., an Orchidaceae endemic to the Guineo-Congolian regional centre of endemism which is only known from very few collections. This method is proved to be appropriate to complete our knowledge on the distribution of rare plant species and to guide the future inventories in tropical Africa. (iii) In ACA, an analysis of the distribution of endemic Orchidaceae confirmed the presence and location of several centres of endemism previously identified on the basis of other plant families. This result again supports the use of Orchidaceae as a chorological marker. The chorological study of the endemic Orchidaceae allowed us to propose a new phytogeographical map for ACA. Phytogeographical elements for each of the ten phytochoria described were identified and their floristic affinities were also discussed. Our results (a) support the existence of a phytogeographical barrier, materialized by the Sanaga River, between the two main centres and area of endemism of the ACA, (b) extend the limits of the afromontane archipelago to the Jos Plateau in Nigeria and (c) show the importance of the Ngovayang-Mayombe line to explain the distribution of endemism in ACA. This mountainous line, stretching along the ocean coast from Southern Cameroon to Congo-Brazzaville, corresponds to several forest refuges identified by many authors, and is here considered as an unique but discontinuous area of endemism.

Environmental factors influence species and habitats on multiple scales creating a mosaic of distribution patterns. Studying factors shaping these patterns are central to our understanding of population dynamics and ultimately ecosystem functioning. Information on the distribution of resources and conservation values are also highly needed in marine management as coastal areas are increasingly influenced by human activities. In this thesis, large-scale field data is used to explore how strong environmental gradients found on multiple scales in the coastal areas of the Baltic Sea influence fish habitats. The underlying concepts are based in the field of species distribution modelling, whereby habitat maps can be produced using environmental layers in a geographic information system. Distribution modelling is further used to address both ecological and applied questions by examining effects of habitat limitation on fish population sizes and to evaluate management actions aimed at habitat conservation. I show that specific habitat requirements for fish species of both freshwater and marine origin can be described using environmental variables and that species-environment relationships can be used to predict the distribution of early life-stages of fish in the Baltic Sea archipelagos. Further, predicted habitat availability of a specific life-stage was directly related to adult population size of Eurasian perch Perca fluviatilis, signifying that the abundance of large predatory fish can be limited by specific recruitment habitats. Lastly, by predicting the distribution of an assemblage of coastal fish species and their associated habitats, an assessment of a network of marine protected areas was performed. Results revealed large gaps in the current network and identified areas suitable for future protection. By demonstrating how current habitat protection can be improved by including critical habitats for coastal fish population sizes this thesis points to the benefits of integrating nature conservation and fisheries management. Based on these findings I conclude that species distribution modelling provides a suitable analytical framework for assessing the habitat requirements of organisms. An increased understanding of habitat-population relationships and an ability to accurately map ecologically important features will be of great value for an ecosystem-based marine management. ­ / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 709

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Os fatores que explicam a distribuição observada em plantas e animais é uma pergunta que intriga naturalistas, biogeógrafos e ecólogos há mais de um século. Ainda nos primórdios da disciplina de ecologia, as tolerâncias ambientais já haviam sido apontadas como as grandes responsáveis pelo padrão observado da distribuição dos seres vivos, o que mais tarde levou à concepção de nicho ecológico das espécies. Nos últimos anos, o estudo das distribuições dos organismos ganhou grande impulso e destaque na literatura. O motivo foi a maior disponibilidade de catálogos de presença de espécies, o desenvolvimento de bancos de variáveis ambientais de todo o planeta e de ferramentas computacionais capazes de projetar mapas de distribuição potencial de um dado organismo. Estes instrumentos, coletivamente chamados de Modelos de Distribuição de Espécies (MDEs) têm sido desde então amplamente utilizados em estudos de diferentes escopos. Um deles é a avaliação de potenciais áreas suscetíveis à invasão de organismos exóticos. Este estudo tem, portanto, o objetivo de compreender, através de MDEs, os fatores subjacentes à distribuição de duas espécies de corais escleractíneos invasores nativos do Oceano Pacífico e ambas invasoras bem sucedidas de diversas partes do Oceano Atlântico, destacadamente o litoral fluminense. Os resultados mostraram que os modelos preditivos da espécie Tubastraea coccinea (LESSON, 1829), cosmopolita amplamente difundida na sua região nativa pelo Indo- Pacífico demonstraram de maneira satisfatória suas áreas de distribuição nas áreas invadidas do Atlântico. Sua distribuição está basicamente associada a regiões com alta disponibilidade de calcita e baixa produtividade fitoplanctônica. Por outro lado, a aplicação de MDEs foi incapaz de predizer a distribuição de T. tagusensis (WELLS,1982) no Atlântico. Essta espécie, ao contrário de sua congênere, tem distribuição bastante restrita em sua região nativa, o arquipélago de Galápagos. Através de análises posteriores foi possível constatar a mudança no nicho observado durante o processo de invasão. Finalmente, o sucesso preditivo para T. coccinea e o fracasso dos modelos para T. tagusensis levantam importantes questões sobre quais os aspectos ecológicos das espécies são mais favoráveis à aplicação de MDEs. Adicionalmente, lança importantes ressalvas na utilização recentemente tão difundida destas ferramentas como forma de previsão de invasões biológicas e em estudos de efeitos de alterações climáticas sobre a distribuição das espécies. / The factors underpinning the observed distribution of plants and animals across time and space are a central question in ecology and has intrigued scientists for over a century. But even back on those early times, the role of climatic tolerances of the species were recognized as one of the main explanations for such distributional patterns. Later, these assumptions gave rise to the concept of niche which triggered several advances in the study of natural history. Recently, these studies were addressed in the light of novel computational techniques capable of providing potential distributional maps for a given species, generically called Species Distribution Models (SDMs). This coupled with the broader availability of species occurrence records and of environmental data from international databases made studies with SDMs very popular and ubiquitous in the literature. One of the main uses of the SDMs approach is the assessment of potentially susceptible areas of invasion by non- indigenous species. Therefore, here we used SDMs to better understand the major factors related to the current distribution of two well established invasive scleractinian coral species in the Atlantic, both from the Pacific Ocean. The results showed that the models were successful in predicting the potentially invaded sites by the cosmopolitan Tubastraea coccinea (LESSON, 1829), broadly distributed throughout the Pacific. This species distribution was basically associated with increasing concentrations of calcite and lower levels of phytoplankton activity. However, the models were incapable of predicting the survival and establishment of T. tagusensis (WELLS, 1982) in the Atlantic. This species, unlike its congener, has a very restricted distribution in its native regions, the Galapagos Islands. A posterior analyzes indeed showed a niche shift during the invasion event of T. tagusensis in the Atlantic. Finally, the good modelling results for T. coccinea contrasted with the failure of modelling T. tagusensis invasion highlight important explanations on methodological procedures in SDMs. It also helps to better understand which ecological aspects of the species are favourable toward good modelling performance. In addition to that, these results calls for precaution when analyzing SDMs results, particularly in invasion and climate change scenarios studies.

Submitted by Valquíria Barbieri (kikibarbi@hotmail.com) on 2018-04-05T22:00:26Z No. of bitstreams: 1 DISS_2014_Luana Aparecida Gomes de Arruda.pdf: 854132 bytes, checksum: e5dce680d3fc443608aec08b5e456321 (MD5) / Approved for entry into archive by Jordan (jordanbiblio@gmail.com) on 2018-04-23T18:21:48Z (GMT) No. of bitstreams: 1 DISS_2014_Luana Aparecida Gomes de Arruda.pdf: 854132 bytes, checksum: e5dce680d3fc443608aec08b5e456321 (MD5) / Made available in DSpace on 2018-04-23T18:21:48Z (GMT). No. of bitstreams: 1 DISS_2014_Luana Aparecida Gomes de Arruda.pdf: 854132 bytes, checksum: e5dce680d3fc443608aec08b5e456321 (MD5) Previous issue date: 2014-12-02 / Pesquisas em campo voltadas para conservação de espécies são necessárias, porém muitas vezes são limitadas, onerosas e trabalhosas. Uma ferramenta que pode ser utilizada para minimizar estes problemas é a Modelagem Preditiva de Distribuição Potencial de Espécies (MPDPE), que permite estimar áreas potenciais de ocorrência atuais e futuras e que vem recebendo destaque em estudos conservacionistas, pois pode ser utilizada com espécies raras ou que estão sofrendo algum grau de ameaça. No presente estudo, a MPDPE foi utilizada para conhecer a distribuição e prever o efeito potencial de mudanças climáticas sobre a distribuição da perereca Phyllomedusa centralis, que possui distribuição conhecida restrita a poucas localidades no estado de Mato Grosso, Brasil. Os modelos foram desenvolvidos com o método de entropia máxima com o auxilio do programa MaxEnt, utilizando variáveis bioclimáticas atuais e futuras. Os modelos de predição de distribuição atual e de cenários futuros obtiveram elevados valores da área sob a curva operador-receptor e a validação apontou alta precisão na qualidade do modelo. Em todos os modelos, a variável ambiental com maior porcentagem de contribuição foi a precipitação. Todos os modelos apresentaram previsão de aumento nas áreas de distribuição potencial em comparação com o modelo atual de distribuição. Apesar de apresentar limitações, o modelo de distribuição potencial é relevante e pode ajudar no planejamento e gestão de reservas, descoberta de novas populações e manejo de espécies, identificação de áreas prioritárias para conservação e definição de onde é necessária a restauração de habitats. / Field surveys aimed at the conservation of species are necessary, but are often limited, costly and onerous. A tool that can be used to minimize these problems is the Predictive Modeling of Potential Species Distribution (PMPSD), which allows estimating current and future areas of potential occurrence and has received attention from conservationists studies, because it can be used with rare species or who are suffering some degree of threat. In the present study PMPSD was used to determine the distribution and predict the potential effect of climate change on the distribution of tree frog Phyllomedusa centralis, which has restricted distribution to a few localities in the state of Mato Grosso, Brazil. The models were developed with maximum entropy method with the aid of the MaxEnt program using current and future bioclimatic variables. The prediction models of current distribution and future scenarios had higher Area Under the receiver-operator Curve values and the validation showed high accuracy of the model quality. In all models the environmental variable with highest percentage of contribution was precipitation. All models showed increased areas of potential distribution compared with the current distribution model. Despite the limitations, the model of potential distribution is important and can help in planning and management of reserves, discovery of new populations, identification of priority areas for conservation, and definitions of regions to habitat restoration.