Comprometida com a compreensão da relação entre hábitat e uso do espaço pelo mico-leão-da-cara-preta (Leontopithecus caissara), esta dissertação se norteia por três perguntas: Diferenças de hábitat entre ilha e continente influenciam o tamanho da área de vida? Há predileção da espécie por alguma classe de vegetação dentro da área de uso? Qual a capacidade suporte em sua área de ocorrência continental, bem como nas áreas potenciais para seu manejo conservacionista? Na tentativa de elucidar essas questões esta dissertação se divide em três capítulos. O primeiro contextualiza o trabalho e a apresenta o estado atual de conhecimento de L. caissara. Os capítulos segundo e terceiro concernem às questões centrais do trabalho - uso e seleção do hábitat pelo mico-leão-da-cara-preta. No capítulo dois apresentamos o uso do espaço pela espécie em sua região continental de ocorrência e comparamos os resultados obtidos com as informações disponíveis para a Ilha do Superagui. No capítulo três tratamos da seleção do hábitat por grupos insulares e continentais de L. caissara e estimamos a capacidade suporte para a espécie considerando seus limites de ocorrência e as áreas passíveis de receber animais em situação de manejo. Ao final desses capítulos apresentamos algumas considerações e recomendações para pesquisa e conservação do mico-leão-da-cara-preta. A preocupação com uma postura crítica e construtiva acerca das metodologias de estudos e análises sobre uso do espaço por espécies animais é transversal aos assuntos tratados ao longo de todo o trabalho. Os resultados apresentados confirmam as grandes áreas de vida de L. caissara, as quais parecem ser compensadas energeticamente pela incorporação de novas áreas e abandono de outras ao longo do tempo. Os tipos de hábitats mais intensamente utilizadas pelos mico-leão-da-cara-preta intercalaram áreas de floresta madura e em clímax edáfico com áreas antropizadas em sucessão, ambos hábitats sobre pouco desnível altimétrico. A capacidade suporte estimada é aparentemente incapaz de sustentar uma população viável e ressalta a urgência de pesquisas genéticas que colaborem para a compreensão do histórico ecológico/evolutivo de L. caissara. Potenciais translocações com vistas ao aumento populacional devem considerar as amplas áreas de diva, a espacialidade dinâmica, a relação uso/disponibilidade do hábitat e as diferenças entre ilha e continente. / This dissertation focuses on the interaction between habitat and space use by the black-faced lion tamarin (Leontopithecus caissara). We seek to answer three questions: 1) Do differences in vegetation between insular and continental habitats influence how the species use the space? 2) Does the species prefer a specific type of vegetation within its home-range? 3) What is the carrying capacity of the continental distribution and which are areas for potential conservation management? The first chapter of this dissertation relates the subjects discussed and introduces what is known about L. caissara. The second and third chapters develop the central questions of the research: the use and selection of habitat by the black-faced lion tamarin. In Chapter Two, we introduce space use by the species in its continental distribution and compare the results with data from Superagui Island. In Chapter Three, we address habitat selection by insular and continental groups of L. caissara and estimate the carrying capacity for the species given its distribution and areas potentially able to receive animals in a management context. The conclusion of each chapter presents considerations and recommendations for research and conservation. The study methods and analyses of space use aim to be critical and constructive and are relevant to the topics addressed throughout the text. The results presented confirm that the large home-ranges of L. caissara undergo dynamic turnovers, with some areas being abandoned and others incorporated throughout the year. The habitat types most intensively used by tamarins include areas of mature and forest mixed with areas of anthropic succession, both occurring at low altitudes. The estimated carrying capacity is apparently insufficient to maintain a viable population and highlights the importance of genetic studies that incorporate the ecological/evolutionary history of the species. Potential translocations meant to increase population size should consider the large home-ranges, dynamic spatial structure, relation of habitat use/availability and the differences between island and continent.

A perda de habitats é, atualmente, a grande ameaça à diversidade de vertebrados terrestres (Crooks, 2002). Muito pouco resta da vegetação nativa no estado de São Paulo, uma vez que é o estado mais desenvolvido do Brasil. Embora sua porção litorânea ainda possua uma grande faixa de Floresta Atlântica, o que restou da vegetação de cerrado em seu interior são pequenos fragmentos, cercados de agricultura e silvicultura. Entretanto, este mosaico de vegetação ainda abriga espécies de médios e grandes mamíferos. Este estudo foi desenvolvido numa área com fragmentos de cerradão, cerrado sensu stricto, floresta semidecídua, além de cultivos de eucalipto e cana-de-açúcar, nos municípios de Santa Rita do Passa-Quatro e Luiz Antônio. Registraram-se 22 espécies de mamíferos de médio e grande porte por meio de armadilhamento fotográfico, canteiro de pegadas, identificação de fezes, vestígios e avistamentos diretos. Dessas 22 espécies, dez eram carnívoros os quais exploravam o ambiente independentemente de sua cobertura vegetal. Numa abordagem mais espacializada notou-se alguma diferença no uso dos habitats da área de estudo, inclusive do eucaliptal, que se mostrou um habitat importante na dinâmica das populações de carnívoros do local. Dessa forma concluiu-se que ambientes modificados pelas culturas humanas podem representar habitats efetivamente utilizados pela mastofauna de uma região antropizada. Diferentes métodos podem ser usados para monitorar populações ou comunidades faunísticas. O armadilhamento fotográfico e o registro em canteiro de pegadas são bastante utilizados para médios e grandes mamíferos. Os dois métodos possuem viéses na sua amostragem, além de custos e eficiências bem distintos, no entanto o uso conjunto desses dois métodos parece registrar de forma adeqüada a riqueza da mastofauna de uma determinada região. / Habitat\'s loss is the great jeopardy to the diversity of terrestrial vertebrates nowadays (Crooks, 2002). There\'s too little left from the native vegetation in São Paulo State, since it\'s the most developed state in Brazil. Although its coastal area still has a large tract of the Atlantic Forest, just small patches of Brazilian savanna (cerrado) vegetation are found in it, surrounded by agriculture and silviculture. However this vegetation mosaic still shelters both medium and large mammals\' species. This study was held in an area with remnant fragments of woodland savanna (cerradão), cerrado sensu stricto, semideciduous forest as well the cultivation of eucalyptus and sugar-cane in Santa Rita do Passa-Quatro e Luiz Antônio - Brazil. Twenty-two species of large and medium sized mammals were reported by the use of camera trapping, track plots recording, identification of dungs, vestiges and sights. Among these 22 species, ten were carnivore which exploit the environment regardless its vegetation coverage. During a more spatial approach, some difference in the use of the habitats was noted, concerning the study area, including the eucalyptus plantation, which turned out to be an important habitat on the dynamics of the carnivore population of the region. Thus one realizes that environments which were altered by human cultures can represent habitats actually used by mammals from an anthropogenic region. Different procedures can be applied to observe faunal populations or communities. The camera trapping and the track plot recording are often used for medium and large-sized mammals. Both methods present bias in their showing, besides these 2 methods seem to be suitable to the register the wealth of the mammals of a specific region.

In the face of biodiversity loss due to agricultural expansion and intensification, agroforestry has been proposed as an environmentally friendly form of agriculture capable of conserving biodiversity while supporting local livelihoods. However, how social drivers related to farmers’ decision-making and ecological processes affect the potential of agroforestry systems to serve as reservoirs for native species diversity and community composition is unclear. This dissertation aims to describe patterns of tree diversity and community composition in coffee (Coffea arabica) agroforestry systems as they compare to surrounding forests, and uncover the social drivers related to farmers’ decision-making and ecological processes giving rise to those patterns. Worldwide, there is an extensive overlap between coffee-growing areas and regions with high species richness and endemism considered biodiversity hotspots. This renders the issue of clarifying the sustainability and conservation value of shade coffee even more urgent. Otherwise, we risk losing important late-succession and conservation concern tree species, and simplifying the structural and floristic composition of mature forests. To uncover how the social factors related to farmers’ decision-making and ecological factors drive tree diversity and community composition in coffee agroforestry systems, a series of empirical studies were conducted based on surveys and field data collected in La Sepultura Biosphere Reserve in Chiapas, Mexico, between 2009-2013. Field research took place in two coffee farming communities within the reserve, where 50 farmers were interviewed, and 31 coffee agroforest sites and 10 forest sites were sampled. Forests were sampled to provide a reference for tree diversity and community composition in the absence of coffee management. Although a higher sample size would have permitted the inclusion of more covariates in statistical analyses without losing statistical power, there is no reason to believe that the results of this dissertation would change if a larger sample size were considered. This is because the magnitude of the effects detected were large and the p-values small, which underscore the robustness of the results of this dissertation. The three chapters in this dissertation correspond to individual studies. Chapter One investigates tree floristic patterns in coffee agroforestry systems and compares them to those in surrounding forests. Findings indicate that although at the landscape level coffee agroforestry systems hold similar tree species richness compared to forests, tree species community composition is significantly distinct. Coffee agroforests had a lower proportion of trees of conservation concern, a higher proportion of pioneer trees, were dominated by Inga spp., harbored lower tree species diversity at the plot level, and were composed of different tree species compared to native forests. This chapter raised questions with regards to whether these results were the result of farmers’ intentional tree selection criteria and preferences, or an unintended consequence of management practices. Chapter Two addressed these questions by examining the use of knowledge by farmers to manage coffee agroforests and the consequences on tree community composition relative to forests. In Chapter Two, results indicate that differences between agroforests and forests are primarily driven by farmers’ manipulation of tree community composition, which occurs according to their beliefs about the benefits and disservices of trees for coffee production. Tree community composition in coffee agroforest is dominated by the trees that farmers prefer and practically void of the trees they dislike as compared to the trees’ natural abundances in forests. These findings are novel and important because they clarify that the community composition changes observed in coffee agroforests are mostly an intentional consequence of management and not a byproduct. Finally, Chapter Three focuses on a subset of trees of particular conservation importance, trees of conservation concern (CC) and typical of old growth or late succession (LS) forests. This chapter investigates how management practices that affect shade tree density, basal area, and the proportion of Inga trees, mediated by land use legacies, affect the proportions of CC and LS trees in coffee agroforests. Findings indicate that management practices that sought to increase the proportion of Inga spp. trees had the largest negative impact on the proportions of trees of LS and CC, but the magnitude of the effects were dependent on land-use legacy. Among farms established on land previously used for pastureland or crop cultivation, the impact of farmers’ tree preferences and selection criteria on LS and CC trees were significantly higher than on farms established on forests without an agricultural history. These findings underscore that farmers’ sharp preference for Inga spp. trees undermines the potential of agroforests to conserve higher proportions of CC and LS trees. The results presented in each chapter of this dissertation allow for a more thorough understanding of the tree diversity patterns conserved in coffee agroforestry systems and the underlying social drivers related to farmers’ decision-making and ecological drivers that generate such patterns. The results of this dissertation seek to contribute new knowledge not only to the scientific community, but also to society so that better policies and strategies be devised that successfully conserve floristic diversity in the biodiverse areas of the world where coffee is cultivated.

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.

Le réseau hydrographique français présente deux lignées de truite commune (Salmo trutta, L.) génétiquement et phénotypiquement distinctes : les lignées Atlantique (ATL) et Méditerranéenne (MED) qui occupent les bassins versant du même nom. Les repeuplements intensifs pratiqués de manière systématique depuis un siècle avec des souches domestiques ATL ont entrainé dans la zone méditerranéenne une introgression plus ou moins importante des populations naturelles. La persistance de populations peu introgressées amène les gestionnaires à prendre en compte dans leur démarche de conservation ces populations autochtones. La gestion de cette problématique d'hybridation passe par une meilleure connaissance de la dynamique de biodiversité intra-spécifique et donc des mécanismes évolutifs qui régulent les flux de gènes entre les lignées MED et ATL.Cette thèse s'appuie sur un travail collaboratif entre scientifiques et gestionnaires et comporte plusieurs objectifs. Sur le plan théorique nous avons testé deux barrières reproductives pré-zygotiques potentielles liées au comportement reproducteur (compétition intra-sexuelle mâle et préférence inter-sexuelle femelle) ainsi qu'une possible barrière post-zygotique correspondant à un différentiel de survie embryo-larvaire lié à la température. Un large jeu de données a également été analysé pour mettre en évidence un potentiel différentiel de survie entre lignée à l'âge adulte. Enfin, ces résultats ont été inclus dans un modèle démo-génétique (modèle Mediterranea, plate-forme CAPSIS-4). Cet outil informatique d'aide à la décision adapté aux besoins des gestionnaires permettra à terme l'évaluation des stratégies de gestion et de conservation.Les résultats montrent une préférence intersexuelle hétérogame qui tendrait à accélérer le mélange des deux lignées. L'étude de la survie embryo-larvaire montre un avantage sélectif pour les descendants de femelles MED, particulièrement dans des conditions de températures basses. Enfin, l'analyse de la distribution de l'âge chez les adultes montrent un avantage aux individus MED ce qui pourrait traduire une adaptation locale pour cette lignée au sein du territoire haut-savoyard. Les simulations préliminaires effectuées avec le modèle Mediterranea intègrent ces résultats et mettent en évidence le rôle de la structure du réseau hydrographique dans la variabilité spatiale de l'introgression. Ces résultats concordent avec les patrons d'introgression observés in situ et apportent de nouvelles connaissances pouvant se révéler utiles dans la gestion future de la biodiversité intra-spécifique de la truite commune. / The natural distribution area of brown trout (Salmo trutta, L.) in the French hydrographic landscape reveals the existence of two genetically and phenotypically distinct lineages: the Atlantic lineage (ATL) and the Mediterranean lineage (MED) that are initially respectively present in the Atlantic and Mediterranean drainage basins. Intensive and systematic stocking practices carried out over a century with ATL domestic strains have resulted, in the Mediterranean area, in heterogeneous patterns of introgression of native MED populations. The persistence of some low introgressed MED populations led managers to focus on these native populations in their conservation plans. To efficiently account for these introgression processes, a better understanding of intraspecific biodiversity dynamics is required, with a specific focus on how evolutionary mechanisms may regulate gene flow between MED and ATL lineages.The present manuscript is based on a collaborative work between scientists and managers in Haute-Savoie, France, and investigates several potential mechanisms for introgression. We explored two potential pre-zygotic reproductive barriers related to reproductive behavior (male intra-sexual competition and female inter-sexual preference) and also a possible post-zygotic barrier corresponding to a differential of embryo-larval survival linked to temperature. A large dataset was also analyzed to identify a potential differential survival between lineages at adult stage. Finally, these results were included into a demogenetic model (Mediterranea Model, CAPSIS-4 platform). This computer based aid for decision making will ultimately allow evaluating various management strategies.The results show a heterogamous intersexual female preference which should promote the genetic admixture between the two lineages. However, the study of embryo-larval survival shows a selective advantage for the offspring of MED females, especially in low temperature conditions. Finally, the analysis of the distribution of age in adults suggests a potential higher survival for MED individuals, which could indicate a local adaptation for this lineage in the territory of Haute-Savoie. The preliminary simulations performed with the Mediterranea model incorporate these results and highlight the role of hydrogeographic network structure in the spatial variability of introgression. Both results and simulations are consistent with the introgression patterns observed in situ and provide new knowledge that can be applied to the management of intraspecific biodiversity of brown trout.

This thesis fills a research gap in our knowledge of kokako song by looking at how song evolves in multi-dialect areas. Kokako only exist in small remnant populations separated by large tracts of unsuitable land. Kokako are very poor flyers, only able to fly for approximately 100 metres at a time. In order to prevent inbreeding and a loss of genetic diversity in the remaining kokako populations, managers are carrying out translocations to establish new populations, maintain gene flow and prevent inbreeding. However, these translocations have the potential to be unsuccessful because kokako exhibit macrogeographic variation in their dialects, and tend not to breed with individuals who do not share the same dialect as them. If the purpose of the translocation is to enhance genetic diversity by having kokako from different areas breed then song is an important factor that must be dealt with. Song is extremely important to kokako for a number of reasons. Chiefly, it is hypothesised that song is their primary means of territory defence. A kokako gains all its resources from its territory, so it is imperative that they successfully defend it. Their duet song functions in territory defence, but also acts to form and maintain pair bonds. In order to try and address the problem that song causes in translocations I studied if and how song evolves in a multiple dialect area. I conducted research at Pukaha Mount Bruce, where there is a population of kokako originating from two different source populations, and thus two different dialects, Northern Mapara and Mangatutu. I looked at the Northern Mapara dialect, and recorded kokako belonging to three groups; kokako currently living in the source population, kokako that were translocated to Pukaha and kokako that were born at Pukaha. In order to determine how the song may be changing I looked at element repertoires, the levels of sharing between groups, the number of unique elements in repertoires and the syntactical and temporal characteristics of phrases. This study shows that translocation into multiple dialect areas can affect kokako song. Translocation did not affect the size of the kokako repertoire, but it seemed to affect the amount of sharing within and between different groups of kokako. Currently the level of sharing within the groups at Pukaha is lower than the level of sharing within the source Mapara population, indicating that the song may be diverging. There also seem to be more unique elements found at Pukaha, which in part explains the lack of sharing. There appears to be microgeographic variation at Pukaha, with birds clustered around the second (Mangatutu) dialect sharing less with the source population than do those kokako whose territories are lower down in the reserve. The phrases which are used are also evolving, with only one phrase truly shared among all groups. There are other phrases which show additions or deletions of elements, and so are evolving. The main change found in the phrases is the timing between elements, with six out of seven phrases examined showing changes. These results have repercussions for future kokako translocations, and the future of the Pukaha kokako. A low amount of phrase and element type sharing combined with changes of intra-phrase timing could lead to the Pukaha kokako’s inability to successfully defend their territories. This research shows how kokako song can give conservation managers information on the status of their populations in regards to interbreeding and raises questions which can be answered by further research, both at Pukaha and in other mixeddialect kokako populations.

This thesis fills a research gap in our knowledge of kokako song by looking at how song evolves in multi-dialect areas. Kokako only exist in small remnant populations separated by large tracts of unsuitable land. Kokako are very poor flyers, only able to fly for approximately 100 metres at a time. In order to prevent inbreeding and a loss of genetic diversity in the remaining kokako populations, managers are carrying out translocations to establish new populations, maintain gene flow and prevent inbreeding. However, these translocations have the potential to be unsuccessful because kokako exhibit macrogeographic variation in their dialects, and tend not to breed with individuals who do not share the same dialect as them. If the purpose of the translocation is to enhance genetic diversity by having kokako from different areas breed then song is an important factor that must be dealt with. Song is extremely important to kokako for a number of reasons. Chiefly, it is hypothesised that song is their primary means of territory defence. A kokako gains all its resources from its territory, so it is imperative that they successfully defend it. Their duet song functions in territory defence, but also acts to form and maintain pair bonds. In order to try and address the problem that song causes in translocations I studied if and how song evolves in a multiple dialect area. I conducted research at Pukaha Mount Bruce, where there is a population of kokako originating from two different source populations, and thus two different dialects, Northern Mapara and Mangatutu. I looked at the Northern Mapara dialect, and recorded kokako belonging to three groups; kokako currently living in the source population, kokako that were translocated to Pukaha and kokako that were born at Pukaha. In order to determine how the song may be changing I looked at element repertoires, the levels of sharing between groups, the number of unique elements in repertoires and the syntactical and temporal characteristics of phrases. This study shows that translocation into multiple dialect areas can affect kokako song. Translocation did not affect the size of the kokako repertoire, but it seemed to affect the amount of sharing within and between different groups of kokako. Currently the level of sharing within the groups at Pukaha is lower than the level of sharing within the source Mapara population, indicating that the song may be diverging. There also seem to be more unique elements found at Pukaha, which in part explains the lack of sharing. There appears to be microgeographic variation at Pukaha, with birds clustered around the second (Mangatutu) dialect sharing less with the source population than do those kokako whose territories are lower down in the reserve. The phrases which are used are also evolving, with only one phrase truly shared among all groups. There are other phrases which show additions or deletions of elements, and so are evolving. The main change found in the phrases is the timing between elements, with six out of seven phrases examined showing changes. These results have repercussions for future kokako translocations, and the future of the Pukaha kokako. A low amount of phrase and element type sharing combined with changes of intra-phrase timing could lead to the Pukaha kokako’s inability to successfully defend their territories. This research shows how kokako song can give conservation managers information on the status of their populations in regards to interbreeding and raises questions which can be answered by further research, both at Pukaha and in other mixeddialect kokako populations.

The chevron skink (Oligosoma homalonotum) is one of the largest, yet least observed skink species in New Zealand. The species was thought to have once been widespread in Northern New Zealand, however currently it is only found on Great Barrier and Little Barrier Islands. Great Barrier Island is the apparent stronghold for the species although it appears to be in decline there, despite a net increase in habitat. Recent studies have increased the understanding of the general ecology of the species, however little is known about the threats to the survival of this species. This study had two main objectives; the first was to establish if rats are a threat to chevron skinks, and the second was to increase current knowledge of the species ecology. The research was undertaken in an area of extensive rodent control (Glenfern Sanctuary) and an adjacent unmanaged reserve in Port Fitzroy, on Great Barrier Island in 2008. The first objective of this study involved confirming that rat densities in the treatment (Glenfern Sanctuary) were sufficiently different to allow meaningful comparisons of chevron skink population characteristics between sites. This was achieved by determining absolute rat densities using Zippin’s removal method at four sites, and correlating these with a relative abundance measure (tracking rates) to give confidence in the observed trends. Rat densities were high (1.94 - 3.00 rats ha-1) in the control, and low (0.00 and 0.06 rats ha-1) in the treatment sites, and these correlated well with tracking rates. In light of these clear differences between the treatment and control, the population structure and condition of chevron skinks were compared between sites. The population structure showed erosion of juvenile and sub-adult size categories, which indicated differences in vulnerabilities between size categories. Physical evidence of failed rat predation was also observed in adult skinks in the unmanaged control, which confirmed that rats were interacting with chevron skinks. Although the adults survived the attacks they suffered injuries including eye damage, punctures, cuts and tail loss. Smaller skinks would be unlikely to survive such attacks due to the severity and scale of the injuries, supporting the assertions of the population structure that smaller skinks may be more vulnerable than adults. The extent of tail loss was converted to a condition index to determine if failed rat predation was more widespread in the population, than was observed by conspicuous injuries. This condition index (body-tail condition index) was stable through all size categories in the treatment, but significantly reduced in adults in the unmanaged sites. That there was no reduction in the condition of smaller skinks in the unmanaged control sites despite high rat densities suggests that interactions between rats and smaller skinks are fatal, and thus not represented in the data. Nine chevron skinks were radio-tracked to determine habitat use, home range and ranging behaviour. Habitat use of chevron skinks was similar to a previous study and demonstrated that trees, crevices and logs were important refuge sites. Chevron skinks were more likely to be found at sites with trees, crevices and debris dams. Chevron skink home ranges indicated that adults moved further away from streams than previously anticipated at this time of year, and skinks demonstrated site fidelity. There was also overlap in home ranges between individuals, and skinks with overlapping home ranges shared common refuges. During flooding events, chevron skinks exhibited an arboreal response that appears to be a behaviour specific to stream associated animals, which allows them to avoid being taken by floodwaters.

The chevron skink (Oligosoma homalonotum) is one of the largest, yet least observed skink species in New Zealand. The species was thought to have once been widespread in Northern New Zealand, however currently it is only found on Great Barrier and Little Barrier Islands. Great Barrier Island is the apparent stronghold for the species although it appears to be in decline there, despite a net increase in habitat. Recent studies have increased the understanding of the general ecology of the species, however little is known about the threats to the survival of this species. This study had two main objectives; the first was to establish if rats are a threat to chevron skinks, and the second was to increase current knowledge of the species ecology. The research was undertaken in an area of extensive rodent control (Glenfern Sanctuary) and an adjacent unmanaged reserve in Port Fitzroy, on Great Barrier Island in 2008. The first objective of this study involved confirming that rat densities in the treatment (Glenfern Sanctuary) were sufficiently different to allow meaningful comparisons of chevron skink population characteristics between sites. This was achieved by determining absolute rat densities using Zippin’s removal method at four sites, and correlating these with a relative abundance measure (tracking rates) to give confidence in the observed trends. Rat densities were high (1.94 - 3.00 rats ha-1) in the control, and low (0.00 and 0.06 rats ha-1) in the treatment sites, and these correlated well with tracking rates. In light of these clear differences between the treatment and control, the population structure and condition of chevron skinks were compared between sites. The population structure showed erosion of juvenile and sub-adult size categories, which indicated differences in vulnerabilities between size categories. Physical evidence of failed rat predation was also observed in adult skinks in the unmanaged control, which confirmed that rats were interacting with chevron skinks. Although the adults survived the attacks they suffered injuries including eye damage, punctures, cuts and tail loss. Smaller skinks would be unlikely to survive such attacks due to the severity and scale of the injuries, supporting the assertions of the population structure that smaller skinks may be more vulnerable than adults. The extent of tail loss was converted to a condition index to determine if failed rat predation was more widespread in the population, than was observed by conspicuous injuries. This condition index (body-tail condition index) was stable through all size categories in the treatment, but significantly reduced in adults in the unmanaged sites. That there was no reduction in the condition of smaller skinks in the unmanaged control sites despite high rat densities suggests that interactions between rats and smaller skinks are fatal, and thus not represented in the data. Nine chevron skinks were radio-tracked to determine habitat use, home range and ranging behaviour. Habitat use of chevron skinks was similar to a previous study and demonstrated that trees, crevices and logs were important refuge sites. Chevron skinks were more likely to be found at sites with trees, crevices and debris dams. Chevron skink home ranges indicated that adults moved further away from streams than previously anticipated at this time of year, and skinks demonstrated site fidelity. There was also overlap in home ranges between individuals, and skinks with overlapping home ranges shared common refuges. During flooding events, chevron skinks exhibited an arboreal response that appears to be a behaviour specific to stream associated animals, which allows them to avoid being taken by floodwaters.

<p>One of the main reasons for the massive loss in plant species diversity is the fragmentation of habitats. In Europe, open pastures and meadows are the habitats going through the most changes during the 20th century, according to the agricultural changes. In this study vascular plants were invented at five different islands in the Lurö archipelago, Vänern, Sweden. The aim of the study was to sort out whether the diversity of plants has gone through any changes in abandoned managed grasslands compared to continuous managed grasslands. The aim was also to study if a change in the landscape has made any differences for the species development or decline. The results indicate that the number of vascular plants were significantly lower in the abandoned areas than the still managed areas. Results, only from the field layer, showed same results. There was a significant difference between the number of indicators in managed lands than lands that were abandoned for 30-40 and 100 years ago. A comparison from earlier study, from a time when grazing had just ceased at some islands, showed a significant difference in plant species diversity between the years. Just a few decades can impoverish a plant community that might have taken hundreds or even thousands of years to build up. To preserve the biological diversity formed by human impact, one must continue managing the lands.</p> / <p>En av de största orsakerna till den massiva förlusten av växtarter, är fragmenteringen av habitat. I Europa är öppna naturbetesmarker och ängar de habitat som genomgått de största förändringarna i och med jordbrukslandskapets omstruktureringar under 1900-talet. I den här studien inventerades kärlväxter på 5 olika öar i kulturlandskapet Lurö skärgårds naturreservat. Syftet var att ta reda på hur diversiteten bland kärlväxtarter skiljer sig mellan hävdade gräsmarker och f.d. gräsmarker där hävd upphört och hur ett förändrat landskap spelat roll för artantalets utveckling eller tillbakagång. Resultat visade att antalet kärlväxter var signifikant lägre i marker som slutat hävdas, än marker som fortfarande hävdas. Även jämförelser i enbart fältskiktet visade ett signifikant högre artantal hos välhävdade marker än marker där hävd upphört. Det fanns en signifikant skillnad mellan antalet indikatorarter i marker som var under hävd och marker som slutat hävdas för 30-40 år sedan, kontra 100 år sedan. Vid jämförelser med en tidigare studie, som ägt rum precis efter att hävden upphört på ett flertal lokaler visade resultat att det fanns en signifikant skillnad i artantal mellan de båda åren. På några få decennier kan ett helt växtsamhälle som byggts upp under hundratals eller kanske till och med tusentals år utarmas. För att bevara den biologiska mångfald som formas av en störningsregim beroende av människans inverkan, måste hävd fortsätta kontinuerligt.</p>