Translocations are an important aspect of the management of natural populations in an increasingly fragmented landscape. Maintaining connectivity and gene flow is beneficial for both contemporary fitness and adaptive potential in the face of environmental change. Genetic rescue (GR) can alleviate inbreeding depression, genetic load, and increase adaptive potential of populations. Here, I have translocated 10 (5 of each sex) brook trout (Salvelinus fontinalis) to four geographically proximate and environmentally similar fragmented stream-dwelling populations of brook trout in Virginia to test for genetic rescue. The translocated brook trout contributed to more families than would be expected under neutral introgression, and hybridization resulted consistently in larger full-sibling family sizes. In the cohort immediately following translocation I observed relatively high (>20%) introgression in 3 of the 4 recipient sites, and in one recipient population 57.7 % of the offspring had at least one migrant parent. During the post-translocation period favorable regional climatic conditions resulted in large cohorts across recipient sites and controls, however the percent increase in juvenile abundance scales to initial genetic diversity and patch size. I observe strong evidence of hybrid vigor through consistently larger body sizes of hybrid offspring. At this point I cannot rule out potential negative effects of translocations such as outbreeding depression with out sampling more cohorts following genetic recombination. However, I provide an empirical and replicated foundation to begin assessing the efficacy of GR-motivated translocations for headwater fish conservation, and make a substantial contribution to the growing body of GR-literature.

No description available.

Abstract :The main goal of this stud y was to quantify the effect s of landscape structure on the abundance of Ruby-throate d Hummingbird s (Archilochus colubris) in forest patches and this, while accounting for its indirect effects on open flower community an d the occurrence of Yellow-bellied Sapsucker s (Sphympicus varius), a potential commensal of hummingbirds. We sampled 40 forest patches (0. 5 to >10 0 ha ) where we had installed 2 nectar feeders (forest edge and 40 m within forest ) during 2 breeding season s (2006 and 2007) . We visited forest patches weekly and recorded the number of hummingbirds detected within 10 m of feeders during 10 min. Mean daily artificial nectar consumption by hummingbirds, as well as their relative total abundance an d the respective relative abundance of adult males and females, were all affected by forest cover. Except for the relative total abundance, this effect of forest cover depended upon the size of forest patches. Nectar consumption and abundance generally peaked in forest patches of intermediate size found in landscapes characterized by intermediate forest cover. Mea n daily artificial nectar consumption and the relative total abundance, a s well as that of males, were higher at feeders located on the forest edge compared to 40 m inside forest patches. Regarding indirect landscape effects, landscape structure influenced the structure of open flower communities surrounding feeders, which in turn, affected the relative total abundance of hummingbirds, a s well as that of adult males. On the other hand, we failed to find strong evidence that landscape structure affected the occurrence of Yellow-bellied Sapsuckers or that the latter influenced Ruby-throated Hummingbird abundance patterns. These results support the idea that landscape structure may affect the abundance pattern of a species directly as well as through mechanisms which are themselves dependent upon the composition and configuration of landscapes //Résumé : La structure des paysages peut influencer l'écologie d'une espèce directement, en contraignant ses mouvements, par exemple, de même qu'indirectement en affectant, entre autres, l'abondance de ses proies ou prédateurs. Quoique plusieurs études aient tenté de quantifier l'influence de la structure du paysage sur les patrons d'abondance, rares sont celles qui ont mesuré simultanément les effets directs et indirects du paysage. L'objectif de ce mémoire consiste à modéliser simultanément les effets directs de la structure du paysage sur l'abondance relative du Colibri à gorge rubis ( Archilochus colubris ) et sa consommation de nectar artificiel ainsi que les effets indirects par lesquels le paysage peut aussi agir tels la disponibilité en ressources alimentaires (communautés floristiques) et la relation interspécifique de commensalisme avec le Pic maculé ( Sphyrapicus varius ). Pour ce faire, j'ai échantillonné 40 îlots forestiers (0,5 à >100 ha) dans la région de l'Estrie (Québec, Canada). À chacun d'eux, j'ai installé deux abreuvoirs (en bordure et 40 m à l'intérieur) durant les étés 2006 et 2007 et ont été visités de façon hebdomadaire. J'ai détecté une relation quadratique du couvert forestier dans le paysage avec l'abondance totale relative, celle des mâles et des femelles ainsi que pour la consommation quotidienne moyenne. Ces effets varient en fonction de la taille d'îlot sauf pour l'abondance relative totale. Les valeurs maximales se situent à des niveaux intermédiaires de couvert forestier et de taille d'îlots. Certaines caractéristiques mesurées étaient à l'échelle locale comme la position de l'abreuvoir dans l'îlot forestier ou la structure de la végétation. J'ai détecté un effet de bordure pour toutes les variables sauf l'abondance des femelles. L'indice de structure de végétation n'avait d'influence que sur l'abondance des mâles. Concernant les effets indirects, l'ensemble des variables du paysage explique 69,61% de l'indice de communauté floristique et ce dernier a un effet significatif sur l'abondance totale et l'abondance des colibris mâles. Pour la relation avec le pic, les variables du paysage mesurées n'ont pas permis de détecter un effet. De plus, bien qu'étant une variable non significative, les modèles incluant la présence du Pic maculé étaient généralement parmi les plus performants. L'ensemble de ces résultats soutient l'importance de combiner l'écologie du paysage et l'écologie comportementale dans les mêmes modèles afin de tenir compte non seulement des effets directs mais aussi des effets indirects du paysage //

Dissertation presented for the degree of Doctor of Philosophy (PhD) at Stellenbosch University. / Thesis (PhD (Conservation Ecology and Entomology))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: The South African Cape lowlands have been severely transformed and reduced to fragments embedded in matrices of various activities. With the need to prioritise conservation efforts, information on the conservation worthiness and management of these fragments is required. This study aimed to better understand how fragmentation affects the Cape lowland vegetation patterns and dynamics and more specifically, to determine if, and if so to what extent these fragments contribute to regional plant diversity and more importantly their functionality. The novel approach adopted focused on plant functional traits, which are better predictors of ecosystem response to global change than individual species. Species were sampled at four scales in four sites of decreasing sizes, including: a mainland and three fragments of three Cape lowland vegetation types i.e. Atlantis Sand Fynbos (ASF), Swartland Shale Renosterveld (SSR) and Langebaan Dune Strandveld (LDS). Traits such as dispersal, pollination, breeding mode and longevity were selected based on relevance to species’ and plantfunctional types’ (PFTs) responses to fragmentation. The findings revealed different effects on species richness and PFTs. The effect of reduced patch size on species richness was more evident in ASF where fragments below 600 ha had significantly fewer species than the mainland. This effect was not unequivocal in SSR and LDS due to several confounding factors (notably the grazing history of the sites). The SSR fragment grazed by indigenous herbivores had significantly more species than the ungrazed sites. Also, the largest LDS fragment grazed by livestock had significantly more species than the ungrazed mainland, indicating that grazing rather than fragment size influences species richness, although the smallest fragments of these two vegetation types had significantly fewer species than the larger fragments. Species turnover and complementarity were high for all three vegetation types, reflecting the degree of habitat heterogeneity and high contribution of beta diversity to overall gama diversity. The effect of reduced patch size was higher on PFT diversity than on PFT richness, with Langebaan Dune Strandveld where habitat fragmentation was more recent being the least affected of the three vegetation types. This indicates a degree of functional redundancy in the Cape lowlands, which is important for ecosystem resistance and resilience. The ASF mainland and the largest fragment had higher PFT diversity than the medium-sized and the smallest fragments; the mainland had also higher PFT diversity than all the fragments combined. Similarly, the smallest SSR fragment had significantly lower PFT diversity and richness than the other sites. The grazed SSR fragment had higher PFT richness and diversity than the ungrazed mainland and smallest fragment, indicating the role of grazing in maintaining renosterveld vegetation. The PFTs absent from the different sites were mostly short-distance dispersed dioecious and non-dioecious species, and some with highly specialised pollination systems. This suggests that dispersal and pollination are vital functional attributes for the persistence of the studied fragmented ecosystems. Habitat fragmentation effects plant community composition and ecological functions in the Cape lowlands, a conclusion supported also by the revealed significant trait-convergence and divergence assembly patterns. These communities result from various fragmentation filters that operate at different spatial-temporal scales and selecting species with suitable responses. All three vegetation types are susceptible to fragmentation, albeit at varying degree. The fragmentation effect was confounded by the sampling and temporal scales, the nature of disturbance regime, and the traitmediated differences in species’ response. The role of the surrounding matrix on fragment connectivity and gene flow appears to be of crucial importance, hence mitigation measures focusing on improving connectivity between patches, monitoring threatened taxa, and promoting dispersal and pollination have been recommended. / AFRIKAANSE OPSOMMING: Suid-Afrika se Kaapse laagland het dramaties verander en weggekwyn tot fragmente wat in matrikse van verskeie bedrywighede veranker is. Gedagtig aan die voorkeuraandag wat bewaringspogings tans geniet, is inligting oor die bewaringswaardigheid en bestuur van hierdie fragmente nodig. Hierdie studie stel dit ten doel om beter begrip te vorm van hoe fragmentasie die plantegroeipatrone en -dinamiek in die Kaapse laagland raak, en meer bepaald om vas te stel óf, en indien wel, in watter mate, hierdie fragmente tot streeksplantdiversiteit en -funksionaliteit bydra. Die ongewone studiebenadering konsentreer op funksionele kenmerke van plante, wat beter aanwyser van ekosisteemreaksie op wêreldwye verandering is as individuele spesies. Spesiemonsters is op vier skale by vier terreine van wisselende grootte ingesamel, wat insluit moederstrook en drie fragmente van elk van drie plantegroeisoorte in die Kaapse laagland, naamlik Atlantis-sandfynbos (ASF), Swartland-skalierenosterveld (SSR) en Langebaan-duinestrandveld (LDS). Kenmerke soos verspreiding, bestuiwing, voortplantingsmetode en lewensduur is gekies op grond van die tersaaklikheid daarvan vir spesies en plantfunksionele tipes (PFT’s) se reaksie op fragmentasie. Die studie bring verskillende uitwerkings op spesie-oorvloed en PFT’s aan die lig. Wat spesie-oorvloed betref, was die uitwerking van kleiner strookgrootte (“patch size”)duideliker te sien by ASF, waar fragmente kleiner as 600 ha beduidend minder spesies as die moederstrook bevat het. Hierdie uitwerking kon nie so duidelik by SSR en LDS waargeneem word nie weens verskeie strengelingsfaktore, veral die weidingsgeskiedenis van die terreine. Die SSR-fragment waarop inheemse herbivore gewei het, het beduidend meer spesies as die onbeweide terreine bevat. Voorts het die grootste LDS-fragment waarop vee gewei het heelwat meer spesies as die onbeweide moederstrook gehad, wat daarop dui dat weiding eerder as fragmentgrootte spesie-oorvloed beïnvloed, hoewel die kleinste fragmente van hierdie twee plantsoorte steeds aansienlik minder spesies as die groter fragmente bevat het. Spesie-omset en -aanvullendheid was hoog vir ál drie plantsoorte, wat aanwyser is van die mate van habitat-heterogeniteit en die groot bydrae wat betadiversiteit tot algehele gammadiversiteit lewer. Die uitwerking van kleiner strookgrootte was duideliker te bespeur op PFT-diversiteit as PFT-oorvloed – in dié verband het LDS, waar habitatfragmentasie mees onlangs plaasgevind het, die ligste van die drie plantsoorte afgekom. Dít dui op mate van funksionele oorbodigheid in die Kaapse laagland wat belangrik is vir ekosisteemweerstandigheid en -gehardheid. Die ASF-moederstrook en die grootste ASF-fragment het hoër PFT-diversiteit getoon as die medium- en kleinste fragmente; die moederstrook het in werklikheid oor hoër PFT-diversiteit as ál die fragmente saam beskik. Insgelyks het die kleinste SSR-fragment beduidend minder PFT-diversiteit en -oorvloed as die ander terreine getoon. Die beweide SSR-fragment was hoër in PFT-oorvloed én -diversiteit as die onbeweide moederstrook en die kleinste fragment, wat die rol van weiding in die instandhouding van renosterveldplantegroei beklemtoon. Die PFT’s wat nié op die verskillende terreine voorgekom het nie, was meestal tweehuisige en nietweehuisige spesies wat oor kort afstande versprei, en sommige spesies met hoogs gespesialiseerde bestuiwingstelsels. Dít dui daarop dat verspreiding en bestuiwing noodsaaklike funksionele kenmerke vir die voortbestaan van die bestudeerde gefragmenteerde ekosisteme is. Habitatfragmentasie raak die samestelling en ekologiese funksies van plantgemeenskappe in die Kaapse laagland. Dié gevolgtrekking word ook gerugsteun deur die bewese patrone van beduidende kenmerkkonvergensie (“trait convergence”) en divergensiesamekoms (“divergence assembly”). Hierdie plantgemeenskappe spruit uit verskeie fragmentasiefilters wat op verskillende ruimte-tydskale funksioneer, en wat spesies met geskikte reaksies kies. Ál drie plantsoorte is ontvanklik vir fragmentasie, hoewel in wisselende mate. Die fragmentasie-uitwerking is beïnvloed deur monsterinsameling- en tydskale, die soort versteuringsbedeling, en die kenmerkbemiddelde (“traitmediated”) verskille in spesiereaksie. Die rol van die omringende matriks op fragmentverbondenheid en geenvloei blyk van die allergrootste belang te wees, en dus word temperingsmaatreëls aanbeveel wat daarop gemik is om verbondenheid tussen stroke te verbeter, bedreigde taksa te moniteer, en verspreiding en bestuiwing aan te help.

Chameleons are an understudied taxon facing many threats, including collection for the international pet trade and habitat loss and fragmentation. A recent field study reports a highly female-biased sex ratio in the Eastern Arc Endemic Usambara three horned chameleon, Trioceros deremensis, a large, sexually dimorphic species. This species is collected for the pet trade, and local collectors report males bring a higher price because only this sex has horns. Thus, sex ratios may vary due to differential rates of survival or harvesting. Alternatively, they may simply appear to be skewed if differences in habitat use biases detection of the sexes. Another threat facing chameleons is that of habitat loss and fragmentation. Despite enormous amounts of research, the factors of fragmentation that different species respond to is still under debate. Understanding these responses is important for current mitigation efforts as well as predicting how species will respond to future habitat alteration and climate change. My study suggests that differences in survival and detection may explain much of the observed seasonal sex skew in adult T. deremensis. Within fragmented habitat chameleons consistently responded more to edge effects and vegetative characteristics associated with fragmentation than to area or isolation effects. This may bode poorly for chameleon populations in the coming decades as climate change further alters vegetative communities and exacerbates edge effects.

Este estudo enfocou a importância do contexto de ambientes alterados do entorno para a distribuição de diferentes grupos de espécies de pequenos mamíferos não-voadores em paisagens fragmentadas de Mata Atlântica. Na primeira abordagem (capítulo 2), usando a distribuição de pequenos mamíferos em remanescentes florestais e nos quatro principais habitats alterados de uma paisagem de Mata Atlântica, investigamos (1) como o poder explanatório dos modelos que descrevem a distribuição das espécies em fragmentos florestais varia entre as variáveis da estrutura da paisagem que incorporam ou não a qualidade da matriz e (2) a importância da escala espacial para analisar a influência da estrutura da paisagem. Usamos amostragem padronizada nos remanescentes e habitats alterados para gerar dois índices de qualidade de habitat, correspondentes à abundância e à ocorrência de pequenos mamíferos. Para cada remanescente, calculamos a quantidade de habitat e a conectividade em diferentes escalas espaciais, considerando ou não a qualidade dos habitats ao redor. A incorporação da qualidade da matriz aumentou o poder explanatório dos modelos para todas as escalas espaciais para metade das espécies que ocorreram na matriz, mas apenas quando consideramos a distância entre as manchas de habitat (conectividade). Os resultados indicam a importância da matriz para a dinâmica de paisagens fragmentadas e sugere que índices relativamente simples podem melhorar nosso entendimento sobre a distribuição das espécies, e poderiam ser aplicados na modelagem, monitoramento e manejo de paisagens tropicais complexas. Na segunda abordagem (capítulo 3), testamos duas hipóteses relacionadas à importância do contexto da paisagem para a diversidade biológica encontrada em áreas agrícolas usando os pequenos mamíferos da Mata Atlântica como modelo: (1) que o contexto em que cultivos agrícolas estão inseridos, em particular a quantidade de florestas remanescentes, determina a assembléia de pequenos mamíferos encontrada nestas áreas produtivas; (2) que essas respostas ao contexto são escala-dependentes, sendo observadas em escalas espaciais mais amplas. Para tanto, amostramos 36 sítios em áreas agrícolas em duas paisagens fragmentadas de Mata Atlântica com diferentes proporções de florestas nativas remanescentes, os quais foram selecionados de forma a abranger ampla variação na quantidade e agregação de áreas abertas no entorno imediato. Construímos e comparamos 12 modelos candidatos que diferem quanto à contribuição dos efeitos do contexto em escala espacial ampla e em escala local, incluindo todas as combinações possíveis entre essas variáveis, a interação das variáveis medidas em diferentes escalas, e um modelo nulo. De acordo com as expectativas iniciais, as espécies restritas a biomas florestais foram mais comuns e bem distribuídas em áreas agrícolas circundadas por maiores quantidades de floresta em escala ampla. No entanto, as espécies invasoras e não-restritas a biomas florestais dominaram as áreas agrícolas das duas paisagens estudadas, independentemente da quantidade de floresta remanescente em escala ampla, tendo respondido principalmente, mas de maneira oposta, ao contexto em escalas menores. Os resultados indicam que: (1) a resposta diferencial entre os grupos de espécies é condicionada por diferenças nos requerimentos de habitat entre eles; (2) a manutenção de espécies mais exigentes em áreas agrícolas depende de estratégias de manejo que considerem a escala da paisagem; (3) mesmo áreas de agricultura convencional podem ser importantes para a conectividade da paisagem para espécies exigentes, desde que inseridas em contexto de maior quantidade de matas remanescentes; (4) o controle das populações de espécies invasoras que podem atuar como reservatórios de patógenos causadores de doenças no homem e pestes na agricultura depende de manejo em escala local, pelo menos em paisagens onde as áreas agrícolas são predominantes. / This study focused on the importance of the context of altered habitats in the neighborhoods to the distribution of different groups of species of non-flying small mammals in fragmented landscapes of the Atlantic forest. In the first approach (chapter 2), using the distribution of small mammals in forest remnants and in the four main altered habitats in an Atlantic forest landscape, we investigated 1) how explanatory power of models describing species distribution in forest remnants varies between landscape structure variables that do or do not incorporate matrix quality and 2) the importance of spatial scale for analyzing the influence of landscape structure. We used standardized sampling in remnants and altered habitats to generate two indices of habitat quality, corresponding to the abundance and to the occurrence of small mammals. For each remnant, we calculated habitat quantity and connectivity in different spatial scales, considering or not the quality of surrounding habitats. The incorporation of matrix quality increased model explanatory power across all spatial scales for half the species that occurred in the matrix, but only when taking into account the distance between habitat patches (connectivity). Results indicate the importance of the matrix for the dynamics of fragmented landscapes and suggest that relatively simple indices can improve our understanding of species distribution, and could be applied in modeling, monitoring and managing complex tropical landscapes. In the second approach, (chapter 3), we aimed at testing two hypotheses related to the importance of landscape context to the biological diversity found in areas of agriculture using Atlantic forest small mammals as a model: (1) that the context in which the areas of agriculture are inserted, in particular the quantity of remnant forests, determines the assemblage of small mammals found in those productive areas; (2) that those responses to the context are scale-dependent, being observed at larger spatial scales. To accomplish that, we sampled 36 sites in areas of agriculture in two fragmented Atlantic forest landscapes presenting different proportions of native forest remnants, which were selected aiming at including the widest variation in quantity and aggregation of open anthropogenic areas in the local neighborhood. We built and compared 12 candidate models which differed in relation to the contribution of the effects of context at large and local spatial scales, including all possible combinations between these variables, the interaction of the variables measured at different scales, and the null model. According to our initial expectations, the species that are restricted to forest biomes were the commonest and best-distributed ones, in areas of agriculture surrounded by higher quantities of forest at the large scale. However, the invasive species and the species that are not restricted to forest biomes dominated the areas of agriculture in the two studied landscapes, independently from the quantity of remnant forest at the large scale, and they responded mainly, but in the opposite way, to the context at smaller scales. The results indicate that: (1) the differential response between the groups of species is conditioned by differences in habitat requirements between them; (2) the maintenance of more demanding species in agricultural lands depends on management strategies which consider the landscape scale; (3) even areas of conventional agriculture can be important to the connectivity of the landscape for the most demanding species, as far as they are inserted in a context of higher quantities of remnant forest; (4) the control of the populations of invasive species that can act as reservoirs of pathogens that cause disease in men, and that can be pests in agriculture, depends on the management at local scale, at least in landscapes where the areas of agriculture predominate.

A intensa degradação do bioma cerrado tem tido grandes conseqüências na disponibilidade de habitats de boa qualidade para muitos animais e a busca por métodos rápidos e confiáveis que localizem áreas de valor ecológico para diferentes grupos de animais tem despertado grande interesse. A análise geográfica computadorizada foi utilizada como ferramenta para caracterização da heterogeneidade (diversos graus de qualidade e tipo de cobertura fitofisionômica) dos habitats existentes no remanescente estudado, buscando fornecer informações que pudessem levar ao entendimento de como as espécies de mamíferos de médio e grande porte utilizam estes habitats alterados, além de fornecer informações que pudessem ser utilizadas para o delineamento da amostragem. Desta forma, a primeira etapa foi a elaboração de uma base cartográfica que produziu dois mapas de caracterização ambiental, um mapa geral e outro da mata ripária. O primeiro foi utilizado para a realização de uma análise preliminar da qualidade dos habitats e distribuição das armadilhas fotográficas, transecções e canteiros de pegadas, buscando capturar toda a heterogeneidade existente no remanescente. Desta forma, houve a sistematização das amostragens. A utilização destes métodos permitiu a detecção de 22 espécies de mamíferos de médio e grande porte em 28 dias de amostragem, quando a curva acumulativa de espécies (Sobs Mao Tau) atingiu sua assíntota. O teste do qui quadrado permitiu afirmar que houve influência das fitofisionomias na distribuição das espécies observadas. Desta forma, partindo-se do pressuposto de que a heterogeneidade de habitats certamente irá influir na diversidade de recursos alimentares, admitiu-se que a grande riqueza obtida no remanescente estudado esteja principalmente relacionada à disponibilidade de recursos alimentares. A segunda etapa da análise espacial foi a elaboração de um modelo de tomada de decisão que espacializou as informações relacionadas à biologia e ecologia de algumas espécies de mamíferos. O modelo desenvolvido permitiu produzir novas informações importantes em relação à qualidade dos habitats e o uso dos mesmos pelas espécies-alvo, por meio da sobreposição dos dados de detecção nos Mapas de Oportunidades gerados (validação do modelo de tomada de decisão desenvolvido). O uso destes habitats também foi testado por meio do qui quadrado e o resultado obtido permitiu afirmar que houve a influência da qualidade do habitat na distribuição das espécies neste estudo. Esta informação enfatiza que o modelo de tomada de decisão aplicado pode ser uma ferramenta muito importante em estudos relacionados ao uso de habitats, alterados ou intactos, por espécies de mamíferos de médio e grande porte, em função de suas necessidades ambientais, ou seja, cada espécie possui requerimentos ambientais específicos e que devem ser levados em consideração para o desenvolvimento de qualquer plano de manejo e conservação em um determinado local. / The intense degradation of the Cerrado biome has had great consequences over the habitat quality available for many animals. The search for rapid and reliable methods to allocate areas with ecological values for different groups of animals has arising great interest now-a-days. The developed methodology at the present work aim to determine the variation of the habitat quality within a São Paulo State cerrado remnant (2,098ha), using remote sensing and geoprocessing techniques. According to the environmental needs of each species, were selected abiotic and biotic criteria that could be inserted on a decision making model in order to influence habitat quality and infer seven mammals species occurrence: Myrmecophaga tridactyla - great anteater, Tapirus terrestris - tapir, Tayassu tajacu - collared peccary, Mazama americana - red brocket deer, Eira barbara tayra, Puma concolor puma and Leopardus pardalis ocelot. Those criteria were evaluated by experts, who assign specific weights according to species environmental needs. Thus, seven Opportunity Maps were developed through a Multi Criteria Evaluation, which were validated in the field (trace sensing and cam trapping). The model used showed very robust in predicting coherently the habitat quality using the occurrence of the target species. The most detections were obtained in favorable areas (40%), followed by very favorable areas (20%), regular areas (18%), unfavorable areas (15%) and very unfavorable areas (6%). The most species were detected more often in favorable areas and less often in very unfavorable areas, excepted T. terrestris and T. tajacu, which were detected in very favorable areas.

Invasões biológicas são consideradas uma das maiores ameaças atuais à biodiversidade global. O cão doméstico é hoje o carnívoro mais abundante no mundo, e tem invadido áreas de vegetação nativa, podendo causar impactos negativos à fauna silvestre através da predação, competição e transmissão de doenças. A partir de dois extensos bancos de dados obtidos através de armadilhas fotográficas, esta dissertação pretende contribuir com o entendimento das causas e consequências da invasão por cães domésticos de remanescentes florestais e agroflorestas na Mata Atlântica. A dissertação está organizada em dois capítulos. No primeiro, usamos dados obtidos em duas paisagens rurais do Planalto Atlântico de São Paulo com diferentes proporções de florestas remanescentes, e (1) descrevemos o tipo de manejo e as características dos cães que visitam fragmentos florestais, (2) comparamos, entre estas paisagens, a frequência e horário de visitas e o tamanho de grupos de cães invasores assim como os fatores determinantes da intensidade de invasão, e (3) investigamos o impacto da intensidade de invasão sobre a distribuição de mamíferos silvestres de maior porte. No segundo capítulo, usamos dados obtidos em um mosaico agroflorestal do Sul da Bahia, e (4) verificamos se a conversão de florestas nativas em agroflorestas e a intensificação das agroflorestas favorecem a invasão por cães domésticos, e (5) se a invasão por estes animais está mais associada à presença humana nas agroflorestas do que nas florestas. Em conjunto, os resultados dessa dissertação sugerem que: (1) a intensidade da invasão por cães em paisagens antropizadas de Mata Atlântica é altíssima, tanto em termos do número de indivíduos e de visitas como em termos do número de sítios ocupados; (2) a invasão é favorecida pelo tipo de manejo dos animais, que são em grande parte criados soltos, e parece estar fortemente associada à presença do homem; (3) a intensidade de invasão afeta negativamente a distribuição de um maior número de espécies de mamíferos de maior porte do que a perda de 40% de floresta na paisagem; (4) características dos remanescentes florestais associadas à perda de habitat (quantidade e qualidade dos remanescentes) são mais importantes que a pressão de propágulo para determinar a intensidade da invasão; (5) a intensificação do manejo de agroflorestas acentua a invasão. Visto que a intensificação de agroflorestas e de outros sistemas agrícolas vem se acentuando globalmente e que, apesar da diminuição das taxas de desmatamento das florestas tropicais nos últimos anos, a maior parte das áreas remanescentes é constituída de vegetação degradada ou secundária, a quantidade de áreas susceptíveis à invasão e os danos causados por cães domésticos devem aumentar no futuro. / Biological invasions are considered one of the most important threats to global biodiversity. Domestic dogs, the most abundant carnivore in the world, are known to invade areas of native vegetation and impact wildlife through competition, predation and disease transmission. Drawing on two extensive dataset obtained through camera-trapping, this dissertation intends to contribute to the understanding of the causes and consequences of the invasion by domestic dogs of forests fragments and agroforests in the Atlantic Forest. The dissertation is organized into two chapters. In the first chapter, we use data from two rural landscapes of São Paulo Atlantic Plateau with different proportions of remaining forests, and (1) describe the management and the characteristics of dogs that visit forest fragments, (2) compare, between these landscapes, the frequency and time of visits, the size of groups of invading dogs, and the drivers of invasion intensity, and (3) investigate the impacts of invasion intensity on the distribution of native large mammals. In the second chapter, using data from an agroforestry mosaic in southern Bahia, we investigate (4) if the conversion of native forests into agroforests and agroforestry intensification favor the invasion by dogs, and (5) if invasion by these animals is more associated with human presence in agroforests than in forests. Our findings highlight that: (1) the intensity of the invasion by dogs in human-modified landscapes in the Atlantic Forest is extremely high, both in terms of the number of individuals and of visits and in terms of the number of occupied sites; (2) invasion is favored by the type of management, with dogs kept free, and seems to be strongly associated with the presence of humans; (3) invasion intensity negatively affects the distribution of a larger number of large mammals than the loss of 40% of forest in the landscape; (4) characteristics of forest fragments associated with habitat loss (quantity and quality of remnants) are more important than propagule pressure to determine the intensity of invasion; (5) management intensification in agroforests intensifies invasion. As intensification of agroforestry and other agricultural systems has increased globally and, despite the decrease in the rates of deforestation in recent years, most tropical forest remnants consist of degraded or secondary vegetation, the amount of areas susceptible to invasion and the damages caused by domestic dogs should increase in the future.

Conservation managers worldwide are increasingly faced with the challenges of managing and protecting fragmented landscapes, largely as a consequence of human activities. Over recent decades, ecological theory has made a significant contribution to the development of landscape-scale conservation and practice. However, recommendations accounting for what is practically achievable in the modern-day landscape are currently lacking, while criteria for conservation planning and prioritisation continue to neglect the role of habitat networks at the required spatial scale for the long-term persistence of biodiversity. In this thesis, I test and apply ideas surrounding the complexities of managing and conserving species in a landscape context, using a suite of bird species endemic to papyrus (Cyperus papyrus) swamps in East and Central Africa as a model system. In the face of large-scale habitat loss and degradation, practical measures that account for the fragmented nature of this system, the needs of multiple specialist species, and the reliance on this habitat by local people, are urgently required. I first review the concepts originating from reserve design theory to provide a decision-making framework for those involved in landscape-scale conservation amid 21st century challenges to biodiversity, highlighting the key principles to be considered for informed choices to be made. Second, I show that the needs of local people can be compatible with conservation planning in the tropics, and may play an important part in maintaining habitat quality for species residing in historically disturbed landscapes. Third, I develop a novel framework to make an explicit link between metapopulation dynamics and conservation planning. Despite differences in the patch-level dynamics of individual species, areas of habitat where populations of multiple species are resistant to extinction, and resilient because of high chances of (re)colonization can be identified, highlighting where resources could be invested to ensure species have the capacity to respond to future change. Finally, I simulate the metapopulation dynamics of the papyrus-endemic birds to demonstrate that the optimal conservation strategy for the long-term persistence of all species residing in a network depends on the characteristics of individual species, and the total area that can be protected. Overall, this thesis develops and tests the ecological theory used in spatial conservation planning, emphasising the importance of habitat disturbance and interspecific ecological differences for the effective management of habitat networks. The results increase the evidence base for the conservation of wetland birds in Africa, as well as for species residing in fragmented landscapes more generally.

Nessa dissertação, avaliei a eficiência e congruência de métodos para amostragem de mamíferos de maior porte e investiguei a influência de fatores múltiplos correlacionados, comuns em paisagens fragmentadas, sobre a distribuição destes animais em remanescentes de Mata Atlântica. Através de amostragens padronizadas em 24 remanescentes florestais de uma paisagem rural com 49% de remanescentes florestais no Planalto Paulista e de um delineamento pareado, no capítulo 2 comparei o desempenho e a congruência de dois métodos (pegadas em parcelas de areia e armadilhas fotográficas) e de dois tipos de isca (banana e iscas de cheiro) para a estimativa da riqueza e taxa de ocorrência de mamíferos de maior porte. Ambos os métodos se mostraram adequados para o estudo destes animais em florestas tropicais e dos fatores que afetam sua distribuição em paisagens alteradas, pois (1) registram as espécies de menor porte e noturnas, (2) podem ser padronizados entre áreas heterogêneas, (3) apresentam desempenho semelhante no registro da maioria das espécies e da riqueza de espécies, e (4) refletem de maneira similar o padrão de ocorrência das espécies entre diferentes áreas. Frente às iscas de cheiro utilizadas, a banana foi a isca mais eficiente na amostragem tanto das espécies herbívoras/frugívoras quanto das espécies onívoras, destacando a necessidade da padronização das iscas utilizadas e do uso de iscas complementares ou de iscas que atraiam uma ampla gama de animais. Usando os dados obtidos com armadilhas fotográficas, avaliei quais fatores condicionam a presença e a freqüência de ocorrência de cães domésticos (capítulo 3) e de mamíferos de maior porte (capítulo 4) nos remanescentes. Esta avaliação foi realizada através da seleção de modelos de regressão construídos com base na relação causal entre os fatores estudados - que pode ser estabelecida a partir de como usualmente se dá a expansão das atividades humanas em florestas neotropicais - e comparados através do critério de informação AIC (The Akaike Information Criterion). Para o cão doméstico, foram considerados quatro fatores: extensão de estradas, quantidade de mata e número de cães domésticos no entorno, e qualidade da vegetação. Foi observada uma forte relação positiva entre o total de residentes e o total de cães domésticos no entorno dos remanescentes. Dentro dos remanescentes, o cão doméstico foi mais registrado do que sete das 11 espécies nativas, sua ocorrência foi mais bem explicada pela quantidade de cães no entorno, e sua freqüência de ocorrência pela diminuição da quantidade de mata no entorno, o que mostra a necessidade de controle populacional desta espécie no entorno de áreas naturais e da manutenção de áreas florestadas mais extensas, menos suscetíveis a entrada deste invasor. Para os mamíferos de maior porte, os fatores considerados foram: quantidade de mata e número de residentes no entorno dos remanescentes, distância à estrada de asfalto, freqüência de ocorrência de cães domésticos nos remanescentes, e qualidade da vegetação dos remanescentes. Os resultados demonstraram que, apesar da ampla variação na resposta das espécies a estes fatores, a distância a estradas de asfalto e a freqüência de ocorrência de cães domésticos, fatores que são correlacionados a disponibilidade de habitat e não são freqüentemente considerados, determinaram a distribuição de um número maior de espécies. A comunidade de mamíferos de maior porte encontrada é simplificada, dominada por espécies generalistas e com poucos dispersores e predadores de sementes e plântulas, o que pode levar a conseqüências negativas para outras espécies e para o funcionamento e regeneração das florestas remanescentes. Estes resultados sugerem que para a conservação de uma comunidade íntegra de mamíferos de maior porte na Mata Atlântica é necessário, não apenas a manutenção de grandes contínuos de mata nativa ou de paisagens com percentual alto de matas remanescentes, mas a redução drástica das perturbações associadas à ocupação e atividades humanas. O manejo e restauração de paisagens devem considerar a proximidade entre os remanescentes florestais e estradas, principalmente as asfaltadas e de alto tráfego, e a importância de campanhas de controle populacional e vacinação de cães domésticos. / In this master thesis, I evaluated the efficiency and congruence of methods for sampling large mammals, and investigated the influence of multiple and correlated factors, common in fragmented landscapes, on the distribution of these animals in Atlantic Forest remnants. Through standardized surveys at 24 forest remnants in a rural landscape with 49% of remaining forest in the Planalto Paulista and using a paired design, in chapter 2 I compared the performance and the congruence of two methods (tracks in sand plots and camera-trapping) and of two types of baits (banana and scent lures) for estimating richness and rate of occurrence of large mammals. Both methods are suitable for studying these animals in tropical forests as well as the factors that affect their distribution in disturbed landscapes, because (1) they record medium-sized and nocturnal species, (2) can be standardized among heterogeneous sites, (3) present similar performance for recording most species and richness, (4) reflect in similar ways the pattern of species occurrence among different sites. Compared with scent lures, banana was the most efficient bait for sampling herbivores/frugivores as well as omnivores, highlighting the need to standardize baits and use complementary baits or baits that attract a wide range of animals. Using camera-trapping data, I evaluated which factors determine the presence and the frequency of occurrence of domestic dogs (chapter 3) and of large mammals (chapter 4) in remnants. This evaluation was done through the selection of regression models buit based on the causal relationship among studied factors which can be established from the way expansion of human activities usually happens in neotropical forests and compared through the AIC, The Akaike Information Criterion. For the domestic dog, four factors were considerate: extension of roads, amount of forest and number of domestic dogs in the surroundings, and vegetation quality. It was observed a strong positive relationship between the total number of residents and the total number of domestic dogs in the surroundings. Inside remnants, the domestic dog was more frequently recorded than seven of the 11 native species, its occurrence was better explained by the number of dogs in the surroundings, and its frequency of occurrence by the reduction of the amount of forest in the surroundings, which indicates the need of population control of this invasive species in the surroundings of natural areas and of the maintenance of extensive forests areas that are less susceptible to the entrance of this invasive species. For native large mammals, the considered factors were: amount of forest and number of residents in the surroundings, distance from paved roads, frequency of occurrence of domestic dogs and vegetation quality. Results suggested that, despite the large variation in the responses of species to the studied factors, distance from paved roads and frequency of occurrence of domestic dog, factors that are correlated with habitat availability and are not frequently considered, determined the distribution of a larger number of species. The large mammal community found is simplified, dominated by generalist species and with few seed and seedling dispersers and predators, which can lead to negative consequences to other species and to forest functioning and regeneration. These results suggest that for conserving a complete large mammal community at the Atlantic Forest, not only the maintenance of large tracts of continuous forest or landscapes with high percentage of remaining forest is needed, but also a drastic reduction of disturbances associated with human activities and occupation. Landscape management and restoration should consider the proximity between forest remnants and roads, especially those that are paved and present high traffic, and the importance of campaigns of domestic dog population control and vaccination.