Humans are modifying the global landscape at an unprecedented scale and pace. As a result, species are declining and going extinct at an alarming rate. Here, I investigate two main aspects of species’ declines: what factors are contributing to their declines and how effective our conservation efforts have been. I assessed one of the main mechanisms for protecting species by looking at the Endangered Species Act (ESA) in the United States. I examined three separate indicators of species declines for different groups of species: range contractions in Canadian imperilled species, declines in abundance in global amphibian populations and increases in temporal variability in abundance in North American breeding birds. I found that change in recovery status of ESA listed species was only very weakly related to the number of years listed, number of years with a recovery plan, and funding. These tools combined explained very little of the variation in recovery status among species. Either these tools are not very effective in promoting species’ recovery, or species recovery data are so poor that it is impossible to tell whether the tools are effective or not. I examined patterns of species’ declines in three different groups in relation to a number of anthropogenic variables. I found high losses of Canadian imperiled bird, mammal, amphibian and reptile species in regions with high proportions of agricultural land cover. However, losses of imperiled species are significantly more strongly related to the proportion of the region treated with agricultural pesticides. This is consistent with the hypothesis that agricultural pesticide use, or something strongly collinear with it (perhaps intensive agriculture more generally), has contributed significantly to the decline of imperiled species in Canada. Global increases in UV radiation do not appear to be a major cause of amphibian population declines. At individual sites, temporal changes in amphibian abundance are not predictably related to changes in UV intensity. Variability in species’ abundance of North American breeding birds, after accounting for mean abundance, is not systematically higher in areas of high human-dominated land cover or climate change. Rather, it appears that areas with a high proportion of human-dominated cover come to have a higher proportion of highly abundant, and thus more variable, species.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

With an increased human impact, natural resources are under great pressure.  Deforestation is one effect of this, and the largest threat against biodiversity.. Changes in tropical habitats is a major concern for conservation biologists, due to its high biodiversity and rapid decreased area. Recently, developmental activities and habitat destruction have caused a major decline in the abundance of the terrestrial mega-fauna.This is especially evident in areas with a high human population and a rich mega-fauna as in India. The purpose of this project was to determine the land-use cover change (LUCC) in the area of Karbi Anglong, which lies in the middle of Assam, India. This was done by identifying different vegetation types from satellite images, from the years 1992, 2002 and 2011 using a remote sensing application (ERDAS) and ArcGIS. Interviews in the area werealso operated, and data about how animal use the corridors were used along with registered human-tiger conflicts. The results show that during the first period, a total of 360 km2 of the area changed vegetation type, mostly due to an increase of agricultural areas. The second largest change (79 km2) was an increase of moist mixed deciduous forest which seems to have taken over some of the semi evergreen forest’s previous area. If that is the case it is most likely an effect of selective logging from the local people, who use fire wood as fuel.All in all, there has been a great habitat loss along withfragmentation of the landscape. The conflict data shows that tigers are present between the core areas, and the interviews show that the migrations of other animals are also common.To maintain the high ecological values in Karbi Anglong, it is of great importance to maintain connectivity between core areas and stop further habitat loss and fragmentation.

Earlier studies have found that endangered species recovery is only weakly associated with the tools enabled by the U.S. Endangered Species Act (ESA). With habitat loss often cited as a leading cause of species declines, we tested whether the recovery of ESA-listed species is instead associated with the protection of critical habitat (CH) by protected areas. We tested the relationship for 299 species using recovery indices derived from the biennial status reports to Congress (1990-2010), as well as NatureServe and IUCN population status data. We found no overall relationship between recovery and the extent to which CH is protected. However, restricting the analysis to recovering species, listed species with larger areas of protected (R2 = 0.158) or strictly protected (R2 = 0.194) CH fared better than species with less protected or strictly protected CH areas. Declining species (199 of 273 species studied) fared no better with more protected habitat. We conclude that the abatement of habitat loss alone does not necessarily facilitate recoveries for the majority of ESA-listed species. We also note that the weak relationships we observed in this study may be reflective of poor recovery status estimates.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

A dispersão de sementes por vertebrados é um processo ecológico muito importante para a manutenção da biodiversidade, especialmente nas regiões tropicais. Estas interações mutualistas podem ser rompidas devido à caça e a perda e fragmentação de habitats, na medida em que estas ameaças podem levar os parceiros mutualistas à extinção. No presente trabalho, buscamos entender as consequências de possíveis extinções de aves frugívoras sobre a organização de sistemas de dispersão de sementes na floresta Atlântica brasileira. Primeiro, nós caracterizamos o papel que cada uma das espécies desempenha em estruturar as redes de interação de que fazem parte. Em seguida, investigamos possíveis correlatos biológicos deste papel estrutural e vimos que as plantas com sementes pequenas e com períodos de frutificação extensos tendem a ser estruturalmente mais importantes. Por outro lado, características morfológicas (tamanho do bico e massa corpórea) e ecológicas (abundância e grau de frugivoria) não se mostraram relevantes em explicar o papel das aves nas redes de dispersão de sementes. O risco de extinção, no entanto, está associado ao papel estrutural das espécies de aves, de tal modo que aves mais ameaçadas tendem a ser mais importantes para a estrutura das redes. Estes resultados indicam que a perda de espécies ameaçadas pode ter consequências para a organização dos sistemas de dispersão de sementes de que fazem parte. Em um capítulo posterior, buscamos entender como os sistemas de dispersão de sementes responderiam a crescentes perdas de habitat. Com base em dados empíricos, estimamos uma sequência de extinções de aves decorrentes da perda de habitat na floresta Atlântica. Simulamos esta sequência de extinções em redes de dispersão de sementes provenientes de uma área protegida, avaliando os impactos de tais remoções de espécies sobre a organização das interações. Nossos resultados sugerem relativa robustez das redes de dispersão de sementes à remoção de espécies decorrente da perda de habitat. Por outro lado, a estrutura das redes parece colapsar quando a porcentagem de habitat é reduzida a menos de 30% da paisagem. É possível que um limiar de riqueza de espécies gere também um limiar na resposta da estrutura das redes à perda de habitat. Por fim, em um capítulo de perspectivas sobre os impactos da defaunação, avaliamos a importância de grandes vertebrados frugívoros como dispersores de sementes. Sugerimos que a inclusão de aspectos da história natural dos grandes frugívoros na abordagem de redes complexas pode trazer novas contribuições e permitir avanços nos estudos que investigam como esses dispersores podem influenciar a dinâmica das comunidades de plantas. Considerando o conjunto de resultados apresentados nesta tese, ilustramos como a abordagem de redes pode ser útil ao se estudar sistemas com muitos elementos, como é o caso da dispersão de sementes. Contribuímos para um melhor entendimento dos aspectos da biologia das espécies que influenciam a posição que ocupam dentro das redes de dispersão de sementes. Ademais, procuramos combinar princípios da ecologia de paisagens e análises de redes complexas para entender as consequências da perda de habitat sobre a organização de sistemas de dispersão de sementes / Seed dispersal by vertebrates is a key ecological process for biodiversity maintenance, particularly in tropical regions. These mutualistic interactions can be disrupted due to hunting and habitat loss and fragmentation, threats that may lead mutualistic partners to extinction. In the present work, we seek to understand the consequences of possible extinctions of frugivorous birds on the organization of seed dispersal systems in the Brazilian Atlantic forest. First, we described the role each species plays in structuring the interaction networks they are part of. Then, we investigated potential biological correlates of these structural roles and we found that plants with small seeds and long fruiting periods tend to be more important to network structure. On the other hand, morphological traits (bill size and body mass) and ecological traits (abundance and degree of frugivory) were not relevant to explain the role bird species play in seed dispersal networks. Extinction risk, however, is associated with the structural role of bird species, so that higher-risk species tend to me more important for network structure. Our results suggest that the loss of higher-risk bird species may affect the organization of seed dispersal systems. In a later chapter, we seek to understand how seed dispersal systems would respond to increasing habitat loss. Based on empirical data, we estimated a sequence of bird species extinctions following habitat loss in the Atlantic forest. We simulated that sequence of extinctions in seed dispersal networks from a protected area, evaluating the impacts of such species deletions on the organization of interactions. Our results point out relative robustness of seed dispersal networks to removal of species due to habitat loss. On the other hand, the structure of the networks seems to collapse when the percentage of habitat cover shrinks to less than 30% of the landscape. It is possible that a threshold in species richness creates a threshold in network structure response to habitat loss. Finally, in a chapter of perspectives on the impacts of defaunation, we evaluated the importance of large frugivorous vertebrates as seed dispersers. We suggest that the inclusion of aspects of the natural history of large frugivores in complex networks may allow new insights and advances in studies investigating how these seed dispersers can influence the dynamics of plant communities. Considering the overall results presented in this work, we illustrate how the network approach can be useful when studying systems with many components, such as seed dispersal. We contribute to a better understanding of the biological aspects that affect the position species occupy within seed dispersal networks. Furthermore, we combined principles from landscape ecology and analysis of complex networks to understand the consequences of habitat loss on the organization of seed dispersal systems

Florestas tropicais comportam dois terços de todas as espécies existentes no mundo, mas a perda de habitat, fragmentação e alteração na qualidade do habitat estão levando esta biodiversidade à extinção. Apesar de haver uma extensa literatura sobre este assunto, há um consenso geral de que o conhecimento gerado por muitos estudos é dependente do contexto e permeado por dificuldades metodológicas, como a alta correlação entre os fenômenos ocorrentes em paisagens alteradas pela ação humana e a miríade de respostas biológicas encontradas entre espécies. Desta forma, há ainda muita incerteza sobre a generalidade dos padrões observados e sua efetiva aplicação para a conservação de áreas naturais. Assim, nesta tese o objetivo foi de contribuir para esta discussão ao responder as seguintes perguntas: (i) Qual papel que bordas ecossistêmicas e efeitos de borda desenvolvem em comunidades naturais? (ii) A comunidade de aves é afetada pela fragmentação do habitat de maneira semelhante em matas primárias e secundárias? (iii) Seriam os efeitos de área e de borda análogos, e estariam estes associados em uma relação causal? (iv) Como a comunidade de aves se comporta com relação à variação na cobertura florestal, configuração do fragmento e qualidade do habitat, e será possível separar o efeito de cada variável? (v) Diferenças no protocolo amostral poderiam alterar as estimativas de atributos da comunidade e mudar a magnitude dos padrões ecológicos observados assim como a probabilidade de detectá-los? E (vi) qual estratégia é mais eficiente em identificar locais com alta integridade da comunidade, espécies indicadoras ou métricas indicadoras, como métricas da paisagem? Para responder estas perguntas foram usados dados provenientes de mais de 7000 aves capturadas com redes de neblina em 65 pontos amostrais localizados em seis paisagens de diferentes proporções de cobertura florestal e graus de perturbação na Mata Atlântica do Planalto Atlântico Paulista. Os resultados mostram que: (i) bordas estão presentes tanto em habitats naturais quanto alterados pela ação humana e produzem grandes efeitos sobre espécie e comunidades; (ii) apesar de matas secundárias possuírem uma comunidade de aves empobrecida, a forma como as aves são afetadas pela fragmentação nestes habitats é semelhante a matas primárias; (iii) efeitos de borda não são apenas análogos, mas podem ser a causa dos efeitos de área de fragmento; (iv) os efeitos de mudanças na cobertura florestal, configuração do fragmento e qualidade do habitat são altamente correlacionados e só podem ser separados com o uso de técnicas estatísticas que controlem explicitamente esta correlação; (v) a forma como o protocolo de amostragem é estruturado temporalmente afeta os padrões encontrados da relação espécie-área em paisagens fragmentadas; e por fim, (vi) métricas indicadoras, produzem resultados mais fortes e consistentes do que espécies indicadoras na identificação de áreas com alta integridade da comunidade. Assim, conclui-se que as aves de sub-bosque na Mata Atlântica são fortemente afetadas pela perda de habitat, fragmentação e mudanças na qualidade do habitat, mas esta influência é muito dependente do contexto temporal e espacial em que o estudo é realizado. Ainda, devido à baixa consistência dos resultados obtidos com amostras de curta duração, aliado ao grande poder explicativo dos modelos contendo métricas da paisagem, métricas indicadoras devem ser consideradas como a melhor estratégia para a identificação de áreas com alta integridade da comunidade. / Tropical forests hold two thirds of all species in the world, but alterations in habitat cover, fragmentation and quality are driving tropical biodiversity to the brink of extinction. Despite the extended literature on this subject, there is a general agreement that the knowledge gained from many of these studies are context-specific and pervaded by methodological difficulties, such as high inter-correlations among many phenomena in human-altered landscapes and diverse biological responses to landscape change that depend on species traits. Because of these issues, there is great uncertainty about the generality of observed patterns and the effective application of results in the conservation of natural areas. Thus, in this thesis the aim was to bring light to some of these concerns by answering the following questions: (i) What is the role of ecosystem boundaries and edge effects on natural communities? (ii) Do bird communities show similar patterns of responses to habitat fragmentation in secondary forests as those previously reported for primary forest? (iii) Are edge and area effects on bird species functionally similar and even causally associated? (iv) How does a tropical understory bird community respond to the highly inter-correlated variation in forest cover, patch configuration and habitat quality; and is it possible to set these influences apart? (v) Could differences in sampling protocol alter community estimates or change the magnitude of ecological trends and the probability of detecting them? And (vi), which strategy is more efficient in identifying sites with the highest community integrity, indicator species or structural indicators, such as landscape metrics? To address these questions I used data from more than 7000 birds captured using mist nets in 65 sites from six landscapes with different proportions of forest cover and habitat degradation in the Atlantic Forest of Brazil. The results showed that: (i) edges are ubiquitous features of natural and human-altered landscapes and strongly influence most species; (ii) even though the bird community in secondary forests is degraded relative to primary communities, birds from these areas show similar responses to edge and area effects found for primary forests; (iii) edge effects are not only functionally similar, but might also be the main drivers of area effects in fragmented landscapes; (iv) the effects of changes in forest cover, patch configuration and habitat quality are highly confounded and without the use of analyses that explicitly model this correlation it is impossible to pull apart the relative influence of each variable; (v) the way the sampling protocol is designed temporally affects the perceived patterns of how species respond to area effects; and finally, (vi) structural indicators generate stronger and more consistent results than indicator species in predicting changes in community integrity. In conclusion, the results show that understorey birds are highly affected by changes in habitat cover, fragmentation and habitat quality in the Atlantic forest, but this influence is strongly dependent on the temporal and spatial context of the study. Also, because of the low consistency of results obtained from short-surveys, and the large explanatory power of models containing landscape metrics, structural indicators should be viewed as the best strategy for identifying sites with high community integrity.

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North American river otters are considered common in the state of Florida, but their populations have not been studied since the 1980’s. Since that time, Florida’s human population has more than doubled, and many natural areas of Florida have been developed. The aim of this study was to determine the presence or absence of river otters at locations in Florida which they historically inhabited. Forty-six sample sites where otters were historically found were obtained from the Florida Museum of Natural History Mammals Master Database (FMNH MMD). These sites were condensed to two focus areas, in and around Alachua and Collier Counties, where the sites were most highly clustered. Each site was surveyed to determine the presence or absence of river otters and to determine the suitability of the site’s environment for otter habitation. Sites with favorable habitat features for otters were surveyed a second time. River otters were not found at any site. Only 9 of the 46 sites had permanent water and only 8 of those had other habitat features preferred by otters. Therefore, only 17.39% of sites that historically supported otters likely still have the ability to do so. Loss of water over time is most likely the result of human disturbances such as the draining, damming, and canalizing of wetlands. As a result of this loss of natural habitat, river otters have become increasingly common in urban areas wither preferred habitat features, even if they are man-made. The increased presence near humans may have led to the apparently inaccurate assumption that otters are common, and, therefore, do not need protection.

Human activities have transformed natural landscapes into human-dominated areas at unprecedented rates in the last centuries. Land cover transformation is associated with loss of natural habitat, thus a threat to biodiversity. Because habitat loss will likely continue in the future due to population growth and increase demand for natural resources, an important question in ecological studies is whether land cover features (i.e. amount, variety, shape, configuration) can be used as predictors to estimate species loss from habitat modification. This thesis investigates the predictive ability of landscape features in predicting species distributions at the landscape level and across large regions. It tests several predictions from classic hypotheses such as the species-area relationship and habitat fragmentation, utilizing a macroecological approach. Response variables (e.g. species richness, species’ probability of occurrence) and independent variables (e.g. proportion of natural areas, metrics of fragmentation, temperature, etc.) are analysed in cell sizes of 25-900km2 covering large regions (e.g. southern Ontario, New York State). Bird species were chosen as the main biological model. Most literature assumes that species richness should vary positively as a function of remaining natural area, following the well-known species–area relationship (i.e. classic SAR). Prior studies have shown that avian species richness has a peaked, rather than a monotonic increasing, relationship with the proportion of natural land cover in landscapes of southern Ontario. The first chapter of the thesis showed improvements in the predictive power of classic SARs by proposing the “Lost-habitat SAR”, which demonstrates that richness of open-habitat species can be predicted when we partition human-dominated land cover into an ‘‘available human-dominated’’ component and ‘‘lost’’ habitat (i.e. parts of the landscape that can no longer be utilized by any species). The second chapter addresses a current contention in the literature about the effect of habitat fragmentation beyond habitat amount at the landscape level. Specifically, I tested the effect of fragmentation (e.g. number of patches) on both avian richness and the probability of occurrence (pocc) of individual species, after controlling for habitat amount in 991 landscapes, each 100-km2, in southern Ontario. The analysis showed that overall species richness responds primarily to habitat amount, and that the effect of habitat fragmentation, holding the total amount of habitat constant, is negligible. The probability of occurrence of a few bird species did relate negatively to the size, number and isolation of the patches within the landscape. We argue that the evidence is inconsistent with the hypothesis that reducing habitat fragmentation would be an effective conservation strategy for birds at the landscape level. Chapter 3 tested the speculation in the climate change literature that habitat loss may impede the colonization or movement of species whose ranges are shifting northwards in response to climate. Using the same 100-km2 landscapes of southern Ontario, I examined individual bird species’ probability of occupancy as a function of the amount of remaining natural land cover for three groups of species: i) those whose northern range limit falls within the study area, ii) those whose southern range limit is in the study area, and iii) those whose ranges cover the entire study area. The results showed that the probability of occupancy of southern-edge species is a positive function of the amount of natural land cover (forest) in the landscape, while the probability of occupancy of northern-edge species is a negative function of natural land cover. Hence, I conclude that at southern range limits species faces the dual stresses of climatic warming and habitat conversion. Whereas, at northern (potentially expanding) range edges, partially disturbed landscapes are more readily occupied than undisturbed landscapes. In the final chapter, I challenge widely accepted hypothesis that habitat loss causes biodiversity loss by testing whether conserving natural land cover would conserve species diversity. More specifically, I tested whether broad-extent relationships between avian species richness and natural land cover are independent of: 1) whether species distribution data come from systematic censuses (atlases) versus range maps, and 2) the grain size of the analysis in grid cells covering southern Ontario, CA, and New York State, US. My findings showed that over regional extents, range-map-based richness relates strongly to temperature, irrespective of spatial grain, and that censused species richness relates to temperature less strongly. Moreover, range-map richness is a negative function of the proportion of natural land cover, while realized richness is a peaked function. Therefore, I conclude that conserving natural land cover would not conserve species diversity in southern Ontario or in New York State, since greater natural cover does not imply higher richness. We argue that habitat loss has become a panchreston. It may be misguiding conservation biology strategies by focusing on a threat that is too general to be usefully predictive.