The selection of sites for biodiversity conservation is best done if it anticipates future challenges and efficiently accomplishes targets, given limited funding for such efforts. The first chapter of this thesis discusses how conservation practitioners might manage and enhance long-term survival for species whose ranges must shift as climate changes, across regions that present significant mobility barriers. I describe recommendations highlighting connectivity, refugia from climate change, adaptation, and restoration within agricultural landscapes in North America, but these recommendations are transferable elsewhere. The second chapter examines patterns of change in agricultural intensity and land price within Canada’s species-rich farmland between 1986 and 2011, and creates sequential cost-efficient plans to conserve resident species-at-risk within that time period, to determine how environmental and cost changes erode the efficiency of conservation plans. While sites initially selected as cost-efficient remained so through time, total plan costs increased, decreasing each plan’s ability to represent all species for a given budget. This emphasizes the urgent need for conservation within Canada’s farmland.

Examining how ecological processes are influenced by spatial variation can provide valuable insights into how communities are formed and how they may change in dynamic landscapes. In this thesis I address three objectives surrounding the spatial and temporal variation in species’ recruitment and predation, the influence of habitat isolation on consumer-resource relationships, and the influence of habitat fragmentation on a multi-trophic system. I used marine invertebrates, specifically crustaceans, bivalves, and sessile species as a model system. First, I address the spatial and temporal variation in local and regional processes in a multispecies assemblage of marine sessile invertebrates. Using diverse communities of marine sessile invertebrates as a model system I tested the hypothesis that spatial and temporal variation in recruitment and predation would shape local communities, and that both recruitment and predation would have significant effects on the abundance and structure of adult communities. I found that both recruitment and predation vary through time and space leading to the emergence of regional community divergence. I also address how habitat isolation interacts with top-down and bottom-up processes in seagrass ecosystems. Spatial structure of the habitat may mediate top-down and bottom-up controls of species abundances through decreased habitat connectivity and increased habitat isolation. I manipulated top down and bottom up processes by excluding mesograzers, adding resources, or altering both factors in isolated and contiguous patches of artificial seagrass. I then measured epiphyte recruitment, epiphyte abundances, and macroalgae abundance. I paired this with epiphyte sampling from isolated natural seagrass patches. I found that habitat isolation significantly decreased the abundance of epiphytes settling on seagrass blades due to dispersal limitation for epiphytic invertebrates. I found that consumers had strong effects on epiphyte biomass in continuous habitats, but not isolated habitats. Resource additions increased macroalgae cover and epiphyte biomass only in isolated habitats. The results suggest that isolated habitats may be nutrient limited and that top-down effects are stronger in continuous habitats, while bottom-up effects may dominate in isolated habitats. In my third objective, I address how habitat fragmentation may alter marine food webs. I examined whether predation rates, prey, and predator behavior differed between continuous and fragmented seagrass habitat in a multi-trophic context at two sites in Barnegat Bay, NJ. I hypothesized that blue crab predation rates and foraging would decrease in fragmented seascapes, due to a reduction in adult blue crab densities, increasing survival rates of juvenile blue crabs and hard clams. I expected hard clams to exhibit weaker predator avoidance behavior in fragmented habitats because of decreased predation. I found that species’ responses to fragmentation were different based on trophic level. Clams experienced higher predation and burrowed deeper in continuous habitats at both sites. Densities of blue crabs, the primary predator of hard clams, were higher in continuous habitats at both sites. Predation on juvenile blue crabs was significantly higher in fragmented seagrass at one site. Our results suggest that in fragmented seascapes, the impact of fragmentation on higher trophic level predators may drive predation rates and prey responses across the seascape, which may lead to trophic cascades in fragmented habitats. / Biology

Habitat loss, habitat fragmentation and species invasions have been recognized as three of the leading threats to biodiversity. I examined the effects of habitat loss and fragmentation on native and invasive plants in central Texas. During the last century, the density and abundance of woody plants has been increasing in the savannas of eastern Edwards Plateau. This process, known as woody plant encroachment, not only reduces the amount of open herbaceous habitat but also fragments that habitat creating smaller and more isolated patches. In three studies, I investigated the consequences of this habitat loss and fragmentation for plants which do not occur under the cover of woody plants including native grasses and forbs and the invasive Eurasian bunchgrass, Bothriochloa ischaemum (King Ranch Bluestem). In the first study, I show that woody plant encroachment reduces native herbaceous species richness (the number of species in a given area). Using a collection of historical aerial photographs, I demonstrate that current native herbaceous species richness was most strongly related to recent habitat amount, but to the degree of habitat fragmentation at least 50 years ago. In a second study, I show that the presence of B. ischaemum was negatively related to the degree of fragmentation in the surrounding landscape. Finally, I found that B. ischaemum had higher rates of germination and growth in experimental plots where the species commonly lost with woody plant encroachment were removed than in unmanipulated control plots. Together, this work suggests that woody plant encroachment is directly slowing the spread of an invasive species while indirectly facilitating its establishment. / text

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 destruction and fragmentation of natural habitat is the leading driver of the current extinction crisis. As a result, a research area has emerged focused on studying ecology in islands of natural habitat surrounded by a sea of anthropogenic land uses, so called ‘habitat islands’. However, this research has largely been undertaken on small-medium scales, generally in single systems. Furthermore, many habitat island studies have used previous results and theory derived in the context of oceanic island research. Thus, this thesis aims to examine a variety of macroecological and biogeographical patterns using a large number of purely habitat datasets sourced from both the literature and my own sampling, with the objective of teasing out any general statistical patterns. The various macroecological and biogeographical patterns can be grouped under four broad headings: 1) species–area relationships (SAR), 2) nestedness, 3) species abundance distributions (SADs), and 4) species incidence functions (function of area). Overall, it was found that there were few hard macroecological generalities that hold in all cases across habitat island systems. This is because most habitat island systems are highly disturbed environments, with a variety of confounding variables and undesirable species (e.g. species associated with human land uses) acting to modulate the patterns of interest. Nonetheless, some clear patterns did emerge. In particular, it was found that the power model was by the far the best general SAR model for habitat islands. The slope of the island species–area relationship (ISAR) was related to the matrix type surrounding archipelagos, such that habitat island ISARs were shallower than true island ISARs. Significant compositional and functional nestedness was rare in habitat island datasets, although island area was seemingly responsible for what nestedness was observed. Species abundance distribution models were found to provide useful information for conservation in fragmented landscape, but the presence of undesirable species substantially affected the shape of the SAD. Species incidence function curves were found to vary across space for a given species, but not in any systematic manner. In conclusion, this thesis finds that the application of standard island biogeography theory to habitat islands is too simplistic. It is hoped that the results of this thesis will act as a catalyst for a more macroecological approach to habitat island research, and a starting point for the development of an integrated theory of habitat islands.

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.

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

Saltmarshes in SE England are eroding rapidly and one potential impact is the loss of habitat for fishes. Saltmarshes have been created by setting back the existing line of flood defence through managed realignment. The use by fishes of natural and managed realignment habitats at Tollesbury, Abbotts Hall and Orplands was examined (2005-07). Three seasonal groups were apparent in the fish assemblages of the managed realignment sites: February-April (Pomatoschistus microps and Sprattus sprattus), May-September (Dicentrarchus labrax and Atherina presbyter) and October-January (Liza aurata and Liza ramada). The sites were used mainly by 0- and 1-group fishes and adult P. microps. The mean abundance (July - August 2007) was 558 0.1 ha' (range 76 - 2699 0.1 ha'). In summer, small (< 30 mm) zooplanktivorous D. labrax fed successfully at all sites. Larger (30-59 mm) D. labrax consumed more macroinvertebrates in the Tollesbury managed realignment and two established marshes than at Abbotts Hall and Orplands. By autumn there were no site-specific differences in gut fullness of D. labrax. Stable isotope ratio analysis and gut contents analysis revealed that small (< 50 mm) D. labrax, S. sprattus and A. presbyter assimilated zooplankton which eat detritus, resuspended microphytobenthos and some phytoplankton. L. aurata assimilated zooplankton and microphytobenthos. P. microps (20-50 mm) and A. presbyter (80-99 mm) assimilated benthic meiofauna. Larger (50-230 mm) D. labrax assimilated macroinvertebrates which eat microphytobenthos, Ulva spp., C3 plants and detritus. Some recommendations for saltmarsh restoration are provided with an estimate of the economic value of bass in saltmarshes,to highlight further areas of research.

Orientador: Ariovaldo Pereira da Cruz Neto / Resumo: A perda de habitat é vista como um dos principais efeitos decorrentes das perturbações da paisagem causada pelo homem aos ambientes naturais. Essa gera maior isolamento dos fragmentos e diminui as áreas de contato entre habitat e matriz, com efeitos negativos sobre a biodiversidade. Os efeitos da perda de habitat nos padrões de biodiversidade são geralmente analisados usando dados de distribuição de espécies e / ou abundância relativa. No entanto, eles não podem ser identificados em populações em que esses efeitos ainda não foram refletidos na abundância e incidência de espécies, e não nos informam sobre os mecanismos causais subjacentes às respostas diferenciais de espécies ou populações a essas perturbações. Uma opção para preencher esta lacuna é concentrar-se em quantificar a miríade de processos fisiológicos em que diferentes espécies lidam com ambientes em mudança. Os morcegos apresentam uma grande diversidade morfológica, fisiológica e comportamental, estando presentes em uma diversa variedade de nichos ecológicos, estabelecendo diversas relações críticas para a manutenção dos ecossistemas onde ocorrem. Os morcegos frugívoros estão entre os mais importantes dispersores de sementes do Neotrópico. Juntamente com os morcegos, investigações com seus ectoparasitas específicos são de grande relevância, visto que, os ectoparasitas exercem pressões seletivas importantes sobre a evolução dos seus hospedeiros. Assim, perda de habitat pode trazer importantes mudanças para as popul... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Habitat loss is seen as one of the main effects of man-made landscape disturbances on natural environments. This generates greater isolation of the fragments and reduces the contact areas between habitat and matrix, with negative effects on biodiversity. The effects of habitat loss on biodiversity patterns are generally analyzed using species distribution and / or relative abundance data. However, they cannot be identified in populations where these effects have not yet been reflected in species abundance and incidence, and do not inform us of the causal mechanisms underlying the differential responses of species or populations to these disturbances. One option to bridge this gap is to focus on quantifying the myriad physiological processes in which different species deal with changing environments. Bats have a great morphological, physiological and behavioral diversity, being present in a diverse variety of ecological niches, establishing several critical relationships for the maintenance of the ecosystems where they occur. Fruit bats are among the most important seed dispersers of the Neotropic. Together with bats, investigations with their specific ectoparasites are of great relevance, as ectoparasites exert important selective pressures on their host evolution. Thus, habitat loss can bring about major changes to bat populations and in some biotic interactions such as parasitism. In this context, we use some physiological analysis to (1) evaluate the impacts of habitat los... (Complete abstract click electronic access below) / Mestre

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.