This thesis uses a range of different size spectra to compare contrasting benthic habitats in the aquatic realm. Temporal and spatial variation in benthic size spectra were investigated across a full salinity gradient (i.e. from freshwater, through estuarine to marine) in the River Yealm, south Devon, in order to gauge the influence of large differences in taxonomy and evolutionary history. Abundance and biomass size spectra showed a similar pattern among sites in all seasons but winter, suggesting that the size structure of benthic communities may be similar in sites with very different community compositions. A subsequent study comparing size spectra across salinity by employing artificial substrata suggested that substratum type also had little effect on the size structure of these benthic communities. A technique was developed for obtaining microbial size distributions for benthic communities and showed that microbial size structures were also similar between the marine and freshwater sites within the Yealm system. A final study demonstrated that the shape of size spectra was clearly affected by metal contamination. Size spectra across a salinity gradient -(i.e. from freshwater to lower estuary) in the highly contaminated Fal system were very different to those in the uncontaminated Yealm, due mostly to the low macrofaunal abundance in the former. This thesis is the first to assess patterns in benthic size spectra across a full salinity range in the same system. It is hoped that it will provide a base line for further studies in this exciting research area in macroecology and that biomass spectra might also prove useful as metrics for biomonitoring.

<p> Macroevolution and macroecology are concerned with the patterns in evolutionary and ecological data, respectively, which arise when observing multiple species over time and/or space. Species extinction and species pool functional composition are the macroevolutionary and macroecological patterns at the heart of this dissertation. The hypotheses and analyses in the three studies forming this dissertaiton were all framed in terms of how species functional traits can shape these emergent patterns. </p><p> In my first study, I analyzed the Cenozoic fossil record of North American mammals to test two long standing hypotheses: the survival of the unspecialized hypothesis, and the Law of Constant Extinction. My analysis centers around a model of species duration as a function of multiple species traits, species&rsquo; phylogenetic relatedness, and species&rsquo; origination cohort. My results support the conclusion that generalist species will, on average, have a greater duration than more specialized species. I also find that species extinction risk increases with species duration, a result that is counter the Law of Constant Extinction. Additionally, I find that only some of the factors associated with extinction risk for Modern mammals could be considered risk factors for mammals from the rest of the Cenozoic, indicating a difference between the modern biodiversity crisis and &ldquo;normal&rdquo; extinction dynamics. </p><p> My second study also deals with the survival of the unspecialized and the Law of Constant Extinction, but focuses on a different system: post-Cambrian Paleozoic brachiopods. An additional aspect of this study is an analysis of the relationship between extinction intensity and the strength of trait selection. I find support for greater survival among environmental generalists than specialists. I also find evidence that for geographic range and environmental preference, as extinction intensity increases, the selective importance of these traits increases. This result is evidence for a qualitative difference between background and mass extinction. The final study is an analysis of the changing functional composition of the North American mammal regional species pool over the last 65 million years. The goals of this analysis are to understand when functional groups are enriched or depleted, and how changes to environmental context may shape these changes. I find that mammal diversity is more strongly shaped by changes to origination probability rather than changes to extinction probability. I also find that all arboreal ecotypes declined throughout the Paleogene and disappeared from the species pool by the Neogene. Additionally, I found that most herbivore ecotypes expand their relative contribution to functional diversity over time. </p><p> My desire with this dissertation is to present the types of analyses and results that are possible through a synthesis of macroevolution and macroecology. The first step to building any dialogue is to agree on a common language and I&rsquo;ve emphasised an expressive statistical framework with which to phrase our questions in a common tongue. My hope is that this studies serve as an example of how to use paleontological data to unite questions about the processes underlying macroevolutionary and macroecological patterns.</p><p>

<p>Billions of dollars have been invested in land protection as a strategy to conserve biodiversity based on the assumption that protected areas buffer species from processes that drive extinction. Increasingly, protected area expansion and connectivity are being incorporated into climate change adaptation strategies to facilitate anticipated shifts in species ranges in response to predicted changes in temperature and precipitation. However, the effectiveness of protected areas at maintaining biodiversity, either by reducing the risk of extinction or facilitating colonization into new areas, has not been well established. In addition, the growing reliance on multiple-use protected areas that allow resource extraction, such as timber harvest and mineral mining, has raised questions about whether multiple-use protected areas are equally beneficial for long-term biodiversity conservation as more strictly protected areas that limit active resource management. In order to address these questions using repeated Breeding Bird Atlas data, I first had to confront the limitations of existing approaches to account for imperfect detection by developing a novel modelling approach to addresses the gap between requirements of other multi-season occupancy models (i.e. repeated sampling) and existing datasets. I then applied that single-visit dynamic occupancy modelling approach to Atlas data in New York and Pennsylvania for 97 species to quantify drivers of colonization and extinction while accounting for imperfect detection in landscapes that varied by type and amount of land cover and area under protection. In general, protected areas increased colonization and lowered extinction probabilities to an increasing degree as both forest cover and neighborhood protection decreased, with particular benefits for forest breeding birds. Both strict and multiple-use protected areas increased colonization and reduced extinction more for mature forest species than early forest species, with the greatest benefits accruing when forest cover was relatively low. These results provided the most comprehensive evidence to date that protected areas can facilitate species persistence by both reducing the risk of extinction and providing attractive colonization sites as species? ranges shift and that biodiversity conservation can be compatible with renewable resource extraction.

O nosso conhecimento sobre a distribuição das espécies vem avançando desde as primeiras observações feitas séculos atrás. Recentemente uma melhoria nos métodos e na cobertura geográfica das amostragens tem melhorado significativamente nosso conhecimento sobre padrões de distribuição. O que tem permito diversos tipos de análises, revelando padrões macroecológicos com os observados aqui onde riqueza de répteis e anfíbios apresenta uma forte relação com o ambiente, sendo maiores em aras mais baixas, com temperatura e precipitação estáveis e maior estrutura no ambiente, enquanto que para endemismo e diversidade beta a relação é mais fraca. Porém este conhecimento sobre a distribuição das espécies não está homogeneamente distribuído por todas as regiões, sendo especialmente baixo na região Amazônica, que é justamente a região que abriga a maior riqueza local de espécies, estando concentrado ao longo das margens dos rios. Isto que pode indicar que os valores que temos disponíveis ainda são subestimados, e que quaisquer inferências sobre estes valores devem ser interpretados com cautela / Our knowledge on species distribution has advanced since the first observations made centuries ago. Recently the improvement on techniques and geographical coverage of samplings activities has improved significantly our knowledge on distribution patterns. This advance has allowed several analyses to be done, and macroecological patterns to emerge, such as the one observed ibn here with reptile and amphibian richness presenting a strong relationship with environmental conditions, with higher values at lower areas, with more stable precipitation and temperature, an higher environmental structure, while endemism and beta diversity have a weaker signal. However the knowledge on species distribution is not homogeneously distributed across all regions, being especially low at the Amazon, which is precisely the area that harbors the highest richness values, being concentrated at the rivers\' shores, suggesting that the values we have today may be far underestimated, and thus any inference using them should be interpreted with caution

<p> Rhamphichthyoidea is a monophyletic clade of Neotropical electric fishes (Ostariophysi, Gymnotiformes), with about 55 known species, some still awaiting formal description. These species are widespread in tropical and subtropical freshwaters of South America, with a single species reaching Costa Rica in southern Central America. Rhamphichthyoid species inhabit a variety of lowland habitats including small sandy streams, floodplain oxbow lakes, and the benthos of deep river channels. Rhamphichthyoidea displays substantial morphological disparity, ranging in maximum total body size from 62 millimeters to about 1 meter, and exhibiting diversity of distinctive snout shapes. This phenotypic diversity is reflected in a broad range of ecological interactions and foraging modes. Here I studied the diversity of Rhamphichthyoidea at three levels: alpha diversity, species interrelationships, and macroevolutionary patterns. The first chapter presents results of a species level phylogeny using a total evidence approach, including a new classification based on phylogenetically diagnosed clades. The second and third chapters review the species diversity and boundaries of the poorly studied genera <i>Rhamphichthys</i> (7 spp.) and <i>Gymnorhamphichthys</i> (5 spp.). The fourth chapter presents an analysis of diversification through time, linking habitat occupancy with morphological aspects of snout shape in the radiation of Rhamphichthyoidea. In summary, this dissertation provides information on the species diversity, morphological characteristics, biogeography of the long-snouted rhamphichthyids; the phylogenetic relationships and a newly proposed classification of Rhamphichthyoidea; and adds to the understanding of general patterns of diversification within the Neotropical ichthyofauna.</p>

The thesis explores how the range sizes of carnivorans are shaped by geographic and evolutionary constraints. Employing modern spatial analyses and phylogenetic comparative methods, we illustrate that phylogenetically conserved climate tolerances delimit species? geographic constraints, which in turn shape the species? range size. Range size heritability patterns emerge as a consequence of this interplay between geographic and evolutionary constraints.

O nosso conhecimento sobre a distribuição das espécies vem avançando desde as primeiras observações feitas séculos atrás. Recentemente uma melhoria nos métodos e na cobertura geográfica das amostragens tem melhorado significativamente nosso conhecimento sobre padrões de distribuição. O que tem permito diversos tipos de análises, revelando padrões macroecológicos com os observados aqui onde riqueza de répteis e anfíbios apresenta uma forte relação com o ambiente, sendo maiores em aras mais baixas, com temperatura e precipitação estáveis e maior estrutura no ambiente, enquanto que para endemismo e diversidade beta a relação é mais fraca. Porém este conhecimento sobre a distribuição das espécies não está homogeneamente distribuído por todas as regiões, sendo especialmente baixo na região Amazônica, que é justamente a região que abriga a maior riqueza local de espécies, estando concentrado ao longo das margens dos rios. Isto que pode indicar que os valores que temos disponíveis ainda são subestimados, e que quaisquer inferências sobre estes valores devem ser interpretados com cautela / Our knowledge on species distribution has advanced since the first observations made centuries ago. Recently the improvement on techniques and geographical coverage of samplings activities has improved significantly our knowledge on distribution patterns. This advance has allowed several analyses to be done, and macroecological patterns to emerge, such as the one observed ibn here with reptile and amphibian richness presenting a strong relationship with environmental conditions, with higher values at lower areas, with more stable precipitation and temperature, an higher environmental structure, while endemism and beta diversity have a weaker signal. However the knowledge on species distribution is not homogeneously distributed across all regions, being especially low at the Amazon, which is precisely the area that harbors the highest richness values, being concentrated at the rivers\' shores, suggesting that the values we have today may be far underestimated, and thus any inference using them should be interpreted with caution

Abstrakt​: Brown et al. (2011) navrhli fundamentální podobnost mezi organismy a ekonomikami národních států založenou na rozvodných sítích nutných k fungování metabolismu/ekonomiky a omezeních z nich vyplývajících podle Metabolické teorie ekologie. Tato práce má primárně za účel prozkoumat zda tyto omezení figurují i v rámci jednotlivých sektorů ekonomiky a jejich vztahu k některým dalším makroekonomickým a demografickým ukazatelům. Klíčová slova​: ekologie, makroekologie, metabolická teorie ekologie, ekonomie, energie

Abstract​: Brown et al. (2011) proposed a fundamental similarity between organisms and the economies of nation­states based on the distribution networks necessary for the functioning of the metabolism / economics and limitations arising from them according to the Metabolic theory of ecology. This work is primarily intended to investigate whether these limitations figure even within individual sectors of the economy and their relation to some other macroeconomic and demographic indicators. Key words​: ecology, macroecology, metabolic theory of ecology, economy, energy

A variação batimétrica nos oceanos e suas mudanças ambientais associadas impõem limites à distribuição de espécies, modulando a ocorrência de indivíduos com diferentes formas, funções e histórias de vida de acordo com a profundidade, e sendo, portanto, importante para o entendimento de padrões da biodiversidade marinha. Este estudo objetiva inferir padrões de distribuição de hidroides no Oceano Atlântico e mares árticos e antárticos adjacentes a mais de 50 m de profundidade, buscando contribuir para o entendimento da diversificação e estruturação associadas à variação batimétrica que propiciaram a ocupação dos diferentes ambientes pelo grupo. Apresentamos pela primeira vez inferências das amplitudes de distribuição batimétrica das espécies, da variação de características funcionais de indivíduos e espécies com a profundidade e da distribuição da composição de espécies ao longo da profundidade e da latitude. Em conjunto, os resultados indicam que a distribuição de hidroides no Atlântico profundo está relacionada a fatores históricos e a gradientes ambientais associados às variações latitudinal e batimétrica. Os tamanhos reduzidos e a baixa fertilidade em mar profundo sugerem que a colonização e a evolução de hidroides ao longo da profundidade são principalmente influenciadas pela disponibilidade de alimento e pelas baixas densidades populacionais. Ainda, a maior proporção de espécies e indivíduos solitários em mar profundo e o maior uso de substratos não-consolidados sugerem influência da disponibilidade de substrato. A proporção de espécies capazes de liberar medusas abaixo de 50 m é geralmente menor que em águas rasas costeiras, mas a proporção aumenta com a profundidade, principalmente abaixo de 1.500 m. A liberação de medusas seria desvantajosa em um ambiente com baixas densidades populacionais, por aumentar a incerteza da fecundação dada pela dispersão de gametas, e despender mais energia para reprodução em um cenário de poucos recursos alimentares. Amplas distribuições batimétricas sugerem capacidade de dispersão vertical e alta tolerância às mudanças ambientais associadas à variação batimétrica. Os resultados indicam também que a colonização de hidroides em mar profundo ocorre em um sistema de fonte-sumidouro, no qual as populações de mar profundo seriam sustentadas por imigração de águas mais rasas. Mostramos neste estudo que hidroides são importantes habitantes do mar profundo e que o entendimento da diversidade do grupo neste ambiente se beneficiará de investigações em áreas ainda pouco amostradas, como latitudes tropicais sul e profundidades abaixo de 1.000 m / The bathymetric variation in the oceans and associated environmental changes impose limits on the distribution of species, modulating the occurrence of individuals with different forms, functions and life histories according to depth, and is therefore important for the understanding of marine biodiversity patterns. This study aims to infer patterns of hydroid distribution in the Atlantic Ocean and adjacent Arctic and Antarctic seas at more than 50 m deep, seeking to contribute to the understanding of the diversification and structuring associated with the bathymetric variation that favored the occupation of the different environments by the group. We present for the first time inferences on the bathymetric ranges of distribution of the species, on the variation of functional traits of individuals and species with depth, and on the distribution of the species composition along depth and latitude. Together, the results indicate that the distribution of hydroids in the deep Atlantic is related to historical factors and to the environmental gradients associated with latitudinal and bathymetric variations. Reduced sizes and low fertility in deep sea suggest that colonization and evolution of hydroids along depth are mainly influenced by food availability and low population densities. Also, the greater proportion of solitary species and individuals in the deep sea and the greater use of unconsolidated substrates suggest influence of substrate availability. The proportion of species capable of releasing medusae below 50 m deep is generally lower than in shallow coastal waters, but the proportion increases with depth, especially below 1,500 m. The release of medusae would be disadvantageous in an environment with low population densities, by increasing the uncertainty of fertilization given by the dispersion of gametes, and expending more energy for reproduction in a scenario of few food resources. Wide bathymetric distributions suggest vertical dispersal capacity and high tolerance to the environmental changes associated to the bathymetric variation. The results also indicate that colonization of hydroids in the deep sea occurs in a source-sink system in which deep-sea populations would be sustained by shallower water immigration. We show in this study that hydroids are important inhabitants of the deep sea and that the understanding of the diversity of the group in this environment will benefit from investigations in areas still poorly sampled, such as southern tropical latitudes and depths below 1,000 m