[Truncated abstract] The malleefowl (Leipoa ocellata) is a large, ground-dwelling bird that is listed as threatened in all states of Australia in which it occurs. Its range encompasses much of southern Australia; however, much of it has been cleared for agriculture. Malleefowl are thought to have suffered substantial decline owing to multiple threats that include habitat loss, predation from exotic predators, grazing of habitat by introduced herbivores and fire - common threats in the decline of many Australian vertebrate species. The malleefowl has an unmistakeable appearance, unique biology, and widespread distribution across Australia. Consequently, it has been the focus of much scientific and community interest. In the Western Australian wheatbelt, community groups are working to conserve the species and have been actively collecting data on its distribution for over 15 years. The vast majority of these data are presence-only and have been collected in an opportunistic manner but, combined with long-term data from government agencies and museums spanning over 150 years, they present a significant opportunity to inform ecological questions relevant to the conservation of the species. The purpose of this study was to answer key ecological questions regarding the distribution, status and habitat preferences of malleefowl using unstructured occurrence records supplemented by reliable absences derived from Bird Atlas data sets and targeted surveys. Malleefowl in the Western Australian wheatbelt were used as a case study to illustrate: 1) how the decline of a species can be quantified and causes of that decline identified; and 2) how threats can be identified and responses to threats explored. I used bioclimatic modelling to define and explore variation within the climatic niche of the Malleefowl across Australia. '...' This thesis provides substantial additional knowledge about the ecology, distribution and status of malleefowl in Western Australia. It also illustrates how opportunistic and unstructured data can be augmented to investigate key aspects of a species' ecology. Despite the limitations of these data, which primarily relate to variation in observer effort across time and space, they can provide important outcomes that may not be achieved using standard survey and data collection techniques. The utility of opportunistic data is greatest in situations where the species: is recognisable and easily observed; is relatively sedentary; and occurs within a landscape containing consistent land use and habitat types. The approaches used in this study could be applied by researchers to situations where community interest exists for species with these attributes. At a national scale, the malleefowl is predicted to decline by at least 20% over the next three generations. The findings of this thesis suggest that the future for the species in the Western Australian wheatbelt may not be as dire as predicted elsewhere within its range, owing largely to the easing and cessation of threatening processes (e.g. land clearing, grazing of habitat by livestock) and the ability of the species to occupy a variety of habitat types. Despite this perceived security, some caution must be exercised until there is a more complete knowledge of the impact of fox predation and reduced rainfall due to climate change on malleefowl populations. Furthermore, the status of the species beyond the agricultural landscapes in Western Australia requires closer examination.

[No abstract supplied]

New Zealand's South Island tussock grasslands have been highly modified by human activities, including burning, grazing and introductions of exotic plants for pastoralism. Studies suggest that tussock grasslands are degraded, in that native species have declined, and exotic species have increased in both diversity and abundance. These trends are primarily thought to be related to the impacts of grazing and subsequent grazing removal. Few studies have assessed long-term changes that have occurred in tussock grasslands, and those that have are generally limited to one particular location. This thesis aimed to investigate temporal changes in community structure in tussock grasslands, and relate these changes to environmental variables and land tenure. Data were used from 90 permanently-marked vegetation transects, which were set up on 19 geographically widespread properties in areas of tussock grassland across Canterbury and Otago in the South Island of New Zealand. The transects were on land in both conservation and pastoral tenure. Each transect was 100 m, and consisted of 50 0.25 m² quadrats. The transects were measured between 1982 and 1986 (first measurement), were re-measured between 1993 and 1999 (second measurement) and again between 2005 and 2006 (third measurement). A total of 347 vascular species were observed over the 90 transects and three measurement times. Species richness declined between the first and second measurements (first time interval), and increased between the second and third measurements (second time interval), at both the small (quadrat) and large (transect) scales. Both native and exotic species declined in mean quadrat species richness during the first time interval, and then increased during the second time interval. Changes in mean quadrat species richness were similar on transects in both conservation and pastoral tenure. Multivariate analysis of species' occurrences in quadrats identified a long gradient in species composition for these 90 transects. Four key plant communities were identifed along this gradient and differed in their mean elevation: (1) Highly-modified pastoral community, (2) Short-tussock grassland community, (3) Tall-tussock grassland community, (4) Alpine mat-forming species community. A detailed investigation into temporal changes that occurred on 53 transects that occurred in short- and tall-tussock grassland communities showed that changes in species composition were not consistent over time. Transects on different properties changed in species composition by different amounts. Specifically, in ordination space, transects on two properties changed in composition significantly more than transects on one other property. The property that a transect was on also affected the way that it changed in composition, i.e. native species were more likely to have increased on transects on some properties. Transects in conservation tenure did not change in species richness or composition differently from those in pastoral tenure. Considering that many native plants in tussock grasslands are relatively slow-growing, and that these areas have been grazed and burned for more than a century, we may expect it to be some time before we can detect differences in vegetation dynamics on conservation land from that on pastoral land. The changes in the community structure of these tussock grasslands were related to a combination of environmental factors, such as soil chemistry, climate, and management factors. This study has allowed greater understanding of vegetation change in tussock grasslands, and demonstrates the importance of long-term ecological monitoring in making reliable and accurate predictions about landscape-scale changes in tussock grassland community structure.

<p>The work in this thesis deals with effects of changed species richness on process rates among stream-living macroinvertebrates. Global biodiversity is decreasing rapidly and it is poorly known what the consequences of this loss may be for ecosystems and the services they provide. Hence, it is important to investigate the potential effects of losing species. In streams, deforestation, introduction of non-native species, pollution and channelization are examples of events that may affect species richness negatively. In this thesis emphasis is on changes in species richness within functional feeding groups (FFGs) of stream-living macroinvertebrates. The FFGs used were shredding detritivores, grazers, filter feeders and predators - all of which uphold important ecological processes in streams. Along with an observational field study, species richness was manipulated in laboratory and field experiments to investigate the effects of changed species richness on process rates and thus ecosystem functioning.</p><p>The results show that effects of changed species richness on process rates may be dramatic. Among the shredding detritivores there were negative effects on leaf mass loss, regardless whether fixed, random or predicted sequences of species loss was investigated. These effects could be attributed to either species richness per se or species composition. However, among the other FFGs the relationship between species richness and process rates was less consistent. In filter feeders, there was no or a negative effect of decreasing species richness while both grazers and predators showed positive effects of species loss.</p><p>The results also show that the most important interactions between species in an experiment, thus potentially in a natural community, are likely to determine what the effect of species loss on process rates will be. Facilitation and niche differentiation lead to reduced process rates if species are lost, while mechanisms, such as interspecific resource or interference competition, produce the opposite effect. Furthermore, in systems with a diminishing resource, the first two mechanisms may become more important over time enhancing the effect of species loss in the long term.</p><p>In conclusion, effects of species loss may be dramatically negative or positive even if lost species are classified as redundant. The effect in the short term most likely depends on which species are lost, on the original species composition and on the underlying mechanisms. Questions remaining to be answered are how important the observed effects are in more complex systems and if they are persistent over time? Future studies will tell. </p>

<p>The minimum ecologically viable population size (MEVP) of a species describes the minimum size at which the species itself or another species in the same ecosystem goes extinct as a result of the loss of inter-specific interactions. The MEVP shows a good potential for use as a tool for exploring the mechanisms behind species extinctions, but presently only a small amount of research has been done that takes advantage of this. In this study the MEVP is used to investigate what properties of species can be used as good indicators of ecological importance. 100 large computer generated food webs were created with an assembly model and the reduction in density that was necessary to induce an extinction event in the web was subsequently determined for each species within the webs. This change in density was then correlated with 28 different properties, measured for each species. The results show that properties that measure how well connected a species is, as well as measures of the species role as a prey item in the web are the ones with the greatest potential to find species with high MEVP. Further, the results put emphasis on the importance of regarding the web as a whole when working with species extinctions, while also highlighting the usefulness of the MEVP concept.</p>

Tumor necrosis factor (TNF) is upregulated in a number of cardiomyopathies. This thesis investigates TNF in triggering the expression and activation of matrix metalloproteinases (MMPs) in pressure overload cardiac disease, and explores the role of superoxide. Cardiac pressure overload was generated in adult wild-type and TNF-/- mice by transverse aortic constriction. Isolated cardiomyocytes and cardiofibroblasts from neonatal mice ventricles were treated with recombinant TNF (rTNF), and MMP induction and activation were assessed, with and without apocynin (a NADPH-oxidase inhibitor). TNF-/- mice showed less superoxide production and MMP activation, compared to wild-type mice, following pressure overload. rTNF upregulated the production of NADPH-dependent superoxide in cardiomyocytes as early as 1 hour (24 hours in cardiofibroblasts). rTNF also increased the expression of MMP-9 and MMP-12 in cardiomyocytes more than in cardiofibroblasts, and MMP-8 and MMP-13 more in cardiofibroblasts. This induction in both cardiac cell types was concomitant with superoxide production.

The work in this thesis deals with effects of changed species richness on process rates among stream-living macroinvertebrates. Global biodiversity is decreasing rapidly and it is poorly known what the consequences of this loss may be for ecosystems and the services they provide. Hence, it is important to investigate the potential effects of losing species. In streams, deforestation, introduction of non-native species, pollution and channelization are examples of events that may affect species richness negatively. In this thesis emphasis is on changes in species richness within functional feeding groups (FFGs) of stream-living macroinvertebrates. The FFGs used were shredding detritivores, grazers, filter feeders and predators - all of which uphold important ecological processes in streams. Along with an observational field study, species richness was manipulated in laboratory and field experiments to investigate the effects of changed species richness on process rates and thus ecosystem functioning. The results show that effects of changed species richness on process rates may be dramatic. Among the shredding detritivores there were negative effects on leaf mass loss, regardless whether fixed, random or predicted sequences of species loss was investigated. These effects could be attributed to either species richness per se or species composition. However, among the other FFGs the relationship between species richness and process rates was less consistent. In filter feeders, there was no or a negative effect of decreasing species richness while both grazers and predators showed positive effects of species loss. The results also show that the most important interactions between species in an experiment, thus potentially in a natural community, are likely to determine what the effect of species loss on process rates will be. Facilitation and niche differentiation lead to reduced process rates if species are lost, while mechanisms, such as interspecific resource or interference competition, produce the opposite effect. Furthermore, in systems with a diminishing resource, the first two mechanisms may become more important over time enhancing the effect of species loss in the long term. In conclusion, effects of species loss may be dramatically negative or positive even if lost species are classified as redundant. The effect in the short term most likely depends on which species are lost, on the original species composition and on the underlying mechanisms. Questions remaining to be answered are how important the observed effects are in more complex systems and if they are persistent over time? Future studies will tell.

This thesis focuses on phylogenetic, taxonomic, ecological, and conservation aspects of the crustose lichen genus Lecania (Ramalinaceae, lichenized Ascomycota). Lecania has previously been defined on basis of relatively few morphological characters, and the genus had never been treated in molecular phylogenies. The molecular phylogeny of the genus is inferred from DNA sequences. Twenty-five species traditionally placed in Lecania are included in the study along with 21 species from closely related genera. Lecania is a polyphyletic genus. A well-supported monophyletic group containing 16 Lecania species, including the type species L. fuscella is discovered, i.e. Lecania s. str. Nine species formerly included in Lecania do not belong in the genus. A new species, L. belgica, is described. The relationships of a group of morphologically similar Lecania species, i.e. the L. cyrtella group are investigated using morphological and molecular methods. Haplotype network and phylogenetic analyses indicate that the included species, as conceived in the morphological examinations, all are monophyletic. Two new species, L. leprosa and L. madida, are described, L. proteiformis is resurrected from synonymy, and the known range of L. prasinoides is greatly expanded. The type species Lecania fuscella has become endangered in many countries. Twelve localities in Sweden where the species had been found historically are investigated, but L. fuscella is only recovered in one locality. The species composition in these 12 localities, 58 old and 5 new collections with L. fuscella is determined and analyzed. The vegetation community differs between the old and the new collections, and between the locality where the species is recovered and those where it is not. Lecania fuscella has not been able to adapt to environmental changes and now only appears in a specific type of vegetation community. The phylogenetic diversity of the species is calculated, but does not reflect the species’ evolutionary potential.

Background It is debated whether a low total diversity of the gut microbiota in early childhood is more important than an altered prevalence of particular bacterial species for the increasing incidence of allergic disease. The advent of powerful, cultivation-free molecular methods makes it possible to characterize the total microbiome down to the genus level in large cohorts. Objective We sought to assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to atopic eczema development. Methods Microbial diversity and composition were analyzed with barcoded 16S rDNA 454-pyrosequencing in stool samples at 1 week, 1 month, and 12 months of age in 20 infants with IgE-associated eczema and 20 infants without any allergic manifestation until 2 years of age (ClinicalTrials.gov ID NCT01285830). Results Infants with IgE-associated eczema had a lower diversity of the total microbiota at 1 month (P = .004) and a lower diversity of the bacterial phylum Bacteroidetes and the genus Bacteroides at 1 month (P = .02 and P = .01) and the phylum Proteobacteria at 12 months of age (P = .02). The microbiota was less uniform at 1 month than at 12 months of age, with a high interindividual variability. At 12 months, when the microbiota had stabilized, Proteobacteria, comprising gram-negative organisms, were more abundant in infants without allergic manifestation (Empirical Analysis of Digital Gene Expression in R [edgeR] test: P = .008, q = 0.02). Conclusion Low intestinal microbial diversity during the first month of life was associated with subsequent atopic eczema. / <p>Funding Agencies|BioGaia AB, Stockholm, Sweden||Ekhaga Foundation, the Heart and Lung foundation||Research Council for the South-East Sweden|F2000-106|Olle Engqvist Foundation||Swedish Asthma and Allergy Association||Swedish Research Council||University Hospital of Linkoping||Soderberg Foundation||Vardal Foundation for Health Care Science and Allergy Research, Sweden||BioGaia AB||</p>

Throughout history species has gone extinct due to anthropogenic activities. During the last century efforts have been done to reintroduce species back into the wild. Zoos that originally were created as amusement parks for people have today a new purpose; to keep and breed species in captivity for later reintroductions in the wild. However a relaxed environment such as a zoo leads to a general fitness decline of up to 40% per generation in captivity. The probability of a successful reintroduction of a species that has been bred in a zoo will be lower the longer time it has been kept in captivity. The reintroduction of a captive bred species can also cause secondary extinctions and other negative effects on the food-web. Both changes in the community caused by the loss of a species and changes in the species itself caused by captivity can be expected to affect the outcome of a reintroduction attempt. Using a modeling approach I here investigate how the reintroduction of a captive bred species (at three different trophic levels; basal, intermediate and top predator species) affects a food-web and what risks there are in reintroducing it. A Lokta-Volterra model with type II functional response is used. I investigate three scenarios: the reintroduction of a species with 0% change in its attributes, 40% change in its attributes and 75% change in its attributes. It was found that the most important factor for reintroduction success when reintroducing a species is whether it is a producer species (basal species) or a consumer species (intermediate and top predator species). The producer species were most sensitive to the changes in their attributes, whilst consumer species were more sensitive to change in the food-web (Euclidian distance). The producer species were found to cause most secondary extinctions in all scenarios, hence indicating that it is a bottom-up controlled food-web. The present study suggests that the success of a reintroduction attempt is affected both by the degree of changes in the food web caused by the initial loss of the species and the degree of change in the species itself caused by captivity.