Dissertations / Theses on the topic 'Terrestrial biodiversity'

It is widely known that the world is losing biodiversity and primarily it is thought to be caused by anthropogenic activities. Many of these activities have been identified. However, we still lack a clear understanding of the causal relationships between human activities and the pressures they place on the environment and biodiversity. We need to know how ecosystems and individual species respond to changes in human activities and therefore how best to moderate our actions and reduce the rate of loss of biodiversity. One of the ways to detect these changes is to use indicators of ecosystem conditions. Indicators are statistics following changes in a particular factor usually over time. These indicators are used to summarise a complex set of data, and are seen as being representative of the wider situation in that field. So it can be assumed that if that particular factor is declining or improving, then the situation in general is also declining or improving. They are used to check the status and trends of biodiversity by both the public and policy makers. Indicators are also used to assess national performance and can be used to identify the actions required at the policy level. In this manner, they provide an important link between policy-makers and scientists collecting the data. The current thesis investigates the possibility of using bird species as indicators of biodiversity for better management of natural terrestrial ecosystems, by identifying their habitats according to various environmental factors. The study is established by drawing upon three main scientific areas: ecology, geographical information system (GIS), and statistical modelling. The Mornington Peninsula and Western Port Biosphere Reserve (MPWPBR) (Victoria, Australia) was chosen for the study area because of the combination of suburban and natural environments that made it optimum for this type of study. Once the study area was defined, the necessary data for the research were obtained from various sources. Birds Australia provided data on recorded observation of 271 bird species within the study area. Based on the nature of this study, seven species were selected for the study. The criteria for this selection are discussed in Chapter 3. Most literature state that the primary determinant for bird abundance is vegetation and land cover. Because of this, Ecological Vegetation Class (EVC) layer was used to determine which type(s) of vegetation have the greatest impact on habitat selection. Each species showed a relationship to a number of v vegetation types. These EVCs were combined to produce vegetation patches, and were considered as potentially suitable habitats of corresponding bird species. For each of the species, these habitat patches were analysed for the different aspects of patch characteristics (such as the level of patchiness, connectivity, size, shape, weighted distance between patches, etc.) by using the Landscape Context Tool (a GIS add-on). This process assisted the understanding of the importance of patch quality in habitat selection among different bird species by analysing the location of bird observation sites relative to habitat patches. In this way, the association between bird presence and the conditions of a habitat patch was identified by performing a discriminant function analysis. To investigate the probability of a species presence according to different environmental factors, a model of species distribution was created. Binary logistic regression was used to indicate the level of effect of each variable. The model was then successfully validated in the field. To define the indicators of environmental factors, it was essential to separate bird species based on their dependency on one or more of the studied variables. For this purpose, One-Way ANOVA was used. This analysis showed that some bird species can be considered as indicators of urban areas, while others could be good indicators of wellpreserved large forests. Finally, it must be mentioned that the type and quality of the datasets are crucial to this type of study, because some species have a higher degree of sensitivity to certain types of vegetation or land cover. Therefore, the vegetation data must be produced as detailed as possible. At the same time, the species data needs to be collected based on the presence and absence (versus presence-only) of the birds.

Die Ökosysteme unserer Erde sind durch das rasante Artensterben infolge von Umweltveränderungen durch den Menschen und des globalen Klimawandels stark betroffen. Mit den Auswirkungen dieses Artenverlustes und der damit einhergehenden Veränderung der Diversität beschäftigt sich die heutige Biodiversitätsforschung. Spezieller wird der Effekt der Diversität auf Ökosystemprozesse wie beispielsweise den Biomasseaufbau von Primärproduzenten oder der Resistenz einer Gemeinschaft gegen die Einwanderung neuer Arten untersucht. Die Quantifizierung des Einflusses der Diversität auf die Primärproduktion und das Verständnis der zugrunde liegenden Mechanismen ist von besonderer Wichtigkeit. In terrestrischen Pflanzengemeinschaften wurde bereits ein positiver Diversitätseffekt auf die Gemeinschaftsbiomasse beobachtet. Dies wird hauptsächlich durch den Komplementaritäts- und/oder den Dominanzeffekt erklärt. Die Komplementarität zwischen Arten ist beispielsweise bei Unterschieden in der Ressourcenausnutzung gegeben (z.B. unterschiedliche Wurzeltiefen). Diese kann zu einer besseren Nährstoffausnutzung in diverseren Gemeinschaften führen, die letztlich deren höhere Biomassen erklärt. Der Dominanzeffekt hingegen beruht auf der in diverseren Gemeinschaften höheren Wahrscheinlichkeit, eine hochproduktive Art anzutreffen, was letztlich die höhere Biomasse der Gemeinschaft verursacht. Diversitätseffekte auf Ökosystemprozesse wurden bisher hauptsächlich auf der Gemeinschaftsebene untersucht. Analysen über die Reaktionen, die alle Arten einer Gemeinschaft einschließen, fehlen bisher. Daher wurde der Einfluss der Diversität auf die individuelle Performance von Pflanzenarten innerhalb des Biodiversitätsprojektes „Das Jena Experiment“ untersucht. Dieses Experiment umfasst 60 Arten, die charakteristisch für Mitteleuropäische Graslandschaften sind. Die Arten wurden in die 4 funktionellen Gruppen Gräser, kleine Kräuter, große Kräuter und Leguminosen eingeteilt. Im Freilandversuch zeigte sich, dass mit steigender Artenzahl die individuelle Pflanzenhöhe zunahm, während die individuelle oberirdische Biomasse sank. Der positive Diversitätseffekt auf die pflanzliche Gemeinschaftsbiomasse kann folglich nicht auf der individuellen oberirdischen Biomassezunahme beruhen. Überdies reagierten die einzelnen funktionellen Gruppen und sogar die einzelnen Arten innerhalb einer funktionellen Gruppe unterschiedlich auf Diversitätsveränderungen. Folglich ist zu vermuten, dass einige Ökosystemprozesse auf Gemeinschaftsebene durch die Reaktionen von bestimmten funktionellen Gruppen bzw. Arten hervorgerufen werden. Diversitätseffekte auf Gemeinschaftsbiomassen wurden bislang hauptsächlich mit terrestrischen Pflanzen und weniger mit frei-schwebenden Algenarten (Phytoplankton) erforscht. Demzufolge wurde der Einfluss der Diversität auf die Biomasse von Phytoplankton-Gemeinschaften experimentell untersucht, wobei es sowohl zu negativen als auch positiven Diversitätseffekten kam. Eine negative Beziehung zwischen Diversität und Gemeinschaftsbiomasse zeigte sich, wenn schnell-wüchsige Algenarten nur geringe Biomassen in Mono- und Mischkultur aufbauten. Die vorhandenen Nährstoffe in der Mischkultur wurden von den schnell-wüchsigen Arten monopolisiert und folglich standen sie den langsam-wüchsigen Algenarten, welche viel Biomasse in Monokultur aufbauten, nicht mehr zur Verfügung. Zu einem positiven Diversitätseffekt auf die Gemeinschaftsbiomasse kam es, wenn die Artengemeinschaft eine positive Beziehung zwischen Wachstumsrate und Biomasse in Monokultur zeigte, sodass die schnell-wüchsige Algenarten viel Biomasse aufbauten. Da diese schnell-wüchsigen Algen in der Mischkultur dominant wurden, bestand die Gemeinschaft letztlich aus hoch-produktiven Algenarten, was zu einer erhöhten Gesamtbiomasse führte. Diese beiden Versuchsansätze verdeutlichen Mechanismen für die unterschiedlichen Reaktionen der Gemeinschaften auf Diversitätsveränderungen, welche auch für terrestrische Pflanzengemeinschaften gefunden wurden. Ein anderer wichtiger Ökosystemprozess, der von der Diversität beeinflusst wird, ist die Anfälligkeit von Gemeinschaften gegenüber invasiven Arten (Invasibilität). Die Invasibilität wird von einer Vielzahl von Faktoren beeinflusst und demzufolge wurde der Effekt der Diversität und der Produktivität (Nährstoffgehalt) auf die Invasibilität von Phytoplankton-Gemeinschaften in An- und Abwesenheit eines Herbivoren untersucht. Die zwei funktionell unterschiedlichen invasiven Arten waren die Blaualge Cylindrospermopsis raciborskii (schlecht fressbar) und der Phytoflagellat Cryptomonas sp. (gut fressbar). Es zeigte sich, dass der Fraßdruck, welcher selber durch die Produktivität beeinflusst wurde, einen bedeutenden Effekt auf die Invasibilität von Phytoplankton-Gemeinschaften hat. Die funktionellen Eigenschaften der invasiven und residenten Arten waren zudem bedeutender als die Artenzahl.
To date, positive relationships between diversity and community biomass have been mainly found, especially in terrestrial ecosystems due to the complementarity and/or dominance effect. In this thesis, the effect of diversity on the performance of terrestrial plant and phytoplankton communities was investigated to get a better understanding of the underlying mechanisms in the biodiversity-ecosystem functioning context. In a large grassland biodiversity experiment, the Jena Experiment, the effect of community diversity on the individual plant performance was investigated for all species. The species pool consisted of 60 plant species belonging to 4 functional groups (grasses, small herbs, tall herbs, legumes). The experiment included 82 large plots which differed in species richness (1-60), functional richness (1-4), and community composition. Individual plant height increased with increasing species richness suggesting stronger competition for light in more diverse communities. The aboveground biomass of the individual plants decreased with increasing species richness indicating stronger competition in more species-rich communities. Moreover, in more species-rich communities plant individuals were less likely to flower out and had fewer inflorescences which may be resulting from a trade-off between resource allocation to vegetative height growth and to reproduction. Responses to changing species richness differed strongly between functional groups and between species of similar functional groups. To conclude, individual plant performance can largely depend on the diversity of the surrounding community. Positive diversity effects on biomass have been mainly found for substrate-bound plant communities. Therefore, the effect of diversity on the community biomass of phytoplankton was studied using microcosms. The communities consisted of 8 algal species belonging to 4 functional groups (green algae, diatoms, cyanobacteria, phytoflagellates) and were grown at different functional richness levels (1-4). Functional richness and community biomass were negatively correlated and all community biomasses were lower than their average monoculture biomasses of the component species, revealing community underyielding. This was mainly caused by the dominance of a fast-growing species which built up low biomasses in monoculture and mixture. A trade-off between biomass and growth rate in monoculture was found for all species, and thus fast-growing species built up low biomasses and slow-growing species reached high biomasses in monoculture. As the fast-growing, low-productive species monopolised nutrients in the mixtures, they became the dominant species resulting in the observed community underyielding. These findings suggest community overyielding when biomasses of the component species are positively correlated with their growth rates in monocultures. Aquatic microcosm experiments with an extensive design were performed to get a broad range of community responses. The phytoplankton communities differed in species diversity (1, 2, 4, 8, and 12), functional diversity (1, 2, 3, and 4) and community composition. The species/functional diversity positively affected community biomass, revealing overyielding in most of the communities. This was mainly caused by a positive complementarity effect which can be attributed to resource use complementarity and/or facilitative interaction among the species. Overyielding of more diverse communities occurred when the biomass of the component species was correlated positively with their growth rates in monoculture and thus, fast-growing and high-productive species were dominant in mixtures. This and the study mentioned above generated an emergent pattern for community overyielding and underyielding from the relationship between biomass and growth rate in monoculture as long as the initial community structure prevailed. Invasive species can largely affect ecosystem processes, whereas invasion is also influenced by diversity. To date, studies revealed negative and positive diversity effects on the invasibility (susceptibility of a community to the invasion by new species). The effect of productivity (nutrient concentration ranging from 10 to 640 µg P L-1), herbivory (presence/absence of the generalist feeder) and diversity (3, 4, 6 species were randomly chosen from the resident species pool) on the invasibility of phytoplankton communities consisting of 10 resident species was investigated using semi-continuous microcosms. Two functionally diverse invaders were chosen: the filamentous and less-edible cynaobacterium C. raciborskii and the unicellular and well-edible phytoflagellate Cryptomonas sp. The phytoflagellate indirectly benefited from grazing pressure of herbivores whereas C. raciborskii suffered more from it. Diversity did not affect the invasibility of the phytoplankton communities. Rather, it was strongly influenced by the functional traits of the resident and invasive species.

This thesis makes a contribution to the growing body of literature examining the institutional dimension of human-environment interactions. It has been guided by an interest in the problem of loss of terrestrial biodiversity in the state of Queensland, Australia and its institutional determinants. The study explored two research questions: • How to conceptualise and evaluate the effectiveness of institutions contributing to the resolution of environmental problems? • How effective is the Queensland land use planning and development assessment system in achieving biodiversity protection outcomes? The first part of the study established a theoretical and analytical foundation for the effectiveness assessment of institutional environmental performance, by examining a wide range of theoretical, conceptual and analytical questions regarding the conceptualisation of institutions, their causal role and evaluation. The study was built on an understanding of institutions as systems of rules that structure social interactions, and it defined institutional ‘performance’ as an institutional influence on, or contribution to, the behavioural response of targeted actors. It argued that institutions play a significant role in social interactions, and are an important explanatory factor for many behavioural phenomena. Building on the literature review, the study established that biodiversity protection is a highly complex and multi-faceted problem. Institutional designs are required to address a range of problem attributes, such as the existing knowledge base, value and incentive systems, distribution of decision-making authorities, and coordination of interactions among a large number of actors. In this context, the study examined two analytical problems. The first was how to approach a large diversity of problem attributes that may contribute to the resolution or creation of complex environmental problems. The second was how to examine diverse and complex institutional designs.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
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The main subject of my papers has been the phylum Tardigrada, with particular emphasis on the Antarctic fauna. While this is one of the ‘lesser known phyla’ the group forms an important element of Antarctic non-marine ecosystems. My work has centred on four interrelated themes: i) taxonomy, predominantly Tardigrada and with an Antarctic bias though including wider global species and high taxon groupings (I have also worked on other taxa such as Fungi-imperfecti and freshwater invertebrates); ii) biodiversity of tardigrades, particularly Antarctic habitats; iii) data-based studies based on the terrestrial Tardigrada and Antarctic freshwater crustaceans; and iv) biogeographic analysis of these databases. The thesis presented consists of papers published in major, peer-reviewed journals, along with book chapters published and in press. Several of my papers have been cited 10-30 times according to the ISI Web of Science citation system. Highlights of my work include being the first to publish a paper on the global terrestrial biogeography of a phylum and showing the extant limno-terrestrial tardigrade fauna reflect the early tectonic break-up of the Laurasia, West and East Gondwana super continents between 65 and 135 million years ago.

The main subject of my papers has been the phylum Tardigrada, with particular emphasis on the Antarctic fauna. While this is one of the ‘lesser known phyla’ the group forms an important element of Antarctic non-marine ecosystems. My work has centred on four interrelated themes: i) taxonomy, predominantly Tardigrada and with an Antarctic bias though including wider global species and high taxon groupings (I have also worked on other taxa such as Fungi-imperfecti and freshwater invertebrates); ii) biodiversity of tardigrades, particularly Antarctic habitats; iii) data-based studies based on the terrestrial Tardigrada and Antarctic freshwater crustaceans; and iv) biogeographic analysis of these databases. The thesis presented consists of papers published in major, peer-reviewed journals, along with book chapters published and in press. Several of my papers have been cited 10-30 times according to the ISI Web of Science citation system. Highlights of my work include being the first to publish a paper on the global terrestrial biogeography of a phylum and showing the extant limno-terrestrial tardigrade fauna reflect the early tectonic break-up of the Laurasia, West and East Gondwana super continents between 65 and 135 million years ago.

This doctoral dissertation was produced in a cooperation between Halmstad University (Wetland Research Centre, School of Business and Engineering) and Lund University (Limnology & Marine Biology, Department of Ecology). Abstract . Wetland creation at large, regional scales is implemented as a measure to abate the biodiversity loss in agricultural landscapes and the eutrophication of watersheds and coastal areas by non-point source nutrient pollution (mainly nitrogen). The consequences of creating many new wetlands for biodiversity conservation and nutrient reten- tion (ecosystem functioning) in agricultural landscapes are still relatively unknown, both on local (per wetland) and regional (per landscape) scales. In Sweden, wetland creation has progressed already since the 1990s, and by now larger numbers of created wetlands are present, mainly in the intensively farmed landscapes of southwestern Sweden. This thesis aimed to investigate the following aspects in these systems: (i) their large-scale effects on biodiversity, (ii) their functional diversity of bacterial denitrifiers, (iii) the abiotic and biotic influences on wetland ecosystem functioning, (iv) the potential for biodiversity-function links, and (v) the potential for functional links and joint functioning.(i) Created wetlands hosted diverse assemblages of macroinvertebrates and plants. They maintained a similar com- position and diversity as natural ponds in agricultural landscapes. The environmental conditions per wetland did hardly affect macroinvertebrate and plant assemblages, and the prerequisites for nutrient retention did neither. In landscapes were wetland creation efforts had increased the total density of small water bodies by more than 30%, macroinver- tebrate diversity of created wetlands was facilitated on both local and regional scales. (ii) Diverse communities of denitrifying bacteria with the capacity for conducting different denitrification steps (functional types) were present in all investigated wetlands. The richness of denitrifying bacteria communities was affected by nitrate concentration and hydraulic loading rate, which may potentially be relevant for the nitrogen retention function of created wetlands. The diversity across different functional types of bacterial denitrifiers increased with nitrate concentration. (iii) Both abiotic and biotic factors influenced ecosystem functions of created wetlands. Variation in nitrogen retention was associated to nitrate load, but even to vegetation parameters. In wetlands with constant nitrate load, planted emergent vegetation facilitated nitrogen retention compared to other vegetation types. In wetlands with variable loads, nitrogen retention was facilitated if nitrate load was high and many different vegetation types were present; nitrogen load could explain the majority of the variation in nitrogen retention compared to vegetation parameters. Phosporus retention of created wetlands was best explained by vegetation parameters. Litter decomposition was inhibited at high nitrate to phosphorus ratios. Methane production increased with age and decreased with plant cover. (iv) Biodiversity may facilitate wetland ecosystem functions, particularly in dynamic wetland ecosystems. Nitrogen retention increased with vegetation type diversity, phosphorus retention capacity with plant richness, and litter decomposition with macroinvertebrate diversity. (v) Created wetlands have the capacity of sustaining several parallel ecosystem services. Some wetland functions were coupled; nitrogen retention increased with fast litter decomposition. On the other hand, methane emission and nitro- gen retention were independent of each other, as were nitrogen and phosphorus retention.In conclusion, created wetlands have the potential to at least partly abate the lost biodiversity and multifunctionality caused by the past extensive destruction of natural wetlands in agricultural landscapes.

[Paper II] Milenkovski S., Thiere G., Weisner S.E.B., Berglund O. & Lindgren P.-E. Variation of eubacterial and denitrifying bacterial biofilm communities among constructed wetlands. Submitted manuscript. [Paper V] Thiere G. & Weisner S.E.B. Influence of biotic and abiotic parameters on ecosystem functioning of created wetlands. Manuscript.

In alpine regions worldwide, climate change is dramatically altering ecosystems, affecting biodiversity across habitats and taxonomic scales. For streams, the associated recession of mountain glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, and basal resources – often threatening the very existence of some habitats and biota. Globally, alpine streams harbor particularly substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity: however, anthropogenic warming threatens to homogenize habitats through the reduction of the cryosphere, thereby reducing biodiversity from micro- to macroscopic organisms and genes to communities. Still, alpine stream biodiversity, particularly in North America, is poorly understood, making it difficult to predict future changes without baselines for comparison. For my dissertation, I used genetic tools to assess biodiversity in alpine streams of the central Rocky Mountains in North America. Here, I begin by reviewing the current state of alpine stream biology from an organismal perspective. Next, I provide two perspectives on macroinvertebrate diversity. The first, a population genetic comparison of three highly similar species, is followed by a fine-scale genomic study of one species, Lednia tumana. I follow these largely macroinvertebrate-centric chapters with a modern synthesis of the microbial ecology of mountain glacier ecosystems. Finally, I conclude with a study of microbial diversity that addresses how microbial diversity is shaped by geography, habitat, and hydrological source in North America. Collectively, this research refines existing themes in alpine stream biology by revealing unexpected differences in population genetic patterns among closely related species, the influence of recent deglaciation on population genetic structure and demographic history of a threatened stonefly, and clarification of the environmental drivers shaping microbial diversity.

In 1994 a new Forestry Act was accepted in Sweden. One of its aims was to raise the consideration for preservation of biodiversity. Since this happened over 15 years ago there is now an interest in analyzing if the law has been effective in its purpose. In this study methods suitable for analysis are being investigated. The study contents a pilot study of methods for five parameters that can validate if the law has been followed. The fieldstudy were executed in Orsa, Dalarna, Sweden in a managed forest and where last clearcut was done after 1994. The work consisted of measuring the parameters in the field and to compare them with data from before 1994. The benefits of the parameters and the current and previous Forestry Act and their differences are discussed in the report. The parameters examined were the distribution of tree species, standing dead wood, smaller areas saved for preservation, big trees and trees with cavities/cavernous trees. All of these plus a few other variables favourable for the diversity of species in the forest are dealt with in the 30 § in the Forestry Act of 1994. The study implied that the variables reported to be favourable for biodiversity, and possible to investigate within the restrictions of this study, seemed to have increased. The results should however be interpreted with care since the study is small and the reference values sometimes were missing or covering larger areas than the field data.

Wetlands contain both aquatic and terrestrial environments which generates high biodiversity. However, they are commonly associated with mosquitoes (Diptera: Culicidae), and mosquitoes are usually regarded as negative by humans because they can cause nuisance and transmit diseases. This thesis aimed to clarify the association between mosquitoes and wetlands and to achieve a more balanced view of biodiversity in wetlands by including mosquito diversity. Studies on adult mosquito diversity and assemblages were performed in 18 wetlands spread over Sweden. The Swedish mosquito species were organized in ten functional groups based on four life-history characteristics. This classification was used as an additional diversity measurement and as a tool for presentation of mosquito data. Mosquito diversity showed several of the well-established diversity patterns such as a latitudinal gradient, a species-area relationship and a distribution-abundance relationship. In a landscape perspective, diversity of both mosquitoes and dytiscids (Coleoptera: Dytiscidae) were positively influenced by a high proportion of permanent water and a high amount of open areas, indicating co-varying diversity patterns. Mosquito assemblages in the Nedre Dalälven region were mainly structured by the extent of flooded areas and wetland type (wet meadow, swamp and bog). In addition to the influence of the proportion of temporary wetlands at a local scale, the proportion of forest gained importance at larger spatial scales and in relation to dispersal distances of species. In southern Sweden, mosquito faunas differed between natural and constructed wetlands, partly reflecting differences in wetland size. In an experiment, different responses of two co-occurring mosquito species to rapid larval habitat desiccation indicate that weather conditions after a flood could influence mosquito assemblages. The conclusions of this thesis provide suggestions on how to construct and position wetlands for increased insect diversity, and indicate that low abundance of major nuisance species might be crucial for acceptance of wetlands near human settlements.

Det svenska kulturlandskapet har förändrats radikalt under de senaste 200 åren från ett varierat och heterogent landskap till ett mer monotont, homogeniserat landskap som följd av att olika former av mänskligt resursutnyttjande har effektiviserats. Detta har lett till en fragmentering av livsmiljöerna för flera av kulturlandskapets arter. Kraftledningsgator kan tänkas hysa naturtyper som påminner om vissa av de nu försvunna eller fragmenterade livsmiljöerna (t ex betad skogsmark och vissa typer av ängsmarker) och skulle kunna ha en viktig betydelse som reträttplats och/eller spridningskorridor för dessa arter.

I en fallfällsinventering i Köpings och Strängnäs kommun i Mälardalen undersöktes förekomst och abundans av marklevande evertebrater i kraftledningsgator, skog och betesmark. Jämförelser i förekomst och abundans gjordes mellan dessa marktyper (d v s kraftledningsgator, skog och betesmark), samt mellan positioner inom kraftledningsgator (centrala och distala delar) och närliggande skogsmark. Jämförelserna innefattade dels analyser av artantal (eller snarare antal taxa) och flera olika biodiversitetsindex och dels analyser av likhet i artförekomst och individantal med "likhetsindex" (similarity index). Separata analyser gjordes inom olika taxonomiska grupper (t ex alla taxa, endast inom insekter, endast inom spindeldjur). Antalet replikat tillät statistisk testning av eventuella mönster i antal taxa och biodiversitetsindex.

Inga signifikanta skillnader dokumenterades, varken mellan de olika marktyperna eller mellan positioner inom kraftledningsgator och närliggande skog. Vi tolkar dessa resultat som att kraftledningsgator med avseende på antal taxa respektive biodiversitet inte är (signifikant) sämre än skogs- eller betesmark. Det kan betonas att det inte heller fanns något konsekvent (icke-signifikant) mönster som pekade på att så skulle vara fallet. Antal taxa och biodiversitetsindex tar ingen hänsyn till vilka arter eller taxa som ingår i analyserna. En naturtyp som hyser en individ- och artrik fauna bestående av oönskade arter (introducerade arter, "skadedjur" etc.) registrerar t ex ett högre biodiversitetsindex än en naturtyp med fåtaligt förekommande rödlistade, skyddsvärda arter. Likhetsindex belyser bättre vilka arter som är inblandade. Visserligen tas inte heller här hänsyn till exakt vilka arter som ingår (eller deras eventuella önskvärdhet eller skyddsvärde), men ett högt index indikerar att samma arter förekommer i de jämförda naturtyperna. I denna studie indikerar ett högt likhetsindex dessutom att antalet individer av de inblandade arterna är likartat, eftersom ett index som tar hänsyn till abundans användes.

Resultaten visade överlag höga likhetsindex, speciellt verkade kraftledningsgator och skogsmark hysa likartad evertebratfauna medan likheten mellan kraftledningsgator och betesmark var mindre uttalad. Sammanfattningsvis indikerar studien att kraftledningsgator inte verkar vara lågvärdiga livsmiljöer för de marklevande evertebrat-taxa som ingått i studien. Vi föreslår att kraftledningsgator med väl avvägda rutiner för röjning och skötsel skulle kunna spela en viktig roll i skapandet av artrika kantzoner eller marker som liknar ängs- eller betesmarker med svag hävd.

As a consequence of the intensification of various forms of human resource utilization rural Sweden has changed radically over the past 200 years from offering a varied and diverse landscape to a more monotonous, homogenised type of environment. This has led to fragmentation of habitats for many of the species occurring. Power line corridors might harbour habitats that resemble some of the now lost or fragmented habitats (e.g. grazed forest land and certain types of meadow), and could have important functions as refuge habitats and / or distribution corridors for these species.

In a pitfall trap study in Köping and Strängnäs municipalities in Mälardalen, the occurrence and abundance of ground-living invertebrates were investigated in power line corridors, adjoining forest and pastures. Comparisons were made between these habitat types, and between positions within the power line corridor (central and distal parts) and the nearby forested area. The comparisons included analysis of number of species (or rather the number of taxa) and several biodiversity indexes, as well as analysis of the similarity of the occurrence of certain species and individual numbers by use of "similarity index". Separate tests were made in different taxonomic groups (e.g. all taxa, only within insects, only within spiders). The number of replicates allowed statistical testing of patterns in the number of taxa and biodiversity index.

No significant differences were documented, neither between the different habitat types, nor between positions in the power line corridors and nearby forest. There was also no consistent (non-significant) pattern indicating that this would be the case. We suggest these results to indicate that power line corridors at least are not (significantly) poorer quality habitats than are forest or pasture land with regard to number of taxa and biodiversity. Number of taxa and biodiversity indices take no account of the species or taxa included in the analysis. Thus the same weight is assigned to an unwanted species (e.g. an invasive pest species or parasite) as to a red-listed, highly valued species. Similarity index takes more heed to the species involved. Although similarity indices do not consider the exact identity of involved species (or their possible value or desirability), a high index value indicates that the same species occur in the compared habitats. In this study, where an index that takes into account the abundance of species was used, a high similarity index value also indicates that the numbers of individuals are similar.

Overall, the results showed high similarity between habitat types. This would suggest that, to a large extent, power lines, forest and pasture land had the same composition of taxa, and that the taxa had similar abundances. Power lines and forest seemed to exhibit particularly high similarities, whereas the similarity between power lines and pasture land was less pronounced. Thus, this study indicates, in contrast to several previous suggestions, that power line corridors do not seem to be low quality habitats. We also suggest that power line corridors with well designed management routines could play an important role creating edges and habitats resembling meadow or low intensity grazed pasture land.

L'étude de la biodiversité de la macrofaune et des Oniscoïdes dans l'agroécosystème Majerda (BVM) a été réalisée sur 2 années successives sur 15 parcelles durant 4 saisons de l'année 2008-2009 et sur 11 parcelles de l'année 2009-2010. L'analyse a été faite en fonction des cultures les plus représentées dans la BVM (l'arboriculture, culture maraîchère, fourragère et légumineuse). L'échantillonnage a été réalisé par piégeage. Au total, 19 groupes taxonomiques ont été collectés. Les résultats montrent une variation saisonnière de la diversité de la macrofaune en fonction des parcelles. Les Coléoptères, les Oniscoïdes, les Hyménoptères, les Diptères, les Orthoptères et les Araignées sont les plus constants et abondants dans la BVM. Les Oniscoïdes sont abondants dans les parcelles en cultures fourragères. En passant des parcelles du milieu terrestre vers celui côtier, un gradient ascendant de la diversité de la macrofaune a été observé. Neuf espèces ont été collectées. Porcellio laevis est la plus fréquente durant toutes les saisons d'étude. En fonction de cultures, l'effectif et la richesse spécifique les plus importants ont été enregistrés dans les cultures fourragères et dans la céréaliculture. En fonction des secteurs, les Isopodes terrestres sont abondants dans les parcelles du secteur Pont de Bizerte qui sont irriguées par le mode aspersion et par les eaux usées. L'étude de la variation interannuelle montre qu'il existe un effet du facteur année sur la diversité de la macrofaune et des espèces d'Oniscoïdes. Les espèces d'Oniscoïdes sont corrélées avec la conductivité, la teneur du sol en Mg2+ Ca2+, K+ et de la granulométrie du sol
In Tunisia, few studies on the macrofauna and species diversity of terrestrial isopods in the agroecosystems were performed. To fill this gap, the spatio-tempral (plots, sectors and season) diversity of macrofauna and Oniscidea was analysed. We studied the distribution of Isopods in Majerda agroecosystems related to cultivation types (orchards, market gardening, vegetable crops), irrigations systems (sprinkler, surface and drip) and soil physico-chemical characteristics. Sampling was carried out with pitfalls traps during in 15 plots during 2008-2009 and 11 plots during 2009-2010. Nineteen groups of macrofauna was found. Coleoptera, Oniscidea, Hymenoptera, Diptera, Othoptera and Aranea were the most present and abundant. Isopods were abundant in autum in the vegetable crops cultivation. In the coastal plots (Ghar El Melh sector) diversity was higher than in the terrestrial plots (Utique sector). Nine species of terrestrial isopods belonging to 6 genera were identified. Porcellio laevis was the most frequent species in all seasons. According to cultivation types, the number of individuals and the species richness were important in vegetable crops and barely cultivation. The spatial distribution of Oniscidea showed that isopods were abundant in the plots of Pont of Bizerte irrigated by sprinkler systems and wastewater. Year factor affected the diversity of fauna and isopods. Oniscidea species distribution was correlated to conductivity, texture and the content of Mg2+ Ca2+ and K+ of soil

Plant-pollinator networks have shown to be highly dynamic systems as species and interactions change in time and space. Few studies have incorporated several habitats in their network. In this work I investigate interacting plant and pollinator communities of three adjacent habitats at Gotska Sandön, an island in the Baltic Sea. The networks varied in size between the habitats, and the larger networks of the dune and meadow displayed both nested and modular structure while the smaller forest network was more randomly organised. We found species present in more than one habitat that connected the networks by forming inter-habitat modules of tightly linked species. Species took on different topological roles in the networks depending on how many links they formed and where these attached. The habitat generalists were important to overall network structure as role correlated with habitat generalisation level.

La faune sauvage terrestre est actuellement confrontée a une sixième extinction de masse dont l’origine, contrairement aux extinctions des ères passées, est principalement anthropogénique. Suite à la prise de conscience de la communauté internationale dans les années 70, un nombre sans cesse croissant d’instruments juridiques ont été élaborés en vue de la protection de la faune sauvage terrestre sans pour autant parvenir à endiguer la disparition des espèces. A travers ce constat, c’est l’efficacité du régime juridique relatif à la protection de la faune sauvage terrestre qui est en cause. Le cœur du problème réside dans le fait que la faune sauvage terrestre est considérée comme une ressource naturelle. En ce sens, chaque État a compétence pour gérer, exploiter voire détruire les ressources en faune situées sur son territoire en vertu du principe de souveraineté permanente sur les ressources naturelles. Or, ce principe est en contradiction avec les réalités écologiques et biologiques dans la mesure où la faune sauvage terrestre, outre le fait qu’elle puisse être amenée a se déplacer sur le territoire de plusieurs États, participe à l’entretien d’écosystèmes ou à des processus biologiques qui dépassent bien souvent le cadre des frontières étatiques. L’exploitation des ressources en faune dans un État donné peut donc avoir des effets sur l’environnement des États tiers. En conséquence, la souveraineté des États sur leurs ressources en faune ne peut être absolue, ce que traduit imparfaitement le principe de non-utilisation dommageable du territoire dont l’application concrète et pratique à la faune sauvage terrestre reste incertaine eu égard à la difficile appréhension par le droit de la complexité des processus écologiques transfrontières. La faune sauvage terrestre ne devrait donc pas être soumise au même régime juridique que les ressources naturelles extractives qui sont invariablement situées sur le territoire d’un État donné et qui ne participent à l’entretien d’aucun écosystème ou processus biologique. Il serait sans doute plus pertinent d’envisager pour la faune sauvage terrestre un régime juridique comparable à celui qui s’applique à certains cours d’eau et bassins internationaux basé sur la Coopération. En effet, même s'il n’existe pas de régime juridique général applicable aux cours d’eau, ces derniers sont la plupart du temps considérés comme des ressources partagées de facto impliquant une gestion commune par les États riverains sans que la souveraineté de ces derniers soit remise en cause. Cette solution n’est pas celle qui prévaut actuellement en droit international. En effet, le régime actuel, entièrement construit autour du principe de souveraineté permanente sur les ressources naturelles se caractérise par sa fragmentation. Les obligations étatiques en matière de protection de la faune sauvage terrestre sont majoritairement d’origine conventionnelle. [...]
Terrestrial wildlife is actually facing a sixth mass extinction which is mostly anthropogenic contrary to past mass extinctions. After the international community took notice of the problem in the 70s, an increasing number of legal instruments were adopted in order to protect terrestrial wildlife worldwide. Yet, wildlife populations continued to decline. Through this terrible assessment, it is the efficiency of the international legal regime of wildlife protection which needs to be questioned and scrutinized.The crux of the problem lies in the fact that terrestrial wildlife is considered as a natural resource. As such, each State has jurisdiction to manage, exploit, deplete, or even destroy wildlife resources located on their territory pursuant to the principle of permanent sovereignty over natural resources. However, this principle is in contradiction with ecological and biological realities Indeed, terrestrial fauna, apart from the fact that it may move from one State to the other, is involved in the maintenance of ecosystems and other complex biological processes which effects are felt way outside the borders of a single State. As a result, the exploitation of wildlife resources in one State can have dire consequences on the environment of other States. As such, sovereignty over wildlife resources cannot be absolute which the principle of good neighbourliness imperfectly captures. Yet, it appears that the application of this principle in the context of the conservation of wildlife resources raises a certain number of uncertainties due to the difficulty to translate in legal terms the complexities of the ecological processes involved. Consequently, terrestrial wildlife should not be regulated by the same legal regime as the one applicable to extractive resources which are invariably located within the borders of a single State and are not part of any transnational ecological process. Maybe would it be more relevant to apply a legal regime similar to the one applicable to international waterways, most of them are considered as de facto shared resources implying a regime of common management between Riverine States without their respective sovereignty being challenged in any way. Yet this solution is not the one that prevails under international law as far as wildlife resources are concerned. The actual regime is entirely built around the principle of terrestrial sovereignty over natural resources where each State is responsible for implementing its international obligations in its own territory. [...]

Over the next three decades, there are many predicted disturbances to Earth’s oceans, such as El Nino and hurricanes, which will lead to mass coral bleaching effects. Marine protected areas have been utilized worldwide to maintain coral population sizes and remediate external stressors, such as overfishing or mining. Using a series of modeling techniques, this thesis will propose an experiment that will determine the optimal distance and location for a future MPA in New Zealand. It will also be measuring whether one large reserve or a network of smaller MPAs are more effective in the regeneration of stony corals. These models will be based on Solemosmilia variabilis, the most common stony coral in the region. Based on past studies, it is hypothesized that there will be a significant positive increase with the metapopulation growth of corals in both protected areas. It is also predicted that there will be a higher rate of connectivity within a network of smaller marine protected areas if the MPAs are less than 2 km apart. If the distance is greater, one larger MPA will be more effective due to the lower rates of genetic drift.

Prestonella bowkeri and Prestonella nuptialis are montane specialists endemic to the southern Great Escarpment of South Africa. Phylogeographic analyses of these species based on mitochondrial markers CO1 and 16S reveal extremely high levels of divergence between populations indicating a lack of gene flow between populations. This is not surprising, because P. nuptialis and P. bowkeri have limited dispersal capacity, low vagility, a highly fragmented distribution and are habitat specialists that are restricted to isolated mesic refugia associated with waterfalls and montane seepages. A relaxed Bayesian clock estimate suggests that populations diverged from one another during the mid-late Miocene (12.5-7 MYA) which coincides with the modern trends of seasonal aridity which began during the Miocene. This result should be viewed with caution because the rates used are at best imprecise estimates of mutation rates in snails. There is no clear dichotomy between the two species and P. bowkeri is paraphyletic with respect to P. nuptialis, as a consequence the taxonomy is unclear. Due to the high levels of sequence divergence between populations they may be considered as evolutionary significant units (ESU’s). An assessment of haplotype diversity (h) and nucleotide diversity (π) reveals that populations in the western part of the Great Escarpment are more genetically depauperate than populations in the east. Correlations between genetic diversity and climatic variables show that genetically depauperate populations are found in areas that have lower annual rainfall, less reliable rainfall and higher potential evaporation, all factors associated with a drier, less mesic environment that increases the chances of a population bottleneck. This indicates that a shift towards a more arid environment may be a driver of genetic erosion. Historical climate change may thus have affected the amount and distribution of genetic diversity across the Great Escarpment since the Miocene. This has serious future implications for the survival of Prestonella. With predicted increase in global temperatures, climate change in South Africa is likely to result in range contraction and an eastward range shift for many species in the drier central and western areas (Erasmus et al. 2002) and regions along the Great Escarpment are likely to become more arid. Prestonella populations found living on inselbergs along the Great Escarpment are already restricted to site specific watercourses and seepages. An increase in the periods between stream flow, and increasing rainfall variability and mean annual potential evaporation are likely to have an adverse affect on species living in these habitats, resulting in further bottlenecks and possibly local extinction. An IUCN assessment of P. nuptialis and P. bowkeri suggests that these two species are probably endangered. The issue surrounding the conservation of Prestonella species is that they are threatened by global climate change, which cannot be simply restricted or prevented, which makes dealing with the threat of climate change difficult. Assisted migration (MA) may be considered as a method to prevent possible future extinctions of Prestonella populations, but will only be considered as a last resort. The thermal tolerance (Arrhenius breaking temperature and flat-line temperature) of individual snails from three Prestonella populations (one forest population and two thicket populations) were assessed using infrared sensors that detected changes in heart rate with increasing temperature. The forest population had a significantly lower Arrhenius breaking temperature (ABT) and flat-line temperature (FLT) than the two thicket population (p<0.05). Our results do not show a correlation between upper thermal limits and maximum habitat temperatures or other climatic variables in Prestonella populations. Although no correlation is found between ABT and maximum habitat temperature, it is likely that the differences seen between these populations are due to local micro-climate adaptation. The climatic variables used in this experiment are coarse estimates from GIS data and do not reflect actual microhabitat conditions. Forest environments are less heat stressed than thicket environments due to the forest canopy which may explain the lower ABT and FLT of the forest population.

This dissertation presents a diagnosis of the diversity of terrestrial vertebrates in the Brazilian state of Sergipe. Information on the general and regional distribution, conservation and expected occurrence of species were collected for each taxonomic group. The morphoclimatic domain model was adopted as the geographic baseline for the definition of the ranges of the 547 species identified. Most of the 45 species of amphibian expected for Sergipe are distributed throughout the different domains, although 11 are restricted to the Atlantic Forest. Two species of Phyllomedusa are endangered locally, almost all the 39 confirmed species are restricted to the Atlantic Forest. The 57 reptilian species are mostly widely-distributed lizards and snakes, although 11 are restricted to either the Atlantic Forest or the caatinga. Two species of nemidophorus lizards are endemic, and four have a local distribution, while approximately 30 of the expected species were confirmed. With regard to the 387 bird species, 14 are restricted to the Atlantic Forest and two to the caatinga. The albatross, Thalassarche melanophris, has a restricted distribution, and the passeriform Herpsilochmus pectoralis is on the list of endangered species. Approximately 450 species of birds 95 of which are endangered are expected to occur in Sergipe. Most of the 36 species of nonvolant mammals, plus the 22 bats, are from the Atlantic Forest and caatinga, or more amply distributed. Red-listed species include the Atlantic Forest bat Chiroderma doriae, the titi monkeys Callicebus coimbrai and C. barbarabrownae from the Atlantic Forest and caatinga, respectively, and the capuchin, Cebus xanthosternos. Of the 124 species that probably occur within the area, three are endemic to the caatinga, and four to the Atlantic Forest. The most important areas of the Atlantic Forest and caatinga for ecological studies and biological inventory are identified and discussed.
A dissertação é um diagnóstico da biodiversidade dos vertebrados terrestres da região de Sergipe. Para cada grupo taxonômico foram obtidas informações sobre a distribuição geral e regional das espécies, conservação e espécies de ocorrência esperada. O modelo dos domínios morfoclimáticos foi adotado como unidade geográfica para determinar as distribuições das 547 espécies. A maioria das 45 espécies de anfíbios está amplamente distribuída em todos os domínios, 11 são restritas à mata atlântica. Duas espécies de Phyllomedusa estão ameaçadas localmente, quase todas as 39 espécies esperadas ocorrer são restritas à mata atlântica. As 57 espécies de répteis são compostas principalmente por lagartos e serpentes amplamente distribuídas em todos os domínios, 11 são restritas à mata atlântica e caatinga. Duas espécies de lagartos do gênero Cnemidophorus são endêmicas e 4 têm distribuição localizada; aproximadamente 30 espécies de répteis são esperadas ocorrer. Com relação às 387 espécies de aves, 14 são restritas à mata atlântica e 2 à caatinga. O albatroz Thalassarche melanophris tem distribuição localizada e o passeriforme Herpsilochmus pectoralis está na lista de ameaçados. Aproximadamente 450 espécies de aves são esperadas ocorrer, 95 ameaçadas. A maioria das 36 espécies de mamíferos não voadores, mais 22 morcegos, é da mata atlântica e caatinga ou tem distribuição mais ampla. Nas listas de conservação estão o morcego Chiroderma doriae da mata atlântica, os macacos guigós Callicebus coimbrai da mata e C. barbarabrownae da caatinga, e o macaco-prego Cebus xanthosternos. As espécies de mamíferos de provável ocorrência são 124, endêmicas da caatinga 3, da mata atlântica 4. São apresentados comentários sobre áreas de mata atlântica e caatinga para futuros estudos ecológicos e inventários sobre biodiversidade.

Increasing human population size is increasing the demand for resources like timber, oil, tea, coffee, and other crops. Plantation crops mimic some aspects of native habitats, and there are studies that report the presence of some native anuran biodiversity in plantations. I focused on tea plantations in the Western Ghats-Sri Lanka Biodiversity Hotspot and studied the diversity and health of anurans in different habitats found within a tea cultivation area, near Munnar region in the Western Ghats, India. The landscape includes tea bushes, native evergreen shola forest patches, and eucalyptus forest stands. I reviewed 40 studies comparing amphibian species richness in plantations and primary forests. The age of the plantation, type of plantation, presence in a biodiversity hotspot, number of species in the dominant plantation type, number of species in the paired forest habitat, and latitudinal zone of the study, did not correlate with species richness, but plantations that had periodic harvesting had higher species richness than plantations that practiced clear-cut harvesting. I tested different methods of standard amphibian sampling in the field season 2012 in Munnar, and found that Visual Encounter Surveys (VES) in the shola habitat and Stream Transects (ST) were the most efficient. Using the VES and ST methods, I sampled amphibians in three upland habitats (tea, shola, and eucalyptus) at four different sites, and 150m of stream transects at each site, for two consecutive monsoon seasons. Fourteen species were encountered in both years and the community structure was similar across the years. The community structure at the four sites that was driven by the presence of exclusive species at each site and species composition in streams was similar across the landscape and was driven by the presence of similar species in streams across the four sites. Two hundred and sixteen anurans of 17 species, were tested for the presence of the lethal fungus Batrachochytrium dendrobatidis. The preliminary results from the Polymerase Chain Reactions were negative. My study provides baseline data for anuran diversity, composition, and health in the Munnar region of India and results of this project can be compared with tea plantations around the world.

The aims of this thesis are to (1) analyze the predictability (indicators) of plant and fungal species diversity in old-growth forests, and (2) assess the history and biodiversity of woodland key habitats (WKHs) and their potential to maintain species diversity in fragmented boreal forest landscapes.

Predictability was explored in Granlandet nature reserve, an unexploited landscape composed of discrete old-growth Picea forest patches of varying size isolated by wetland, reflecting conditions of insular biota at stochastic equilibrium. Data from 46 patches (0.2-12 ha) showed that most species were rare. However, species richness and composition patterns exhibited a high degree of predictability, which strengthen the possibility to apply biodiversity indicators in old-growth forest stands. Area was a key factor. The increase in species richness starts to level out at 2-3 ha. Large patches host more Red-list species in their interiors than do small ones, i.e. stand size is an important qualitative aspect of old-growth habitat. Nestedness emerged in relation to area but also in equal-sized plots. Structural complexity and habitat quality were important for species richness and compositional patterns, and small habitats of high quality could harbor many rare species. Monitoring of wood-fungi on downed logs showed that species diversity on downed logs changed over periods of 5-10 years and that the occurrences of annual species were unpredictable. It is suggested that monitoring of species with durable fruit bodies (mainly polypores) is likely to be a feasible approach to obtain comparable data over time.

Assessments of biodiversity of WKHs were performed in two areas with contrasting histories of forest exploitation, namely in south boreal and north boreal Sweden. Analyses of the history of 15 south boreal WKHs showed that fire-suppression, selective logging until mid-20th century and abandonment by modern forestry has shaped their forest structure. These WKHs are not untouched forests, they lack key structural components and harbor few Red-list species. Artificial interventions to restore natural processes and patterns are needed to further increase their suitability for threatned species. Modeling analyses of species richness in 32 WKHs in north boreal Sweden, some of which have not been isolated by modern forestry until recently, indicated an excess of crustose lichen species, i.e. WKHs may face delayed species extinctions. By contrast, the results indicate that wood-fungi have tracked the environmental changes. Differences in substrate dynamics between epiphytes on living trees and species growing on decaying logs may explain the diffeence between species groups. The results indicate that population densities of Red-list species were low, which may result in further depletion of species diversity.

Continuing species declines and extinctions are likely if not conservation of WKHs are combined with other considerations in th managed forest landscape. Both WKHs and their surroundings must be managed and designed to maintain biodiversity over time. For a successful future conservation of boreal forest biodiversity monitoring of WKHs must be combined with monitoring of refeence areas.

Understanding biological responses to climate change is a primary concern in conservation biology. Of the ecosystems being rapidly impacted by climate change, those in the high-elevation tropics are among the most poorly studied. The tropical Andean biosphere includes record elevations above 5000 meters, where extreme environmental conditions challenge many organisms. In the Cordillera Vilcanota of southern Peru, frogs including Pleurodema marmoratum and Telmatobius marmoratus have expanded their ranges to 5244 – 5400 m into habitats created by glacial recession, making them among the highest recorded amphibians on Earth. To understand how hydrologic alterations from loss of glacial meltwater and climatic fluctuations affect these amphibians, I conduct a 36-month field study of reproductive phenology and develop a method to distinguish glacial meltwater-fed ponds and precipitation-fed ponds utilizing natural variation in stable isotopes of water (18O, 2H, and d-excess). My results suggest that some ponds critical for breeding populations may have lost their connection to glacial runoff. Ongoing deglaciation may transform these ponds from permanent to ephemeral habitats, leading to the extirpation of the fully aquatic species, T. marmoratus. The 2015/2016 El Niño delayed the onset of the 2015 wet season and shortened the P. marmoratum breeding and tadpole development period in ephemeral ponds. I examine regional patterns of amphibian occupancy and prevalence of the deadly amphibian pathogen Batrachochytrium dendrobaditis in unexplored high-elevation zones that were until recent decades covered by permanent ice. Next, I examine adaptive strategies that allow these two frog species to persist in the harsh high-elevation environment. Pleurodema marmoratum withstands the daily freeze-thaw cycle by utilizing a wide thermal tolerance range (from below 0ºC to CTmax > 32ºC) and I report the first evidence of frost tolerance in a tropical frog. My research compares divergent strategies allowing two anuran species to persist through disease and variable, extreme conditions in high-mountain environments, providing a better understanding of responses to and consequences of climate change for some of the world's highest life forms.

Roads pose two central problems for wildlife: wildlife-vehicle collisions (WVCs) and habitat fragmentation. Wildlife exclusion fencing can reduce WVCs but can exacerbate fragmentation. In Chapter 1, I summarize the relevant studies addressing these two problems, with a focus on large mammals in North America. Chapters 2 and 3 summarize field assessments of technologies to reduce WVCs and maintain connectivity, specifically jumpout ramps and underpasses, along Highway 101 near San Luis Obispo, CA. In a fenced highway, some animals inevitably breach the fence and become trapped, which increases the risk of a wildlife-vehicle collision. Earthen escape ramps, or “jumpouts”, can allow the trapped animal to escape the highway corridor. Few studies have quantified wildlife use of jumpouts, and none for >2 years. We used wildlife cameras to quantify wildlife use of 4 jumpouts from 2012-2017. Mule deer were 88% percent of our detections and jumped out 20% of the time. After accounting for pseudoreplication, 33% of the events were independent events, and 2 groups of deer accounted for 41% of all detections at the top of the jumpout. Female deer were 86% of the detections and were much more likely than males to return to the jumpout multiple times. This is the first study to document use of jumpouts for more than 3 years, the first to account for pseudoreplication, and the first to quantify differences in jumpout use between male and female mule deer. We recommend a jumpout height between 1.75m-2m for mule deer to increase the jumpout success rate. Chapter 3 addresses factors that may affect the use of undercrossings by mule deer and other wildlife. Wildlife crossings combined with wildlife exclusion fencing have been shown to be the most effective method to reduce wildlife-vehicle collisions while maintaining ecological connectivity. Although several studies have quantified wildlife use of undercrossings, very few have exceeded 24 months, and the factors affecting carnivores use of the undercrossings remain unclear. We quantified mule deer, black bear, mountain lion, and bobcat use of 11 undercrossings along Highway 101 near San Luis Obispo, California from 2012-2017. We constructed zero-inflated Poisson general linear models on the monthly activity of our focal species using underpass dimensionality, distance to cover, substrate, human activity, and location relative to the wildlife exclusion fence as predictor variables. We accounted for temporal variation, as well as spatial variation by quantifying the landscape resistance near each undercrossing. We found that deer almost exclusively used the larger underpasses whereas the carnivores were considerably less selective. Bears used undercrossings more that were within the wildlife exclusion fence, whereas mountain lion activity was higher outside the wildlife exclusion fence. Bobcat activity was highest and most widespread, and was negatively associated with distance to cover. Regional connectivity is most important for bear and mountain lion, and the surrounding habitat may be the most important predictor for their use of undercrossings. We recommend placing GPS collars on our focal species to more clearly document fine-scale habitat selection near the highway.

Terrestrial ecosystems in the southeastern United States have evolved with fire as a common disturbance and as a result many natural communities require the presence of fire to persist over time. Human development precludes natural fires from occurring within these communities; however, prescribed fire is considered to be a critical tool in the effort to restore fire-dependent ecosystems after decades of fire exclusion. Direct effects of fire on individual floral and faunal species as well as benefits to biodiversity at the landscape (gamma diversity) level have largely been supported in previous research. However, information on the effects of natural and prescribed fire on plant diversity at the local level (alpha diversity) is limited, particularly for southeastern forests. The applicability of the Intermediate Disturbance Hypothesis (IDH), which suggests that the highest levels of biodiversity are found at intermediate levels of disturbance, is also untested for North Florida upland plant communities. This study compared the effects of fire on local scale mean plant species diversity by examining burned and unburned portions of three fire-dependent communities to determine if there is an effect of prescribed fire on in alpha biodiversity. Alpha biodiversity was not significantly different (p=0.433) between burned and unburned fire-dependent plant communities in northern Florida, suggesting that prescribed fire does not affect plant species diversity in these communities and/or the IDH for plant communities is not supported at the time scale tested. However, the application of prescribed fire did result in changes in abundance of species, particularly with species such as Dicanthelium acuminatum, Quercus myrtifolia, and Vaccinium myrsinites, that respond positively to fire, which may have implications for associated faunal diversity.

Numerous causes have been implicated in contributing to amphibian population declines since the 1980's, with habitat modification, ultraviolet radiation (UV-B) and environmental contaminants (such as glyphosate-based herbicide) being among the most common. This study identifies the effects of a generic glyphosate-based herbicide (GLY- 4 Plus) on mortality, immune function, body condition, and morphological plasticity of larvae of the spotted salamander (Ambystoma maculatum) under conditions that reflect open and closed canopy light regimes. Larval salamander responses to glyphosate-based herbicide varied depending on UV-B conditions. In general, it appears that an open canopy (i.e. greater UV-B exposure) may confer fitness benefits. In the presence of herbicide, survival was higher in an open canopy UV-B regime and pooled open canopy survival was higher than that of closed canopy treatments. In the absence of herbicide, body condition and immune function were positively related with amount of UV-B. Finally, herbicide presence appeared to affect morphology under low UV-B conditions. UV-induced breakdown of surfactant or a complex interaction between temperature stratification and trophic relations is potentially responsible for the observed patterns in survival and body condition. However, the mechanistic underpinnings of improved immune function and morphological differences are less clear. As deforestation is likely to continue, amphibians may find themselves in ponds with increasingly open canopies. Combined with the knowledge that some amphibians can become locally adapted to UV exposure and develop pesticide tolerance, the probability of surviving exposure to this herbicide may be elevated in open canopy ponds. These results emphasize the complexity of natural systems and the importance of including multiple factors in experiments.

Honeybees (Apis mellifera) are important pollinators of many plant species and are employed globally for crop and honey production. However, little is known about the effects of this species on native pollinator and plant species in areas to which they have been introduced; and previous research has not been able to reach a general consensus as to the type of impact honeybees have on pollination systems. In addition to the effects of exotic pollinators, the loss and fragmentation of natural habitats is also of major concern to the continuing diversity of pollinators and plant populations. Here, the impact of honeybee density on other pollinator guilds, and levels of remaining pollen and nectar standing crop among 18 patches of the New Zealand native shrub – manuka (Leptospermum scoparium) is examined at three different regions within the North Island. The same sites were also used to test the reproductive capabilities of manuka and subsequent pollen limitation among patches. A further 11 sites were utilised to examine biodiversity via intercept and pitfall traps within manuka patches, and the patch variables driving taxa composition. Large fly (Diptera = 5 mm) abundance was negatively correlated with honeybee abundance and instances of physical disturbance of large flies by honeybees were observed. There was no significant correlation between honeybee abundance and other pollinator guilds. Nectar was a limiting resource for both honeybees and large flies, whereas, pollen was not a limiting resource among any of the major pollinating insect guilds. Pollination treatments revealed that manuka is partially self-compatible, but relies more heavily on cross pollination for higher yields of capsule and seed set. Pollen limitation did not occur significantly at any of the sites. A total of 159 Coleoptera, 125 Diptera, 131 Hymenoptera morphospecies, and 50 other groups of taxa from various orders were collected among sites. Invertebrate richness was higher at lower altitudes and litter invertebrate richness was significantly higher with an increase in the proportion of manuka cover. There were distinct differences in taxa composition between the three regions, with plant community composition and altitude the most significant factors. Patch size also played a part, but a lack of overall variation in patch sizes may understate the effect this has on insect composition. Overall, honeybees are competing for nectar resources and displacing large flies as a consequence; however, capsule and seed set among manuka patches did not significantly suffer as a consequence. Regional variation in patch characteristics such as altitude, plant community composition, patch size, proportion manuka cover, and plant evenness appear to be influencing insect composition found within manuka patches to varying degrees. Further investigation into the impact of patch size and patch connectivity is also warranted.

I studied water bird use of two lakes in the Claremont-Upland area to determine what physical, chemical, and biological aspects of these lakes provide suitable water bird habitat and food resources. I censused the Bernard Field Station Lake in Claremont and a gravel pit freshwater area in Upland from 10/85 to 3/86 for water bird use. I also mapped these sites, noted their water surface area and water depth changes, monitored their water chemistry, and censused their vegetation. The results of this work showed more total water birds per hour of observation time, and more birds per hour of observation time of each food preference type, at the Upland Lakes than at the BFS Lake, except for diving ducks, which I found at both sites in similar abundance, and coots, which I found at the BFS Lake in greater abundance than at the Upland Lakes. The Shannon-Weiner Index of Diversity, H', used to determine bird species diversity, was higher for most individual census dates and on average, at the Upland Lakes than at the BFS Lake. The Upland Lakes had fewer species and less abundance of true aquatic plants than the BFS Lake; however, the BFS Lake had fewer different types of habitat (i.e. open shoreline, thick emergent shoreline vegetation, mudflats, grassy areas, etc .) than did the Upland Lakes. The Upland Lakes, although originally very similar to the BFS Lake in total water surface area, came to have four times the water surface area of the BFS Lake as time progressed, due to winter rainfall and runoff. The results of bird censuses also showed many more migrant than resident birds using the Upland Lakes area, while few migrant birds used the BFS Lake. Water bird use differences between these sites are the resuIt of the interaction of the unique ecological factors of each site. The Upland Lakes provide more diverse habitats, greater water surface area, a more accessible, open, isolated location for stopovers for migratory birds than the BFS Lake provides. The BFS Lake provides only two major habitat types for water bird use: thick shoreline emergent vegetation (mostly cattails), and open water. Diving ducks and coots utilize these habitats well and thus, with the exception of migratory flocks of diving ducks, used the BFS Lake as frequently, or more frequently than they used the Upland Lakes. Other birds that forage in muddy, open shore or grassy, open shore areas preferred the Upland Lakes area (dabbling ducks and shorebirds). Additional observation of similar water area in Claremont, Upland, and Montclair, California could produce a larger data base to demonstrate conclusively such tentative findings of this study as size of water surface area being directly proportional to amount of migratory bird use.

The resilience of coral reefs depends, among others, upon local physical and biological characteristics. This dissertation focused on how herbivory, structural complexity, and sedimentation can impact the structure, function, and, ultimately, resilience of Caribbean coral reefs. We filled an important knowledge gap related to trophic niche and ecological roles of surgeonfishes (A. coeruleus and A. tractus), two of the most important herbivorous fishes in the Caribbean. We showed that both species feed primarily on turf algae preventing further progression of algal succession while A. tractus may also help reduce macroalgal abundance by targeting common macroalgal species such as Dictyota spp. We used a factorial experiment to analyze the interactive effects of herbivory (exclosure vs. open plots) and reef structural complexity (vertical vs. horizontal substrate orientation), on the development of benthic communities. We found that vertical substrates were quickly dominated by crustose algae regardless of herbivory treatment while succession of horizontal substrates was determined by herbivory. Our results suggest that at small scale, reef complexity is a major factor determining algal community structure. We investigated why, despite high levels of herbivory, coral cover in South Florida has failed to recover. We surveyed benthic composition, grazing and abiotic characteristics along six spur and groove reefs in the Florida Keys. Using boosted regression tree analyses, we found that sediment abundance was the best predictor of both juvenile and adult corals, which could explain the failure of coral recovery. We studied spatial and temporal changes of reef communities of reefs in Havana, Cuba where global and local stressors have affected coral communities while overfishing and nutrient enrichment has led to low herbivory levels. Our surveys revealed a region-wide high abundance of algae (~60%) as a consequence of heavy overfishing with likely negative consequences on coral recovery. In summary, my dissertation showed context-depend effects of herbivory, structural complexity, and sediment on Caribbean coral reefs. While reduction of herbivory can often suppress coral recovery, on coral reefs with robust herbivore populations, physical factors such as structural complexity and sediment may still limit coral recovery and fundamentally impact reef resilience.

‘Aigarchaeota’, a deeply branching lineage in the domain Archaea with no cultivated representatives, includes both thermophilic and hyperthermophilic microorganisms that reside in terrestrial and marine geothermal environments. The ‘Aigarchaeota’ consists of at least nine proposed genus-level groups that have been confirmed via 16S rRNA sequencing, with ‘Aigarchaeota’ Group 1 (AigG1) being the focus of this study. Based on cultivation-independent genomic data available from several AigG1 members in Great Boiling Spring (GBS), NV, and Yellowstone National Park, 22 different types of growth media were designed and tested for their ability to support growth of AigG1. One of these cultures, G1-10, was found to contain AigG1 at ~5% abundance, as well as other novel thermophilic microbial groups including a new species of the genus Pyrobaculum, members of the candidate phyla ‘Calescamentes’ and ‘Fervidibacteria’, and the novel archaeal lineage NAG1 (‘Geoarchaeota’). To attempt to obtain pure cultures of AigG1 and other novel thermophiles, a single-cell sorting system using an optical trap and a microfluidic device was constructed. The system was validated by sorting E. coli cells, which demonstrated that single, viable cells could be reliably obtained. Using this single cell sorting device on the G1-10 culture, a pure culture of a member of the genus Pyrobaculum was obtained, which was shown to represent a distinct species in this phylum by whole genome sequencing and in silico DNA-DNA hybridization. Additionally, a pure culture of the first representative of the candidate phylum ‘Fervidibacteria’ from an enrichment culture derived from G1-10. Additionally, to aid in morphology-based sorting of AigG1 and stable isotope labeling studies, fluorescence in situ hybridization (FISH) based on catalyzed reporter deposition (CARD-FISH) were developed and an AigG1-specific probe was tested. CARD-FISH was successfully used to detect AigG1 in both the G1-10 culture and in natural sediment samples from GBS. Stable isotope labeling incubations were performed with a variety of 13C-labeled substrates (bicarbonate, amino acids, sugars, and short chain fatty acids) on GBS sediments and G1-10 culture samples, and CARD-FISH was used to specifically detect AigG1 in the fixed samples. Nanometer-scale secondary-ion mass spectrometry (nano-SIMS) will then be used to determine whether AigG1 was capable of taking up the different carbon substrates tested. Overall, the results and accomplishments from this project and follow up nano-SIMS analysis will allow a better understanding of the metabolic potential of AigG1 and will aid future efforts to attempt to obtain pure cultures of this novel lineage.

Biodiversity conservation throughout the world is challenged by the impacts of a changing climate on fragmented landscapes. To mitigate these threats, conservation managers require models which can demonstrate the consequences of both negative impacts and management actions. This need can be addressed through spatial modelling applications. Unfortunately, throughout much of the world, spatial modelling is forgone, being seen as requiring skills and resources beyond the means of many conservation planners and managers. This thesis seeks to address this dilemma by delivering criteria for a successful modelling application and by providing case studies which demonstrate how appropriate modelling can be undertaken without highly specialised skills or prohibitively expensive software and equipment. In this way it facilitates the delivery of better targeted and, consequently more effective, management actions. For my case studies I have used the south-western corner of Australia as a demonstration landscape. This region is recognised internationally as a “biodiversity hotspot,” not only for the biological richness and uniqueness of species but also for the level of threat to which they are subject. Like many landscapes throughout the world, much or this region’s natural biota exists in fragmented, fragile and degraded patches and is therefore highly vulnerable to the anticipated impacts of anthropogenic global warming. In this thesis I have: 1) examined the principles of spatial modelling and reviewed how spatial modelling has been applied to conservation management in this region, 2) conducted examples of different forms of spatial modelling using actual regional conservation management issues, and 3) demonstrated how these examples can be incorporated into conservation management planning. My key findings are: Spatial modelling provides users with an opportunity to effectively test hypotheses, thereby informing the planning process and improving conservation outcomes. Where spatial modelling is omitted from the process, knowledge gaps are often addressed by the axiomatic and by assumption. This is contrary to the principles of effective adaptive management. Modelling tools are inherently more effective when selected for their capacity to meet a planning objective rather than where projects are tailored to meet a model’s capacity. The coordinated use of multiple tools can often provide a more robust understanding of the consequences impacts and mitigating actions. All tools and data sets used should be utilised with a clear and acknowledged understanding of their suitability, strengths and limitations. A wide range of spatial modelling tools (and data sets) are freely and readily available to conservation managers. Most of these come with excellent tutorials and support services. Data gaps can often be addressed through targeted field observations, obtained through complimentary planning processes, or synthesised from accessible data sets. There is a very large body of peer reviewed literature demonstrating means by which others have applied existing modelling tools, or developed tools themselves, to meet a wide range of applications. Accessing this literature is an excellent means of building spatial modelling capacity. New and improved tools, methodologies and data sets are constantly being developed. A failure to implement effective spatial modelling is becoming increasing difficult to justify.

Phylogeography aims to understand the processes that underlie the distribution of genetic variation within and among closely related species. Although the means by which this goal might be achieved differ considerably from those that spawned the field some thirty years ago, the foundation and conceptual breakthroughs made by Avise are nonetheless the same and are as relevant today as they were two decades ago. Namely, patterns of neutral genetic variation among individuals carry the signature of a species’ demographic past, and the spatial and temporal environmental heterogeneity across a species’ geographic range can influence patterns of evolutionary change. Aquatic systems throughout Mexico provide unique opportunities to study phenotypic plasticity and evolution in relation to climatic and environmental selective forces. There are several unique, often isolated aquatic environments throughout Mexico that have a history of geographic isolation and reconnection. The first study presented herein shows significant mitochondrial sequence divergence was also discovered between L. megalotis populations on either side of the Sierra de San Marcos that bisects the valley of Cuatro Ciénegas and that the populations in the valley are genetically distinct from those found outside of the valley. The second study recovered signals of two divergence events in Cuatro Ciénegas for six codistributed taxa, and reveals that both events occured in the Pleistocene during periods of increased aridity suggesting that climatic effects might have played a role in these species’ divergence. The final study presents an Illumina-based high-resolution species phylogeny for Astyanax mexicanus providing added support that there are multiple origins to cave populations and further clarifying the uniqueness of the Sabinos and Rio Subterráneo caves.

Novel ecosystems emerge from alterations to historic abiotic regimes and contain new species combinations. Everglades canals offer an opportunity to understand the function of novel habitat for native and non-native fishes and how novel conditions in turn influence distribution, abundance and assembly patterns. I examined native and non-native fish assemblages collected across a gradient in novelty, defined by the loss of wetland connectivity and habitat complexity. As novelty increased, native species richness and abundance strongly declined, and the contribution of non-natives increased. Community structure vastly differed among canals and was strongly influenced by spatial factors and secondarily by hydrological factors. Natives and non-natives had opposing responses to key hydrologic and habitat parameters. This study represents the first comprehensive assessment of Everglades canal fishes, providing insight into the factors influencing native and non-native abundance and assembly patterns and contributing to our understanding of this novel but permanent habitat.

Shallow sheltered Baltic Sea bays are ecologically important habitats that harbour a unique vegetation community and constitute vital reproduction areas for many coastal fish species. Knowledge about the invertebrate community in these bays is, however, limited. This thesis examines the macroinvertebrate community in shallow sheltered Baltic Sea bays and how it is affected by: (1) the natural morphometric isolation of bays from the sea due to post-glacial land uplift; and (2) differences in vegetation types. The invertebrate biomass and number of taxa was found to decrease with increased bay isolation. The taxon composition changed from dominance by bivalves and gastropods in open bays to a community composed of a larger proportion of insects in isolated bays. Stable isotope analysis indicated epiphytes and periphyton as the major energy resources for most of the examined consumers, but the relative importance of these in relation to larger plants decreased for some consumers with increased bay isolation. A comparison of invertebrate abundance between plants revealed a close relationship with morphological complexity of the plants. More complexly structured plants had higher invertebrate abundance than plants with simpler morphology. The results suggest that management of these coastal habitats should be dynamic and take into consideration the natural change in invertebrate community resulting from the slow bay isolation process. In addition, the results imply that changes in the aquatic vegetation due to anthropogenic influences could induce changes in the invertebrate community as the plant habitat structure is altered. A changed invertebrate community may in turn affect higher trophic levels since invertebrates are important food for many fish and waterfowl species.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 4: In press.

The study evaluated the effects of herbivory pressure, nutrient availability and potential propagule supply on recruitment and succession of coral reef macroalgal communities. Recruitment and succession tiles were placed in a nutrient-herbivory factorial experiment and macroalgal abundances were evaluated through time. Proportional abundances of macroalgal form-functional groups on recruitment and succession tiles were similar to field established communities within treatments, evidencing possible effects of adult macroalgae as propagule supply. Macroalgal abundance of recruitment tiles increased with nutrient loading and herbivory reduction combined whereas on succession tiles nutrient loading increased abundance of articulated-calcareous only when herbivores were excluded. Macroalgal field established communities were only affected by herbivory reduction.

Explosive compounds are broadly distributed across the globe as a result of nearly two centuries of munitions use in warfare and military activities. Two explosive compounds have seen disproportionate use; RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) and TNT (2-methyl- 1,3,5-trinitrobenzene), being the most commonly found explosives in the environment. The effects of explosives on biota have been studied in great detail; however, there is a general lack of understanding with regard to broader ecological impacts of these contaminants. My dissertation objective was to follow the impacts of explosive compounds on vegetation across scales. Impacts on vegetation at the species scale alter community composition via species-specific and age-specific responses to explosives. Results presented here showed that contaminated soils induced a variety of responses in vegetation, yet impacts to water relations were similar regardless of species. Use of novel metrics in monitoring plant responses to explosives compounds aided in delineation of reference and treatment groups. At the community scale the presence of explosives induced species and functional composition shifts. The observed shifts are likely due to physiological impairment as individuals in the field exhibited significant impacts to physiological functions. Effects of explosives contamination also detectable using remote sensing techniques. Impacts to plant morphology and physiology are directly related to community level shifts observed in long contaminated areas. This highlights the long lasting impacts that these largely overlooked contaminants can have on a system and opens avenues for new, at range, vegetation based contaminant detection systems.

Modern methods for managing pine (Pinus sylvestris) create homogenized forests. This decreases nature’s potential for biodiversity and might threaten species in need of different types of milieu. The main purpose of this study was to investigate how important older pine trees are for biodiversity. In the Hall-Hangvar Reserve in the north-west part of Gotland, insects collected from traps showed that more species were found in old or dead trees compared to younger pine trees. A statistically significant difference was found for Coleoptera (beetles). The taxons of greatest interest for this study were Coleoptera and Hymenoptera (wasps). Certain families of Hymenoptera use ducts made by larvae from some families of Coleoptera.These larvae also serve as prey. Relevance concerning enviromental importance to species and diffrenences in inhabiting the three stages of pine trees was of importance.

The Florida Reef Tract (FRT) extends from the tropical Caribbean up the southeast coast of Florida into a temperate environment where tropical reef assemblages diminish with increasing latitude. This study used data from a three-year comprehensive fishery-independent survey to quantify reef fish spatial distribution along the Southeast FRT and define where the assemblage shifts from tropical to temperate. A total of 1,676 reef fish visual census samples were conducted to assess the populations on a stratified-random selection of sites of marine hardbottom habitats between the Miami River and St. Lucie inlet. Multivariate analyses were used to investigate differences in assemblages among sites. Depth (m), general habitat (reef or hardbottom), and slope (high or low) strata were examined to explain the dissimilarities between assemblages. A general trend of cold-tolerant temperate fish dominated the northern assemblages and more tropical species dominated further south. Seven reef fish assemblage biogeographic regions were determined. In shallow habitats the data clustered in three spatial regions: One south of Hillsboro inlet, one in Northern Palm Beach south of Lake Worth inlet, and one north of Lake Worth inlet. The assemblage in deep habitats mainly split in close proximity to the Bahamas Fracture Zone south of Lake Worth Inlet. The presence of reef habitat aided in splitting the southern assemblage regions from the northern all-hardbottom assemblage regions in both the shallow and deep habitats. Substrate relief was significantly correlated with the differences in the northernmost deep assemblages but did not appear to affect the remainder of the shallow and deep assemblages. This bioregional study creates a baseline assessment of reef fish assemblages of the Southeast FRT for future analyses.

Através da amostragem de 28 sítios em diferentes estádios de regeneração em uma área de Mata Atlântica contínua, procuramos nesta dissertação contribuir para o entendimento dos mecanismos relacionados às mudanças faunísticas observadas durante o processo de regeneração em florestas tropicais, e, assim, melhor compreender o valor das florestas secundárias para a conservação da biodiversidade tropical. Para isso, na primeira parte da dissertação investigamos a influência da regeneração sobre características de estrutura da floresta e disponibilidade de alimento consideradas importantes para diversos grupos da fauna. Encontramos maior profundidade do folhiço, volume de galhadas e disponibilidade de frutos de uma abundante palmeira de sub-bosque nas florestas mais maduras, enquanto que nas áreas em estádio mais inicial de regeneração encontramos maior conexão da vegetação, biomassa de artrópodes no solo e disponibilidade de frutos no total e da espécie de planta mais abundante no sub-bosque. Essas modificações podem estar relacionadas às mudanças na fauna observadas durante a regeneração florestal. As espécies que dependem de características só encontradas nas matas mais maduras, como espaços abertos para movimentação, maior complexidade do chão da floresta, ou determinados recursos alimentares poderiam encontrar limitações em áreas em estádios mais iniciais de regeneração, ao passo que espécies que não dependem desses recursos poderiam se beneficiar da maior disponibilidade total de alimentos, ou da maior conexão da vegetação para movimentação, encontradas nessas áreas. Na segunda parte do trabalho, avaliamos a influência da regeneração e de características estruturais e de disponibilidade de alimento sobre espécies endêmicas (especialistas de floresta) e não-endêmicas (generalistas de habitat) de pequenos mamíferos terrestres. Como previsto, observamos que um grupo de espécies (generalistas de habitat) prolifera nas áreas mais jovens, enquanto que o outro grupo (especialistas de floresta) foi mais comum, embora de maneira mais sutil, nas áreas mais maduras. Esses padrões foram em parte explicados pelas variáveis mensuradas, principalmente a disponibilidade de recursos alimentares. Aparentemente, as espécies generalistas estão se beneficiando da maior disponibilidade de alimentos encontrada nas áreas em estádio mais inicial de regeneração, enquanto que as especialistas possuem maior capacidade de ocupação das áreas mais maduras, onde esses recursos são mais escassos. Portanto, esses resultados sugerem um compromisso (trade-off) entre capacidade competitiva e capacidade de utilização de recursos 101 abundantes, como prevê o mecanismo de nicho sucessional, proposto inicialmente para explicar a sucessão de espécies vegetais. As características encontradas nas florestas mais jovens favoreceram a proliferação de espécies de pequenos mamíferos terrestres generalistas de habitat. Entretanto, o efeito positivo da regeneração florestal sobre as espécies especialistas, de maior interesse para a conservação, foi menos acentuado, de forma que as florestas secundárias abrigaram uma assembléia de pequenos mamíferos terrestres rica, podendo, portanto, representar um importante instrumento de aumento de área e conectividade em paisagens altamente modificadas, como as encontradas na Mata Atlântica. Entretanto, esses resultados não reduzem o valor das florestas maduras, principalmente em paisagens fragmentadas e para grupos mais sensíveis da fauna. Essas florestas devem ser protegidas, assim como deve ser garantida (e se preciso auxiliada) a regeneração das florestas secundárias, para que possam adquirir em longo prazo as condições necessárias à manutenção das espécies e dos grupos de espécies da fauna mais severamente afetados pela secundarização das florestas tropicais.
By sampling 28 sites in different regeneration stages in a continuous Atlantic forest area, in this master thesis we aimed to contribute to the understanding of the mechanisms associated with the wildlife changes observed during tropical forest regeneration, and thereby better understand the value of secondary forests for the conservation of tropical biodiversity. In the first part of the thesis we investigated the influence of regeneration on aspects of forest structure and food availability considered to be important to several wildlife groups. We found deeper leaf litter, and higher woody debris volume and fruit availability of an abundant understorey palm in the older-growth areas, while in areas in earlier stages we found higher vegetation connection, higher ground-dwelling arthropod biomass, total fruit availability, and availability of fruits of the most abundant understorey plant species. These modifications may be related to the wildlife changes observed during forest regeneration. Species that rely on features only found in older-growth forests, such as open space for movement, higher complexity of the forest floor, or certain food resources, could find limitations in younger forests, whereas species which do not depend on these resources could benefit from the higher total food availability, or higher 102 vegetation connection for movements, found in these areas. In the second part of the study, we assessed the effect of regeneration and of structural attributes and food availability on endemic (forest specialist) and non-endemic (habitat generalist) terrestrial small mammal species. As expected, we found that a group of species (habitat generalists) proliferate in younger areas, while the other group (forest specialists) is more common, although more subtly, in older-growth areas. These patterns were partly explained by the measured variables, especially food availability. Apparently, the generalist species are benefiting from the increased food availability found in younger forests, while specialist species have greater ability to occupy older-growth areas, where these resources are scarcer. Therefore, our data suggest a trade-off between competitive ability and ability to use abundant resources, as predicted by the successional niche mechanism, initially proposed to explain the succession of plant species. The characteristics observed in younger forests favored the proliferation of habitat generalist terrestrial small mammals. However, the positive effect of forest regeneration on specialist species, of more conservation concern, was less pronounced, so that the secondary forests harbored a rich terrestrial small mammal assemblage, and may therefore be an important tool to increase the area and connectivity in highly modified landscapes, such as those found in the Atlantic forest. However, these results do not diminish the value of old-growth forests, especially in fragmented landscapes and for more sensitive wildlife groups. These forests should be protected, as well as the regeneration of the secondary forests should be guaranteed (and assisted, if necessary), so that these areas could acquire in the long term the necessary conditions to maintain the species and the groups of species most adversely affected by the secondarization of the tropical forests.

This project is comprised of a creative work and accompanying exegesis. The creative work is a collection of poetry which examines the history and ecology of the wetlands and river systems of the Swan Coastal Plain, and which utilises the practice of walking as a research methodology. For the creative practitioner walking reintroduces the body as a fundamental definer of experience, placing the investigation centrally in the corporeal self, using the physical senses as investigative tools of enquiry. As Rebecca Solnit comments in her history of walking, ‘exploring the world is one of the best ways of exploring the mind, and walking travels both terrains’ (Solnit, 2000, p. 13). The context for my poetic walking project Swamp, is a local and global environment undergoing an unprecedented loss of biodiversity, mainly due to the destruction of habitat and changes in climatic conditions (Reid, Partha Dasgupta, Robert M. May, A.H. Zakri, & Henk Simons, 2005, pp. 438-442). The loss of species and ecosystems that have been a part of our earth home results in the human experience of ‘homesickness’ — a longing for the home places that we have known and which have diminished or disappeared. Before the arrival of the British colonists in 1829, the Swan River and adjacent wetlands were an integral part of the seasonal food source for the original inhabitants, the Noongar (Bekle, 1981). In addition wetland places were, and are, deeply embedded in the spiritual and cultural life of the Noongar people of the Swan Coastal Plain (O'Connor, Quartermaine, & Bodney, 1989). In less than two hundred years since the establishment of the Swan River Colony (Western Australia), the lakes and rivers of the Swan Coastal Plain have undergone extreme changes, often resulting in complete draining and in-filling of wetland areas as the city and its suburbs spread beyond the original town limits. This re–engineering of the landscape has had a dramatic and detrimental impact upon biodiversity, water quality and the sense of place experienced by residents. Swamp is a project that has three main facets: a) a body of original poetry which interprets the historical relationship between the British, European, and Chinese newcomers to Noongar country, and the wetlands lakes of the Swan Coastal Plain. The poetry contained in this thesis is copyright to the author, Anandashila Saraswati (Nandi Chinna). b)An essay which contextualises the project within the sphere of walking art, psychogeography, and the philosophical idea of ‘Homesickness’. c) A website, www.swampwalking.com.au, which displays photographs documenting the walks I have carried out over the three year period of the project from February 2009 to February 2012. The exegetical part of this project looks at the notion of ‘homesickness’ as a philosophical condition that can be seen as a motivating force in the practice of writing on walking. I use Debord’s theory of the dérive as a starting point for my walking methodology and examine nostalgia within the Situationist International (Debord, 1958) and subsequent psychogeographical movements. I also investigate the role of homesickness in the work of other writers who walk and who write about their walking practice. Finally I discuss homesickness in the epoch of the Anthropocene (Crutzen & Schwägerl, 2011), the era in which the earth’s biosphere is characterised by human interventions which have changed the meteorological, geological and biological elements of our earth home. In the Anthropocene, the wilderness view of nature needs to be re-evaluated. I posit that walking is a way of reconnecting with the physical landscape and building relationships with small wilds that exist in our home places, and that writing about the walking allows these relationships and encounters to ripple out to readers, contributing to and enabling the development of an ethic of care for ecosystems and beings other than human.

Benthic diatoms are valuable tools for biological monitoring and paleo-ecological reconstruction of past environmental conditions. This thesis aims at describing size-related properties of benthic diatoms and suggests that data assessment for community analysis can be improved by considering the importance of scale. It investigates which environmental factors structure epilithic diatom communities on the coast of the Gulf of Bothnia and identifies environmental factors correlated with phytobenthic biomass. It also contributes to the floristic knowledge of the Baltic Sea.

Diatom species show large variation in size. The responses of large species (≥1000 μm3) in diatom communities to environmental factors are underestimated if solely measured as relative abundance, as is the common practice. However, relative abundance gives the best gradient resolution, as compared to surface area and biovolume, if species are counted separately in two biovolume classes. Small and large species in the same community may respond differently to the same environmental factors.

To assess the principal environmental factors structuring diatom communities in the Gulf of Bothnia, 270 quantitative samples were collected from submerged stones. Sampling was carried out in spring in four areas of the Bothnian Bay, characterized by a stable north-south salinity gradient (0.4-3.3 psu), and in three areas of the Bothnian Sea which has a rather uniform salinity of ca. 5 psu. Canonical correspondence analysis (CCA) identified salinity and exposure to wave action as the principal factors structuring the diatom communities of the Bothnian Bay, whereas exposure to wave action was the principal factor in the Bothnian Sea. Measurements of relative ignition loss suggested that the cover of macroalgae, and thereby the higher abundance of epiphytic diatoms in the epilithic samples, was positively correlated with salinity in the Bothnian Bay and with water movement in the Bothnian Sea.

Two new brackish water species are described, Navicula sjoersii S. Busse & Snoeijs and N. bossvikensis S. Busse & Snoeijs. The new species are compared with N. perminuta Grunow, a common brackish-water species.

Seagrass populations are in decline worldwide. Zostera marina (eelgrass), one of California’s native seagrasses, is no exception to this trend. In the last 8 years, Morro Bay, California has lost 95% of its eelgrass. Eelgrass is an ecosystem engineer, providing important ecosystem services such as sediment stabilization, nutrient cycling, and nursery habitats for fish. The failure of recent restoration efforts necessitates a better understanding of the causes of eelgrass decline in this estuary. Previous research on eelgrass in California has demonstrated a link between population genetic diversity and eelgrass bed health, ecosystem functioning, and resilience to disturbance and extreme climatic events. The genetic diversity and population structure of Morro Bay eelgrass populations has not been assessed until this study. Additionally, we compare Morro Bay eelgrass to Bodega Bay eelgrass in northern California. We conducted fragment length analysis of 9 microsatellite loci on 133 Morro Bay samples, and 20 Bodega Bay samples. We found no population differentiation within the bay, and no difference among samples growing at different tidal depths. Comparison with Bodega Bay in northern California revealed that Morro Bay eelgrass contains three first generation migrants from a northern eelgrass population, but remains considerably genetically differentiated. Despite the precipitous loss of eelgrass in Morro Bay between 2007 and 2017, genetic diversity remains comparable to other populations on the west coast.

Introduced populations of Eichhornia crassipes (Pontederiaceae) possess extremely low levels of genetic diversity due to severe bottleneck events and clonal reproduction. While populations elsewhere have been well studied, North American populations of E. crassipes remain understudied. We used Amplified Fragment Length Polymorphism markers to assess genetic diversity and population structure in North American E. crassipes populations. Patterns of diversity over the past fifty years were analyzed using herbarium specimens. Furthermore, we sampled populations across the Gulf Coast of the United States throughout a year to determine contemporary genetic diversity and assess potential seasonal effects. Genetic diversity was found to be scant in the United States without population structure, agreeing with previous studies from other regions. Genetic diversity has remained consistently low over the past fifty years despite significant changes in selection pressure. However, evidence for and against population structure between seasons was found and the consequences of this are discussed.