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published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

MSc., Faculty of Science, University of the Witwatersrand, 2011 / Sodic soils are salt-affected soils which are high in sodium in relation to magnesium and calcium. Commonly called sodic sites in the Kruger National Park (KNP), these patches exhibit unique functional characteristics due to the high levels of sodium which cause surface crusting, cracking and the dispersion of clay particles. The aim of this study is to use satellite imagery to map sodic sites in the KNP at different spatial and spectral scales, giving the best option for a repeatable, semi-automated classification. The resultant map of sodic sites for the KNP will be used as a management tool and for future research projects. A field test for sodicity was necessary to collect sufficient ground truth samples for robust accuracy assessment of the image classification. Sodic soils are identified by measuring EC, pH and SAR which are highly variable within site and between testing methods, and therefore not useful for rapid ground truth classification of sodic soils in the field. The sodium level at which clay particle dispersion takes place varies between soils, but is measurable in the field using the Emerson dispersion test. Laboratory tested sodic soil sites from previous research re-tested in this study showed positive results for dispersion of clay particles in water. The physical properties of sodic sites described in the literature and observed in the field were applied to classify sodic sites in the KNP in the field using a decision tree, together with results from the dispersion test and the observed presence of the grass species Sporobolus iocladus. Landsat 7 and SPOT 5 imagery cover the whole park, with ASTER, CAO hyperspectral, LiDAR and black and white orthophotos available for selected areas. The topography elements of crest and footslope were derived from the STRM 90m digital elevation model (DEM). Image preprocessing to top of atmosphere reflectance was performed where necessary and visual enhancement techniques and transformations were applied to derive the normalised difference vegetation index (NDVI) and other indices. Spectral signatures were checked against spectral signature libraries, and the class separation was tested using the cluster analysis of spectral signatures. MODIS NDVI averages placed the imagery in phenological context. Object-based image analysis using eCognition was applied to classify the sodic sites of the Shingwedzi and Ripape River catchments. The input imagery was segmented into ecologically meaningful patches and classification accuracy was assessed using the field samples collected using the decision tree to identify four classes: sodic sites (bare and woody), river sand, riverine vegetation and savanna areas. Comparison of the accuracy assessments for the Shingwedzi study site showed that the Landsat 7 and SPOT 5 classification algorithms gave an overall kappa index accuracy of 89% and 78% respectively, and a sodic site kappa index of 90% and 89%. Validation results using the ground truth samples gave an overall kappa index accuracy of 61% for Landsat 7 and 52% for SPOT 5, with a sodic site kappa index of 49% and 39% respectively. The classification algorithms were applied to the Ripape study site for Landsat 7 and SPOT 5 with repeatable results for the SPOT 5 imagery of 88% overall kappa index and 81-93% kappa index for sodic sites using similar seasonal imagery in the wet to early dry season. The Landsat 7 classification algorithm was applied to the entire KNP based on the repeatability results of 56% overall kappa index and 60% sodic site kappa index for the Ripape site. The quest for a repeatable algorithm to classify sodic sites from satellite imagery has been met by the SPOT 5 imagery using scenes acquired at similar seasonal stages. The late wet season or early dry season imagery was used to apply the classification algorithm with the best success. Changes in size or shape of sodic sites over time requires very high resolution imagery and further studies to understand where the edge of sodic sites are detected from imagery, and how the phenology of the vegetation growing on these sites affects detecting any change in size of the sodic site.

<p><a>Natural enemy ecology strives to integrate the fields of disease ecology and community ecology to forge a broader understanding of how pathogens and predators structure communities. To advance this field, we need a greater emphasis on: 1) quantifying pathogen-mediated effects on community structure and comparing these effects to those observed with predators and 2) determining the interactive effects of combined natural enemies on communities. I conducted a mesocosm experiment designed to assess the individual and combined effects of predators (dragonfly larvae and adult water bugs) and a pathogen (ranavirus) on a larval amphibian community. Additionally, I conducted laboratory experiments to assess whether ranavirus exposure increases the vulnerability of tadpoles to predation. In my laboratory experiments, I found that virus exposure increased predation rates with dragonflies, but not water bugs. For tadpoles in the dragonfly treatments, the probability of survival for virus-exposed tadpoles was 66-77% lower compared to unexposed tadpoles. This data suggests that predators may selectively remove infected individuals from the population, which can enhance the magnitude of the healthy herds effect. I found that the risk level of the predators largely explained effects on the community. For instance, high-risk dragonflies reduce overall survival to 30% whereas low-risk water bugs only reduced survival to 67%. Additionally, I found that virus reduce survival to 62%, which was comparable to effect of the low-risk predator. Interestingly, all three natural enemies influenced community structure (i.e. species relative abundance) in unique ways. These results demonstrate that pathogens can have effects similar to predators on communities, and that natural enemy identity is important when considering impacts on community structure. When predators were combined with the virus, I found that mortality was relatively unchanged from the predator-only treatments suggesting less than additive effects of combined natural enemies. This result was driven by the healthy herds effect; the presence of dragonflies reduced overall infection prevalence in the community to 7% compared to 30% in the virus-only treatment. This effect was observed in the water bug treatments, to a lesser degree, suggesting that predator risk or efficiency contributes the magnitude of the effect. Collectively, my work demonstrates the importance of examining the individual and combined effects of natural enemies on ecological communities.</a></p>

It is increasingly recognized that individuals of the same species differ from each other and influence and respond to their environment in unique ways. This thesis deals with size variation among individuals that not only are of the same species but also of similar age. Such variation may develop even when individuals are born in the same environment, i.e. within a cohort. I have studied the sources and consequences of variation within and among cohorts from egg through early ontogeny using young-of-the-year (YOY) perch (Perca fluviatilis) as study organism. In agreement with predictions based on model results only taking exploitative interactions among individuals into account, I found that the broader the initial size distributions were, the more did the degree of size variation among individuals decrease over time. Still, with initially small size variation among individuals, in several experiments also size divergence was observed. Furthermore, size variation among individuals increased more under high compared to at low densities. Increased size variation over time may be explained by size-dependent diet shifts allowing for initially larger individuals to make an early diet shift when the first resource becomes limiting. However, as size divergence also was observed in situations with only shared resources available, it can be concluded that diet shifts are not a prerequisite for size divergence in young animal cohorts. Hence, I also suggest that mechanisms not related to competition for limiting resources, such as genetic variation, stochasticity and behavioural traits must be taken into account, especially when initial size differences are small. The importance of considering size variation among individuals within cohorts was demonstrated in a study of winter mortality in YOY perch cohorts. A large individual size in autumn was shown to increase overwinter survival within cohorts. However, late summer growth rather than average body size reached in autumn explained variation in overwinter survival between cohorts. Higher accumulation to lipid reserves and accordingly lower mortality over winter was observed in years with high growth rates late in the season. In another study I showed that apparent patterns of density-dependent growth can emerge among larval fish, but rather than a result of density-dependent resource limitation this was due to variation in size-selective predation pressure. Individuals in the right end of the size distributions grew in to a high predation pressure from cannibalistic perch when cannibal density was high, coinciding with high larval perch densities. Finally, as substantial size variation among individuals can develop within cohorts, also intra-cohort cannibalism can occur. Using a physiologically structured population model it was shown that the development of size bimodality within cohorts as a result of intra-cohort cannibalism is critically dependent on long hatching periods, high victim densities and density-dependent feedbacks on shared resources. / Det faktum att individer som tillhör samma art skiljer sig från varandra och påverkar och påverkas av sin omgivande miljö på ett unikt sätt tillskrivs allt större betydelse inom ekologin. Den här avhandlingen handlar framför allt om storleksvariation mellan individer som förutom att tillhöra samma art dessutom tillhör samma årsklass. Sådan storleksvariation kan till och med utvecklas mellan individer som föds och växer upp i samma miljö (inom en kohort). Jag har studerat orsaker bakom och konsekvenser av variation inom och mellan kohorter. Som studieorganism har jag använt mig av årsyngel av abborre (Perca fluviatilis). I överensstämmelse med förutsägelser baserade på en modell som enbart tar hänsyn till konkurrens om en gemensam resurs visade det sig såväl i ett dammexperiment som i en naturlig sjö att ju bredare den initiala storleksfördelningen var desto mer minskade graden av variation i kroppsstorlek mellan individer över tid. Å andra sidan, när den initiala variationen var relativt liten observerades i flera oberoende experiment även storleksdivergens över tid mellan individer. Variationen i storlek ökade särskilt i miljöer med höga tätheter av konsumenter (abborrar). För att förstå de bakomliggande mekanismerna av sådana täthetseffekter måste man ta hänsyn till den återkoppling som sker mellan antalet konsumenter och mängden resurser. Ökad storleksvariation över tid skulle kunna förklaras med storleksberoende dietskiften som tillåter individer med en initial storleksfördel att genomgå ett tidigt dietskifte samtidigt som tillgången av den första resursen begränsar övriga individers tillväxt. Eftersom storleksdivergens även observerades i situationer där enbart en delad resurs var tillgänglig kan man dock dra slutsatsen att dietskiften inte är en förutsättning för storleksdivergens inom kohorter. Jag föreslår därför också att mekanismer som inte är relaterade till konkurrens om en begränsad resurs, såsom inneboende variation mellan individer och variation i beteendemönster bör beaktas för att förklara uppkomsten av storleksvariation, speciellt i de fall då den initiala variationen är liten. De resultat som presenteras visar på betydelsen av att ta hänsyn till storleksvariation mellan individer. Storlek efter den första tillväxtsäsongen var viktig för att förklara vilka individer inom en kohort av årsyngel som överlever sin första vinter. För att förklara variation i vinteröverlevnad mellan kohorter (mellan år och sjöar) var däremot hög tillväxt sent på säsongen (oberoende av medelstorlek på hösten) avgörande. Högre ackumulering av fettreserver och lägre mortalitet inom kohorter av årsyngel under vintern observerades under år med hög tillväxt under den senare delen av tillväxtsäsongen. I en annan studie visade jag att mönster som tyder på täthetsberoende tillväxt kan uppkomma hos fiskyngel men att detta fenomen snarare än täthetsberoende resursbegränsning förklaras av variation i storleksberoende predationstryck. De större individerna inom kohorterna växte in i ett högt predationstryck från kannibalistiska abborrar när tätheten av kannibaler var hög, något som samkorrelerade med höga tätheter av yngel. Slutligen, då en hög grad av storleksvariation mellan individer kan utvecklas inom kohorter är även kannibalism mellan individer inom en kohort möjligt. Genom att använda mig av en så kallad fysiologiskt strukturerad populationsmodell kunde jag visa att divergerande tillväxtkurvor mellan kannibaler och deras byten (vilket resulterar i storleksbimodalitet) som ett resultat av kannibalism inom kohorter är beroende av den tid det tar för ynglen att kläcka ut, antalet bytesfiskar per kannibal samt den återkoppling som finns mellan konsumenterna och deras gemensamma resurs (djurplankton).

Unproductive lakes are one of few natural landscape compartments with net release of carbon to the atmosphere. Lakes also generally decrease the net terrestrial carbon uptake, since most of the CO2 production in unproductive lakes are derived from organic carbon produced on land (e.g. in forests). High latitude lakes are predicted to be particularly affected by the global climate change. The carbon cycling in these lakes and their role in the landscape are therefore important to study. In this thesis, carbon turnover processes were studied in two lakes above the arctic circle (Lake Diktar-Erik and Lake Merasjärvi) in year 2004 and 2005. Both lakes were net heterotrophic, with large variations in CO2 concentrations both on shorter (30min) and longer (24h) time-scales. The pelagic habitat supported a major part of the net production of CO2, with larger dynamics in the CO2 production than the sediments. The CO2 variations of the surface water were related to respiration of allochthonous organic carbon, and were affected by the concentration and quality of the DOC, as well as the whole lake water temperatures, and vertical water movements. The emission of CO2 from Lake Merasjärvi was measured with the eddy covariance tech­nique. The results showed that the gas transfer rate during moderate winds were higher than expected, causing the two most commonly used models to underestimate the long term fluxes of CO2 from the lake. Taken together, the results of the thesis show that the studied lakes contributed to bring terrestrial organic carbon back into the atmosphere, driven by a substantial internal CO2 production based on mineralization of allochthonous organic carbon. Major results are that the eddy covariance technique indicated that commonly used models tend to underestimate the net release rate of CO2 from lakes to the atmosphere, and that the lake CO2 dynamics can be the results of interactions between biogeochemical and physical processes in the lake water.

According to the Water Framework Directive of the European Union, macrophytes should be used as indicators in the ecological and environmental monitoring of lakes. In the member state Sweden the Environmental Protection Agency has elaborated assessment criteria for determining lake status based on macrophytes. The main focus of this thesis is to evaluate the efficiency of the assessment criteria for macrophytes. In addition the concordance between the ecological status classes of the four quality factors included was analysed. The assessment criteria for macrophytes are based on the total phosphorus preference of the respective species. The focus is thus mainly on the nutrient level of the investigated lakes and the environmental problem monitored is eutrophication. Macrophytes are one of the five biological quality factors used for lakes. The others are phytoplankton, diatoms, benthic fauna and fish. The two latter were included in this thesis. In addition to the biological factors the chemical factor, nutrients in lakes, i.e. the total phosphorus, was included. The macrophyte composition was investigated in two eutrophic Uppland lakes: Lake Trehörningen and Lake Edasjön. Since the assessment criteria were launched in 2007 there have been problems reported regarding the outcome of the methods. The results are sometimes inconclusive for eutrophicated lakes and especially for lakes with naturally high levels of nutrients. In this study the macrophyte species composition was compared with the nutrient level of different lakes. Some species were found in equal shares in oligotrophic lakes as in eutrophic, e.g. Nymphaea candida and Nuphar lutea. Hence they were considered less suitable as elements in the method evaluated. A couple of species were present in predominantly oligotrophic (e.g. Lobelia dortmanna) or eutrophic (e.g. Hydrocharis morsus-ranae) lakes, respectively. They were regarded as better indicators since they ”preferred” lakes either poor or rich in nutrients. It is important to point out that all the other biological quality factors used, except for macrophytes, are multimetric. I conclude that more parameters are needed for evaluation of macrophytes in lakes. Tentatively, the degree of coverage of the plants and algae, the presence and degree of coverage of invasive nonnative species, lake lowerings and the consequent composition and abundance change, all should be tested as additional parameters.  A high level of concordance was verified for the status classifications of the four quality factors in lakes of oligotrophy as well as in lakes of eutrophy, i.e. no particular  pattern based on trophy level was found. The macrophyte inventories of the two Uppland lakes both resulted in a moderate ecological status for macrophytes.

Den här studien undersöker hur vegetationen förändras mellan 1979 och 2010 i området som idag är Hornborgasjöns naturreservat. Sjösänkningar i området ledde till att ett igenväxt träskområde ersatte en viktig vattenreservoar och närsaltfälla. Restaureringsarbetet under 80-talet var banbrytande och antagligen ett av vår tids mest omfattande naturvårdsarbete. Studien svarar också på om restaureringen uppnådde sitt mål och om resultatet blev som man tänkt sig. I arbetet skapades en aktuell vegetationskarta för 2010, denna jämfördes med en i arbetet digitaliserad vegetationskarta från 1979. Kartbilder skapades och justerades i ArcGIS och vegetationsytornas area framtogs för att möjliggöra en vegetationsanalys mellan kartorna. Vegetationsförändringarna i området visade sig vara omfattande mellan 1979 och 2010, där tydlig igenväxtningsmark med stora monokulturer ersattes med öppnare marker där vegetationstyperna var spridda över hela området i mindre ytor. Mångfalden i området ökade liksom vattenytan. Vattenytans stora utbredning efter restaureringen blev den stora överraskningen tillsammans med att sävvegetationen helt försvann. Undervattensvegetationens stora spridning räddade dock restaureringens syfte att gynna fågellivet trots sävruggarnas frånvaro. En ny viktig naturtyp framkom i vegetationskartan 2010, öppet vatten med död vegetation, där stora delar av vegetationstypen består av den för många hotade arter vitala biotopen död sumplövskog. / This study investigates vegetation changes in the nature reserve of Lake Hornborga between 1979 and 2010. Lowering of the surface of the lake had changed an important water reserve and nutritive salt trap into an overgrown fen and during the 80's a total pioneering restoration, perhaps the most important work of nature conservation of our time, was made. This study claims to answer if the restoration was successful and if its goals were reached. A current vegetation map for 2010 was created and adjusted in ArcGIS and this map was compared with a vegetation map of 1979. Vegetation areas were calculated to facilitate analyses between the maps. Large-scale vegetation changes have occurred between 1979 and 2010. Overgrown fenland with monoculture vegetation has been replaced by a more open landscape with a diversified growth and an open surface of water. The large extension of open surface and the disappearance of rush vegetation are two great surprises of the restoration. Thanks to a large-scale spread of underwater vegetation the aim of furthering birdlife could be reached despite the loss of rush vegetation. A new type of vegetation area has also been created, where  open water submerges dead vegetation, one of which is a biotope of dead marsh broadleaf trees, vital to many threatened species. / Vid kontakt med Lantmäteriet har muntlig bekräftelse getts gällande tillstånd av publicering av deras upphovsrätts skyddade material, där alla högskolearbeten ges sådant tillstånd vid alla Sveriges lärosäten. I mitt arbete gäller detta figur 1.

Title from first page of PDF document. Includes bibliographical references.

Environmental factors influence species and habitats on multiple scales creating a mosaic of distribution patterns. Studying factors shaping these patterns are central to our understanding of population dynamics and ultimately ecosystem functioning. Information on the distribution of resources and conservation values are also highly needed in marine management as coastal areas are increasingly influenced by human activities. In this thesis, large-scale field data is used to explore how strong environmental gradients found on multiple scales in the coastal areas of the Baltic Sea influence fish habitats. The underlying concepts are based in the field of species distribution modelling, whereby habitat maps can be produced using environmental layers in a geographic information system. Distribution modelling is further used to address both ecological and applied questions by examining effects of habitat limitation on fish population sizes and to evaluate management actions aimed at habitat conservation. I show that specific habitat requirements for fish species of both freshwater and marine origin can be described using environmental variables and that species-environment relationships can be used to predict the distribution of early life-stages of fish in the Baltic Sea archipelagos. Further, predicted habitat availability of a specific life-stage was directly related to adult population size of Eurasian perch Perca fluviatilis, signifying that the abundance of large predatory fish can be limited by specific recruitment habitats. Lastly, by predicting the distribution of an assemblage of coastal fish species and their associated habitats, an assessment of a network of marine protected areas was performed. Results revealed large gaps in the current network and identified areas suitable for future protection. By demonstrating how current habitat protection can be improved by including critical habitats for coastal fish population sizes this thesis points to the benefits of integrating nature conservation and fisheries management. Based on these findings I conclude that species distribution modelling provides a suitable analytical framework for assessing the habitat requirements of organisms. An increased understanding of habitat-population relationships and an ability to accurately map ecologically important features will be of great value for an ecosystem-based marine management. ­ / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 709