Conservation Genetics of Exploited Finnish Salmonid Fishes

Genetic diversity is one of the levels of biodiversity that the World Conservation Union (IUCN) has recognized as being important to preserve. This is because genetic diversity is fundamental to the future evolution and to the adaptive flexibility of a species to respond to the inherently dynamic nature of the natural world. Therefore, the key to maintaining biodiversity and healthy ecosystems is to identify, monitor and maintain locally-adapted populations, along with their unique gene pools, upon which future adaptation depends. Thus, conservation genetics deals with the genetic factors that affect extinction risk and the genetic management regimes required to minimize the risk. The conservation of exploited species, such as salmonid fishes, is particularly challenging due to the conflicts between different interest groups. In this thesis, I conduct a series of conservation genetic studies on primarily Finnish populations of two salmonid fish species (European grayling, Thymallus thymallus, and lake-run brown trout, Salmo trutta) which are popular recreational game fishes in Finland. The general aim of these studies was to apply and develop population genetic approaches to assist conservation and sustainable harvest of these populations. The approaches applied included: i) the characterization of population genetic structure at national and local scales; ii) the identification of management units and the prioritization of populations for conservation based on evolutionary forces shaping indigenous gene pools; iii) the detection of population declines and the testing of the assumptions underlying these tests; and iv) the evaluation of the contribution of natural populations to a mixed stock fishery. Based on microsatellite analyses, clear genetic structuring of exploited Finnish grayling and brown trout populations was detected at both national and local scales. Finnish grayling were clustered into three genetically distinct groups, corresponding to northern, Baltic and south-eastern geographic areas of Finland. The genetic differentiation among and within population groups of grayling ranged from moderate to high levels. Such strong genetic structuring combined with low genetic diversity strongly indicates that genetic drift plays a major role in the evolution of grayling populations. Further analyses of European grayling covering the majority of the species’ distribution range indicated a strong global footprint of population decline. Using a coalescent approach the beginning of population reduction was dated back to 1 000-10 000 years ago (ca. 200-2 000 generations). Forward simulations demonstrated that the bottleneck footprints measured using the M ratio can persist within small populations much longer than previously anticipated in the face of low levels of gene flow. In contrast to the M ratio, two alternative methods for genetic bottleneck detection identified recent bottlenecks in six grayling populations that warrant future monitoring. Consistent with the predominant role of random genetic drift, the effective population size (N_e) estimates of all grayling populations were very low with the majority of N_e estimates below 50. Taken together, highly structured local populations, limited gene flow and the small N_e of grayling populations indicates that grayling populations are vulnerable to overexploitation and, hence, monitoring and careful management using the precautionary principles is required not only in Finland but throughout Europe. Population genetic analyses of lake-run brown trout populations in the Inari basin (northernmost Finland) revealed hierarchical population structure where individual populations were clustered into three population groups largely corresponding to different geographic regions of the basin. Similar to my earlier work with European grayling, the genetic differentiation among and within population groups of lake-run brown trout was relatively high. Such strong differentiation indicated that the power to determine the relative contribution of populations in mixed fisheries should be relatively high. Consistent with these expectations, high accuracy and precision in mixed stock analysis (MSA) simulations were observed. Application of MSA to indigenous fish caught in the Inari basin identified altogether twelve populations that contributed significantly to mixed stock fisheries with the Ivalojoki river system being the major contributor (70%) to the total catch. When the contribution of wild trout populations to the fisheries was evaluated regionally, geographically nearby populations were the main contributors to the local catches. MSA also revealed a clear separation between the lower and upper reaches of Ivalojoki river system – in contrast to lower reaches of the Ivalojoki river that contributed considerably to the catch, populations from the upper reaches of the Ivalojoki river system (>140 km from the river mouth) did not contribute significantly to the fishery. This could be related to the available habitat size but also associated with a resident type life history and increased cost of migration. The studies in my thesis highlight the importance of dense sampling and wide population coverage at the scale being studied and also demonstrate the importance of critical evaluation of the underlying assumptions of the population genetic models and methods used. These results have important implications for conservation and sustainable fisheries management of Finnish populations of European grayling and brown trout in the Inari basin.

Element speciation and behaviour in metal-rich Boreal river and estuarine systems using ultrafiltration and chemical modelling

The bioavailability of metals and their potential for environmental pollution depends not simply on total concentrations, but is to a great extent determined by their chemical form. Consequently, knowledge of aqueous metal species is essential in investigating potential metal toxicity and mobility. The overall aim of this thesis is, thus, to determine the species of major and trace elements and the size distribution among the different forms (e.g. ions, molecules and mineral particles) in selected metal-enriched Boreal river and estuarine systems by utilising filtration techniques and geochemical modelling. On the basis of the spatial physicochemical patterns found, the fractionation and complexation processes of elements (mainly related to input of humic matter and pH-change) were examined. Dissolved (<1 kDa), colloidal (1 kDa-0.45 μm) and particulate (>0.45 μm) size fractions of sulfate, organic carbon (OC) and 44 metals/metalloids were investigated in the extremely acidic Vörå River system and its estuary in W Finland, and in four river systems in SW Finland (Sirppujoki, Laajoki, Mynäjoki and Paimionjoki), largely affected by soil erosion and acid sulfate (AS) soils. In addition, geochemical modelling was used to predict the formation of free ions and complexes in these investigated waters. One of the most important findings of this study is that the very large amounts of metals known to be released from AS soils (including Al, Ca, Cd, Co, Cu, Mg, Mn, Na, Ni, Si, U and the lanthanoids) occur and can prevail mainly in toxic forms throughout acidic river systems; as free ions and/or sulfate-complexes. This has serious effects on the biota and especially dissolved Al is expected to have acute effects on fish and other organisms, but also other potentially toxic dissolved elements (e.g. Cd, Cu, Mn and Ni) can have fatal effects on the biota in these environments. In upstream areas that are generally relatively forested (higher pH and contents of OC) fewer bioavailable elements (including Al, Cu, Ni and U) may be found due to complexation with the more abundantly occurring colloidal OC. In the rivers in SW Finland total metal concentrations were relatively high, but most of the elements occurred largely in a colloidal or particulate form and even elements expected to be very soluble (Ca, K, Mg, Na and Sr) occurred to a large extent in colloidal form. According to geochemical modelling, these patterns may only to a limited extent be explained by in-stream metal complexation/adsorption. Instead there were strong indications that the high metal concentrations and dominant solid fractions were largely caused by erosion of metal bearing phyllosilicates. A strong influence of AS soils, known to exist in the catchment, could be clearly distinguished in the Sirppujoki River as it had very high concentrations of a metal sequence typical of AS soils in a dissolved form (Ba, Br, Ca, Cd, Co, K, Mg, Mn, Na, Ni, Rb and Sr). In the Paimionjoki River, metal concentrations (including Ba, Cs, Fe, Hf, Pb, Rb, Si, Th, Ti, Tl and V; not typical of AS soils in the area) were high, but it was found that the main cause of this was erosion of metal bearing phyllosilicates and thus these metals occurred dominantly in less toxic colloidal and particulate fractions. In the two nearby rivers (Laajoki and Mynäjoki) there was influence of AS soils, but it was largely masked by eroded phyllosilicates. Consequently, rivers draining clay plains sensitive to erosion, like those in SW Finland, have generally high background metal concentrations due to erosion. Thus, relying on only semi-dissolved (<0.45 μm) concentrations obtained in routine monitoring, or geochemical modelling based on such data, can lead to a great overestimation of the water toxicity in this environment. The potentially toxic elements that are of concern in AS soil areas will ultimately be precipitated in the recipient estuary or sea, where the acidic metalrich river water will gradually be diluted/neutralised with brackish seawater. Along such a rising pH gradient Al, Cu and U will precipitate first together with organic matter closest to the river mouth. Manganese is relatively persistent in solution and, thus, precipitates further down the estuary as Mn oxides together with elements such as Ba, Cd, Co, Cu and Ni. Iron oxides, on the contrary, are not important scavengers of metals in the estuary, they are predicted to be associated only with As and PO4.

LVDC power distribution system: computational modelling

In the doctoral dissertation, low-voltage direct current (LVDC) distribution system stability, supply security and power quality are evaluated by computational modelling and measurements on an LVDC research platform. Computational models for the LVDC network analysis are developed. Time-domain simulation models are implemented in the time-domain simulation environment PSCAD/EMTDC. The PSCAD/EMTDC models of the LVDC network are applied to the transient behaviour and power quality studies. The LVDC network power loss model is developed in a MATLAB environment and is capable of fast estimation of the network and component power losses. The model integrates analytical equations that describe the power loss mechanism of the network components with power flow calculations. For an LVDC network research platform, a monitoring and control software solution is developed. The solution is used to deliver measurement data for verification of the developed models and analysis of the modelling results. In the work, the power loss mechanism of the LVDC network components and its main dependencies are described. Energy loss distribution of the LVDC network components is presented. Power quality measurements and current spectra are provided and harmonic pollution on the DC network is analysed. The transient behaviour of the network is verified through time-domain simulations. DC capacitor guidelines for an LVDC power distribution network are introduced. The power loss analysis results show that one of the main optimisation targets for an LVDC power distribution network should be reduction of the no-load losses and efficiency improvement of converters at partial loads. Low-frequency spectra of the network voltages and currents are shown, and harmonic propagation is analysed. Power quality in the LVDC network point of common coupling (PCC) is discussed. Power quality standard requirements are shown to be met by the LVDC network. The network behaviour during transients is analysed by time-domain simulations. The network is shown to be transient stable during large-scale disturbances. Measurement results on the LVDC research platform proving this are presented in the work.

Ellagitannins in Finnish plant species – Characterization, distribution and oxidative activity

Ellagitannins are secondary metabolites that are produced by plants. Among other features, they are assumed to function as plants’ defensive compounds against plant-eating herbivores. This thesis focuses on a theory, which suggests that the biological activity of ellagitannins is based on their tendency to oxidize at the highly alkaline gut conditions of insect herbivores (oxidative activity). To study the biological activities of ellagitannins, a wide variety of structurally different ellagitannins were purified from different plant species by using liquid chromatographic techniques. The structures were characterized with the aid of spectrometric methods. Based on the acquired data, it was also possible to create a scheme, which enables the classification and even identification of ellagitannins from plant extracts without the need to isolate each compound for individual characterization. The biological activities of ellagitannins were determined with methods that are based on the abilities of the compounds to scavenge radicals, chelate iron ions, and on their rate of oxidation at high pH. The results showed that ellagitannins possess oxidative activities both at high and neutral pH, and that their activities depend on structure. The occurrence, distribution and content of ellagitannins in Finnish plant species were also studied. The specific ellagitannin profiles of the studied plant species were found to correlate well with their taxonomic classification.

Formal modelling for digital media distribution

Human beings have always strived to preserve their memories and spread their ideas. In the beginning this was always done through human interpretations, such as telling stories and creating sculptures. Later, technological progress made it possible to create a recording of a phenomenon; first as an analogue recording onto a physical object, and later digitally, as a sequence of bits to be interpreted by a computer. By the end of the 20th century technological advances had made it feasible to distribute media content over a computer network instead of on physical objects, thus enabling the concept of digital media distribution. Many digital media distribution systems already exist, and their continued, and in many cases increasing, usage is an indicator for the high interest in their future enhancements and enriching. By looking at these digital media distribution systems, we have identified three main areas of possible improvement: network structure and coordination, transport of content over the network, and the encoding used for the content. In this thesis, our aim is to show that improvements in performance, efficiency and availability can be done in conjunction with improvements in software quality and reliability through the use of formal methods: mathematical approaches to reasoning about software so that we can prove its correctness, together with the desirable properties. We envision a complete media distribution system based on a distributed architecture, such as peer-to-peer networking, in which different parts of the system have been formally modelled and verified. Starting with the network itself, we show how it can be formally constructed and modularised in the Event-B formalism, such that we can separate the modelling of one node from the modelling of the network itself. We also show how the piece selection algorithm in the BitTorrent peer-to-peer transfer protocol can be adapted for on-demand media streaming, and how this can be modelled in Event-B. Furthermore, we show how modelling one peer in Event-B can give results similar to simulating an entire network of peers. Going further, we introduce a formal specification language for content transfer algorithms, and show that having such a language can make these algorithms easier to understand. We also show how generating Event-B code from this language can result in less complexity compared to creating the models from written specifications. We also consider the decoding part of a media distribution system by showing how video decoding can be done in parallel. This is based on formally defined dependencies between frames and blocks in a video sequence; we have shown that also this step can be performed in a way that is mathematically proven correct. Our modelling and proving in this thesis is, in its majority, tool-based. This provides a demonstration of the advance of formal methods as well as their increased reliability, and thus, advocates for their more wide-spread usage in the future.

Modelling of changes in electricity end-use and their impacts on electricity distribution

The electricity distribution sector will face significant changes in the future. Increasing reliability demands will call for major network investments. At the same time, electricity end-use is undergoing profound changes. The changes include future energy technologies and other advances in the field. New technologies such as microgeneration and electric vehicles will have different kinds of impacts on electricity distribution network loads. In addition, smart metering provides more accurate electricity consumption data and opportunities to develop sophisticated load modelling and forecasting approaches. Thus, there are both demands and opportunities to develop a new type of long-term forecasting methodology for electricity distribution. The work concentrates on the technical and economic perspectives of electricity distribution. The doctoral dissertation proposes a methodology to forecast electricity consumption in the distribution networks. The forecasting process consists of a spatial analysis, clustering, end-use modelling, scenarios and simulation methods, and the load forecasts are based on the application of automatic meter reading (AMR) data. The developed long-term forecasting process produces power-based load forecasts. By applying these results, it is possible to forecast the impacts of changes on electrical energy in the network, and further, on the distribution system operator’s revenue. These results are applicable to distribution network and business planning. This doctoral dissertation includes a case study, which tests the forecasting process in practice. For the case study, the most prominent future energy technologies are chosen, and their impacts on the electrical energy and power on the network are analysed. The most relevant topics related to changes in the operating environment, namely energy efficiency, microgeneration, electric vehicles, energy storages and demand response, are discussed in more detail. The study shows that changes in electricity end-use may have radical impacts both on electrical energy and power in the distribution networks and on the distribution revenue. These changes will probably pose challenges for distribution system operators. The study suggests solutions for the distribution system operators on how they can prepare for the changing conditions. It is concluded that a new type of load forecasting methodology is needed, because the previous methods are no longer able to produce adequate forecasts.