Forest owners' acceptance of incentive based policy instruments in forest biodiversity conservation : a choice experiment based approach

Abstract

Statistical Methods for Conservation and Alignment Quality in Proteins

Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the quality of the alignment. However, automatic construction of a multiple sequence alignment for a set of remotely related sequences does not always provide biologically relevant alignments.Therefore, there is a need for an objective approach for evaluating the quality of automatically aligned sequences. The profile hidden Markov model is a powerful approach in comparative genomics. In the profile hidden Markov model, the symbol probabilities are estimated at each conserved alignment position. This can increase the dimension of parameter space and cause an overfitting problem. These two research problems are both related to conservation. We have developed statistical measures for quantifying the conservation of multiple sequence alignments. Two types of methods are considered, those identifying conserved residues in an alignment position, and those calculating positional conservation scores. The positional conservation score was exploited in a statistical prediction model for assessing the quality of multiple sequence alignments. The residue conservation score was used as part of the emission probability estimation method proposed for profile hidden Markov models. The results of the predicted alignment quality score highly correlated with the correct alignment quality scores, indicating that our method is reliable for assessing the quality of any multiple sequence alignment. The comparison of the emission probability estimation method with the maximum likelihood method showed that the number of estimated parameters in the model was dramatically decreased, while the same level of accuracy was maintained. To conclude, we have shown that conservation can be successfully used in the statistical model for alignment quality assessment and in the estimation of emission probabilities in the profile hidden Markov models.

Determinants of Polylepis (Rosaceae) Forest Distribution and Treeline Formation in the High Andes

High elevation treelines are formed under common temperature conditions worldwide, but the functional mechanisms that ultimately constrain tree growth are poorly known. In addition to environmental constraints, the distribution of high elevation forests is largely affected by human influence. Andean Polylepis (Rosaceae) forests are an example of such a case, forests commonly growing in isolated stands disconnected from the lower elevation montane forests. There has been ample discussion as to the role of environmental versus anthropogenic causes of this fragmented distribution of Polylepis forests, but the importance of different factors is still unclear. In this thesis, I studied functional, environmental and anthropogenic aspects determining Polylepis forest distribution. Specifically, I assessed the degree of genetic determinism in the functional traits that enable Polylepis species to grow in cold and dry conditions. I also studied the role of environment and human influence constraining Polylepis forest distribution. I found evidence of genetically determined climatic adaptations in the functional traits of Polylepis. High elevation species had reduced leaf size and increased root tip abundance compared to low elevation species. Thus these traits have potentially played an important role in species evolution and adaptation to high elevation habitats, especially to low temperatures. I also found reduced photosynthesis rate among high elevation tree species compared to low elevation species, supporting carbon source limitation at treelines. At low elevations, Polylepis forest distribution appeared to be largely defined by human influence. This suggests that the absence of Polylepis forests in large areas in the Andes is the result of several environmental and anthropogenic constraints, the role of environment becoming stronger towards high elevations. I also show that Polylepis trees grow at remarkably low air and soil temperatures near treelines, and present new evidence of the role of air temperatures in constraining tree growth at high elevations. I further show that easily measurable indices of accessibility are related to the degree of degradation of Polylepis forest, and can therefore be used in the rapid identification of potentially degraded Polylepis forests. This is of great importance for the conservation and restoration planning of Polylepis forests in the Andes. In a global context, the results of this thesis add to our scientific knowledge concerning high elevation adaptations in trees, and increase our understanding of the factors constraining tree growth and forest distribution at high-­elevation treelines worldwide.

Assessment of Coastal Bird Populations and Habitats on the Finnish Coast of the Baltic Sea: Implications for Monitoring and Management

Coastal birds are an integral part of coastal ecosystems, which nowadays are subject to severe environmental pressures. Effective measures for the management and conservation of seabirds and their habitats call for insight into their population processes and the factors affecting their distribution and abundance. Central to national and international management and conservation measures is the availability of accurate data and information on bird populations, as well as on environmental trends and on measures taken to solve environmental problems. In this thesis I address different aspects of the occurrence, abundance, population trends and breeding success of waterbirds breeding on the Finnish coast of the Baltic Sea, and discuss the implications of the results for seabird monitoring, management and conservation. In addition, I assess the position and prospects of coastal bird monitoring data, in the processing and dissemination of biodiversity data and information in accordance with the Convention on Biological Diversity (CBD) and other national and international commitments. I show that important factors for seabird habitat selection are island area and elevation, water depth, shore openness, and the composition of island cover habitats. Habitat preferences are species-specific, with certain similarities within species groups. The occurrence of the colonial Arctic Tern (Sterna paradisaea) is partly affected by different habitat characteristics than its abundance. Using long-term bird monitoring data, I show that eutrophication and winter severity have reduced the populations of several Finnish seabird species. A major demographic factor through which environmental changes influence bird populations is breeding success. Breeding success can function as a more rapid indicator of sublethal environmental impacts than population trends, particularly for long-lived and slowbreeding species, and should therefore be included in coastal bird monitoring schemes. Among my target species, local breeding success can be shown to affect the populations of the Mallard (Anas platyrhynchos), the Eider (Somateria mollissima) and the Goosander (Mergus merganser) after a time lag corresponding to their species-specific recruitment age. For some of the target species, the number of individuals in late summer can be used as an easier and more cost-effective indicator of breeding success than brood counts. My results highlight that the interpretation and application of habitat and population studies require solid background knowledge of the ecology of the target species. In addition, the special characteristics of coastal birds, their habitats, and coastal bird monitoring data have to be considered in the assessment of their distribution and population trends. According to the results, the relationships between the occurrence, abundance and population trends of coastal birds and environmental factors can be quantitatively assessed using multivariate modelling and model selection. Spatial data sets widely available in Finland can be utilised in the calculation of several variables that are relevant to the habitat selection of Finnish coastal species. Concerning some habitat characteristics field work is still required, due to a lack of remotely sensed data or the low resolution of readily available data in relation to the fine scale of the habitat patches in the archipelago. While long-term data sets exist for water quality and weather, the lack of data concerning for instance the food resources of birds hampers more detailed studies of environmental effects on bird populations. Intensive studies of coastal bird species in different archipelago areas should be encouraged. The provision and free delivery of high-quality coastal data concerning bird populations and their habitats would greatly increase the capability of ecological modelling, as well as the management and conservation of coastal environments and communities. International initiatives that promote open spatial data infrastructures and sharing are therefore highly regarded. To function effectively, international information networks, such as the biodiversity Clearing House Mechanism (CHM) under the CBD, need to be rooted at regional and local levels. Attention should also be paid to the processing of data for higher levels of the information hierarchy, so that data are synthesized and developed into high-quality knowledge applicable to management and conservation.

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.

Taxonomy and Species Richness of Amazonian Pimplinae and Rhyssinae (hymenoptera: ichneumonidae)

The Amazonian region, the biggest rain forest of our planet, is known for its extraordinary biodiversity. Most of this diversity is still unexplored and new species of different taxa are regularly found there. In this region, as in most areas of the world, insects are some of the most abundant organisms. Therefore, studying this group is important to promote the conservation of these highly biodiverse ecosystems of the planet. Among insects, parasitoid wasps are especially interesting because they have potential for use as biodiversity indicators and biological control agents in agriculture and forestry. The parasitoid wasp family Ichneumonidae is one of the most species rich groups among the kingdom Animalia. This group is still poorly known in many areas of the world; the Amazonian region is a clear example of this situation. Ichneumonids have been thought to be species poor in Amazonia and other tropical areas. However, recent studies are suggesting that parasitoid wasps may be quite abundant in Amazonia and possibly in most tropical areas of the world. The aim of my doctoral thesis is to study the species richness and taxonomy of two of the best known ichneumonid subfamilies in the Neotropical region, Pimplinae and Rhyssinae. To do this I conducted two extensive sampling programs in the Peruvian Amazonia. I examined also a large number of Neotropical ichneumonids deposited to different natural history museums. According to the results of my thesis, the species richness of these parasitoids in the Amazonian region is considerably higher than previously reported. In my research, I firstly further develop the taxonomy of these parasitoids by describing many new species and reporting several new faunistic records (I, II, III). In this first part I focus on two genera (Xanthopimpla and Epirhyssa) which were thought to be rather species poor. My thesis demonstrates that these groups are actually rather species rich in the Amazonian region. Secondly, I concentrate on the species richness of these parasitoids in a global comparison showing that the Neotropical region and especially the Peruvian Amazonia is one of the most species rich areas of Pimpliformes ichneumonids (V). Furthermore, I demonstrate that with the data available to date no clear latitudinal gradient in species richness is visible. Thirdly, increasing the macroecological knowledge of these parasitoids I show that some previously unreported ichneumonid subfamilies are present in the Amazonian region (IV). These new insights and the results of the global comparison of ichneumonid inventories suggest that the previous belief of low diversity in the tropics is most likely related to a lack of sampling effort in the region. Overall, my research increases the knowledge of Neotropical ichneumonids highlighting the importance of Peruvian Amazonia as one of the diversity hotspots of parasitoid wasps.