Research Assessment Exercise 2007 University of Oulu
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3. Doctoral theses and degrees3a. List of doctoral theses 2001-2006 in the Department of BiologyA list of links to the electronic versions of doctoral theses can be found at http://cc.oulu.fi/~ehohtola/ra/ Note: The electronic versions of theses contain the summary part (abstract, literature review, main results, discussion) of the thesis, usually 30–70 pages. All theses are based on compilations of published papers or manuscripts. A list of these papers is provided, but they are not reproduced in the electronic version. 3a.1 Year 2001Ari-Pekka Huhta (2001) Restorative mowing on semi-natural grasslands: community-level changes and species-level responses. Acta Universitatis Ouluensis A 365. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514259947/ This thesis operates at two levels of ecological research, describing the effects of withdrawal and re-introduction of management on grasslands. The aim of the community-level survey was to explore the effects of abandonment, mowing and grazing on semi-natural meadows in northern Finland. At the species level, the aim was to evaluate the responses of three monocarpic meadow species to various degrees of simulated grazing under natural growth conditions. The community-level studies suggest that strongly competitive grass species with rapid vegetative growth, especially those forming tussocks, are able to retain or increase their cover in abandoned meadows. However, most species are able to persist in a meadow for a long time after abandonment, even when a group of immigrants arrive. This leads to a temporary increase in species diversity, and it may therefore be used as an indicator of ongoing succession. Nevertheless, abandonment is harmful for the rare archaeophytic species in the long run. Late mowing does not have extensive short-term impacts on grass-dominated semi-natural meadows. Therefore, it is neither an efficient nor a substitutional way of management when the goal is to restore a formerly grazed pasture. Mowing executed early in the season may, however, be a more appropriate way of inducing changes in species composition and enhancing species richness. According to the results of the species-level studies, Erysimum strictum and Rhinanthus minor tolerate well minor apical damage, while more severe damage has a detrimental impact on the performance of both species. The observed differences in regrowth responses between the two species are presumably due to their different habitat requirements in relation to competition. The species-level experiment with two late-flowering populations of field gentian Gentianella campestris ssp. campestris revealed that the southern, Swedish population that has been regularly grazed and mown overcompensated for the intermediate (50%) damage level, whereas the northern, Finnish field gentians growing in unmanaged habitats showed at best partial or full compensation. Regular grazing and mowing have presumably favoured grazing-tolerant plant species, i.e. species with a good regrowth capacity. Herbivory reshapes grassland plant communities in two ways: directly by affecting the survival and reproductive success of individual plants and indirectly by changing the competitive environment. Tall and competitive perennial species suffer relatively more from damage than true grassland species, i.e. small herbs and grasses, which are better able to tolerate regular tissue losses and respond to damage within the ongoing growing season. As a result, certain species benefit from grazing and mowing in the sense that they may gain more through competitive relaxation than they lose in defoliation. Keywords: regrowth capacity, secondary succession, simulated herbivory, vegetation management Auli Karhu (2001) Evolution and applications of pine microsatellites. Acta Universitatis Ouluensis A 357. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514259246/ The evolution of microsatellites was studied within and between the pine species. Sequences showed that microsatellites do not necessarily mutate in a stepwise fashion and that size homoplasy is common due to flanking sequence and repeat area changes within and between the species. Thus, some assumptions of statistical methods based on changes in repeat numbers may not hold. Sequences from cross-species amplifications revealed evidence of duplications of microsatellite loci in pines. On two independent occasions, the repeat area of the microsatellite had undergone a rapid expansion during the last 10-25 million of years. Microsatellite markers were used together with other molecular markers (allozymes, RFLPs, RAPDs, rDNA RFLPs) and an adaptive trait (date of bud set) to study patterns of genetic variation in Scots pine (Pinus sylvestris) in Finland. All molecular markers showed high level of within population variation, while differentiation among populations was low (FST = 0.02). Of the total variation in bud set, 36.4 % was found among the populations which experience a steep climatic gradient. Thus, the markers applied were poor predictors of population differentiation of the quantitative trait studied The distribution of genetic variation was studied in five natural populations of radiata pine (Pinus radiata), species which has gone through bottlenecks in the past. Null allele frequencies were estimated and used in later analyses. Microsatellites showed high level of variability within populations (He = 0.68-0.77). Allele length distributions and average number of alleles per locus showed some traces of bottlenecks. Instead, comparison of observed genetic diversities and expected diversities suggested post-bottleneck expansion of populations. Genetic differentiation (FST and RST) among populations was over 10 %, reflecting situation in the isolated radiata pine populations. Using microsatellites and a newly developed Bayesian method, individual inbreeding coefficients were estimated in five populations of radiata pine. Most individuals were outbred while some were selfed. Presumably, in ancestral radiata pine populations the recessive deleterious alleles have been eliminated after bottlenecks and the mating system has changed as a consequence. Keywords: inbreeding coefficient, microsatellite evolution, Pinus, population structure Sari Kontunen-Soppela (2001) Dehydrins in Scots pine tissues: Responses to annual rhythm, low temperature and nitrogen. Acta Universitatis Ouluensis A 356. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514259114/ Natural seasonal variation and the effects of cold treatment and nitrogen fertilization on protein expression with special emphasis on dehydrin proteins, were studied using different aged Scots pine (Pinus sylvestris L.). Several different dehydrins were found and their expression depended on the tissue type, tree age or specific treatment. Their concentrations fluctuated seasonally and in response to nitrogen fertilization, but no effects of low temperature on the dehydrins of seedlings were observed. A 60-kDa dehydrin was associated with cold acclimation in the bud and bark tissues of mature trees and in the needles of seedlings. In the needles of mature trees, this dehydrin was associated with springtime desiccation, which was detected as a significant decrease in the osmotic potential of needles. The quantity and quality of soluble proteins altered seasonally in Scots pine tissues, but low temperature treatment alone did not have any effect on the proteins. Soluble protein concentration increased during autumn and decreased in spring in buds and bark, but not in the needles of mature trees. In needles of seedlings, however, protein concentrations altered seasonally. Several proteins, of varying molecular weights, were more abundant in winter in all the tissues studied and some increased in concentration in the nitrogen-fertilized seedlings. The role of these proteins as a storage reserve in Scots pine is discussed. The osmotic potential of needles showed seasonal fluctuation, being high in the summer and low during the winter. Low temperature treatment decreased the osmotic and water potential of needles and increased the concentrations of soluble sugars in seedlings. Based on carbohydrate analyses, the metabolism of seedlings acclimated to low temperature in less than ten days. Nitrogen fertilization increased the content of total nitrogen and the soluble protein concentrations in the needles of seedlings and the growth both in the mature trees and seedlings. Although the frost resistance showed no response to nitrogen-fertilization, the soluble proteins and dehydrins were affected in a manner that suggested an earlier growth resumption of spring in the fertilized trees. Keywords: Pinus sylvestris L., carbohydrates, cold acclimation, deacclimation, osmotic potential, soluble proteins, water potential Jouko Kumpula (2001) Productivity of the semi-domesticated reindeer (Rangifer t. tarandus L.) stock and carrying capacity of pastures in Finland during 1960-1990's. Acta Universitatis Ouluensis A 375. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514265556/ Although the present day management of semi-domesticated reindeer (Rangifer t. tarandus L.) and its operational environment have changed from the past, knowledge of the ecological mechanisms typical of traditional herding is still important. The main objective of this study was to examine factors related to stock productivity and carrying capacity of pastures in the Finnish semi-domesticated reindeer management area during 1960-1990's in order to clarify the basis of the present management strategies in Finland. In the Oraniemi district, before 1987, calf production was more affected by the snow conditions of the previous winter, than the weather conditions of the previous summer. Slaughtering mass of calves was more affected by the weather and precipitation in spring and summer than the snow conditions of the previous winter. Thick snow cover and unfrozen soil in early winter also probably affect the quality of natural winter food of reindeer by favouring the growth of certain micro fungi on pastures. Before the mid-1990's in the northern part of the management area, calf production decreased and its variability increased between the districts when reindeer densities on forest and heath land increased, amount of lichen (Cladonia spp.) pastures per reindeer decreased and condition of these pastures deteriorated. Variability in calf production increased especially when the amount of arboreal lichen (Alectoria, Bryoria spp.) pastures per reindeer decreased. The slaughtering mass of reindeer decreased when reindeer densities on all pastures increased. Intensive calf slaughtering increased reindeer stock productivity although it was density dependent. Because of intensified feeding, reindeer densities on winter pastures did not affect stock productivity in the whole management area between 1993 and 1999. Stock productivity could be increased markedly by feeding. Still, slaughtering mass and meat production per reindeer decreased when reindeer densities on summer pastures increased. In the Finnish grazing system, reindeer densities should have remained well below 10 reindeer/km2 lichen range for maintaining lichen ranges in a good condition. The average lichen biomass of lichen ranges in the management area in the mid-1990's was 13% of the lichen biomass at the maximum production. Lichen ranges should have been ungrazed for an average 18 years to recover to the maximum production. The time needed for the lichen ranges to recover to a good condition, would have been 7 years. This study showed that the amount and condition of pastures had a fundamental part in the productivity of Finnish reindeer stock. Calf slaughtering and feeding were effective ways to increase and stabilize stock productivity in the situation where the economic carrying capacity of winter ranges has obvuously been exceeded due to overgrazing and the effects caused by the other land use. This has made reindeer management more and more dependent on feeding. Improvements of the state and condition of winter ranges would only be possible during a long period by regulating reindeer stock size, developing pasture rotation and protecting reindeer pastures from the other land use. Keywords: carrying capacity, density dependent, feeding, management, pastures, semi-domesticated reindeer, slaughtering, stock productivity Anne Laine (2001) Restoring salmonid stocks in boreal rivers. Problems of passage at migratory obstructions and land-derived loading in production areas. Acta Universitatis Ouluensis A 361. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn951425953X/ In this thesis, I examine two important aspects surrounding salmonid reproductive ecology, namely: (i) the problems with passing obstructions during migratory spawning runs and (ii) how the early life stages in boreal streams are influenced by increased levels of fine-grained particulate matter from drained peatlands. These aspects are not only critical to salmonid reproductive success but have grave implications regarding environmental quality and species conservation. Spawning runs can be re-established by constructing fishways at obstructions but the efficiency of fishways depends on several factors. The passage of multi-sea-winter salmon was enhanced in the Isohaara fishway by increasing its water flow and by creating a small waterfall at the entrance. The fishway, which consists of vertical slot and Denil sections, proved to be unsuitable for most freshwater fish, whitefish and river lamprey, whereas salmonids, once they had entered, successfully negotiated the fishway. In fishway design, the migratory behaviour and the demands of the species of interest should be considered. For salmonids, priority should be given to the attractiveness of the fish entrance. When there is a migration corridor, the availability and the quality of spawning and rearing habitats has a major effect on the success of restoration projects. In the humic rivers studied, the survival of incubated brown trout eggs was lower in riffles susceptible to increased levels of fine-grained particulate matter from drained peatlands. Additionally, an increase in the Fe content of high molecular weight dissolved organic matter followed by its precipitation and sedimentation was proposed to be involved. Correspondingly, the recapture rates of stocked yearling salmon were lower in the affected riffles, individual salmon being smaller and thinner and having less food in their stomachs than reference salmon. Based on these results, it seems probable that peatland drainage, by influencing the incubation success of salmonid embryos and the foraging, growth and survival of juveniles, eventually affects the number and quality of smolts produced. In future, such water pollution control measures should be implemented that would enhance the success of natural spawning and help ensure environmental quality. Keywords: fishways, foraging, incubation success, peatland drainage Tuija Liukkonen-Anttila (2001) Nutritional and genetic adaptation of galliform birds: implications for hand-rearing and restocking. Acta Universitatis Ouluensis A 367. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514259904/ The impact of hand-rearing on the morphology and physiology of captive and wild grey partridges (Perdix perdix) and capercaillies (Tetrao urogallus) was studied in three feeding trials conducted under laboratory conditions, and two comparative studies between wild and captive birds. Finally, wild and hand-reared grey partridges from several localities in Europe were sampled and the control region 1 of mitochondrial DNA was sequenced to reveal genetic variation between populations, as well as to compare wild and captive stocks. Wild capercaillies had heavier pectoral muscles, hearts, livers and gizzards, longer small intestines than hand-reared ones, and a higher cytochrome-c oxidase activity in muscle and heart. Invertebrates were essential to the growth, primary and temperature regulation development in grey partridge chicks. Fish was not sufficient to replace invertebrates in the diet. A change in diet from commercial to natural decreased the assimilation efficiency in the grey partridge. It also increased the mass of gizzard reflecting the need for greater grinding ability. Of hepatic P450 enzymes used in this study 7-ethoxyresorufin-0-deethylase and 7-pentoxyresorufin-0-deethylase differed between wild and hand-reared birds. Coumarin-7-hydroxylase activity was higher in grey partridges than capercaillies. Diet differences may have caused these differences. Quebracho tannin added to the diet lowered nitrogen concentration in caecal feces, and elevated the level of excreted tannin. Otherwise its effects were slight. Mitochondrial control region revealed 14 variable sites between two main lineages detected. Nucleotide and haplotype diversities varied greatly between populations. The markedly deep divergence between the two lineages indicated most probably post-glacial recolonisations from geographically isolated refuges. In Finland, wild birds represented the eastern lineage, while the farmstock represented the western lineage. Surprisingly little trace, contrary to expectations, from the large-scale releasing of imported partridges could be seen in the European populations. Keywords: capercaillie, grey partridge, mitochondrial control region, nutrition, Perdix perdix, Tetrao urogallus Kyösti Marjoniemi (2001) Thermogenic mechanisms during the development of endothermy in juvenile birds. Acta Universitatis Ouluensis A 373. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514265424/ The use of regulatory and obligatory heat production mechanisms were studied in juvenile birds during the development of endothermy. The development of shivering thermogenesis was studied in the pectoral and gastrocnemius muscles of the altricial domestic pigeon and in three precocial galliforms (Japanese quail, grey partridge and domestic fowl). The development of shivering was the determinant for the beginning of endothermy. Homeothermy also necessitated avoidance of excess heat loss by insulation and behavioural thermoregulation. In the precocial species, shivering thermogenesis was present in the leg muscles of the youngest age groups (1-2 d) studied. Breast muscles contributed shivering from the second post-hatching week. In the altricial pigeons, significant thermogenesis was apparent later than in the precocials, at the age of 6 d. In contrast to the precocials, the pectoral muscles of the altricials were the most significant heat production tissues. In newly-hatched partridges and pigeons, incipient shivering did not result in significant heat production. The ability to produce heat in cold by putative nonshivering thermogenesis was studied in Japanese quail chicks and domestic ducklings. In both species, three-week cold acclimation resulted in morphometric and physiological changes, but there was no clear evidence of nonshivering thermogenesis. The lack of NST was evident because an increase in shivering amplitude at least in one of the muscles studied paralleled an increase in oxygen consumption. Consequently, shivering thermogenesis was probably the only mode of regulatory heat production. The amplitudes of shivering EMGs measured during cold exposure were dependent on the coexistence of postprandial thermogenesis or exercise. Japanese quail chicks were able to substitute shivering thermogenesis partially with postprandial heat production when nourished. Bipedal exercise both inhibited shivering in pectorals directly via inhibitory neural circuits and stimulated it indirectly via decreased body temperature. Because of increased heat loss, exercise was not used as a substitute for shivering. Shivering is a flexible mode of thermogenesis and its magnitude can be adjusted according to the magnitude of obligatory thermogenesis. The adjustment works towards energy saving by avoidance of the summation of different modes of heat production. The prerequisite for successful adjustment of shivering is adequate insulation, whose role in preventing excessive heat loss is pronounced during exercise. It is concluded that the energetics of posthatching thermoregulation includes the potential for optimizations in energy use in order to avoid dissipation of waste energy as heat. Keywords: exercise, nonshivering thermogenesis, ontogeny, postprandial heat production, shivering, thermoregulation Anna Maria Mattila née Pirttilä (2001) Endophytes in the buds of Scots pine (Pinus sylvestris L.). Acta Universitatis Ouluensis A 369. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514264444/ Although microbes are generally found as endophytes in many plant tissues, the plant shoot meristems have been considered virtually sterile. Plant tissue culture, which utilizes mostly the meristems, has nevertheless given numerous references to microbial existence in these tissues. Since the bud-derived tissue cultures of Scots pine (Pinus sylvestris L.) also become easily occupied by microbes, microbial presence was considered to be one potential cause of the low regeneration capacity of tissues from mature trees. The origin of the microbes occurring in tissue cultures of buds of Scots pine was established in this study. One of the microbes, classified as Hormonema dematioides (Ascomycota), was localized in the scale tissues of a bud. Several other microbes were detected, and were associated especially with the meristematic tissues of Scots pine buds. This group was comprised of the yeast Rhodotorula minuta, and bacteria belonging to Methylobacterium spp., the Pseudomonas fluorescens subgroup, and a Mycobacterium sp. These endophytes were located particularly in the outermost cells of meristems, in the epithelial cells of resin ducts, and in the cells of the developing stem, in the vicinity of the meristems. These endophytes were less frequently found in the vascular tissue or in the intercellular spaces of cells, which are typical locations for the previously known endophytic bacteria. The meristem-associated endophytes were discovered to affect growth of pine tissues, and some of them produced substances that are suitable as precursors for phytohormone synthesis. Additionally, pure cultures of both bacterial and fungal endophytes showed antagonism in vitro against pathogens. When the correlation between the presence endophytes and the degeneration of bud-derived tissue cultures of Scots pine was studied, it was discovered that the endophytes grew uncontrollably once a tissue culture was initiated from the bud. A high level of chitinase production was also detected in these tissue cultures, which was considered to be indicative of a defense reaction. However, the endophytes were not found to colonize excessively in every tissue, but all bud-derived tissue cultures of Scots pine eventually degenerate. Therefore, it was concluded that the endophytes may not exclusively be considered responsible for the degeneration of the cultures. Keywords: biological control, buds, endophytes, meristem, Pinus sylvestris L., regeneration capacity, tissue culture Seliina Päällysaho (2001) Contribution of X chromosomal and autosomal genes to species differences in male courtship songs of the Drosophila virilis group species. Acta Universitatis Ouluensis A 377. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514265831/ In sympatric Drosophila species, songs produced by male wing vibration during courtship are an effective mechanism preventing interspecific matings and maintaining sexual isolation between different species. These songs can vary greatly even between closely related species. The aim of this study was to localise X chromosomal and autosomal genes affecting species differences in male courtship song and to study their interaction in the D. virilis group species. Various genes were probed by in situ hybridisation on the X chromosomes of six species of the group, which enabled us to use localised RFLP markers in QTL studies, as well as to compare gene arrangements of different species. Genetic analyses of differences between the songs of D. virilis and D. littoralis showed that species-specific song traits are affected both by X chromosomal and autosomal genes. The X chromosomal gene(s) having a major impact on pause and pulse length in male song were found to be located at the proximal region of the chromosome. Precise localisation of the song genes was, however, not possible due to multiple chromosome rearrangements restricting recombination between RFLP markers located on this area. The same problem was faced when studying hybrids between D. flavomontana and D. montana with less diverged X chromosomal gene arrangements. Interaction between the X chromosomal and autosomal song genes in determining male song traits was studied in four species belonging to the virilis and montana phylads of D. virilis group. The long pauses in courtship song were found to be mainly caused by X chromosomal song genes (or maternal / cytological factors), while pulse length was determined by X chromosomal genes interacting with autosomal genes. This confirms the important role of X chromosomal gene(s) in song evolution in the montana phylad species. The direction of dominance in hybrid songs suggests that the songs of the montana phylad species have been affected by directional selection favouring shorter pulses and longer pauses between sound pulses during their evolution. The levels and patterns of DNA polymorphism in an X-linked fused (fu) gene was studied in different D. montana populations. These studies revealed that D. montana populations are significantly but not completely isolated, and that a selective sweep at fu (or at a gene linked to fu) may be the reason for the reduced levels and patterns of variability of this gene in Finnish D. montana populations. The methods used in this study will be utilized to study variation in 'song genes' in the future. Keywords: Drosophila virilis, in situ hybridisation, courtship song, DNA sequence variation, inversion, RFLP markers Pasi Reunanen (2001) Landscape responses of the Siberian flying squirrel (Pteromys volans) in northern Finland. The effect of scale on habitat patterns and species incidence. Acta Universitatis Ouluensis A 371. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514264967/ Spatial structure of habitats has been found to affect the species abundance and distribution patterns in heterogeneous environments. In this thesis, I studied landscape responses of the Siberian flying squirrel in a boreal forest context in northern Finland. Studies were conducted at several spatial scales in order to identify landscape characteristics that are associated with the species occurrence at a local scale and its distribution patterns at a regional scale. Data on species presence and absence in forest areas were collected in the field. Habitat patterns in landscapes were analysed from satellite images and landscape metrics concerning landscape structure were quantified in Geographic Information Systems (GIS). Results of this study are in agreement with the general landscape ecological theory and findings in the field. In northern Finland, the distribution of the Siberian flying squirrel primarily follows the spatial extent of spruce-dominated forests but that its actual occurrence is dependent on the scale of observation and the habitat structure. At a home range scale the abundance of deciduous trees in old spruce forest increases the probability that a forest site is occupied by the species, whereas at a local scale the amount of such spruce forests and linkages between habitat patches play an important role. At a regional scale, an increase in open areas and the dominance of pine makes the habitat unsuitable and restricts the presence of the species. Findings of the present research forward practical forest management planning at a large scale and may help set general conservation goals for the Siberian flying squirrel. When managing the species in a complex network of habitat patches in heterogeneous landscapes, spatial dispersion of potential habitat patches as well as connecting habitat and their temporal development should be considered carefully. For this purpose, remote sensed images and GIS are valuable and useful tools. Satellite-image based landscape analysis is presently developing rapidly and hopefully this methodology will soon become a common practice in landscape ecological research and everyday forest management planning. Keywords: GIS, landscape ecology, remote sensing Minna Ruokonen (2001) Phylogeography and conservation genetics of the lesser white-fronted goose (Anser erythropus). Acta Universitatis Ouluensis A 360. University of Oulu, Department of Biology. http://herkules.oulu.fi/isbn9514259483/ The genetic distances among the Anser species ranged from 0.9 to 5.5% in the complete control region sequences and supported the view of close relatedness of these species. Among the four most closely related species, the bean, pink-footed, white-fronted and lesser white-fronted goose, the branching order is uncertain. The short internal branches and low support for the branching order suggest that the species have diverged recently within short time-intervals. The mtDNA tree obtained is incongruent with the traditional view of the species relationships, but the reasons for this remain to be clarified. Two diverged mitochondrial lineages were found in the lesser white-fronted goose and a refugial origin was proposed. Basal haplotypes are geographically widespread and indicate a recent common ancestry for populations. The derived haplotypes are confined to singular breeding populations and suggest restrictions to the present female gene flow. A shift in the frequency of the mtDNA lineages approximately coincides with a migratory divide in the Taimyr Peninsula. Low mtDNA diversity and significant difference in the haplotype frequencies observed in Fennoscandian subpopulation suggested that it should be considered as a management unit. The fossil record was examined to gain additional information about the colonisation history of the species, but was found to be of limited use. The captive lesser white-fronted goose stock used for reintroduction/restocking was shown to be incompatible with the Fennoscandian wild population. Some captive individuals carried the mtDNA of the white-fronted goose suggesting a hybrid origin. Hybridisation has probably occurred during captive propagation, but to clarify further the extent of introgression, nuclear markers should be applied. The structure and evolution of the control region were studied by comparing complete avian sequences. Saturation was found to occur at pairwise divergences of 10% as shown for third codon positions of the mitochondrial genes previously. In pairwise comparisons of the control region and cytochrome b sequences, the rate of divergence varied among the lineages. Two conserved sequence blocks showed considerable sequence conservation when compared to mammalian sequences. Keywords: Anser, conservation genetics, mitochondrial control region, phylogeography |