Landscape-scale soil erosion modelling and ecological restoration for a mountainous watershed in Sichuan, China

Sichuanissa Tiibetin ylängön metsäkato on pysähtynyt mutta eroosio-ongelmat jatkuvat Viikin tropiikki-instituutin tutkija Ping ZHOU kartoitti trooppisen metsänhoidon alaan kuuluvassa väitöskirjatyössään maaperän eroosioalttiutta ja sen riippuvuutta metsäkasvillisuudesta Jangtsen tärkeää sivuhaaraa Min-jokea ympäröivällä n. 7400 neliökilometrin suuruisella valuma-alueella Sichuanin Aba-piirikunnassa. Aineistonaan hän käytti muun muassa satelliittikartoitustietoja ja mittaustuloksia yli 600 maastokoealalta. Tutkimuksen nimi suomeksi on "Maaperän eroosion mallinnus ja vuoristoisen valuma-alueen ekologinen ennallistaminen Sichuanissa Kiinassa". Aikaisempien tutkimusten perusteella oli tiedossa että metsien häviäminen tällä alueella pysähtyi jo 1980-luvun alussa. Sen jälkeen on metsien pinta-ala hitaasti kasvanut etupäässä sen vuoksi, että teollinen puunhakkuu luonnonmetsissä kiellettiin kokonaan v. 1998 ja 25 astetta jyrkemmillä rinteillä myös maatalouden harjoittaminen on saatu lopetetuksi viljelijöille tarjottujen taloudellisten houkuttimien avulla. Täten myös pelto- ja laidunmaata on voitu ennallistaa metsäksi. Ping Zhou pystyi jakamaan 5700 metrin korkeuteen saakka kohoavan vuoristoalueen eroosioalttiudeltaan erilaisiin vyöhykkeisiin rinteen kaltevuuden, sademäärän, kasvipeitteen ja maalajin perusteella. Noin 15 prosentilla tutkitun valuma-alueen pinta-alasta, lähinnä Min-joen pääuomaa ympäröivillä jyrkillä rinteillä, eroosioriski oli suuri tai erittäin suuri. Eri tyyppisellä kasvillisuudella oli hyvin erilainen vaikutus eroosioalttiuteen, ja myös alueen sijainti vuoriston eri korkeuksilla vaikutti eroosioon. Säästyneet lähes luonnontilaiset havumetsät, joita on etupäässä vuoriston ylimmissä osissa 2600-4000 metrin korkeudella, edistävät tehokkaasti metsän luontaista uudistumista ja levittäytymistä vaurioituneille alueille. Säilyneiden metsien puulajikoostumus antoi tutkimuksessa mahdollisuuden ennustaa metsien tulevaa kehitystä koko tutkitulla valuma-alueella sen eri korkeusvyöhykkeissä ja eri maaperätyypeillä. Ennallistamisen kannalta ongelmallisimpia olivat alueet joilta metsäpeite oli lähinnä puiden teollisen hakkuun vuoksi kokonaan hävinnyt ja joilla maaperä yleisesti oli eroosion pahoin kuluttama. Näillä alueilla ei ole tehty juuri mitään uudistamis- tai ennallistamistoimenpiteitä. Niillä metsien ennallistaminen vaatii myös puiden tai pensaiden istuttamista. Tähän sopivia ovat erityisesti ilmakehän typpeä sitovat lajit, joista alueella kasvaa luontaisena mm. sama tyrnilaji joka esiintyy myös Suomessa. Työssä tutkittiin yli kahdeksankymmenen paikallisen luontaisen puulajin (joista peräti noin kolmannes on havupuulajeja) ekologisia ominaisuuksia ja soveltuvuutta metsien ennallistamiseen. Avainasemassa työn onnistumisen kannalta ovat nyt paikalliset asukkaat, joiden maankäytön muutokset ovat jo selvästi edistänet luonnonmetsän ennalleen palautumista. Suomen Akatemia rahoitti vuosina 2004-2006 VITRI:n tutkimushanketta, josta Ping Zhou'n väitöskirjatyö muodosti keskeisen osan. Kenttätyö Sichuanissa avasi mahdollisuuden hedelmälliseen monitieteiseen yhteistyöhön ja tutkijavaihtoon Kiinan tiedeakatemian alaisen Chengdun biologiainstituutin (CIB) kanssa; tämä tieteellinen kanssakäyminen jatkuu edelleen.

Ecological restoration of forests in Fennoscandia : Defining reference stand structures and immediate effects of restoration.

The first aim of this thesis was to explore the structural characteristics of near-natural forests and to quantify how human utilization has changed them. For this, we examined the stand characteristics in Norway spruce Picea abies (L.) Karst-dominated old-growth stands in northwestern Russia and in old Scots pine Pinus sylvestris L.-dominated stands in three regions from southern Finland to northwestern Russia. In the second study, we also compared stands with different degrees of human impact, from near-natural stands and stands selectively cut in the past to managed stands. Secondly, we used an experimental approach to study the short-term effects of different restorative treatments on forest structure and regeneration in managed Picea abies stands in southern Finland. Restorative treatments consisted of a partial cut combined with three levels of coarse woody debris retention, and a fire/no-fire treatment. In addition, we examined burned and unburned reference stands without cutting treatments. Results from near-natural Picea abies forests emphasize the dynamic character of old-growth forests, the variety of late-successional forest structures, and the fact that extended time periods are needed to attain certain late-successional stages with specific structural and habitat attributes, such as large-diameter deciduous trees and a variety of deadwood. The results from old Pinus sylvestris-dominated forests showed that human impact in the form of forest utilization and fire exclusion has strongly modified and reduced the structural complexity of stands. Consequently, small protected forest fragments in Finland may not serve as valid natural reference areas for forest restoration. However, results from the restoration experiment showed that early-successional natural stand characteristics can be restored to structurally impoverished managed Picea abies stands, despite a significant portion of wood volume being harvested. A variety of restoration methods is needed, due to differences in the condition of the forest when restoration is initiated and the variety of successional stages of forest structures after anthropogenic and natural disturbances. Keywords: dead wood, disturbance dynamic, fire, near-natural stand, rehabilitation, succession

Natural regeneration and ecological succession in Pinus kesiya watershed plantations in northern Thailand : Implications on plantation management

Establishment of Pinus kesiya Roy. ex Gord. plantations in Thailand began in the 1960s by the Royal Forest Department. The aim was to reforest abandoned swidden areas and grasslands in order to reduce erosion and to produce timber and fuel wood. Today there are about 150, 000 ha of P. kesiya plantations in northern Thailand. Most of these plantations cannot be harvested due to a national logging ban. Previous studies have suggested that Pinus kesiya plantations posses a capability as a foster environment for native broadleaved tree species, but little is known about the extent of regeneration in these plantations. The general aim of the study was to clarify the extent of forest regeneration and interactions behind it in Pinus kesiya plantations of the Ping River basin, northern Thailand. Based on the results of this study and previous literature, forest management proposals were produced for the area studied. In four different pine plantation areas, a total of seven plantations were assessed using systematic data collection with clustered circular sample plots. Vegetation and environmental data were statistically analysed, so as to recognise the key factors affecting regeneration. Regeneration had occurred in all plantations studied. Regeneration of broadleaved trees was negatively affected by forest fire and canopy coverage. A high basal area of mature broadleaved trees affected the regeneration process positively. Forest fire disturbance had a strong effect also on plantation structure and species composition. Because of an unclear future forest management setting as regards forest laws in Thailand, a management system that enables various future utilisation possibilities and emphasises local participation is recommended for P. kesiya watershed platations of northern Thailand.

Plant species diversity of buffer zones in agricultural landscapes: in search of determinants from the local to regional scale

Buffer zones are vegetated strip-edges of agricultural fields along watercourses. As linear habitats in agricultural ecosystems, buffer strips dominate and play a leading ecological role in many areas. This thesis focuses on the plant species diversity of the buffer zones in a Finnish agricultural landscape. The main objective of the present study is to identify the determinants of floral species diversity in arable buffer zones from local to regional levels. This study was conducted in a watershed area of a farmland landscape of southern Finland. The study area, Lepsämänjoki, is situated in the Nurmijärvi commune 30 km to the north of Helsinki, Finland. The biotope mosaics were mapped in GIS. A total of 59 buffer zones were surveyed, of which 29 buffer strips surveyed were also sampled by plot. Firstly, two diversity components (species richness and evenness) were investigated to determine whether the relationship between the two is equal and predictable. I found no correlation between species richness and evenness. The relationship between richness and evenness is unpredictable in a small-scale human-shaped ecosystem. Ordination and correlation analyses show that richness and evenness may result from different ecological processes, and thus should be considered separately. Species richness correlated negatively with phosphorus content, and species evenness correlated negatively with the ratio of organic carbon to total nitrogen in soil. The lack of a consistent pattern in the relationship between these two components may be due to site-specific variation in resource utilization by plant species. Within-habitat configuration (width, length, and area) were investigated to determine which is more effective for predicting species richness. More species per unit area increment could be obtained from widening the buffer strip than from lengthening it. The width of the strips is an effective determinant of plant species richness. The increase in species diversity with an increase in the width of buffer strips may be due to cross-sectional habitat gradients within the linear patches. This result can serve as a reference for policy makers, and has application value in agricultural management. In the framework of metacommunity theory, I found that both mass effect(connectivity) and species sorting (resource heterogeneity) were likely to explain species composition and diversity on a local and regional scale. The local and regional processes were interactively dominated by the degree to which dispersal perturbs local communities. In the lowly and intermediately connected regions, species sorting was of primary importance to explain species diversity, while the mass effect surpassed species sorting in the highly connected region. Increasing connectivity in communities containing high habitat heterogeneity can lead to the homogenization of local communities, and consequently, to lower regional diversity, while local species richness was unrelated to the habitat connectivity. Of all species found, Anthriscus sylvestris, Phalaris arundinacea, and Phleum pretense significantly responded to connectivity, and showed high abundance in the highly connected region. We suggest that these species may play a role in switching the force from local resources to regional connectivity shaping the community structure. On the landscape context level, the different responses of local species richness and evenness to landscape context were investigated. Seven landscape structural parameters served to indicate landscape context on five scales. On all scales but the smallest scales, the Shannon-Wiener diversity of land covers (H') correlated positively with the local richness. The factor (H') showed the highest correlation coefficients in species richness on the second largest scale. The edge density of arable field was the only predictor that correlated with species evenness on all scales, which showed the highest predictive power on the second smallest scale. The different predictive power of the factors on different scales showed a scaledependent relationship between the landscape context and local plant species diversity, and indicated that different ecological processes determine species richness and evenness. The local richness of species depends on a regional process on large scales, which may relate to the regional species pool, while species evenness depends on a fine- or coarse-grained farming system, which may relate to the patch quality of the habitats of field edges near the buffer strips. My results suggested some guidelines of species diversity conservation in the agricultural ecosystem. To maintain a high level of species diversity in the strips, a high level of phosphorus in strip soil should be avoided. Widening the strips is the most effective mean to improve species richness. Habitat connectivity is not always favorable to species diversity because increasing connectivity in communities containing high habitat heterogeneity can lead to the homogenization of local communities (beta diversity) and, consequently, to lower regional diversity. Overall, a synthesis of local and regional factors emerged as the model that best explain variations in plant species diversity. The studies also suggest that the effects of determinants on species diversity have a complex relationship with scale.

Understanding the organic chain : The framework of the interaction between the actors in organic chains in relation to ecological modernisation of food production

The sustainability of food production has increasingly attracted the attention of consumers, farmers, food and retailing companies, and politicians. One manifestation of such attention is the growing interest in organic foods. Organic agriculture has the potential to enhance the ecological modernisation of food production by implementing the organic method as a preventative innovation that simultaneously produces environmental and economic benefits. However, in addition to the challenges to organic farming, the small market share of organic products in many countries today and Finland in particular risks undermining the achievement of such benefits. The problems identified as hindrances to the increased consumption of organic food are the poor availability, limited variety and high prices of organic products, the complicated buying decisions and the difficulties in delivering the intangible value of organic foods. Small volumes and sporadic markets, high costs, lack of market information, as well as poor supply reliability are obstacles to increasing the volume of organic production and processing. These problems shift the focus from a single actor to the entire supply chain and require solutions that involve more interaction among the actors within the organic chain. As an entity, the organic food chain has received very little scholarly attention. Researchers have mainly approached the organic chain from the perspective of a single actor, or they have described its structure rather than the interaction between the actors. Consequently, interaction among the primary actors in organic chains, i.e. farmers, manufacturers, retailers and consumers, has largely gone unexamined. The purpose of this study is to shed light on the interaction of the primary actors within a whole organic chain in relation to the ecological modernisation of food production. This information is organised into a conceptual framework to help illuminate this complex field. This thesis integrates the theories and concepts of three approaches: food system studies, supply chain management and ecological modernisation. Through a case study, a conceptual system framework will be developed and applied to a real life-situation. The thesis is supported by research published in four articles. All examine the same organic chains through case studies, but each approaches the problem from a different, complementary perspective. The findings indicated that regardless of the coherent values emphasising responsibility, the organic chains were loosely integrated to operate as a system. The focus was on product flow, leaving other aspects of value creation largely aside. Communication with consumers was rare, and none of the actors had taken a leading role in enhancing the market for organic products. Such a situation presents unsuitable conditions for ecological modernisation of food production through organic food and calls for contributions from stakeholders other than those directly involved in the product chain. The findings inspired a revision of the original conceptual framework. The revised framework, the three-layer framework , distinguishes the different layers of interaction. By gradually enlarging the chain orientation the different but interrelated layers become visible. A framework is thus provided for further research and for understanding practical implications of the performance of organic food chains. The revised framework provides both an ideal model for organic chains in relation to ecological modernisation and demonstrates a situation consistent with the empirical evidence.

Genetic and environmental influences on human responses to odors

Olfaction, the sense of smell, has many important functions in humans. Human responses to odors show substantial individual variation. Olfactory receptor genes have been identified and other genes may also influence olfaction. However, the proportion of phenotypic variation in odor response due to genetic variation remains largely unknown. Little is also known about which genes modify specific responses to odors. This study aimed to elucidate genetic and environmental influences on human responses to odors. Individuals from Finnish families (n=146) and Australian (n=413), British (n=163), Danish (n=336), and Finnish (n=399) twins rated intensity and pleasantness of a set of 12 (families) or 6 (twins) odors and tried to identify the odors. In addition, the participants rated their own sense of smell and annoyance experienced with different environmental odors. The odor stimuli of a commercial smell test (The Brief Smell Identification Test; banana, chocolate, cinnamon, gasoline, lemon, onion, paint thinner, pineapple, rose, smoke, soap, and turpentine) were presented in the family study. Based on the results of the family study and a literature survey, a new set of odor stimuli (androstenone, chocolate, cinnamon, isovaleric acid, lemon, and turpentine) was designed for the twin studies. In the family sample, heritabilities of the traits were estimated and underlying genomic regions were searched using a genome-wide linkage scan. In the pooled twin sample, variation in the measured traits was decomposed into genetic and environmental components using quantitative genetic modeling. In addition, associations between nongenetic factors (e.g., sex, age, and smoking) and olfactory-related traits were explored. Suggestive evidence for a genetic linkage for pleasantness of cinnamon at a locus on chromosome 4q32.3 emerged from the family sample. High heritability for the pleasantness of cinnamon was found in the family but not the twin study. Heritability of perceived intensity of androstenone odor was determined to be ~30% in the twin sample. A strong genetic correlation between perceived intensity and pleasantness of androstenone, in the absence of any environmental correlation, indicated that only the genetic correlation explained the phenotypic correlation between the traits (r=-0.27) and that the traits were influenced by an overlapping set of genes. Self-rated olfactory function appeared to reflect the odor annoyance experienced rather than actual olfactory acuity or genetic involvement. Results from nongenetic analyses supported the speculated superiority of females' olfactory abilities, the age-related diminishing of olfactory acuity, and the influences of experience-dependent factors on odor responses. This was the first study to estimate heritabilities and perform linkage screens for individual odors. A genetic effect was detected for only a few responses to specific odors, suggesting the predominance of environmental effects in odor perceptions.

A matter of taste : genetic and environmental influences on responses to sweetness

Diet is a major player in the maintenance of health and onset of many diseases of public health importance. The food choice is known to be largely influenced by sensory preferences. However, in many cases it is unclear whether these preferences and dietary behaviors are innate or acquired. The aim of this thesis work was to study the extent to which the individual differences in dietary responses, especially in liking for sweet taste, are influenced by genetic factors. Several traits measuring the responses to sweetness and other dietary variables were applied in four studies: in British (TwinsUK) and Finnish (FinnTwin12 and FinnTwin16) twin studies and in a Finnish migraine family study. All the subjects were adults and they participated in chemosensory measurements (taste and smell tests) and filled in food behavior questionnaires. Further, it was studied, whether the correlations among the variables are mediated by genetic or environmental factors and where in the genome the genes influencing the heritable traits are located. A study of young adult Finnish twins (FinnTwin16, n=4388) revealed that around 40% of the food use is attributable to genetic factors and that the common, childhood environment does not affect the food use even shortly after moving from the parents home. Both the family study (n=146) and the twin studies (British twins, n=663) showed that around half of the variation in the liking for sweetness is inherited. The same result was obtained both by the chemosensory measurements (heritability 41-49%) and the questionnaire variables (heritability 31-54%). By contrast, the intensity perception of sweetness or the responses to saltiness were not influenced by genetic factors. Further, a locus influencing the use-frequency of sweet foods was identified on chromosome 16p. A closer examination of the relationships among the variables based on 663 British twins revealed that several genetic and environmental correlations exist among the different measures of liking for sweetness. However, these correlations were not very strong (range 0.06-0.55) implying that the instruments used measure slightly different aspects of the phenomenon. In addition, the assessment of the associations among responses to fatty foods, dieting behaviors, and body mass index in twin populations (TwinsUK n=1027 and FinnTwin12 n=299) showed that the dieting behaviors (cognitive restraint, uncontrolled eating, and emotional eating) mediate the relationship between obesity and diet. In conclusion, the work increased the understanding of the background variables of human eating behavior. Genetic effects were shown to underlie the variation of many dietary traits, such as liking for sweet taste, use of sweet foods, and dieting behaviors. However, the responses to salty taste were shown to be mainly determined by environmental factors and thus should more easily be modifiable by dietary education, exposure, and learning than sweet taste preferences. Although additional studies are needed to characterize the genetic element located on chromosome 16 that influences the use-frequency of sweet foods, the results underline the importance of inherited factors on human eating behavior.

Responses of soil microbial communities to clonal variation of Norway spruce

In boreal forests, microorganisms have a pivotal role in nutrient and water supply of trees as well as in litter decomposition and nutrient cycling. This reinforces the link between above-ground and below-ground communities in the context of sustainable productivity of forest ecosystems. In northern boreal forests, the diversity of microbes associated with the trees is high compared to the number of distinct tree species. In this thesis, the aim was to study whether conspecific tree individuals harbour different soil microbes and whether the growth of the trees and the community structure of the associated microbes are connected. The study was performed in a clonal field trial of Norway spruce, which was established in a randomized block design in a clear-cut area. Since out-planting in 1994, the spruce clones showed two-fold growth differences. The fast-growing spruce clones were associated with a more diverse community of ectomycorrhizal fungi than the slow-growing spruce clones. These growth performance groups also differed with respect to other aspects of the associated soil microorganisms: the species composition of ectomycorrhizal fungi, in the amount of extraradical fungal mycelium, in the structure of bacterial community associated with the mycelium, and in the structure of microbial community in the organic layer. The communities of fungi colonizing needle litter of the spruce clones in the field did not differ and the loss of litter mass after two-years decomposition was equal. In vitro, needles of the slow-growing spruce clones were colonized by a more diverse community of endophytic fungi that were shown to be significant needle decomposers. This study showed a relationship between the growth of Norway spruce clones and the community structure of the associated soil microbes. Spatial heterogeneity in soil microbial community was connected with intraspecific variation of trees. The latter may therefore influence soil biodiversity in monospecific forests.

Postglacial climate changes and vegetation responses in northern Europe

Postglacial climate changes and vegetation responses were studied using a combination of biological and physical indicators preserved in lake sediments. Low-frequency trends, high-frequency events and rapid shifts in temperature and moisture balance were probed using pollen-based quantitative temperature reconstructions and oxygen-isotopes from authigenic carbonate and aquatic cellulose, respectively. Pollen and plant macrofossils were employed to shed light on the presence and response rates of plant populations in response to climate changes, particularly focusing on common boreal and temperate tree species. Additional geochemical and isotopic tracers facilitated the interpretation of pollen- and oxygen-isotope data. The results show that the common boreal trees were present in the Baltic region (~55°N) during the Lateglacial, which contrasts with the traditional view of species refuge locations in the south-European peninsulas during the glacial/interglacial cycles. The findings of this work are in agreement with recent paleoecological and genetic evidence suggesting that scattered populations of tree species persisted at higher latitudes, and that these taxa were likely limited to boreal trees. Moreover, the results demonstrate that stepwise changes in plant communities took place in concert with major climate fluctuations of the glacial/interglacial transition. Postglacial climate trends in northern Europe were characterized by rise, maxima and fall in temperatures and related changes in moisture balance. Following the deglaciation of the Northern Hemisphere and the early Holocene reorganization of the ice-ocean-atmosphere system, the long-term temperature trends followed gradually decreasing summer insolation. The early Holocene (~11,700-8000 cal yr BP) was overall cool, moist and oceanic, although the earliest Holocene effective humidity may have been low particularly in the eastern part of northern Europe. The gradual warming trend was interrupted by a cold event ~8200 cal yr BP. The maximum temperatures, ~1.5-3.0°C above modern values, were attained ~8000-4000 cal yr BP. This mid-Holocene peak warmth was coupled with low lake levels, low effective humidity and summertime drought. The late Holocene (~4000 cal yr BP-present) was characterized by gradually decreasing temperatures, higher lake levels and higher effective humidity. Moreover, the gradual trends of the late Holocene were probably superimposed by higher-frequency variability. The spatial variability of the Holocene temperature and moisture balance patterns were tentatively attributed to the differing heat capacities of continents and oceans, changes in atmospheric circulation modes and position of sites and subregions with respect to large water bodies and topographic barriers. The combination of physical and biological proxy archives is a pivotal aspect of this work, because non-climatic factors, such as postglacial migration, disturbances and competitive interactions, can influence reshuffling of vegetation and hence, pollen-based climate reconstructions. The oxygen-isotope records and other physical proxies presented in this work manifest that postglacial climate changes were the main driver of the establishment and expansion of temperate and boreal tree populations, and hence, large-scale and long-term vegetation patterns were in dynamic equilibrium with climate. A notable exception to this pattern may be the postglacial invasion of Norway spruce and the related suppression of mid-Holocene temperate forest. This salient step in north-European vegetation history, the development of the modern boreal ecosystem, cannot be unambiguously explained by current evidence of postglacial climate changes. The results of this work highlight that plant populations, including long-lived trees, may be able to respond strikingly rapidly to changes in climate. Moreover, interannual and seasonal variation and extreme events can exert an important influence on vegetation reshuffling. Importantly, the studies imply that the presence of diffuse refuge populations or local stands among the prevailing vegetation may have provided the means for extraordinarily rapid vegetation responses. Hence, if scattered populations are not provided and tree populations are to migrate long distances, their capacity to keep up with predicted rates of future climate change may be lower than previously thought.

Ecological processes and large-scale climate relationships in northern coniferous forests

Ilmasto vaikuttaa ekologisiin prosesseihin eri tasoilla. Suuren mittakaavan ilmastoprosessit, yhdessä ilmakehän ja valtamerien kanssa, säätelevät paikallisia sääilmiöitä suurilla alueilla (mantereista pallopuoliskoihin). Tämä väistöskirja pyrkii selittämään kuinka suuren mittakaavan ilmasto on vaikuttanut tiettyihin ekologisiin prosesseihin pohjoisella havumetsäalueella. Valitut prosessit olivat puiden vuosilustojen kasvu, metsäpalojen esiintyminen ja vuoristomäntykovakuoriaisen aiheuttamat puukuolemat. Suuren mittakaavan ilmaston löydettiin vaikuttaneen näiden prosessien esiintymistiheyteen, kestoon ja levinneisyyteen keskeisten sään muuttujien välityksellä hyvin laajoilla alueilla. Tutkituilla prosesseilla oli vahva yhteys laajan mittakaavan ilmastoon. Yhteys on kuitenkin ollut hyvin dynaaminen ja muuttunut 1900-luvulla ilmastonmuutoksen aiheuttaessa muutoksia suuren mittakaavan ja alueellisten ilmastoprosessien välisiin sisäisiin suhteisiin.

Joint Regression and Association Models for Repeated Categorical Responses

The focus of this study is on statistical analysis of categorical responses, where the response values are dependent of each other. The most typical example of this kind of dependence is when repeated responses have been obtained from the same study unit. For example, in Paper I, the response of interest is the pneumococcal nasopharengyal carriage (yes/no) on 329 children. For each child, the carriage is measured nine times during the first 18 months of life, and thus repeated respones on each child cannot be assumed independent of each other. In the case of the above example, the interest typically lies in the carriage prevalence, and whether different risk factors affect the prevalence. Regression analysis is the established method for studying the effects of risk factors. In order to make correct inferences from the regression model, the associations between repeated responses need to be taken into account. The analysis of repeated categorical responses typically focus on regression modelling. However, further insights can also be gained by investigating the structure of the association. The central theme in this study is on the development of joint regression and association models. The analysis of repeated, or otherwise clustered, categorical responses is computationally difficult. Likelihood-based inference is often feasible only when the number of repeated responses for each study unit is small. In Paper IV, an algorithm is presented, which substantially facilitates maximum likelihood fitting, especially when the number of repeated responses increase. In addition, a notable result arising from this work is the freely available software for likelihood-based estimation of clustered categorical responses.

Bayesian analysis of community dynamics

Elucidating the mechanisms responsible for the patterns of species abundance, diversity, and distribution within and across ecological systems is a fundamental research focus in ecology. Species abundance patterns are shaped in a convoluted way by interplays between inter-/intra-specific interactions, environmental forcing, demographic stochasticity, and dispersal. Comprehensive models and suitable inferential and computational tools for teasing out these different factors are quite limited, even though such tools are critically needed to guide the implementation of management and conservation strategies, the efficacy of which rests on a realistic evaluation of the underlying mechanisms. This is even more so in the prevailing context of concerns over climate change progress and its potential impacts on ecosystems. This thesis utilized the flexible hierarchical Bayesian modelling framework in combination with the computer intensive methods known as Markov chain Monte Carlo, to develop methodologies for identifying and evaluating the factors that control the structure and dynamics of ecological communities. These methodologies were used to analyze data from a range of taxa: macro-moths (Lepidoptera), fish, crustaceans, birds, and rodents. Environmental stochasticity emerged as the most important driver of community dynamics, followed by density dependent regulation; the influence of inter-specific interactions on community-level variances was broadly minor. This thesis contributes to the understanding of the mechanisms underlying the structure and dynamics of ecological communities, by showing directly that environmental fluctuations rather than inter-specific competition dominate the dynamics of several systems. This finding emphasizes the need to better understand how species are affected by the environment and acknowledge species differences in their responses to environmental heterogeneity, if we are to effectively model and predict their dynamics (e.g. for management and conservation purposes). The thesis also proposes a model-based approach to integrating the niche and neutral perspectives on community structure and dynamics, making it possible for the relative importance of each category of factors to be evaluated in light of field data.