Ecological communities in variable environments : dynamics and diversity under coloured environmental stochasticity

While environmental variation is an ubiquitous phenomenon in the natural world which has for long been appreciated by the scientific community recent changes in global climatic conditions have begun to raise consciousness about the economical, political and sociological ramifications of global climate change. Climate warming has already resulted in documented changes in ecosystem functioning, with direct repercussions on ecosystem services. While predicting the influence of ecosystem changes on vital ecosystem services can be extremely difficult, knowledge of the organisation of ecological interactions within natural communities can help us better understand climate driven changes in ecosystems. The role of environmental variation as an agent mediating population extinctions is likely to become increasingly important in the future. In previous studies population extinction risk in stochastic environmental conditions has been tied to an interaction between population density dependence and the temporal autocorrelation of environmental fluctuations. When populations interact with each other, forming ecological communities, the response of such species assemblages to environmental stochasticity can depend, e.g., on trophic structure in the food web and the similarity in species-specific responses to environmental conditions. The results presented in this thesis indicate that variation in the correlation structure between species-specific environmental responses (environmental correlation) can have important qualitative and quantitative effects on community persistence and biomass stability in autocorrelated (coloured) environments. In addition, reddened environmental stochasticity and ecological drift processes (such as demographic stochasticity and dispersal limitation) have important implications for patterns in species relative abundances and community dynamics over time and space. Our understanding of patterns in biodiversity at local and global scale can be enhanced by considering the relevance of different drift processes for community organisation and dynamics. Although the results laid out in this thesis are based on mathematical simulation models, they can be valuable in planning effective empirical studies as well as in interpreting existing empirical results. Most of the metrics considered here are directly applicable to empirical data.

Microbial diversity in the municipal composting process and development of detection methods

Composting refers to aerobic degradation of organic material and is one of the main waste treatment methods used in Finland for treating separated organic waste. The composting process allows converting organic waste to a humus-like end product which can be used to increase the organic matter in agricultural soils, in gardening, or in landscaping. Microbes play a key role as degraders during the composting-process, and the microbiology of composting has been studied for decades, but there are still open questions regarding the microbiota in industrial composting processes. It is known that with the traditional, culturing-based methods only a small fraction, below 1%, of the species in a sample is normally detected. In recent years an immense diversity of bacteria, fungi and archaea has been found to occupy many different environments. Therefore the methods of characterising microbes constantly need to be developed further. In this thesis the presence of fungi and bacteria in full-scale and pilot-scale composting processes was characterised with cloning and sequencing. Several clone libraries were constructed and altogether nearly 6000 clones were sequenced. The microbial communities detected in this study were found to differ from the compost microbes observed in previous research with cultivation based methods or with molecular methods from processes of smaller scale, although there were similarities as well. The bacterial diversity was high. Based on the non-parametric coverage estimations, the number of bacterial operational taxonomic units (OTU) in certain stages of composting was over 500. Sequences similar to Lactobacillus and Acetobacteria were frequently detected in the early stages of drum composting. In tunnel stages of composting the bacterial community comprised of Bacillus, Thermoactinomyces, Actinobacteria and Lactobacillus. The fungal diversity was found to be high and phylotypes similar to yeasts were abundantly found in the full-scale drum and tunnel processes. In addition to phylotypes similar to Candida, Pichia and Geotrichum moulds from genus Thermomyces and Penicillium were observed in tunnel stages of composting. Zygomycetes were detected in the pilot-scale composting processes and in the compost piles. In some of the samples there were a few abundant phylotypes present in the clone libraries that masked the rare ones. The rare phylotypes were of interest and a method for collecting them from clone libraries for sequencing was developed. With negative selection of the abundant phylotyps the rare ones were picked from the clone libraries. Thus 41% of the clones in the studied clone libraries were sequenced. Since microbes play a central role in composting and in many other biotechnological processes, rapid methods for characterization of microbial diversity would be of value, both scientifically and commercially. Current methods, however, lack sensitivity and specificity and are therefore under development. Microarrays have been used in microbial ecology for a decade to study the presence or absence of certain microbes of interest in a multiplex manner. The sequence database collected in this thesis was used as basis for probe design and microarray development. The enzyme assisted detection method, ligation-detection-reaction (LDR) based microarray, was adapted for species-level detection of microbes characteristic of each stage of the composting process. With the use of a specially designed control probe it was established that a species specific probe can detect target DNA representing as little as 0.04% of total DNA in a sample. The developed microarray can be used to monitor composting processes or the hygienisation of the compost end product. A large compost microbe sequence dataset was collected and analysed in this thesis. The results provide valuable information on microbial community composition during industrial scale composting processes. The microarray method was developed based on the sequence database collected in this study. The method can be utilised in following the fate of interesting microbes during composting process in an extremely sensitive and specific manner. The platform for the microarray is universal and the method can easily be adapted for studying microbes from environments other than compost.

Characterization of genomic diversity in extraintestinal pathogenic Escherichia coli (ExPEC) and development of a diagnostic DNA microarray for the differentiation of ExPEC isolates causing urinary tract infections

Extraintestinal pathogenic Escherichia coli (ExPEC) represent a diverse group of strains of E. coli, which infect extraintestinal sites, such as the urinary tract, the bloodstream, the meninges, the peritoneal cavity, and the lungs. Urinary tract infections (UTIs) caused by uropathogenic E. coli (UPEC), the major subgroup of ExPEC, are among the most prevalent microbial diseases world wide and a substantial burden for public health care systems. UTIs are responsible for serious morbidity and mortality in the elderly, in young children, and in immune-compromised and hospitalized patients. ExPEC strains are different, both from genetic and clinical perspectives, from commensal E. coli strains belonging to the normal intestinal flora and from intestinal pathogenic E. coli strains causing diarrhea. ExPEC strains are characterized by a broad range of alternate virulence factors, such as adhesins, toxins, and iron accumulation systems. Unlike diarrheagenic E. coli, whose distinctive virulence determinants evoke characteristic diarrheagenic symptoms and signs, ExPEC strains are exceedingly heterogeneous and are known to possess no specific virulence factors or a set of factors, which are obligatory for the infection of a certain extraintestinal site (e. g. the urinary tract). The ExPEC genomes are highly diverse mosaic structures in permanent flux. These strains have obtained a significant amount of DNA (predictably up to 25% of the genomes) through acquisition of foreign DNA from diverse related or non-related donor species by lateral transfer of mobile genetic elements, including pathogenicity islands (PAIs), plasmids, phages, transposons, and insertion elements. The ability of ExPEC strains to cause disease is mainly derived from this horizontally acquired gene pool; the extragenous DNA facilitates rapid adaptation of the pathogen to changing conditions and hence the extent of the spectrum of sites that can be infected. However, neither the amount of unique DNA in different ExPEC strains (or UPEC strains) nor the mechanisms lying behind the observed genomic mobility are known. Due to this extreme heterogeneity of the UPEC and ExPEC populations in general, the routine surveillance of ExPEC is exceedingly difficult. In this project, we presented a novel virulence gene algorithm (VGA) for the estimation of the extraintestinal virulence potential (VP, pathogenicity risk) of clinically relevant ExPECs and fecal E. coli isolates. The VGA was based on a DNA microarray specific for the ExPEC phenotype (ExPEC pathoarray). This array contained 77 DNA probes homologous with known (e.g. adhesion factors, iron accumulation systems, and toxins) and putative (e.g. genes predictably involved in adhesion, iron uptake, or in metabolic functions) ExPEC virulence determinants. In total, 25 of DNA probes homologous with known virulence factors and 36 of DNA probes representing putative extraintestinal virulence determinants were found at significantly higher frequency in virulent ExPEC isolates than in commensal E. coli strains. We showed that the ExPEC pathoarray and the VGA could be readily used for the differentiation of highly virulent ExPECs both from less virulent ExPEC clones and from commensal E. coli strains as well. Implementing the VGA in a group of unknown ExPECs (n=53) and fecal E. coli isolates (n=37), 83% of strains were correctly identified as extraintestinal virulent or commensal E. coli. Conversely, 15% of clinical ExPECs and 19% of fecal E. coli strains failed to raster into their respective pathogenic and non-pathogenic groups. Clinical data and virulence gene profiles of these strains warranted the estimated VPs; UPEC strains with atypically low risk-ratios were largely isolated from patients with certain medical history, including diabetes mellitus or catheterization, or from elderly patients. In addition, fecal E. coli strains with VPs characteristic for ExPEC were shown to represent the diagnostically important fraction of resident strains of the gut flora with a high potential of causing extraintestinal infections. Interestingly, a large fraction of DNA probes associated with the ExPEC phenotype corresponded to novel DNA sequences without any known function in UTIs and thus represented new genetic markers for the extraintestinal virulence. These DNA probes included unknown DNA sequences originating from the genomic subtractions of four clinical ExPEC isolates as well as from five novel cosmid sequences identified in the UPEC strains HE300 and JS299. The characterized cosmid sequences (pJS332, pJS448, pJS666, pJS700, and pJS706) revealed complex modular DNA structures with known and unknown DNA fragments arranged in a puzzle-like manner and integrated into the common E. coli genomic backbone. Furthermore, cosmid pJS332 of the UPEC strain HE300, which carried a chromosomal virulence gene cluster (iroBCDEN) encoding the salmochelin siderophore system, was shown to be part of a transmissible plasmid of Salmonella enterica. Taken together, the results of this project pointed towards the assumptions that first, (i) homologous recombination, even within coding genes, contributes to the observed mosaicism of ExPEC genomes and secondly, (ii) besides en block transfer of large DNA regions (e.g. chromosomal PAIs) also rearrangements of small DNA modules provide a means of genomic plasticity. The data presented in this project supplemented previous whole genome sequencing projects of E. coli and indicated that each E. coli genome displays a unique assemblage of individual mosaic structures, which enable these strains to successfully colonize and infect different anatomical sites.

Regulation of GABAergic neuron identity and diversity in the developing midbrain

Gamma-aminobutyric acid (GABA) is the most abundant inhibitory neurotransmitter in the vertebrate brain. In the midbrain, GABAergic neurons contribute to the regulation of locomotion, nociception, defensive behaviours, fear and anxiety, as well as sensing reward and addiction. Despite the clinical relevance of this group of neurons, the mechanisms regulating their development are largely unknown. In addition, their migration and connectivity patterns are poorly characterized. This study focuses on the molecular mechanisms specifying the GABAergic fate, and the developmental origins of midbrain GABAergic neurons. First, we have characterized the function of a zink-finger transcription factor Gata2. Using a tissue-specific mutagenesis in mouse midbrain and anteror hindbrain, we showed that Gata2 is a crucial determinant of the GABAergic fate in midbrain. In the absence of Gata2, no GABAergic neurons are produced from the otherwise competent midbrain neuroepithelium. Instead, the Gata2-mutant cells acquire a glutamatergic neuron phenotype. Ectopic expression of Gata2 was also sufficient to induce GABAergic in chicken midbrain. Second, we have analyzed the midbrain phenotype of mice mutant for a proneural gene Ascl1, and described the variable and region-dependent requirements for Ascl1 in the midbrain GABAergic neurogenesis. These studies also have implications on the origin of distinct anatomical and functional GABAergic subpopulations in midbrain. Third, we have identified unique developmental properties of GABAergic neurons that are associated with the midbrain dopaminergic nuclei, the substantia nigra pars reticulata (SNpr) and ventral tegmental area (VTA). Namely, the genetic regulation of GABAergic fate in these cells is distinct from the rest of midbrain. In accordance to this phenomenon, our detailed fate-mapping analyses indicated that the SNpr-VTA GABAergic neurons are generated outside midbrain, in the neuroepithelium of anterior hindbrain.

Phylogenetics, taxon delimitation and phylogenetic diversity

Throughout the history of Linnean taxonomy, species have been described with varying degrees of justification. Many descriptions have been based on only a few ambiguous morphological characters. Moreover, species have been considered natural, well-defined units whereas higher taxa have been treated as disparate, non-existent creations. In the present thesis a few such cases were studied in detail. Often the species-level descriptions were based on only a few specimens and the variation previously thought to be interspecific was found to be intraspecific. In some cases morphological characters were sufficient to resolve the evolutionary relationships between the taxa, but generally more resolution was gained by the addition of molecular evidence. However, both morphological and molecular data were found to be deceptive in some cases. The DNA sequences of morphologically similar specimens were found to differ distinctly in some cases, whereas in other closely related species the morphology of specimens with identical DNA sequences differed substantially. This study counsels caution when evolutionary relationships are being studied utilizing only one source of evidence or a very limited number of characters (e.g. barcoding). Moreover, it emphasizes the importance of high quality data as well as the utilization of proper methods when making scientific inferences. Properly conducted analyses produce robust results that can be utilized in numerous interesting ways. The present thesis considered two such extensions of systematics. A novel hypothesis on the origin of bioluminescence in Elateriformia beetles is presented, tying it to the development of the clicking mechanism in the ancestors of these animals. An entirely different type of extension of systematics is the proposed high value of the white sand forests in maintaining the diversity of beetles in the Peruvian Amazon. White sand forests are under growing pressure from human activities that lead to deforestation. They were found to harbor an extremely diverse beetle fauna and many taxa were specialists living only in this unique habitat. In comparison to the predominant clay soil forests, considerably more elateroid beetles belonging to all studied taxonomic levels (species, genus, tribus, and subfamily) were collected in white sand forests. This evolutionary diversity is hypothesized to be due to a combination of factors: (1) the forest structure, which favors the fungus-plant interactions important for the elateroid beetles, (2) the old age of the forest type favoring survival of many evolutionary lineages and (3) the widespread distribution and fragmentation of the forests in the Miocene, favoring speciation.

Regeneration ecology and woody species diversity in the remnant natural forest at Wondo Genet, Ethiopia – Potential for landscape restoration

Regeneration ecology, diversity of native woody species and its potential for landscape restoration was studied in the remnant natural forest at the College of Forestry and Natural Resources at Wondo Genet, Ethiopia. The type of forest is Afromontane rainforest , with many valuable tree species like Aningeria adolfi-friederici, and it is an important provider of ecological, social and economical services for the population that lives in this area. The study contains two parts, natural regeneration studies (at the natural forest) and interviews with farmers in the nearby village of the remnant patch. The objective of the first part was to investigate the floristic composition, densitiy and regeneration profiles of native woody species in the forest, paying special attention to woody species that are considered the most relevant (socio-economic). The second part provided information on woody species preferred by the farmers and on multiple uses of the adjacent natural forest, it also provided information and analysed perceptions on forest degradation. Systematic plot sampling was used in the forest inventory. Twenty square plots of 20 x 20 m were assessed, with 38 identified woody species (the total number of species was 45), representing 26 families. Of these species 61% were trees, 13% shrubs, 11% lianas and 16% species that could have both life forms. An analysis of natural regeneration of five important tree species in the natural forest showed that Aningeria adolfi-friederici had the best regeneration results. An analysis of population structure (as determined by height classes) of two commercially important woody species in the forest, Aningeria adolfi-friederici and Podocarpus falcatus, showed a marked difference: Aningeria had a typical “reversed J” frequency distribution, while Podocarpus showed very low values in all height classes. Multi dimensional scaling (MDS) was used to map the sample plots according to their similarity in species composition, using the Sørensen quantitative index, coupled with indicator species analysis .Three groups were identified with respective indicator species: Group 1 – Adhatoda schimperiana, Group 2 – Olea hochstetteri , Group 3 – Acacia senegal and Aningeria adolfi-friederici. Thirty questionnaire interviews were conducted with farmers in the village of Gotu Onoma that use the nearby remant forest patch. Their tree preferences were exotic species such as Eucalyptus globulus for construction and fuelwood and Grevillea robusta for shade and fertility. Considering forest land degradation farmers were aware of the problem and suggested that the governmental institutions address the problem by planting more Eucalyptus globulus. The natural forest seemed to have moderate levels of disturbance and it was still floristically diverse. However, the low rate of natural regeneration of Podocarpus falcatus suggested that this species is threatened and must be a priority in conservation actions. Plantations and agroforestry seem to be possible solutions for rehabilitation of the surrounding degraded lands, thereby decreasing the existent pressure in the remnant natural forest.

Juvenile diversity of tree species in Theobroma cacao L. agroforestry and primary forest – Central Sulawesi, Indonesia

This thesis studies the tree species’ juvenile diversity in cacao (Theobroma cacao L.) based agroforestry and in primary forest in a natural conservation forest environment of Lore Lindu National Park, Sulawesi, Indonesia. Species’ adult composition in Lore Lindu National Park is relatively well studied, less is known about tree species’ diversity in seedling communities particularly in frequently disturbed cacao agroforestry field environment. Cacao production forms a potentially serious thread for maintaining the conservation areas pristine and forested in Sulawesi. The impacts of cacao production on natural environment are directly linked to the diversity and abundance of shade tree usage. The study aims at comparing differences between cacao agroforestry and natural forest in the surrounding area in their species composition in seedling and sapling size categories. The study was carried out in two parts. Biodiversity inventory of seedlings and saplings was combined with social survey with farmer interviews. Aim of the survey was to gain knowledge of the cacao fields, and farmers’ observations and choices regarding tree species associated with cacao. Data was collected in summer 2008. The assessment of the impact of environmental factors of solar radiation, weeding frequency, cacao tree planting density, distance to forest and distance to main park road, and type of habitat on seedling and sapling compositions was done with Non-metric Multidimensional Scaling (NMS). Outlier analysis was used to assess distorting variables for NMS, and Multi-Response Permutation Procedures (MRPP) analysis to differentiate the impact of categorical variables. Sampling success was estimated with rarefaction curves and jackknife estimate of species richness. In the inventory 135 species of trees and shrubs were found. Only some agroforestry related species were dominating. The most species rich were sapling communities in forest habitat. NMS was showing generally low linear correlation between variation of species composition and environmental variables. Solar radiation was having most significance as explaining variable. The most clearly separated in ordination were cacao and forest habitats. The results of seedling and sapling inventory were only partly coinciding with farmers’ knowledge of the tree species occurring on their fields. More research with frequent assessment of seedling cohorts is needed due to natural variability of cohorts and high mortality rate of seedlings.

Current Debates on Classifying Diversity Management: Review and a Proposal

This paper discusses various theoretical approaches to diversity management, analysing their similarities and differences. I start with a review of certain previously presented classifications, and then proceed to describing the different approaches in more detail. In this paper, I propose that the various viewpoints can be categorized into three groups: 1) practitioner/consultant approach, 2) mainstream approach, and 3) critical approaches. Although there are differences within these groups, in particular regarding the critical approaches, these differences appear less significant than those between the groups. Those representing the first group are mainly interested in how to get most out of a diverse workforce, while those in the second group focus on the effects of diversity on performance or work group functioning. While some of the mainstream writers can be rather critical towards earlier research, they hardly ever discuss or even recognize the wide ranging criticism put forward by critical scholars. The critical researchers, then, remain a rather scattered group who do not always share much more than a conviction that the mainstream research keeps missing highly significant issues. Nonetheless, in order to increase our understanding of how different persons can and do work together, more dialogue is required between the varying standpoints.

Models of Dispersal and Diversification

Ecology and evolutionary biology is the study of life on this planet. One of the many methods applied to answering the great diversity of questions regarding the lives and characteristics of individual organisms, is the utilization of mathematical models. Such models are used in a wide variety of ways. Some help us to reason, functioning as aids to, or substitutes for, our own fallible logic, thus making argumentation and thinking clearer. Models which help our reasoning can lead to conceptual clarification; by expressing ideas in algebraic terms, the relationship between different concepts become clearer. Other mathematical models are used to better understand yet more complicated models, or to develop mathematical tools for their analysis. Though helping us to reason and being used as tools in the craftmanship of science, many models do not tell us much about the real biological phenomena we are, at least initially, interested in. The main reason for this is that any mathematical model is a simplification of the real world, reducing the complexity and variety of interactions and idiosynchracies of individual organisms. What such models can tell us, however, both is and has been very valuable throughout the history of ecology and evolution. Minimally, a model simplifying the complex world can tell us that in principle, the patterns produced in a model could also be produced in the real world. We can never know how different a simplified mathematical representation is from the real world, but the similarity models do strive for, gives us confidence that their results could apply. This thesis deals with a variety of different models, used for different purposes. One model deals with how one can measure and analyse invasions; the expanding phase of invasive species. Earlier analyses claims to have shown that such invasions can be a regulated phenomena, that higher invasion speeds at a given point in time will lead to a reduction in speed. Two simple mathematical models show that analysis on this particular measure of invasion speed need not be evidence of regulation. In the context of dispersal evolution, two models acting as proof-of-principle are presented. Parent-offspring conflict emerges when there are different evolutionary optima for adaptive behavior for parents and offspring. We show that the evolution of dispersal distances can entail such a conflict, and that under parental control of dispersal (as, for example, in higher plants) wider dispersal kernels are optimal. We also show that dispersal homeostasis can be optimal; in a setting where dispersal decisions (to leave or stay in a natal patch) are made, strategies that divide their seeds or eggs into fractions that disperse or not, as opposed to randomized for each seed, can prevail. We also present a model of the evolution of bet-hedging strategies; evolutionary adaptations that occur despite their fitness, on average, being lower than a competing strategy. Such strategies can win in the long run because they have a reduced variance in fitness coupled with a reduction in mean fitness, and fitness is of a multiplicative nature across generations, and therefore sensitive to variability. This model is used for conceptual clarification; by developing a population genetical model with uncertain fitness and expressing genotypic variance in fitness as a product between individual level variance and correlations between individuals of a genotype. We arrive at expressions that intuitively reflect two of the main categorizations of bet-hedging strategies; conservative vs diversifying and within- vs between-generation bet hedging. In addition, this model shows that these divisions in fact are false dichotomies.