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One of the most unforgiving processes in nature is that of Muller's ratchet, a seemingly irreversible accumulation of deleterious mutations that all organisms have to deal with or face extinction. The most obvious way to avoid fitness collapse is recombination, though asexual populations usually do not have the luxury of recombining freely. With the aid of computational and mathematical models, we have studied other situations where this threat is averted and the organism can survive the ratchet. The results show that a ratchet where all mutations have the same deleterious fitness effect is very effectively stalled for large effects. However, if mutations are allowed to have a broad range of effects, the fitness-loss rate can be substantial even with the same mean effect as the one-type ratchet, but we have identified parameter regions where even the broad-range effects are effectively stopped. The fitness-loss from a ratchet is very sensitive to the mutation rate and a mutation that increases the mutation rate (mutator) can easily start an otherwise stalled ratchet. Large effect mutators are heavily counter-selected, but smaller mutators can spread in the population. They can be stopped by reversals (antimutators), but even if the mutation rate is equilibrated in this way, there will be large fluctuations in mutation rate and even larger in the fitness-loss rate due to the feedback amplification in their coupling. Another way of preventing the ratchet is by reversal of the deleterious mutations themselves through back-mutations or compensatory mutations. The rate required to stop the ratchet using only back-mutations before the fitness collapses is very large. A detailed comparison between the deleterious mutations in the ratchet and in a sexual population was made and the difference was found to be greatest for large populations with large genomes. There are obviously many ways to survive the ratchet, but even more ways to drive a species to extinction by enh

This thesis investigates the ecological and evolutionary implications of a recent secondary contact between two closely related bird species: collared (Ficedula albicollis) and pied (F. hypoleuca) flycatchers. Collared flycatchers started to colonize the Swedish island of Öland, where pied flycatchers were already present, in the late 1950s-early1960s. My major aims were to investigate which factors are acting against versus for long-term coexistence between the two species. Specifically, I investigated the relative importance of allopatric divergence, interspecific competition, hybridization and learning in promoting or inhibiting coexistence. The combined effects of interspecific competition and hybridization drives pied flycatchers towards local extinction in their preferred deciduous habitat. However, my results also show that pied flycatchers are better able to tolerate harsh environmental conditions. This trade-off between competitive ability and resilience in the face of harsh conditions facilitates a regional coexistence between the species. Coexistence is furthermore favoured by competition-mediated divergence in breeding habitat choice, timing of breeding and male breeding plumage colouration. Due to interspecific competition, male pied flycatchers are forced to breed in a more mixed forest type with a later peak in food abundance, which is accompanied by a divergence in breeding time between the two species. In areas shared with collared flycatchers, male pied flycatchers with brown plumage coloration, most divergent from that of collared flycatchers, are favoured by selection. In addition to facilitating coexistence, the observed shift in habitat occupancy increases reproductive isolation between the two species. By using cross-fostering experiments I demonstrate that natal habitat imprinting has the potential to additionally speed up habitat segregation. Finally I show that hybrid nestlings express an intermediate response to harsh environments, indicat

Cost and benefits of high individual growth rates are likely to vary across different environments leading to geographic differentiation in growth strategies. In ectotherms, habitats constrained by short growing seasons favour rapid growth and development leading to adaptive latitudinal clines in these traits. Geographic variation in growth strategies should be influenced by physiological variation as well as environmental factors, however many of these mechanisms remain largely unexplored. In my thesis, I studied hormonal correlates of growth strategies, and compensatory responses to phenological variation and environmental stress in anuran tadpoles. I tested the hypotheses that fast growing high latitude common frog Rana temporaria tadpoles have higher growth hormone (GH) expression, and low stress hormone (CORT) elevation in response to predator stress. I found no relationship between GH expression and latitude, but CORT response decreased with latitude after 24 hours of predator exposure. Lower CORT response at high latitude can be adaptive as it may enable the tadpoles to maintain high growth in time constrained habitats. I also found that breeding phenology affected latitudinal variation in growth, development and anti-predator strategies. Northern R. temporaria tadpoles were phenotypically more similar to southern tadpoles when breeding occurred early, suggesting that part of the latitudinal variation is plastic and affected by yearly variation in phenology. When time stress was manipulated by delaying hatching, tadpoles were able to compensate by increasing their development and growth during the larval stage, decreasing the cost of the delayed development. In the final study, I found that northern tadpoles showed stronger compensatory growth during the larval stage than southern tadpoles after being delayed by low food, however, temperature manipulation did not induce differences in the compensatory responses. In general, my results highlight the roles of b, Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 735

Sexual conflict is broadly defined as a conflict between the evolutionary interests of the two sexes. Depending on the genetic architecture of the traits involved, it can occur at the level of male-female interactions or take the form of selection acting to change the mean of a shared trait against the sign of its genetic correlation. The aim of my thesis was to use genome-wide expression profiles in the model organism Drosophila melanogaster to provide novel insights in the study of sexual conflict. First, we studied the female post-mating response to partition transcriptional changes associated with reproduction from male-induced effects, which are known to be harmful to females. We found substantial changes in expression of metabolic pathways associated with the activation of reproduction, while male-specific effects were dominated by the onset of an immune response. Changes in female response under different mating strategies was studied using experimental evolution: we found that monogamous females suffered decreased fecundity and their gene expression profiles suggested an overall weaker response to mating. To identify sexually antagonistic genes, we used hemiclonal lines and associated their sex-specific fitness with genome-wide transcript abundance. We confirmed the presence of a negative covariance for fitness and identified a group of candidate genes experiencing sexually antagonistic selection. We then focused on mitochondria, which can enable the accumulation of deleterious mutations with sex-specific effects due to their maternal inheritance, and found few effects on nuclear gene expression in females but major effects in males, predominantly in male-specific tissues. Finally, we used published data to compare intraspecific and interspecific genetic variation for a set of transcripts, to test whether speciation occurs along lines of maximum genetic variance. In conclusion, gene expression techniques can generate useful results in the study of sexual con

In times with elevated CO2 levels and global warming there is a need of finding alternatives to carbon based energy carriers. One such environmental friendly solution could be H2 produced by living organisms. Cyanobacteria are good candidates since they can produce H2 from sunlight and water through the combination of photosynthesis and H2 producing enzymes i.e. nitrogenases and/or [NiFe]-hydrogenases. This thesis investigates the maturation and transcriptional regulation of [NiFe]-hydrogenases in cyanobacteria, with a special focus on hydrogenase specific proteases. The core of all hydrogenases consists of the small and large subunit. The large subunit in which the catalytic site is located goes through an extenstive maturation process which ends with a proteolytic cleavage performed by a hydrogenase specific protease (HupW/HoxW). This thesis shows that within the maturation process of hydrogenases, the proteolytic cleavage is probably the only step that is specific with respect to different types of hydrogenases i.e. one type of protease cleaves only one type of hydrogenase. Further in-silico analysis revealed that these proteases and the hydrogenases might have co-evolved since ancient time and that the specificity observed could be the result of a conserved amino acid sequence which differs between the two types of proteases (HupW/HoxW). A number of different transcription factors were revealed and shown to interact with the promoter regions of several of the genes encoding maturation proteins. The results indicate that the hydrogenase specific proteases are regulated on a transcriptional level in a similar manner as the hydrogenases they cleave. This thesis contributes with knowledge concerning transcriptional regulation and protein regulation of hydrogenases which will be useful for designing genetically engineered cyanobacteria with an improved and adjustable H2 production., Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 722

In this thesis, I used the filamentous ascomycete genus Neurospora as a model to test theoretical predictions on the evolutionary consequences of different reproductive strategies and reproductive gene evolution. The genus Neurospora contains taxa representing a diversity of reproductive strategies, and here I constructed a phylogeny by which I was able to show that several independent transitions in reproductive mode have occurred in the evolutionary history of the genus. This feature makes Neurospora a suitable model for the evolution of reproductive modes. Molecular evolutionary analysis of housekeeping genes revealed an accelerated protein evolution in the highly inbreeding homothallic taxa, in accordance with theory predictions of lower efficiency of selection in asexual and highly inbreeding taxa. Furthermore, self-sterile (heterothallic) taxa capable of asexual propagation was found to be associated with a three-fold higher neutral substitution rate, indicative of a higher mutation accumulation due to elevated number of cell divisions per unit time in these taxa. Further, I have shown a general pattern of rapid evolution of genes involved in reproduction in Neurospora, thus extending the pattern of general high divergence of reproductive genes previously well known in animals, to fungi. Two rapidly evolving reproductive genes: the pheromone receptor genes pre-1 and pre-2 involved in mate recognition were studied in detail. For the gene pre-1 the rapid divergence was found to be driven by positive selection in both heterothallic and homothallic taxa. The rapid divergence of the pheromone receptor gene pre-2 cannot be explained by positive selection and for this gene a subtle differences in evolutionary constraints between heterothallic and homothallic taxa were found. The general similarity in evolutionary constraints of pre-genes in taxa of both mating-systems indicates that these genes serve other functions beside mate recognition.

Biodiversity in the tropics is disproportionately high compared to other habitats, and also under disproportionate threat from human impact. It is necessary to understand how this diversity evolved and how it is partitioned across space in order to preserve it. In this thesis I construct phylogenies of tropical forest dependent vertebrates from Southeast Asia and the islands of the Sunda shelf, a region referred to as Sundaland. I focus on the tree squirrels (genus Sundasciurus) and Asian barbets (Aves: Family Megalaimidae), two taxa with similar ecological characteristics. I use these phylogenies to test hypotheses that have been put forward to explain high levels of tropical diversity including the Pleistocene pump and museum hypotheses. I also use phylogenies to elucidate phylogeographic patterns within the region. I find no evidence for an increase in speciation in the Pleistocene, but I do find within species structure that dates to this period. Common phylogeographic patterns were identified between many forest dependent vertebrates that suggest that populations on the island of Sumatra are generally more closely related to Malay Peninsula populations than to populations on Borneo. From a methodological viewpoint we propose careful usage of universal primers in ancient DNA studies because of our finding of increased risk of amplifying pseudogenes of the mtDNA.

Black grouse (Tetrao tetrix) is a bird species with a lek mating system found in the Palearctic boreal taiga. It is assumed that it has a continuous distribution along Scandinavia and Siberia, whereas in Central Europe it has declined during the last decades. The primary objective of this thesis was to obtain a deeper understanding of the history, systematic classification and the genetic structure of black grouse on different geographical scales using microsatellites and control region mtDNA sequences (CR). I determined how much the mating system, habitat fragmentation and historical population processes have influenced the partitioning of genetic diversity in this species. Phylogeographical results are consistent with a demographic population expansion, and the patterns of postglacial dispersal suggest that a glacial refugium was located somewhere in central Asia, and from there black grouse spread out to Europe following the retreat of glacial ice sheets. I suggest that the two European black grouse subspecies, T. t. Tetrix and T. t. britannicus correspond to only one subspecies: T. t. tetrix, and that this lineage has diverged from T.t. viridanus, a subspecies found in Kazakhstan. The British population is significantly divergent from the remaining Eurasian samples for microsatellites but it is not for mtDNA. Therefore, they should regard as a separate Management Unit and not as a subspecies. Furthermore, British black grouse occur in three independent genetic units, corresponding to Wales, northern England/southern Scotland and northern Scotland. There was also genetic structure within Sweden. Habitat fragmentation is the main cause of population genetic structure in southern Swedish black grouse. In contrast, low levels of genetic differentiation and high connectivity were found in northern Sweden due to female-biased dispersal. On a finer geographical scale, I found genetic differences between leks due to a mixture of related and unrelated individuals within

Cross-boundary movements of energy and material are ubiquitous. Freshwater ecosystems receive nutrients, dissolved, and particulate organic matter from adjacent terrestrial ecosystems, whereas terrestrial ecosystems mainly receive prey organisms and detritus deposited by physical processes such as floods from freshwater ecosystems. Within lakes, fish are considered as integrators between habitats due to their high mobility, although they often occupy either near-shore littoral or open-water pelagic habitats and develop habitat-specific morphologies. Such intra-population divergence in morphological traits might limit the use of multiple habitats. In this thesis, I first focused on quantity and quality of reciprocal fluxes of particulate organic matter between freshwater and terrestrial ecosystems and responses of recipient consumers. Freshwater ecosystems generally received higher amounts of externally-produced resources than terrestrial ecosystems. Despite this discrepancy, aquatic and terrestrial consumer responses were similar, likely due to the differences in resource quality. Second, I investigated the potential of particulate organic carbon (POC) supporting benthic food webs in lakes; a pathway that has largely been neglected in previous studies. I found that POC can substantially subsidize the benthic food web and that the effects on the benthic food web were transferred to the pelagic habitat, thus emphasizing the importance of benthic pathways for pelagic production. Third, I examined how water transparency can affect intra-population divergence in perch (Perca fluviatilis). I observed that increased water transparency can considerably increase morphological divergence between littoral and pelagic populations likely due to its effects on foraging. Finally, I investigated the effects of such intra-population divergence on littoral-pelagic food web coupling. I found that low morphological divergence corresponded with high overlap in resource use, whereas stro

There is considerable evidence that pollinator shifts can explain many differences in flower morphology between closely related plant species, but the extent to which pollinator shifts can explain the maintenance of among-population variation in floral traits within species is poorly known. In this thesis, I combined comparative and experimental approaches to examine the evolution of floral traits in the moth-pollinated orchid Platanthera bifolia. More specifically, I investigated (1) the relationship between flower and pollinator morphology, (2) phenotypic selection on morphology and phenology in populations in contrasting environments, (3) components of prezygotic reproductive isolation among divergent populations, and (4) the adaptive and functional significance of two correlated floral traits. A study of Scandinavian of P. bifolia populations revealed that spur length was positively correlated with proboscis length of local pollinators, which suggests that variation in spur length reflects adaptive evolution in response to geographically variable pollinator-mediated selection. A phenotypic selection study on Öland, SE Sweden, suggested that disruptive selection on spur length contributes to the maintenance of a bimodal distribution of spur length in mixed habitats, but provided very limited evidence of divergent selection on plant morphology and flowering phenology in grassland and woodland habitats. Field experiments revealed strong reproductive isolation between divergent populations on Öland, due to differences in spatial distribution, flowering phenology, and pollinators, and among-population incompatibility. The results suggest that prezygotic reproductive isolation contributes to the maintenance of population differentiation in floral traits in P. bifolia. A field manipulation experiment demonstrated that spur length but not perianth size affects pollination success and seed production. This suggests that among-population differentiation in perianth size m

MADS-box genes are important regulators of reproductive development in seed plants, including both flowering plants and conifers. In this thesis the evolution of the AGAMOUS subfamily of MADS-box genes, and what the ancestral function of this group of genes might have been in the early seed plants about 300 million years ago, was addressed by the discovery of two novel conifer genes, both basal to all previously known AGAMOUS subfamily genes. DAL20, the most basal of these genes, was exclusively expressed in roots, unlike all previously known AGAMOUS subfamily genes. I also studied the evolutionary mechanisms leading to functional diversification of duplicated genes in two different subfamilies of MADS-box genes; the AGAMOUS and AGL6 subfamilies. Focus was on studying changes in gene expression pattern, representing changes in the transcriptional regulation between the genes, and on comparing the functional properties of the gene products, representing changes in the protein-coding sequence between the genes. Duplicated genes in the AGL6 subfamily were found to have evolved by both mechanisms. In the AGAMOUS subfamily I found duplicated spruce genes; DAL2 and DAL20, that appear to have functionally diversified mainly by changes in the transcriptional regulation. Conifer AGAMOUS subfamily genes were also used in a comparative developmental-genetics approach to evaluate hypotheses, based on the morphology of fossil and extant conifer seed cones, on the identity of the female reproductive organ, the ovuliferous scale, and the evolution of seed cone morphology in the conifer families Pinaceae, Taxodiaceae and Cupressaceae. Seed cones in these families have been hypothesized to have homologous ovule-bearing organs, but I found substantial differences in the expression patterns of orthologous AGAMOUS subfamily genes in seed cones of these families that are not compatible with this hypothesis, indicating that the evolutionary history of conifer seed cones is more diverse t

Environmental factors influence species and habitats on multiple scales creating a mosaic of distribution patterns. Studying factors shaping these patterns are central to our understanding of population dynamics and ultimately ecosystem functioning. Information on the distribution of resources and conservation values are also highly needed in marine management as coastal areas are increasingly influenced by human activities. In this thesis, large-scale field data is used to explore how strong environmental gradients found on multiple scales in the coastal areas of the Baltic Sea influence fish habitats. The underlying concepts are based in the field of species distribution modelling, whereby habitat maps can be produced using environmental layers in a geographic information system. Distribution modelling is further used to address both ecological and applied questions by examining effects of habitat limitation on fish population sizes and to evaluate management actions aimed at habitat conservation. I show that specific habitat requirements for fish species of both freshwater and marine origin can be described using environmental variables and that species-environment relationships can be used to predict the distribution of early life-stages of fish in the Baltic Sea archipelagos. Further, predicted habitat availability of a specific life-stage was directly related to adult population size of Eurasian perch Perca fluviatilis, signifying that the abundance of large predatory fish can be limited by specific recruitment habitats. Lastly, by predicting the distribution of an assemblage of coastal fish species and their associated habitats, an assessment of a network of marine protected areas was performed. Results revealed large gaps in the current network and identified areas suitable for future protection. By demonstrating how current habitat protection can be improved by including critical habitats for coastal fish population sizes this thesis points to the benefits, Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 709

Divergence in the face of gene flow is perhaps the most wildly disputed subject among researchers through time. The debate is an old one and we find its origin as far back as the era of Darwin. The theories dealing with sympatric and parapatric speciation, its processes and ecological conditions, are numerous and the empirical data supporting the ideas is constantly growing. However, the reach of a consensus almost seem as distant as ever. Two fundamental prerequisites can be identified for the evolution of divergence with gene flow, the act of disruptive selection, and the development of assortative mating. A set of models in which speciation with gene flow seem particularly likely is when a shift occurs in host preference in phytophagous insects and mating takes place on the host. In the work behind this thesis, the role of assortative mating in the initial stages of sympatric and parapatric speciation has been studied, as has the interaction between assortative mating and inbreeding and how it effects speciation in small sympatric populations, an aspect not much attended to earlier in the literature. My results show that assortative mating based on resource preference, can evolve rapidly upon secondary contact, and even in parapatric populations with a migration rate of 8% (13-15 individuals) per generation. However for assortative mating to be maintained selection against hybrids is needed. My results also suggests that small inbred populations have a hard time coping with strong assortative mating an as a consequence tend to relax their mating preferences to avoid inbreeding depression. Based on these results, I advocate for the importance of considering not only assortative mating in itself, but also the joint effects of assortative mating and inbreeding when dealing with theories of speciation with gene flow.

Chitin belongs to the most abundant biopolymers on earth where it has an important role as a structural element in crustaceans, insects, fungi and some phytoplankton. Missing evidence for long-term accumulation of chitin in nature implies fast turnover and as chitin is composed of aminosugar subunits it holds central roles in both carbon and nitrogen cycles. The aim of this thesis was to contribute to a better understanding of organic matter cycling by learning more about the diversity, function and ecology of bacteria that degrade chitin. A metagenome-enabled study of the spatial distribution of chitinolytic bacteria in aquatic ecosystems identified salinity as the major environmental factor for shaping their community composition. To address the role of alternative environmental variables controlling chitinolytic communities, a temporally resolved study was completed in a dimictic freshwater lake. Pronounced seasonal change in the indigenous chitinolytic community was observed and parallel measured environmental parameters pointed to the availability and crystalline form of chitin as significant controlling factors. The different ecological niches occupied by microbes that utilize chitin for growth were studied in an experimental study. Single-cell quantification of chitinolytic cells and cells incorporating chitin hydrolysis products suggested that commensal use of chitin hydrolysis products without simultaneous chitinase activity could be an important ecological strategy in freshwater bacterioplankton communities. Members of the ubiquitous and often quantitatively dominant group of freshwater Actinobacteria Ac1 were identified as particularly active in this “cheater” lifestyle. Further experiments based on artificially created gradients in bacterial diversity demonstrated the importance of specific bacterial populations and community composition rather than overall community richness in controlling more specific functions such as chitin and cellulose degradatio, Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 700

RNA is a highly versatile molecule with functions that span from being a messenger in the transfer from DNA to protein, a catalytic molecule important for key processes in the cell to a regulator of gene expression. The post-genomic era and the use of new techniques to sequence RNAs have dramatically increased the number of regulatory RNAs during the last decade. Many of these are antisense RNAs, as for example the miRNA in eukaryotes and most sRNAs in bacteria. Antisense RNAs bind to specific targets by basepairing and thereby regulate their expression. A major step towards an understanding of the biological role of a miRNA or an sRNA is taken when one identifies which target it regulates. We have used RNA libraries to study the RNA interference pathway during development in the unicellular model organism Dictyostelium discoideum. We have also, by combining computational and experimental methods, discovered the first miRNAs in this organism and shown that they have different expression profiles during development. In parallel, we have developed a novel approach to predict targets for sRNAs in bacteria and used it to discover sRNA/target RNA interactions in the model organism Escherichia coli. We have found evidence for, and further characterized, three of these predicted sRNA/target interactions. For instance, the sRNA MicA is important for regulation of the outer membrane protein OmpA, the sRNAs OmrA and OmrB regulate the transcription factor CsgD, which is important in the sessile lifestyle of E. coli, and MicF regulates its own expression in a feed forward loop via the regulatory protein Lrp. In conclusion, we have discovered novel antisense RNAs, e.g. miRNAs in D. discoideum, developed an approach to identify targets for antisense RNAs, i.e. a target prediction program for sRNAs in bacteria, and verified and characterized some of the predicted antisense RNA interactions.

Studies of demography and population structure give insight into important evolutionary processes such as speciation and diversification. In the present work I perform such studies in the genus Capsella, which has three species: C. grandiflora, an outcrossing diploid, C. rubella a selfing diploid, and C. bursa-pastoris a selfing tetraploid. These three species make a good model system for evolutionary studies because they encompass two major plant evolutionary processes: mating system shifts and polyploidization. To conduct my studies I have gathered a large number of samples across the distributions of each species and scored them both phenotypically and genotypically: more specifically we measured flowering time and collected DNA sequence data. In the tetraploid C. bursa-pastoris we applied an association mapping approach which takes population structure into account to search for genetic variation associated with variation in flowering time. Flowering time is an important and highly adaptive trait which is frequently subject to natural selection. We found evidence of association between flowering time and several single nucleotide polymorphisms (SNPs) within the flowering locus C (FLC) and cryptochrome 1 (CRY1). In the case of FLC these SNPs code for nonconsensus splice site variation in one of the two copies of the gene. The SNPs could potentially have functional consequences and our results imply that non-functionalization of duplicate genes could be an important source of phenotypic variation. Using a novel coalescent based approach, we investigated the polyploid origin of C. bursa-pastoris and find evidence supporting a recent autopolyploid origin of this species. In the two diploid species, I use sequence data to investigate population structure and demographic history and to assess the effects of selfing on C. rubella. Observed patterns of population structure and genetic diversity in C. rubella can be explained by a combination of both demographic history, Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 725

This thesis investigated the developmental neurotoxic effects of neonatal exposure to highly brominated diphenyl ethers (PBDEs) and perfluorinated compounds (PFCs), alone or in combinations, during a critical period of the brains’ rapid growth and development, in mice. The compounds investigated were the decaBDE (PBDE 209), nonaBDE (PBDE 206), octaBDE (PBDE 203), heptaBDE (PBDE 183), and three PFCs, PFOS, PFOA, and PFDA. PBDEs and PFCs have been identified as emerging classes of persistent environmental compounds, present in wildlife as well as humans, and present at higher levels in infants/children, compared to older persons. Individuals can be exposed to these compounds throughout her/his lifetime and newborn/children can be exposed to toxicants both via the mothers’ milk and directly via ingestion and inhalation. The brain growth spurt (BGS) is defined by rapid growth and developmental of the brain. For rodents (mice and rats), the BGS is postnatal spanning the first 3-4 weeks after birth. In humans this period begins during the third trimester of pregnancy and continues throughout the first two years of life. It has been shown that several environmental toxicants can induce permanent disorders in brain function when administered to the neonatal mouse, during the BGS. This thesis shows that highly brominated PBDEs, including PBDE 209, PBDE 206, and PBDE 203 can cause developmental neurotoxic effects, when given directly to the neonatal mouse. Of the investigated PFCs, PFOS and PFOA were shown to cause similar effects as the PBDEs. Furthermore, PBDE 209 and PFOA can at low doses interact and enhance the neurotoxic effects in mice. Effects in the adult animal included; deranged spontaneous behavior, reduced or lack of habituation, decreased learning and memory abilities, and increased susceptibility of the cholinergic system. Both classes of compounds were shown to affect proteins (CaMKII, GAP-43, synaptophysin, and tau) important for neuronal growth and synaptoge

A wave energy park has been established on the Swedish west coast outside Lysekil and pioneer work about its interactions with the marine environment has been conducted. So far, little is known about the effects of offshore energy installations on the marine environment, and this thesis assists in minimizing environmental risks as well as in enhancing potential positive effects on the marine environment. The Lysekil research site is situated about two kilometres offshore and has been under development since 2005. During this time 26 “environmental devices”, without generators, consisting of a steel buoy attached via a wire to a foundation on 25 m depth have been placed out for ecological studies on macrofauna in surrounding sediments and on colonization of the foundations and the buoys. Sediment samples to examine macrofauna in the seabed have been taken during five seasons. Biomass, abundance and diversity of infauna in the test site were generally low, but higher than in a nearby control site. The species composition was typical for the area and depth. In addition to sediment analysis, the effect of wave power concrete foundations on the marine environment has been investigated by scuba diving. The surface orientation and its effect on colonization by sessile organisms was examined on the first five foundations, placed out in 2005, and observations of habitat use by fish and crustaceans were made. The results show a succession of colonization over time (three years of investigation) with a higher cover by sessile organisms on vertical surfaces. Mobile fauna abundance on and around the foundations was generally low. Three months after the deployment of the 21 new foundations in 2007, assemblages of mobile organisms were examined visually. Also here, mobile species exhibit a low density, but still higher than on surrounding soft bottoms. The edible crab used artificial holes in the foundations frequently. The foundations were placed in two different clusters, north

Male-female coevolution is at the heart of biology. It is responsible for much of the diversity we see in behaviour and morphology, and it is thought to be an important engine of speciation. The pattern of intersexual coevolution is well established in many taxa, yet understanding of the processes responsible for male-female coevolution remains incomplete. By studying interspecific variation within a closely related group of species, we can gain important information about how traits and behaviours have evolved. In the work done for this thesis, we studied a group of seed beetle species. Our results show that male-female coevolution has been a strong force in shaping both behaviour and morphological traits that are associated with mating and reproduction such as, morphology of male and female genitalia and remating behaviour. The evolution of harmful male genitalia has often been suggested to be a product of sexually antagonistic coevolution, but understanding of these extraordinary adaptations is limited. By combining comparative and experimental methods we show that as seed beetle males evolve more spiny genitalia, harm to females is elevated. We provide evidence for the correlated evolution between these antagonistic adaptations in males, and a female counter adaptation (the amount of connective tissue in the copulatory duct). We also demonstrate that imbalance of relative armament of the sexes affects evolution of the costs and benefits of reproduction. As males evolve genitalia that are more harmful relative to the level of female counteradaptation, costs associated with mating for females increase and population fitness is depressed. Our results unveil a coevolutionary arms race between the sexes and are consistent with a proposed link between sexual conflict, species’ viability and the risk of extinction.

Altitudinal gradients offer attractive opportunities for studies of population differentiation in response to environmental heterogeneity. In this thesis, I examined population differentiation along altitudinal gradients by combining common-garden experiments with field studies and experiments in alpine, subalpine and boreal populations of the perennial herb Solidago virgaurea. More specifically, I determined whether leaf physiology in terms of nitrogen concentration and resorption, flowering phenology, flower production and reproductive effort vary along altitudinal gradients. Nitrogen concentration in green leaves were higher in alpine than in subalpine and boreal populations. These differences persisted when plants were grown from seeds in a common-garden experiment at two sites, suggesting that the differences have a genetic component. There was mixed support for a trade-off between maximized carbon gain through the maintenance of high nitrogen concentration, and minimized nitrogen loss through high resorption. In their natural habitats alpine populations began flowering later than subalpine populations, but this difference was reversed when plants were grown in a common environment. This suggests that genetic differences among populations counteract environmental effects and reduce phenotypic variation in flowering time among populations. Flowering time thus shows countergradient genetic variation in S. virgaurea. In a common-garden experiment, boreal populations produced more flowers and had a higher reproductive effort than subalpine and alpine populations indicating habitat-specific genetic differences in reproductive allocation. In a field study, which included three populations, seed set was close to zero in the alpine population, intermediate in the subalpine population, and high in the boreal population. Experimental flower removal showed that seed production was associated with a considerable cost in terms of reduced flowering propensity the following y

The first half of the thesis deals with the seed morphology of members of the ANITA grade at the base of the angiosperm phylogeny (Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileyaceae), especially Illiciaceae and Schisandraceae. Seed characters support a major division between the New World and Old World species of Illicium. Fossil seeds previously assigned to Illiciaceae were re-evaluated. In Schisandraceae, seed and leaf epidermal characters were added to a previously published morphological data matrix. Phylogenetic analysis using the extended data matrix shows that Kadsura and Schisandra appear to be supported as monophyletic sister taxa by a number of synapomorphies in reproductive and vegetative characters. Fossil seeds from the Eocene of North America show some similarities to the modern Schisandra glabra from North America, whereas fossils from Europe are more similar to modern Asian species. In the second half of the thesis, seed morphology of Lysimachia and closely related taxa (Anagallis, Ardisiandra, Asterolinon, Glaux, Pelletiera, Trientalis) was investigated. The phylogenetic relationships among the endemic Hawaiian species of Lysimachia was also studied, using nuclear ribosomal DNA (ETS, ITS) and chloroplast DNA (rpl16, rpl20-rps12, rps16, trnH-psbA, trnS-G) sequence data. The seeds in Lysimachia and related taxa vary in, e.g., shape, seed coat structure and surface patterns. Seed surface patterns are mostly congruent with molecular phylogenetic relationships. A reticulate surface pattern is diagnostic for, e.g., the subgenus Palladia and the Hawaiian endemic subgenus Lysimachiopsis. Mapping seed characters onto a recent molecular-based phylogenetic tree, reveals that they provide potentially synapomorphic character states for various subclades of Lysimachia. The phylogenetic analysis based on the combined data set using nuclear ribosomal DNA and chloroplast DNA data provides new insights into the relationships within the Hawaiian s

Uncovering and understanding the processes that have led to the biological diversity we observe today are of fundamental interest in biology. Since direct observation of speciation is usually impossible, knowledge about the processes behind species formation can be gathered by studying mutations, natural/sexual selection, and genetic drift. In this thesis I aim to identify evolutionary processes that cause species divergence and, ultimately, speciation using Swedish cyprinid fish as a model system. Assuming that the demographic history of a population is mirrored in the genome, I studied the effects of a bottleneck on genetic variability in populations of roach. As expected, I found that a decrease in population size caused a decrease in genetic variability, a pattern that was obtained from both microsatellite and mitochondrial data. The importance of hybridization for speciation is debated, however, by analyzing morphology and microsatellites I could show that common bream and white bream and their interspecific hybrids are phenotypically and genetically differentiated and that ongoing geneflow is mainly unidirectional. Ongoing geneflow antagonizes the effect of genetic drift, but by studying isolated populations (= no gene flow) the impact of genetic drift can be assessed. Long-term isolated populations of roach and perch surprisingly showed stable levels of genetic diversity over time despite decreasing effective population size. However, each population genetically diverged during the period of investigation, a finding that is consistent with the effect of drift. An analysis of the systematic relationship of the 18 species of Swedish cyprinids revealed low congruence of phylogenies based on two different genetic markers. The position of the tench remains unresolved and the relationship of common bream and white bream as sister species cannot be confirmed. Within cyprinid fishes, diversification rates reveal a slowdown with time, a pattern that I found also in ot

The long-term genetic consequences of supportive breeding programs are not well understood. Nevertheless, stocking populations with hatchery-produced fish to compensate for losses of natural production are common practice, for example after constructions of hydroelectric power dams. Hatcheries typically fertilize eggs using ‘mixed-milt fertilizations’, without consideration to natural reproductive behaviours, and hence, natural selective regimes would be altered. Here, a series of experiments with focus on Mhc and mate choice in a population of brown trout (Salmo trutta L.) with a history of long-term stocking are presented. The major histocompatibility complex (Mhc) constitutes of genes coding for antigen presentation in the vertebrate immune system. In addition to the immunological function, Mhc genes might also influence reproductive behaviours such as mate choice. For example, in some species individuals are able to recognize Mhc genotypes of potential mates and to some extent base their mate choice on this information. Here, I address these questions on brown trout. Can the phenomena be observed in brown trout? Could such mechanisms help individuals to avoid inbreeding, or are other mechanisms important? How does the artificial rearing of fish for enhancement of natural populations relate to these issues? The results presented here, in combination with previous work, shows that several factors are important in the process of pair formation in salmonid species. For example, females of the studied population used more than a single criterion when choosing among the available mates Mhc genes and males with certain Mhc genotypes achieved more matings, possibly an effect from increased fighting ability. Further, the population appears to contain an unnatural high level of Mhc variation, and some results indicate that the population might suffer from outbreeding depression at the Mhc. These negative effects are most likely derived from compression of sub-populations

Today, mankind faces a new challenge in energetic terms: a new Industrial Revolution is imperative, already called by some as an Energetic Revolution. This corresponds to a conversion to clean, environmentally friendly and renewable energy sources. In this context, hydrogen arises as a valid alternative, since its combustion produces a considerable amount of energy and releases solely water as a by-product. In the present thesis, two model cyanobacteria, namely Synechocystis sp. strain PCC 6803 and Anabaena/Nostoc sp. strain PCC 7120, were used to examine the hydrogen metabolism. The efforts were focused on to understand the transcription regulation of the hox genes, encoding the structural elements of the bidirectional hydrogenase enzyme. Here, it is shown that such regulation is operated in a very distinct and intricate way, with different factors contributing to its delicate tuning. While in Synechocystis sp. strain PCC 6803 the hox genes were shown to be transcribed as a single operon, in Anabaena/Nostoc sp. strain PCC 7120 they were shown to be transcribed as two independent operons (possibly three). Two transcription factors, LexA and AbrB-like protein, were identified and further characterized in relation to the hydrogen metabolism. Furthermore, different environmental conditions were demonstrated to operate changes on the transcription of the bidirectional hydrogenase genes. In addition, functional studies of three open reading frames found within the hox operon of Synechocystis sp. strain PCC 6803 suggest that this may be a stress responsive operon. However, based on the gained knowledge, it is still not possible to connect the signal transduction pathways, from the environmental signal, through the response regulator, to the final regulation of the hox genes. Nevertheless, the crucial importance of studying the transcription regulation of the different players involved in the hydrogen metabolism is now established and a new era seems to be rising.

When food is heated, a vast number of compounds are formed. Some of these are known to be toxic. Among these are furan, HMF, PhIP, IQ, and MeIQx, the subjects of this thesis. All these compounds are known or suspected carcinogens but the detailed mechanisms behind their carcinogenicity have not yet been fully examined. The aim of this thesis was to study genotoxic properties of these compounds using both in vitro and in vivo methods. Clastogenic effects of all five compounds were assessed with the flow cytometer-based micronucleus assay in vivo and for furan also with the micronucleus assay in vitro. DNA-damaging effects of HMF were studied using the comet assay. No induction of micronuclei was obtained after exposure to IQ, MeIQx or furan. Hence, it can be argued that non-genotoxic mechanisms are partly responsible for the carcinogenic properties of these compounds. PhIP, on the other hand, generated a clear response in the in vivo test. Comparing these result with previous results on acrylamide indicates that PhIP is much more potent. However, acrylamide probably poses a higher risk for humans as the intake is considerably higher. For HMF no effects were seen using the in vivo setup. To further investigate the influence of bioactivation of HMF by sulfotransferases (SULTs) the comet assay was performed in cell lines expressing different levels of SULT. However, no correlation between SULT-expression and DNA-damage was observed. Thus, the DNA-damaging effects found in our experimental setup is probably due to other factors than SULT mediated effects. Furthermore, in this thesis the effects of folic acid on chromosomal stability in healthy people were studied. A negative correlation was found between micronucleus frequency and folate status. The results gained within this thesis will hopefully contribute to the risk assessment of compounds present in our diet.

Mast cells (MC) are potent inflammatory cells that are known primarily for their prominent role in IgE mediated allergies. However, they also provide beneficial functions to the host, e.g. in bacterial and parasitic defence. MCs react rapidly upon stimulation by releasing potent granule-stored mediators, and serine proteases of the chymase or tryptase families are such major granule constituents. As a first step towards a better understanding of the biological function of these proteases, we have determined the extended cleavage specificities of four mammalian mast cell chymases, by utilizing a substrate phage display approach. The specificities of these enzymes have then been used to compare their functional characteristics. The major mucosal MC chymase in mice, mMCP-1, was found to possess a strict preference in four amino acid positions of the peptide substrate. Using this sequence to search the mouse proteome for potential in vivo substrates led to the identification of several very interesting potential novel substrates. Some of them may explain the increased epithelial permeability provided by this enzyme. Human MCs, express only one single α-chymase, and the rodent α-chymases have secondarily gained elastase-like primary cleavage specificity. However, rodents express additional chymases, the β-chymases, and rodent β-chymases may have adopted the function of the α-chymases. The cleavage specificities of the human chymase and two rodent β-chymases were therefore determined (rat rMCP-1 and mouse mMCP-4). N-terminal of the cleaved bond the three chymases showed similar preferences, but C-terminal the human chymase and mMCP-4 shared a high preference for acidic amino acids in the P2´ position and therefore seem to be functional homologues. The molecular interactions mediating the preference for acidic amino acids in position P2´ were further investigated. By site-directed mutagenesis of the human chymase, amino acids Arg143 and Lys192 were concluded to synergistic

This thesis investigates the neurotoxic effects in mice neonatally co-exposed to different toxic environmental agents during a defined critical period of the brains's rapid growth and development. Environmental toxic agents are incorporated in our environment. The agents investigated in this thesis are ortho-substituted polychlorinated biphenyls (PCBs 52, and 153), co-planar PCB (PCB 126), polybrominated diphenyl ether (PBDE 99), methyl mercury (MeHg), and γ-radiation. Several epidemiological studies show that human exposure to environmental agents during early development can affect childhood cognitive development. The brain growth spurt (BGS) is defined by rapid growth and development of the immature brain. For rodents (rats and mice) the BGS is postnatal spanning the first 3-4 weeks after birth. For humans this period begins during the third trimester of pregnancy and continues throughout the first two years of life. Several studies have shown that the BGS period of the brain's development renders the brain vunerable and susceptible to insults caused by environmental agents. The combinations of environmental agents used in this thesis were: PCB 52 + PBDE 99, PCB 153 + MeHg, PCB 126 + MeHg, PBDE 99 + MeHg, and γ-radiation + MeHg. The studies presented in this thesis show that co-exposure to low doses of environmental agents lead to interaction effects. These effects of interaction include defective spontaneous behavior, diminished habituation capabilities and hyperactive condition, decreased learning and memory abilities, and reduction in the nicotinic cholinergic receptor densities. Traditionally environmental agents are evaluated one at a time to investigate their effects of toxicity. This thesis indicates that the effects of interaction caused by co-exposure were often seen at doses where exposure to the individual environmental agent alone did not cause any effect. The observed effect of co-exposure were often as pronounced as a dose up to ten times the indivi

The genus Arnica (Asteraceae) was investigated for phylogenetic relationships and sesquiterpene lactone (STL) content with the aims to trace the evolutionary history of the genus and to investigate possible congruencies between DNA sequence data, secondary chemistry, and biological activity. Complex evolutionary patterns in Arnica are evident from phylogenetic analyses of chloroplast regions (the rpl16 and rps16 introns and the psbA–trnH, ycf4–cemA, and trnT–L spacers), nuclear ribosomal regions (the internal and external transcribed spacers) and the nuclear low-copy DNA region coding for the second largest subunit of RNA polymerase II (RPB2) between exons 17 and 23. Polymorphism was detected in nuclear ribosomal and low-copy regions, likely caused by polyploidy and agamospermy. Lineage sorting and/or hybridization is a possible explanation for incongruencies between topologies of the different DNA regions. None of the five subgenera in Arnica constitute a monophyletic group according to any of our analyses. Sesquiterpene lactone profiles were compared to nuclear ribosomal DNA data using phylogenetic inference and principal component analysis for 33 accessions of 16 species. Clusters supported by both STL chemistry and ribosomal DNA sequence data consist of multiple accessions of the same species (e.g. A montana and A. longifolia), indicating that these species are well defined both genetically and chemically, based on our sampling. Support for subspecies classification of A. chamissonis and A. parryi was found in chemical data. For the first time STLs are reported from subtribe Madiinae, sister to Arniciinae. Anti-inflammatory properties, as measured by inhibition of human neutrophil elastase release from neutrophils and inhibition of the binding of transcription factor NF-κB to DNA, were investigated for extracts of 12 Arnica species. Arnica montana, A. chamissonis and A. longifolia accessions show high inhibitory effects in both bioassays. Generally, species with

This thesis focuses on phylogenetic and taxonomic studies of Catenulida (Platyhelminthes). Catenulida is a group of microscopic free-living worms mainly found in freshwater habitats. The Swedish catenulid fauna was previously virtually unknown. The taxonomy of Catenulida is difficult because of the paucity of good morphological characters, which makes species identification extremely difficult. Molecular phylogenies are inferred from DNA sequences. Based on two molecular markers, 18S rDNA and 28S rDNA, the phylogenetic position of Catenulida has now been well established as the sister group to the rest of the flatworms, Rhabditophora. Within Catenulida there is a basal split between two major clades: Retronectidae + Catenulidae and Stenostomidae. The hypothesis of the marine Retronectidae as the sister group of the limnic Catenulida is rejected. Four molecular markers, 18S rDNA, 28S rDNA, ITS-5.8S and CO1, are used as a backbone to infer phylogeny and to generate hypotheses about species delimitation in Catenulida using parsimony jackknifing and Bayesian analysis. Anokkostenostomum comes out non-monophyletic, and Suomina nested within Catenula, so two new synonymies are proposed: Stenostomum Schmidt, 1848 (Anokkostenostomum Noreña et al. 2005) and Catenula Duges, 1832 (Suomina Marcus, 1945) are proposed. A first report on Swedish freshwater Catenulida are given. A total of 13 species are reported from Sweden. Four of them, all belonging to the taxon Stenostomum are new to science: S. gotlandense n.sp.; S. handoelense n.sp.; S. heebuktense n.sp. and S. steveoi n.sp.

The first objective of this thesis was to investigate effects of endocrine disruptors on the developing brain and gonads of bird embryos. The substances studied were the insecticide methoxychlor, and nine UV-filters (3-benzylidene camphor (3BC), 4 methyl benzylidene camphor (4MBC), benzophenone (BP) 1,2 and 3, 4 hydroxy benzophenone (4 HB), 4 dihydroxy benzophenone (4DHB), benzyl salicylate (BS), and ethyl-4-aminobenzoate Et-PABA)), commonly used in cosmetic products. Some of these substances have no estrogenic effect in vitro, but have been shown to be estrogenic in vivo. The PCB-mixture Clophen A50 is a well-known inducer of biotransformation enzymes and was co-administered with methoxychlor and the UV-filters 3BC and 4MBC. Exposure to 3BC or 4MBC caused ovotestis formation and malformations of the Müllerian ducts in Japanese quail embryos. Co-exposure to one of these compounds and Clophen A50 enhanced the effects, indicating that Clophen A50 potentiates the effects of the UV-filters. Embryonic co-exposure to Clophen A50 and methoxychlor caused a disturbed male sexual behaviour. The metabolites of methoxychlor are estrogen receptor (ER)α-selective, which indicates that the effects on behaviour following embryonic treatment were mediated by ERα. Another objective in this thesis was to localize estrogen receptors (ERs) in the brain of adult and embryonic Japanese quail. The ER localization provides a basis for mechanistic studies on effects of endocrine disruptors, by the identification of estrogen-responsive areas in the brain. We found that ERβ, not previously implicated in sex-differentiation of the brain, was the only ER-subtype present in a sexually dimorphic brain area during differentiation. In conclusion, the estrogenic effects of 3BC, 4MBC and methoxychlor were increased by co-exposure to PCB. These results raise concern since many wildlife species, as well as humans, carry large body burdens of persistent organic pollutants like PCBs, which potentially can

Amphibian populations are declining world-wide and one of the suggested reasons is environmental pollutants. Studies of long-term effects on the reproductive system in frogs following larval exposure to environmental pollutants are scarce. It is therefore important to develop methods to study developmental reproductive toxicity in amphibians. In this thesis the usefulness of Xenopus tropicalis (the West African clawed frog) as a model species for a test system was investigated. Effects on the reproductive system after larval exposure to the pharmaceuticals ethynylestradiol (EE2) and clotrimazole were evaluated. The susceptibility to EE2 exposure was compared between the model species and a wild species, the European common frog (Rana temporaria). Larval exposure to EE2 caused female-biased sex ratios in both examined frog species, indicating male-to-female sex-reversal. In adult Xenopus tropicalis, male frogs that were not sex-reversed had reduced fertility and decreased amount of mature spermatozoa in the seminiferous tubules. The proportion of frogs with ovaries but lacking oviducts increased with increasing EE2-concentrations. A female frog without oviducts is sterile. The development of ovaries in sex-reversed male frogs was implied to be similar to control females. The combination of a reduced number of males, due to sex-reversal, and impaired fertility could have severe effects on frog populations. Larval exposure to clotrimazole modulated aromatase activity in gonads and brain in Xenopus tropicalis. Brain aromatase activity was decreased at the time for gonadal differentiation and gonadal aromatase activity was increased at metamorphosis. The findings in this thesis indicate that reproduction in wild frogs might be impaired by estrogenic compounds in the environment. The results combined with the short generation time supports the use of Xenopus tropicalis as a model species when evaluating long term effects of endocrine disruptors on the reproductive system

Two distinct stress coping strategies, proactive and reactive, have been stated in various animal studies, each associated with a set of behavioural and physiological characteristics. In a given challenging situation, proactive animals show more aggression, a higher general activity and a predominant sympathetic reaction. In contrast, the reactive copers respond more with immobility and avoidance, and a predominant parasympathetic/hypothalamic activation. This divergence in coping has also been indicated in salmonid fish. Interestingly, many of the differences reported between sea-ranched and wild fish resembles characteristics that differentiate proactive and reactive copers. In the present thesis it is shown that individuals with divergent stress coping styles are identifiable in several brown trout (Salmo trutta) populations. Further, the results show that the distribution of individuals displaying these distinct stress coping strategies differs between populations. This strongly indicates that these traits are heritable and that the variation in selection regime in the native rivers influences these traits. In addition, the results show that populations with hatchery origin are biased towards having higher frequencies of trout displaying a proactive style than populations having wild origin. Also, even though the frequency of early sexual maturation, known as a viable alternative life history in salmonids, differs between populations of brown trout, no link between stress coping strategy and early sexual maturation were found. However, this thesis show that maternal contribution, in the form of egg size, is of major importance whether the progeny will sexually mature early and that it also might be of importance for stress coping strategy. Further, correlations of traits commonly associated with stress coping strategies and behavioural syndromes across context and over time is investigated. The results show that individuals with a strong sympathetic reactivity a

In nature, environments are often variable and heterogeneous influencing ecological and evolutionary processes. This thesis focus on how animals interact with their environment and how that affects the reproductive decisions they make. Using empirical data collected from wild collared flycatcher populations, experiments and molecular approaches I try to unveil some of these relationships and the evolutionary, ecological and conservation implications of these findings are discussed. Firstly, collared flycatchers were shown to use breeding densities of their own and other species using similar resources when assessing costs and benefits associated to breeding in specific habitats. However, species will vary in how informative they are, and the worst competitor – with whom you overlap most in resources needs – also provides the best source of information. Collared flycatcher parents will also benefit differentially from investments in sons and daughters due to habitat characteristics and dispersal differences between the sexes. Here, I show that they will produce more of the sex that will give the highest expected fitness return given the environment they are in. These results also provide a reciprocal scenario to Clark's (1978) classical study of sex ratio adjustment in relation to local resource competition (LRC), as more of the natal philopatric sex is produced when LRC is low. Secondly, the effect of elaborated ornaments on paternity in the socially monogamous collared flycatcher was shown to be of more importance in areas where the intensity of intra- and intersexual conflicts are expected to be elevated. Hence, ornamentation by environmental interactions determines paternity, illustrating that sexual selection through extra-pair paternity is context dependent. Finally, even though the collared flycatcher populations that this thesis is based on have been studied on their breeding grounds for more then 25 years, we know little of where they are when they are not b

Although polyploidy is believed to be a major source of evolutionary novelty, few studies have examined the genetic basis of phenotypic variation in wild polyploids. In this thesis I have studied the genetic basis of flowering time variation in the wild tetraploid crucifer Capsella bursa-pastoris, as well as the evolutionary history of this species. First, phylogenetic methods were employed to test hypotheses on the origin of C. bursa-pastoris. Based on DNA sequences from two chloroplast DNA loci and three independent nuclear genes, we found no support for the notion of C. bursa-pastoris as an autopolyploid of the diploid C. grandiflora, or an allopolyploid of C. grandiflora and C. rubella, even though some C. bursa-pastoris accessions shared alleles with C. rubella at nuclear loci. Using divergence population genetic methods, a larger sample of accessions and data for six duplicated nuclear genes, we found that allele sharing in sympatry was better explained by introgressive hybridization than by multiple origins of the tetraploid. The genetic basis of flowering time variation was examined using three approaches. A gene expression microarray study revealed that early- and late-flowering accessions differ in circadian rhythm, as well as in the gibberellin pathway affecting flowering time. Second, two QTL (Quantitative Trait Loci) for flowering time map to duplicated linkage groups. Third, polymorphisms at the candidate genes CRYPTOCHROME1 (CRY1), in one of the QTL regions, and FLOWERING LOCUS C (FLC) are associated with natural flowering time variation. Different FLC splice site polymorphisms are associated with flowering time in samples from Western Eurasia and China. The CRY1 association is only found in Europe, where alleles introgressed from C. rubella have an effect on flowering time. In conclusion, duplicated genes, introgressive hybridization and splicing variation may all have played a role in the evolution of flowering time variation in C. bursa-pastoris.

Comparative studies of bacterial genomes, now counting in the hundreds, generate massive amounts of information. In order to support a systematic and efficient approach to genomic analyses, a database driven system with graphic visualization of genomic properties was developed - GenComp. The software was applied to studies of obligate intracellular bacteria. In all studies, ORFs were extracted and grouped into ORF-families. Based on gene order synteny, orthologous clusters of core genes and variable spacer ORFs were identified and extracted for alignments and computation of substitution frequencies. The software was applied to the genomes of six Chlamydia trachomatis strains to identify the most rapidly evolving genes. Five genes were chosen for genotyping, and close to a 3-fold higher discrimination capacity was achieved than that of serotypes. With GenComp as the backbone, a massive comparative analysis were performed on the variable gene set in the Rickettsiaceae, which includes Rickettsia prowazekii and Orientia tsutsugamushi, the agents of epidemic and scrub typhus, respectively. O. tsutsugamushi has the most exceptional bacterial genome identified to date; the 2.2 Mb genome is 200-fold more repeated than the 1.1 Mb R. prowazekii genome due to an extensive proliferation of conjugative type IV secretion systems and associated genes. GenComp identified 688 core genes that are conserved across 7 closely related Rickettsia genomes along with a set of 469 variably present genes with homologs in other species. The analysis indicates that up to 70% of the extensively degraded and variably present genes represent mobile genetic elements and genes putatively acquired by horizontal gene transfer. This explains the paradox of the high pseudogene load in the small Rickettsia genomes. This study demonstrates that GenComp provides an efficient system for pseudogene identification and may help distinguish genes from spurious ORFs in the many pan-genome sequencing projects goi

Polyblastia A. Massal. is a genus of lichenized fungi belonging to Verrucariaceae (Ascomycota). Traditional classification heavily rested on a few cardinal characters, primarily ascoma structure and spore morphology, but the delimitation of Polyblastia was problematic. Using DNA sequences from nucLSU, and RPB1 the position of the ‘Polyblastia group’, as a strongly supported clade within Verrucariaceae, was confirmed. A three marker phylogeny (including nucITS) based on a wide taxon sampling reveals strongly supported clades within the ‘Polyblastia group’. Thus Polyblastia s.str. is recognized. The phylogeny of the strongly supported Thelidium clade is not completely resolved. In a different clade, Verrucaria rupestris, the type of Verrucaria, is a sister to the Henrica melaspora/H. theleodes clade. Trimmatothele perquisita, the type of Trimmatothele, forms a strongly supported group with a Verrucaria species. The genus Sporodictyon, until recently included in Polyblastia, is resurrected. Species delimitation in Sporodictyon is investigated, and the morphological variation within and between the monophyletic groups is evaluated in an effort to reconcile morphological and molecular data. A taxonomic revision of Sporodictyon, occurring in Northern Europe and the adjacent Arctic is provided, and two new species are described. A comprehensive material is investigated, a key to the species is provided. A generic revision of the family Verrucariaceae, based on recent molecular phylogenetic analyses and previous morphological studies, is offered. Three new genera (Hydropunctaria, Parabagliettoa and Wahlenbergiella) are proposed. Several other monophyletic groups are identified for which the taxon sampling is insufficient for proposing taxonomic changes. The nomenclature of the genera in the family is revised, including the study of type materials and several lectotypifications are suggested. The new genus Atla (Verrucariaceae) is described, and three new species to science

For ectotherms living in seasonal environments, time available for development and growth is often constrained by the length of the growth season. Declining season length towards higher latitudes often select for latitudinal clines in development and growth rates, exhibiting increasing growth and developmental rates towards the north. However, the physiological and ecological factors enabling these clines are poorly understood. Our study system included eight populations of Rana temporaria along a 1500 km latitudinal gradient. We found increased growth rates in populations at higher latitudes to be the result of higher growth efficiency, partly due to increased relative gut length. Populations with higher growth rates also exhibited lower standard metabolic rates, implying that fast-growing individuals are able to achieve high growth rates by spending less energy on maintenance metabolism under low activity conditions. Predator densities, and antipredatory defenses in prey, are assumed to decrease towards higher latitudes. While all study populations responded to predator presence by decreasing activity and foraging, high latitude populations maintained higher activity levels in the presence of the predator. In trials with a free-ranging predator, high latitude tadpoles experienced higher mortality than those from the low latitudes. The higher activity level in the northern populations increases mortality under predation risk, but is probably needed to maintain high growth and development rates. When competing over resources, tadpoles from the low latitude population were inferior competitors, as indicated by their longer development time when raised together with high latitude tadpoles. We found no effect of latitude on size-corrected burst speed. The general effect of predator presence on burst speed depended on food availability, with well fed tadpoles being faster in the absence, and food restricted being faster in the presence of a predator.

Many chemicals present in the aquatic environment can interfere with physiological functions in fish. Exposure to chemicals can be revealed by the use of biomarkers. Induction of 7-ethoxyresorufin O-deethylase (EROD) activity is a commonly used biomarker for exposure to CYP1A inducers such as dioxins and polyaromatic hyrdrocarbons. Vitellogenin is a frequently used biomarker for estrogenic compounds in various fish species whereas a biomarker for androgens, spiggin, is only found in sticklebacks. The main objectives of this thesis were to evaluate gill EROD activity as a biomarker and the three-spined stickleback as a model species in ecotoxicological studies. EROD activities were measured in gill, liver and kidney in rainbow trout (Oncorhynchus mykiss) caged in urban areas in Sweden. EROD induction was most pronounced in the gill. Also in fish caged at reference sites, with an expected low level of known CYP1A inducers, a marked gill EROD induction was found. One suggested inducer in rural waters is humic substances (HS). To evaluate the EROD-inducing capacity of HS, three-spined sticklebacks (Gasterosteus aculeatus) were exposed to HS of natural or synthetic origin. Both kinds of HS caused significant EROD induction. Gill EROD activities were also induced in sticklebacks exposed to ethynylestradiol (EE2) and β-naphthoflavone (βNF), alone and in combinations. Production of vitellogenin was induced in sticklebacks exposed to ≥50 ng EE2/l and a significant decrease in spiggin production was observed in individuals exposed to 170 ng EE2/l. Results from this thesis further strengthen the contention that gill EROD activity is a very sensitive biomarker for CYP1A inducers and that the stickleback is a suitable biomonitoring species, especially for exposure to CYP1A inducers. The finding that not only classical CYP1A inducers but also HS and high EE2 concentrations stimulate gill EROD activity is of significance for the interpretation of biomonitoring data.

The decrease in number and area of managed hay-meadows over the last century, in combination with the reduction of traditional management, threatens the biodiversity connected to these habitats. I experimentally examined how management intensity affected meadow characteristics and long-term population viability of three vascular plant species in wooded hay-meadows on the Swedish island of Gotland in the Baltic Sea. I discovered that intensified management (extra raking and/or extra mowing) reduced the amount of litter and biomass, even in well-managed meadows. The effects of intensified management on population growth rate varied among species. Deterministic demographic models revealed that intensified management increased population growth rate in Succisa pratensis. Stochastic modelling confirmed this; all meadows displayed larger projected population sizes 50 years into the future with intensified management. Polygala amarella responded with lower growth rates in raked plots, a consequence of the plant’s morphology, which makes it prone to being pulled out by raking. Hypochoeris maculata had population growth rates close to unity, and showed no response to an increase in management. Examination of the life-history characteristics of Polygala amarella showed that the species’ strategy is aimed at reproduction and fast growth, which is in contrast to the other two species, with their success relying on the survival of older plants. The species-specific responses to management show that several species should be considered when evaluating management practices for conservation of semi-natural grasslands. Furthermore, I suggest that data on stage distributions alone may not be sufficient for identifying threatened populations. In a study of artificial dispersal between meadows, I found that establishment was twice as successful for planted plug-plants compared to sown seeds. Both methods may be useful for introducing or augmenting meadow populations, depending on acces

This thesis describes the characterization of the Arabidopsis thaliana mutant terminal flower2 (tfl2), the cloning of the corresponding gene, and the analysis of TFL2 function in plant development. The tfl2 mutant is pleiotropic, exhibiting early floral induction in both long and short day conditions, a terminating inflorescence and dwarfing. TFL2 was isolated using a positional cloning strategy, and was found to encode a homolog to HETEROCHROMATIN PROTEIN1 (HP1), previously identified in yeast and animals where it is involved in gene regulation at the level of chromatin, as well as in the structural formation of constitutive heterochromatin. Investigating the light response during seedling photomorphogenesis I found that the tfl2 hypocotyl is hypersensitive to red and far-red light and that tfl2 is impaired in phytochrome mediated light responses such as the shade avoidance response. In the tightly regulated transition to flowering, we have shown that tfl2 might contribute to the interpretation of both external signals such as light and temperature as well as endogenous cues, via FCA, in the autonomous pathway. The Arabidopsis inflorescence meristem is indeterminate, and TFL2 possibly acts to maintain this indeterminate fate by repression of the floral meristem genes APETALA1 and AGAMOUS. In yeast two hybrid experiments TFL2 was shown to interact with IAA5, a protein with suggested functions in auxin regulation. Further, in tfl2 mutants the levels of the auxin indole-3-acetic acid decrease with age in aerial tissues, suggesting a function of TFL2 in regulation of auxin homeostasis and response. In summary, TFL2 contributes to regulation of several aspects of plant development, in accordance with the mutant phenotype and the identity of the TFL2 protein.

The majority of the vertebrate genome sequence is not coding for proteins. In recent years, the evolution of this noncoding fraction of the genome has gained interest. These studies have been greatly facilitated by the availability of full genome sequences. The aim of this thesis is to study evolution of the noncoding vertebrate genome through bioinformatic analysis of large-scale genomic datasets. In a first analysis we addressed the use of conservation of sequence between highly diverged genomes to infer function. We provided evidence for a turnover of the patterns of negative selection. Hence, measures of constraint based on comparisons of diverged genomes might underestimate the functional proportion of the genome. In the following analyses we focused on length variation as found in small-scale insertion and deletion (indel) polymorphisms and microsatellites. For indels in chicken, replication slippage is a likely mutation mechanism, as a large proportion of the indels are parts of tandem-duplicates. Using a set of microsatellite polymorphisms in chicken, where we avoid ascertainment bias, we showed that polymorphism is positively correlated with microsatellite length and AT-content. Furthermore, interruptions in the microsatellite sequence decrease the levels of polymorphism. We also analysed the association between microsatellite polymorphism and recombination in the human genome. Here we found increased levels of microsatellite polymorphism in human recombination hotspots and also similar increases in the frequencies of single nucleotide polymorphisms (SNPs) and indels. This points towards natural selection shaping the levels of variation. Alternatively, recombination is mutagenic for all three kinds of polymorphisms. Finally, I present the program ILAPlot. It is a tool for visualisation, exploration and data extraction based on BLAST. Our combined results highlight the intricate connections between evolutionary phenomena. It also emphasises the importance of

Induction of the cytochrome P450(CYP)1A protein and the connected increase in 7-ethoxyresorufin O-deethylase (EROD) activity are common biomarkers in fish. Enhanced activity of this protein signals exposure to Ah-receptor agonists such as chlorinated dioxins, co-planar polychlorinated biphenyls (PCBs) and certain polycyclic aromatic hydrocarbons (PAHs). The EROD biomarker is commonly analyzed in liver microsomes. However, the gill is directly exposed to waterborne pollutants, and in this thesis the gill filament EROD assay was therefore evaluated as a monitoring tool for waterborne CYP1A inducers in fish. Originally developed in rainbow trout (Oncorhynchus mykiss), the assay was here applied in various limnic and marine species. Following exposure to low waterborne concentrations of the readily metabolized CYP1A inducers benzo(a)pyrene (BaP) and indigo, a strong EROD induction was observed in the gill but not in the liver. This likely reflected metabolic clearance of the inducers in gill and other extrahepatic tissues. The high sensitivity of the gill was confirmed in studies of fish caged in waters in urban and rural areas in Sweden where the gill consistently showed a more pronounced EROD induction compared with the liver and the kidney. Fish caged in the reference waters showed surprisingly strong gill EROD induction and CYP1A immunostaining. Consequently, there may be CYP1A inducers present in the aquatic environment that are not yet identified. The assay was further applied in Atlantic cod (Gadus morhua) as a biomarker of exposure to crude oil and produced water (PW) from oil fields in the North Sea. The assay was finally adapted to detect inhibiting compounds, and an imidazole, a triazole and a plant flavonoid turned out to be potent gill EROD inhibitors. The overall conclusion from the studies of this thesis is that the gill filament EROD assay is a practical and sensitive biomarker of exposure to waterborne CYP1A inducers in various fish species. The inducti

Antibiotic-resistant bacteria are increasingly a major healthcare problem but very few new classes of antibiotics have been discovered or launched in recent decades. Approaches to dealing with the problem include learning how bacteria evolve to resistance and improving dosing regimens with current antibiotics so as to reduce the selection of resistant bacteria. This thesis presents studies examining whether antibiotic dosing at high levels can prevent the selection of fluoroquinolone-resistant mutants in Escherichia coli. It also addresses the genetics of fluoroquinolone resistance in E. coli in relation to fitness costs for the resistant bacteria, and the evolution of E. coli to reduce the costs of resistance. The mutant prevention concentration (MPC) of ciprofloxacin was measured for a set of clinical urinary tract infection E. coli strains showing that MPC could not be predicted from the minimum inhibitory concentration (MIC). Results from an in vitro kinetic model showed that an AUC/MPC >22 for ciprofloxacin was the single best pharmacodynamic index that predicted prevention of resistance emergence in the wild-type. Simulating currently approved dosing regimens for three different fluoroquinolones it was found that only a few were effective in preventing the selection of a small sub-population of pre-existing mutants. Step-wise selection of fluoroquinolone resistance showed that the accumulation of mutations usually reduced bacterial fitness in vitro and in vivo. Systematic construction of isogenic resistant strains confirmed this result and revealed that some combinations of resistance mutations mutually compensate and increase both resistance and fitness. It was discovered that mutations altering RNA polymerase could ameliorate the fitness costs of fluoroquinolone resistance. Thus, the major fitness cost of fluoroquinolone resistance is due to defective transcription. The finding that fluoroquinolone resistance mutations can increase resistance while mutual

Bacteria of the genus Bartonella inhabit the red blood cells of many mammals, including humans, and are transmitted by blood-sucking arthropod vectors. Different species of Bartonella are associated with different mammalian host species, to which they have adapted and normally do not cause any symptoms. Incidental infection of other hosts is however often followed by various disease symptoms, and several Bartonella species are considered as emerging human pathogens. In this work, I have studied the genomic diversity within and between different Bartonella species, with focus on the feline-associated human pathogen B. henselae and its close relatives, the similarly feline-associated B. koehlerae and the trench-fever agent B. quintana which is restricted to humans. In B. henselae, the overall variability in sequence and genome content was modest and well correlated, suggesting low levels of intra-species recombination in the core genome. The variably present genes were located in the prophage and the genomic islands, which are also absent from B. quintana and B. koehlerae, indicating multiple independent excision events. In contrast, diversity of genome structures was immense and probably associated with rearrangements between the repeated genomic islands located around the terminus of replication, possibly to avoid the host’s immune system. In both B. henselae and the mouse-associated species B. grahamii a large portion of the chromosome was manifold amplified in long-time cultures and packaged into phage particles, allowing for different recombination rates for different chromosomal regions. In B. quintana, diversity was studied by sequencing non-coding spacers. The low variability might be due to the recent emergence of this species. Surprisingly, also this species displayed high variability in genome structures, despite its lack of repeated sequences. The results indicate that genome rearrangements and gain or loss of mobile elements are major mechanisms of evolut

The genetic basis for behavioural traits is largely unknown. The overall aim of this thesis was to find genes with importance for behavioural traits related to fear and anxiety. Microarray analysis was used to screen expression profiles of brain regions important for emotional behaviour in dogs, wolves, foxes and mice. In a first experiment, dogs and their wild ancestors the wolves were compared. Our results suggested that directed selection for behaviour might have resulted in expression changes in few genes acting on several brain functions, possibly affecting behaviour. However, the observed expressional differences were confounded with environmental effects. This was addressed in a second study on domesticated silver foxes. By correlating behaviour and brain gene expression in foxes selected for tameness to non-selected foxes raised in the same environment, we found large behavioural differences but only few genes with differential expression in the brain. Fifteen of the 40 genes showing evidence of expression difference were related to haem or haemoglobins. Further studies showed an additive genetic effect on brain gene expression, similar to the additive genetic inheritance of behaviour, indicating an involvement in domestication. Transcriptional profiling was also used for finding genes involved with the sleep disorder narcolepsy. Narcoleptic Doberman pinschers homozygous for the canarc-1 mutation were compared to their unaffected heterozygots revealing reduced expression of three genes, TAC1, PENK and SOCS2, with relevance to the narcoleptic phenotype. Finally gene expression was investigated in relation to anxiety-related traits in a mouse model. Surprisingly, as in the fox study, genes coding for haemoglobins indicated differential expression in the brain between animals with different anxiety levels. Our combined results suggest that genes like haemoglobins, best known for their function in oxygen transport in blood, may also participate in brain function

This thesis focuses on phylogenetic, taxonomic, ecological, and conservation aspects of the crustose lichen genus Lecania (Ramalinaceae, lichenized Ascomycota). Lecania has previously been defined on basis of relatively few morphological characters, and the genus had never been treated in molecular phylogenies. The molecular phylogeny of the genus is inferred from DNA sequences. Twenty-five species traditionally placed in Lecania are included in the study along with 21 species from closely related genera. Lecania is a polyphyletic genus. A well-supported monophyletic group containing 16 Lecania species, including the type species L. fuscella is discovered, i.e. Lecania s. str. Nine species formerly included in Lecania do not belong in the genus. A new species, L. belgica, is described. The relationships of a group of morphologically similar Lecania species, i.e. the L. cyrtella group are investigated using morphological and molecular methods. Haplotype network and phylogenetic analyses indicate that the included species, as conceived in the morphological examinations, all are monophyletic. Two new species, L. leprosa and L. madida, are described, L. proteiformis is resurrected from synonymy, and the known range of L. prasinoides is greatly expanded. The type species Lecania fuscella has become endangered in many countries. Twelve localities in Sweden where the species had been found historically are investigated, but L. fuscella is only recovered in one locality. The species composition in these 12 localities, 58 old and 5 new collections with L. fuscella is determined and analyzed. The vegetation community differs between the old and the new collections, and between the locality where the species is recovered and those where it is not. Lecania fuscella has not been able to adapt to environmental changes and now only appears in a specific type of vegetation community. The phylogenetic diversity of the species is calculated, but does not reflect the species’ evolutio

The DDT metabolite 3-methylsulphonyl-DDE (3-MeSO2-DDE) induces cell death specifically in the adrenal cortex of mice after a cytochrome P45011B1 (CYP11B1)-catalysed bioactivation. This substance is not only an environmental pollutant, but also a suggested lead compound for an improved chemotherapy of adrenocortical carcinoma (ACC). The aim of the thesis was to further investigate this compound in terms of kinetics, cell death mechanisms and species differences. The pharmacokinetics of 3-MeSO2-DDE and the current drug for ACC, o,p’-DDD, was studied during 6 months following a single dose in minipigs. The elimination was slower for 3-MeSO2-DDE than for o,p’-DDD, indicated by a lower clearance and longer t½ in plasma and subcutaneous fat. Both substances remained in fat tissue during the whole study period. Unlike o,p’-DDD, 3-MeSO2-DDE was retained also in liver. The adequacy of the murine adrenocortical cell line Y-1 was evaluated for studies of adrenotoxic compounds. The Y-1 cells proved to be an appropriate test system for future mechanism studies, since CYP-catalysed irreversible binding, inhibited corticosterone production induced by 3-MeSO2-DDE and o,p’-DDD were successfully demonstrated. Cell death of 3-MeSO2-DDE in the mouse adrenal cortex was implied to be necrotic. Early apoptotic signalling (i.e. up-regulation of caspase-9) was observed, although it seemed to be interrupted by ATP-depletion and anti-apoptotic actions by heat shock protein 70, resulting in lack of activation of caspase-3. Using cultured adrenal tissue slices, two not previously studied species were examined ex vivo regarding adrenal binding of 3-MeSO2-[14C]DDE. Binding was found in the hamster adrenal cortex and in assumed cortical cells in the medulla, while the guinea pig adrenal was devoid of binding. This emphasises the species specificity in bioactivation of 3-MeSO2-DDE. The thesis forms a basis for further investigations in the human adrenocortical cell line H295R and provides new knowl

Speciation is the process describing the formation of new species and is at the heart of evolutionary biology. According to the biological species concept only reproductively isolated forms are regarded good species. This thesis aims at identifying evolutionary processes that cause population divergence and, ultimately, speciation. Natural and sexual selection are two major candidates driving changes in traits that could render populations reproductively incompatible. In recent years, biologists have recognized that most animal species are polygamous. Therefore, sexual selection does not end at mating but continues to include interactions between individuals after mating has occurred but before zygote formation. Male-male sperm competition and cryptic female choice are two main forms of postmating sexual selection shaping reproductive traits like behaviour. The studies presented in this thesis focus on laboratory experiments attempting to identify the role of postmating sexual selection in causing reproductive divergence across populations in beetles. The majority of studies were performed using a Bruchid beetle, Callosobruchus maculatus, a common, worldwide pest on stored leguminose seeds. I used two major methodological approaches. One approach seeks to identify the traces left by past selection among extant conspecific populations, by assessing the pattern of female reproductive responses to mating with males of decreasing relatedness. Second, I used a selection experiment to disentangle the joint effect of natural and sexual selection acting simultaneously on diverging replicated selection lines. In general, these experiments revealed that postmating sexual selection can be a powerful engine of incipient divergence between allopatric populations. Changes in traits underlying variables such as female reproductive output, female mating rate or male success in sperm competition evolved rapidly and could in some cases effectively reduce gene flow between conspecific

In this thesis, I examine variation in occurrence and performance of glabrous and trichome-producing plants of the perennial herb Arabidopsis lyrata. I combine field studies and genetic analysis to (1) examine the function of trichomes as a resistance character in natural populations, (2) compare the magnitude of population differentiation in trichome-production and at putatively neutral marker loci, (3) examine the molecular genetic basis of trichome-production, and (4) quantify the effects of herbivore removal on population growth and relative performance of glabrous and trichome-producing plants. In a survey of 30 populations of A. lyrata in Norway and Sweden, I documented spatiotemporal variation in damage from insect herbivores. With few exceptions, glabrous plants were more damaged by herbivorous insects than trichome-producing plants in polymorphic populations. Damage levels varied substantially among populations and among years. The intensity of herbivory quantified as mean leaf removal to glabrous plants was higher in polymorphic populations than in monomorphic glabrous populations. Within the Swedish range, populations were more strongly differentiated at the locus coding for glabrousness than at eight putatively neutral isozyme loci. This is consistent with the hypothesis that trichome production is subject to divergent selection. A study of the genetic basis of trichome production showed that glabrousness was associated with mutations in an orthologue to GLABROUS1, a regulatory gene known to cause glabrousness in A. thaliana. Comparative data indicate that the genetic basis of glabrousness varies among populations. Experimental removal of insect herbivores in a natural A. lyrata population increased population growth rate and the relative fitness of the glabrous morph. The results suggest that insect herbivory may influence both population dynamics and selection on trichome production in A. lyrata.

This thesis presents a comprehensive phylogenetic and taxonomic study of an acoel subgroup, the Childiidae. Members of this taxon are characterized by well-developed male copulatory organs with conical/cylindrical stylets. The phylogenetic analyses, by means of total evidence approach, based on three molecular markers (18S and 28S rRNA genes and Histone H3) and 50 morphological characters reaffirm the non-monophyly of the Childiidae sensu Dörjes, 1968 (Actinoposthiidae and Childia+Paraphanostoma). The total evidence phylogeny strongly support the Childia+Paraphanostoma clade separate from other former members of the Childiidae, which are now placed in Actinoposthiidae. The monophyly of Childia+Paraphanostoma is well corroborated by several morphological characters. A new taxon Childia is defined, in accordance with the PhyloCode, comprising all former Paraphanostoma species and a member of the monotypic genus C. groenlandica. A new diagnosis for the current members of Childia is provided. Several structures, shown to hold promising phylogenetic signals for unraveling acoel relationships, such as musculature pattern, sperm and male copulatory organs, are investigated, using a combination of traditional and modern techniques (ultrastructure, immunocytochemistry and confocal microscopy), with main focus on Childia and its closest relatives. New characters are described and their phylogenetic significance assessed. Morphological characters relating to body-wall musculature, statocyst muscles, male copulatory organ musculature and ultrastructure, and sperm cytoplasmic granules are shown to carry important phylogenetic signals at lower taxonomic levels, while most of the characters related to sperm ultrastructure are useful at higher taxonomic levels within the Acoela. The data obtained undermine the phylogenetic use of the seminal bursa in Childia. In addition to this, it is shown that most of the classical morphological characters used in acoel taxonomy, obtained using