Sammandrag Enligt Förenta nationernas livsmedel och agrikulturorganisation (FAO) är 51% av världens fiskbestånd fullt exploaterade och 17% överexploaterade. Denna andelen har ökat kraftigt de senaste hundra åren och en art som varit hårt drabbad av detta är den populära matfisken torsk (Gadus morhua). Havet runt svenska kusten har tidigare ett av världens mest produktiva torskbestånd, men har de två senaste decennierna minskat drastiskt pga. överfisket. Den intressanta frågan blir då hur torsken påverkats av detta hårt riktade fisket? Den här sammanfattningsartikeln diskuteras först om livshistorieteorin, om torsken och hur fisket på Grand banks utanför Kanada fick hela beståndet att kollapsa. Där efter kommer mera ingående om hur det fisket kan ha påverkat torskens evolution och livshistoria. Torskens fenotypiska variation har minskat under det senaste århundradet. Tillväxten har gått ner pga. av denna anledningen. Regimskiften i ekosystemet, som klimat eller föda, har inte påverkat lika mycket som yrkesfisket. Konkurrensen mellan torskens och yrkesfisket efter samma bytesdjur har en inverkan på torsken genom direkta och fördröjda effekter. Skyddade marina områden kan ha gynnsamma effekter på torskbeståndet genom Allee-effekter som en hårt fiskad population kan besitta, som hämmar tillväxten. Slutligen en diskussion om hur hållbart fiske med en jämförelse mellan aktiva och passiva redskap. Sedan om hur dagens fiske i svenska vatten ser ut och en analys av de nya fiskereglerna för år 2022 i delar av Östersjön. Till sist en kort diskussion om skyddade marina områden kan gynna torskbestånden runt Sveriges kuster. Sammanfattningsvis behöver fisket efter torsk runt Sveriges kuster moderniseras och bedriva ett fiske som tar hänsyn till torskens livshistoria.

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A central point of Darwin’s theory of evolution is that accumulation of many small changes during the evolutionary process can result in significant change over time. In light of his theory, plant scientists seek for and compare different plant traits among species e.g., from morphology, DNA or proteins in order to discover the underlying evolutionary patterns and processes. The Gnetales, an intriguing family that comprises Ephedra, Gnetum and Welwitschia, have puzzled scientists for over a century. Their features are evolutionarily difficult to understand in comparison with other seed plants and this has hampered analyses of evolution and phylogeny regardless of whether morphological or molecular data has been utilized. In this thesis, I first attempt (Paper I) to seek for a new evolutionary indicator; a protein profile from pollination drops of Ephedra is compiled, and the results are compared with those from conifers and other seed plants. The aim of this proteomic study was also to investigate whether proteomic profiles vary among Ephedra species and are affected by different selection factors, e.g., pollination mode, ovule protection etc. The results indicate, however, that proteins are present only in very small amounts in pollination drops of Ephedra, and mainly as waste products from degrading cells. This is surprising since proteins are considered important for defense of the naked ovules of gymnosperms, e.g., against pathogens. Pollination drops of Ephedra have a very high sugar concentration and it is possible that carbohydrates are responsible for ovule defense in Ephedra. The second chapter of my thesis (Paper II) is devoted to Gnetum; a phylogenetic study based on genetic markers derived from both nuclear ribosomal regions and chloroplast regions is conducted. Previous studies have been hampered by difficulties with outgroup comparison and homology assessments of informative gene regions. A few attempts have been made to estimate the deepest splits in the genus, all with a limited ingroup sampling. We address the phylogeny of Gnetum and make a first assessment of the monophyly of species, using a denser sampling of taxa and a combination of faster and more slowly evolving molecular markers. The results are discussed in comparison with previous classification and morphology, and will provide a basis for further studies of taxonomy, ecology, and biogeography in Gnetum.

The Repeat-Induced Point (RIP) mutation pathway is a fungal-specific genome defence mechanism that mitigates the deleterious consequences of repeated motifs and transposable elements (TEs). RIP is an ancient pathway that evolved early in the evolutionary history of fungi. It most likely evolved before the divergence of the fungal subkingdom Dikarya and has been observed in both Ascomycota and certain Basidiomycota. Despite its prevalence, the genetic consequences and taxonomic range of RIP remains ill defined. For these reasons this thesis particularly focusses on fungi representing varying degrees of divergence in order to investigate the influence of RIP on genome evolution, divergence and development of genomic regions underlying important fungal biological traits. The Fusarium fujikuroi species complex (FFSC) represents a diverse assemblage of fungi that are distributed globally. Many of these fungi can cause disease on numerous crops and plants and threaten tree health in both natural and plantations settings. Due to their agricultural importance, and the biological and genomic interest in this taxon, whole genome sequences have been determined for many FFSC species. The availability of this information assembled into chromosome-sized scaffolds allows for unique opportunities to study the occurrence and extent of RIP on a genome-wide level. Moreover, the availability of these genomes, in varying stages of divergence, will prove invaluable in the understanding of the genetic and molecular factors driving genome evolution, lineage divergence, and ultimately speciation. The first chapter of this thesis is a critical review of the literature on the developments made in studying the RIP process in fungi. The different aspects of fungal biology and genome content that can contribute to variation in RIP strength and capabilities are discussed. As this thesis deals with the evolutionary implications of RIP on the FFSC, the current research progress made on RIP in Fusarium lineages is reviewed. Attention is also given to the functional consequences brought about by RIP, particularly how RIP can contribute to reinforcing species boundaries and ultimately drive lineage divergence and speciation. Chapter two introduces The RIPper, a web-based set of tools for genome-wide investigation of RIP in fungi in the phylum Ascomycota. This chapter discusses the development of this software and further demonstrates the ability of this set of software tools to detect the occurrence and extent of RIP in known RIP affected fungal sequences. The work presented in xix Chapter 2 has been published in the journal PeerJ as an application for genome-wide RIP analyses of fungal sequences. Chapter three presents detailed investigation on the extent and occurrence of RIP in the genome of the pitch canker pathogen, Fusarium circinatum and its relatives in the FFSC. Comparative genome-wide RIP analyses were undertaken to determine the influence of RIP on genome divergence amongst these fungi. This chapter provides valuable information on the independent divergence of chromosomes and changes to chromosome architecture brought about by RIP among this economic important group of fungi. The work presented was published in the journal Pathogens. Fusarium pininemorale is a recently recognized member of the American clade of the FFSC and is the focus of chapter 4. Overall, little is known regarding the biology and genetics of this species, even less so for the genetic determinants of host range in the broader American clade of the FFSC. The aim of chapter four was to determine the full genome sequence for F. pininemorale which will allow further studies to investigate genomic aspects of not only genome evolution but will also provide information of its biology and evolution amongst members of the FFSC. The chapter has been published in the journal IMA Fungus. In chapter 5 data on the genome-wide occurrence and extent of RIP in the Ascomycota is presented. This study considered the effects of the RIP amongst these fungi using whole genome sequences. To overcome the typical challenges associated with RIP analyses, genomewide RIP data is produced by using an alignment-free method, based on a sliding-window approach. This study provides valuable information on the taxonomic distribution of RIP amongst the Ascomycetes, occurrence and extent of RIP in regions with TEs and repeats, as well as where RIP occurred due to leakage. This work provides valuable insights on the cumulative influence of RIP and its contribution to chromosome evolution of Ascomycete fungi. This chapter has been submitted to the journal Microorganisms for peer review. The cumulative influence of RIP on the overall base composition in the different genomic regions and sub-genomic compartments of F. circinatum is the focus of chapter six. The results of this study present important information on the manner that RIP drives genomic variation and contributes to the evolution of the genetic landscape and differentiation of diverse sub-genomic compartments of this important fungal pathogen. / Thesis (PhD)--University of Pretoria, 2020. / National research Foundation of South Africa; The Forestry and Agricultural Biotechnology Institute; Center of Plant Health and Biotechnology; Tree Protection co operative programme / Microbiology and Plant Pathology / PhD / Restricted

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Ecologists have long known that complex habitats often provide prey with refugia from predation in a wide variety of habitat types and for a wide variety of prey species. Despite the recognized importance of structural habitat complexity, ecologists have measured complexity in many different ways. I propose four new indices of structural habitat complexity that are dimensionless, that can be applied across various habitat types and scales, and that directly measure how structural complexity interferes with a predator's foraging ability. These indices are: (1) Ct/At, the total area of cover within a habitat (Ct) divided by the area of the habitat (At), (2) Cw/Pw, the average width of the individual structures within a habitat (Cw) divided by the appropriate width of the prey organism (Pw), (3) Sp/Pr, the average inter-structural space size within a habitat (Sp) divided by the width of the predator (Pr), and Sp/Py, the average inter-structural space size within a habitat (Sp) divided by the width of the prey (Py). I predicted that prey survivorship should (1) increase hyperbolically with increasing Ct/At, (2) increase hyperbolically with increasing Cw/Pw, and (3) decrease sigmoidally with increasing Sp/Pr. I also predicted that different sized fauna should respond differently to artificial seagrass plots deployed in a seagrass bed, based upon the size of the inter-structural spaces relative to their body sizes (Sp/Py). I found that prey survivorship increased hyperbolically with increasing Ct/At, and decreased sigmoidally with increasing Sp/Pr. I found no effect of Cw/Pw on prey survivorship. I found that small fauna responded positively to increased structure in artificial seagrass plots deployed in a seagrass bed, but after controlling for structural surface area within each plot there was no difference between treatments, indicating no effect of Sp/Py on small fauna. Larger fauna responded slightly differently than the small fauna, but the pattern of their response did not support the hypothesis that Sp/Py was important. The smaller fauna also appeared to respond positively to increased water flow speeds within the seagrass bed. Overall, these indices may be useful to both ecologists and managers interested in predator-prey-habitat issues.

Management of fisheries resources is increasingly broadening its scope from single-species approaches to more holistic, ecosystem-based approaches that account for interactions of fish with a variety of ecological factors, such as predators, prey, and habitat. This ecosystem based fisheries management (EBFM) approach requires thorough biological and ecological understanding of systems pertaining to community structure, habitat suitability, and food web interactions. to strengthen the ecological underpinnings of EBFM efforts in Chesapeake Bay, the largest estuary in the USA, I conducted synoptic analyses examining the structure, function, and patterns of the bay's demersal fish community. This research relied on I0 years of data from a multi-species, bimonthly bottom trawl survey of the Chesapeake Bay mainstem. The unifying objectives of this work were to 1) synthesize basic biological and ecological information of many Chesapeake Bay fishes, and 2) examine the environmental drivers of community structure and trophic interactions in the Bay. One major hypothesis underlying the more detailed research objectives for each component was that bay-wide patterns in biomass and feeding habits of Chesapeake Bay fishes were mostly driven through bottom-up processes governed by a blend of small- and large-scale environmental factors. as food web structure and trophic interactions are governed by the presence, distribution, abundance, and behavior of species, Chapter 1 focused on evaluating patterns for these basic biological characteristics for a large suite of 50 species and investigating environmental factors that influence the community trends. Univariate and multivariate statistical modeling revealed that the demersal fish community (dominated by five species) was strongly structured along a salinity gradient, and other factors (e.g. dissolved oxygen, temperature, month, and year) helped regulate biomass and diversity trends. Chapter 2 synthesized diet information for 47 fish species, demonstrated the role of five prey groups (mysids, fishes, bivalves, polychaete worms, and crustaceans) in differentiating feeding guilds, and highlighted the importance of non-pelagic prey groups (especially the hyper-benthic mysids) in supporting the nutritional needs of fishes. Diets of 12 predator species were investigated in more detail in Chapter 3 to infer the dynamics of four important prey groups (mysids, bay anchovy, polychaetes, and bivalves) using advanced statistical modeling techniques. Results revealed generally coherent consumption trends across predators for a given prey, suggestive of prey availability driving consumptive patterns. Synchronous annual peaks in prey consumption were indicative of pulses in prey production (particularly mysids and bivalves) that were exploited by predator populations. to evaluate the population-scale effects of these bottom-up alterations in prey productivity, Chapter 4 relied on a simulation model to examine the potential effects that these annual changes in prey availability could have on consumption and production of one representative predator species. The model indicated that enhanced individual growth resulting from pulses in prey production could generate substantial gains in predator spawning stock biomass, recruitment, and fishery yield. However, the bottom-up effects on predator production had only modest effects on rebuilding times of a depleted population relative to controls on fishing mortality. This research represents one of the largest studies on community structure and trophic interactions for demersal fishes in an estuarine environment, contributing to a broader understanding of fish ecology within a complex and dynamic system. By filling research gaps identified for EBFM in Chesapeake Bay, this body of work also supports a more holistic management approach for the sustainable use of resources from the Chesapeake Bay and coastal waters of the Northwest Atlantic Ocean.

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A chemically defined synthetic medium was developed in which Phytophthora infestans (Mont.) de Bary race 1.2.4 grew extensively. This medium consisted of: 90.0 grams maltose, 20.0 grams DL-alanine, 20.0 grams L-proline, 1.0 gram KNO3, 0.5 gram KH2PO4, 0.25 gram MgSO4. 7H2O, 1.0 milligram thiamin per liter of distilled water. The average level of growth in this medium was 0.5864 gram dry weight mycelium per 50 milliliters medium. The glycoalkaloids, solanidine and solanine, were synthesized by Phytophthora infestans in the above medium with 62.5 percent of the samples positive and an overall average of 0.85 milligram total glycoalkaloids per 25 milliliters medium. The level of alkaloids detected in the medium ranged from 0.0 to 5.9 milligrams per 25 milliliters medium. No glycoalkaloid production was detected when the level of growth of the fungus was below 0.35 gram dry weight mycelium per 50 milliliters medium. Phytophthora infestans was also cultured on the following semisynthetic media: chick pea medium, rye seed medium, and lima bean medium. The fungus grew extensively in each medium, but produced alkaloids in only the chick pea medium. Fifty percent of the samples of this medium were positive for alkaloids with an overall average of 0.67 milligram total glycoalkaloids per 25 grams chick peas. Sodium salts of the macronutrients were individually substituted for the potassium and magnesium salts of the basal medium and sodium chloride and sodium acetate were singly added to the medium. Maximum growth levels were demonstrated when 0.04 percent phosphate or 0.04 percent chloride was employed in the medium. Sodium acetate was inhibitory to Phytophthora infestans. Glycoalkaloid production was significantly reduced in media containing sodium salts of the macronutrients. Regression analysis showed that the concentration of phosphate in the medium had the most influence on the level of glycoalkaloids synthesized by the fungus. Raising the concentration of phosphate in the medium resulted in increasing amounts of alkaloids being produced by Phytophthora infestans. Upon addition of micronutrients to the enriched basal medium, growth of Phytophthora infestans was stimulated by levels of ferrous iron in the concentration range of 1.0-5.0 milligram 1-1. Phytophthora infestans was inhibited by all concentrations of cobalt, copper, manganese, nickel, and by concentrations of calcium greater than 0.001 milligram 1-1. No glycoalkaloid production by Phytophthora infestanswas detected in media containing cobalt, copper, calcium, nickel, or manganese. Glycoalkaloids were produced in media containing iron at all concentrations except 5.0 milligrams 1-1 with the highest amount of alkaloids occurring in media containing 0.001 milligram 1-1. Ferrous iron seems to inhibit glycoalkaloid synthesis by Phytophthora infestans. As the level of iron in the media was increased the quantity of glycoalkaloids produced in the media declined. Studies were carried out to determine the effect of mineral nutrition on the resistance of potato foliage to infection by Phytophthora infestans. Results indicated that the level of phosphate had little or no effect on the susceptibility of potato leaflets to late potato blight. Levels of nitrate (1.0-10.0 percent) had little effect on the blight resistance of foliage, whereas higher levels of nitrate (20.0- 25.0 percent) significantly increased the susceptibility of leaflets to infection by Phytophthora infestans. Growth of common saprophytic and enteric bacteria was not inhibited by glycoalkaloids in the concentration range of 1 to 200 milligrams total glycoalkaloids per 100 milliliters.

Predation, especially by canid predators, is a significant cause of sheep loss for many producers. In recent years, the use of llamas to protect sheep from predators has gained recognition as a depredation control method. I conducted a field experiment to test the effectiveness of llamas in reducing canid predation on domestic sheep. Twenty-one llamas were placed with Utah sheep producers. Data collected from these flocks over 20 months were compared to similar data collected from flocks without llamas. Comparisons between treatment and control flocks included (l) proportion of flocks with losses to predators, (2) mean predation rates on ewes and lambs, and (3) lamb predation rate distributions. Two surveys were conducted during the study to assess producer opinions on the inclusion of llamas in their sheep management programs. In all 3 comparisons of lamb losses between treatments and controls, losses sustained by control flocks in Lambing Season l (LS l) were significantly higher than those of flocks with llamas. Among treatment flocks, losses were similar for LS l and Lambing Season 2 (LS2). Among controls, LS2 losses dropped to the level of treatment flocks. My results suggest predation may have to reach some threshold before guard llamas have an effect on losses. Results of surveys of producers with llamas indicated they support the use of llamas as guard animals for sheep.