Recent studies have found populations of European Whitefish (Coregonus lavaretus) to be under the process of divergence induced by a predator (pike, Esox lucius). This has caused whitefish to diverge into similar ecotypes but in separate lakes. Even though there are established ecotypes, these do display a high degree of variation, especially among whitefish dwarfs. The underlying mechanisms has not been fully understood and other determining ecological factors than predation are yet to be explored. In this study, I examine whether there are phenotype-environment correlation between whitefish dwarfs that could help identifying the selection pressures shaping this variation between whitefish dwarfs in different lakes. The morphological features of interest were body size and number of gill rakers since these are determining features of divergence. The environmental variables of interest were features of the lake in questions and its surrounding area. No significant correlations were found between the environmental variables and the body size of whitefish dwarfs. I was however through this study able to conclude significant results regarding phenotype-environment correlations between the number of gill rakers in whitefish dwarfs and the combined effects of lake percentage, lake area, temperature and number of (other fish) species in the lake from which they were sampled. It is probable that this is due to these variables affecting the niche space in which the whitefish dwarfs can diverge. Lakes with more potential refuges from pike will result in more divergence in whitefish dwarfs and vice versa. I can hereby propose a model containing these four environmental variables for how they affect the number of gill rakers in whitefish dwarfs.

Research designed to elucidate artificial reef efficacy in attraction and production is lacking. Delineation of the rock reef habitat, coupled with faunal patterns of substrate use within artificial and natural reef regions, will allow elucidation of the potential of artificial reefs to attract sport fishes, and function as surrogate natural habitat for the conservation of endemic fish species. We compared faunal assemblages and habitat complexity between artificial and natural reefs to access the efficacy of artificial reefs in conservation of the native community, and attraction of sport fishes. We used hydroacoustics to map artificial and natural rock reefs within Bear Lake. We compared the accuracy of Visual Bottom Typer (VBT, BioSonics, Seattle, WA) software to observed substrate in three regions of varying slope and rock complexity within Bear Lake. VBT demonstrated an ability to distinguish substrates regardless of rock complexity and slope, although inaccuracies were present. VBT biased classification towards predominant substrate in the survey regions. We compared benthic invertebrate and fish catch in natural and artificial reef regions to assess the utility of artificial reefs in fisheries management. We assessed the potential of artificial reefs to function as foraging habitat for endemic fishes within Bear Lake. We compared benthic invertebrate taxa abundances and diversity between one region of artificial reefs, and two natural reefs in spring and summer. The artificial reefs hosted prey consumed by endemic Bonneville whitefish and Bear Lake sculpin. We assessed the potential of artificial reefs to function in attraction of sport fishes, and conservation of endemic fishes. We compared differences in fish catch per unit effort (CPUE) and diversity on rock and soft substrate between one artificial and two natural reef regions. Sport fishes attraction to the artificial reefs was minimal. Winter cisco and whitefish used the artificial reefs similarly to natural reefs. Fall lake trout, crayfish, and yellow perch used artificial and natural reefs dissimilarly.

A review of the genus Cisticola was published in 1930 by Rear-admiral Lynes. While subsequent authors have modified Lynes' original groupings, his work remains the basis for modern syntheses of cisticolas. This study tests Lynes' hypotheses by analysing data that he presented in his review and with measurement and plumage data collected from museum specimens. Lynes' groupings were well recovered (98%) when data captured from his review were analysed phenetically, suggesting that he grouped species mostly by similarity. In contrast, when morpho-behavioural data were analysed using cladistic methods, many of his groupings were not monophyletic and the resultant cladogram had very little nodal support due to their highly conservative morphology. To resolve the structure of the genus and the relationships within it, two mitochondrial and four nuclear regions were sequenced from toe-pad samples taken from museum specimens. The molecular analyses included 44 of the 49 currently recognised species and represents the most taxon-dense molecular phylogeny of the genus. The resultant phylogeny separates species into five main clades, but many of Lynes' groupings were not monophyletic and there was also very little support for more recent groupings. Vocalisation analyses indicated that frequency components of songs were correlated with habitat type and body size. These correlations, though, disappeared when phylogeny was controlled for indicating that phylogenetic history rather than habitat preference influenced song character distribution. Some song types are mismatched to their environment, and some sympatric sister species appear to give similar calls. Cisticolas may overcome these attenuation and identification difficulties with behavioural adaptations and aerial displays. The biogeographic distribution of closely related species does not agree with many of the previously proposed hypotheses and a dated phylogeny estimates that most of the diversification in the genus has occurred within the last five million years. Most of the mean divergence date estimates correlated with periods of climate variability and episodes during which there is evidence for high lake levels in Africa, rather than correlating with Plio-Pleistocene glaciation, offering evidence that open habitats may have become fragmented during extremes of both arid and humid climates.

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.

No description available.

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

It has been argued that much of evolution takes place in the absence of fitness gradients. Such periods of evolution can be analysed by examining the mutational network formed by sequences of equal fitness, that is, the neutral network. It has been demonstrated that, in large populations under a high mutation rate, the population distribution over the neutral network and average mutational robustness are given by the principal eigenvector and eigen- value, respectively, of the network's adjacency matrix. However, little progress has been made towards understanding the manner in which the topology of the neutral network influences the resulting population distribution and robustness. In this work, we build on recent results from spectral graph theory and utilize numerical methods to enhance our understanding of how populations distribute themselves over neutral networks. We demonstrate that, in the presence of certain topological features, the population will undergo an exploration catastrophe and become confined to a small portion of the network. We further derive approximations, in terms of mutational biases, for the population distribution and average robustness in networks with a homogeneous structure. The applicability of these results is explored, first, by a detailed review of the literature in both evolutionary computing and biology concerning the structure of neutral networks. This is extended by studying the actual and predicted population distribution over the neutral networks of H1N1 and H3N2 influenza haemagglutinin during seasons between 2005 and 2016. It is shown that, in some instances, these populations experience an exploration catastrophe. These results provide insight into the behaviour of populations on neutral networks, demonstrating that neutrality does not necessarily lead to an exploration of genotype/phenotype space or an associated increase in population diversity. Moreover, they provide a plausible explanation for conflicting results concerning the relationship between robustness and evolvability.

No description available.

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.