The present thesis concerns the population history, evolutionary processes and phylogenetic relationships of lineages of the redfin minnow genus Pseudobarbus. First, the population history and evolutionary processes within P. quathlambae were determined, mainly to decide the conservation value of the Mohale population. The Mohale dam threatens its survival. A divergence in mitochondrial control region and cytochrome b sequences and frequency differences in the distribution of major histocompatibility alleles were found between the Mohale population and an “Eastern” lineage. The Mohale population has therefore been historically isolated and was deemed indispensable for the conservation of P. quathlambae. Differentiation among populations of the P. afer and P. phlegethon complex were investigated, in relation to geological and climatic processes. Sea levels were about – 130 m below present levels during the last glacial maximum, about 18 000 years ago. Five historically isolated lineages were identified through analysis of mitochondrial control region sequences. The four P. afer lineages showed a strong association with proposed palaeoriver systems. A “Forest” lineage, however, reaches across two proposed palaeoriver systems. Surprisingly, this lineage is closely related to P. phlegethon. Pseudobarbus asper and P. tenuis were analysed together, because of their close phylogenetic relationship and because they occur in sympatry in the Gourits River system. Pseudobarbus tenuis showed divergence in mitochondrial control region only between the Keurbooms and Bitou River systems compared to the Gourits River system. Within P. asper, divergence was low, suggesting recent inland exchange opportunities between populations of the Gourits and Gamtoos River systems. River capture of south-eastern tributaries of the Gourits River system by the Keurbooms River would have resulted in unidirectional colonization, suggesting that speciation between P. asper and P. tenuis occurred within the Gourits River system with or without the Gamtoos River system being involved. Lower sea levels during the last glacial maximum also played an important role in the population history of P. burchelli. Differentiation in P. burchelli did not occur between two proposed palaeoriver systems, but rather within a western palaeoriver system. Divergence in mitochondrial control region and cytochrome b sequences showed that the “Breede” and “Tradou” lineages diverged within the Breede River system, before the “Heuningnes” lineage became isolated in the Heuningnes River system. Fifteen historically isolated Pseudobarbus lineages were included in a phylogenetic analysis on which biogeographic hypotheses were based. Phylogenetic relationships based on mitochondrial control region, cytochrome b and 16S and a combined dataset of all these were compared to relationships recovered from a previous morphological dataset. Conflicts between the molecular and morphological analyses, suggests that several morphological characters evolved in a complex manner. The molecular phylogenies suggest that the earliest divergence in the Pseudobarbus was between P. quathlambae in the Orange River system and the other species that occur in the Cape Foristic Region. Pseudobarbus lineages with two pairs of barbels and those with a single pair of barbels (excluding P. quathlambae) grouped together. In terms of currently described species, only the two lineages of P. quathlambae and the three lineages of P. burchelli were clearly monophyletic. Copyright / Thesis (PhD (Genetics))--University of Pretoria, 2007. / Genetics / unrestricted

tRNA genes have the fundamental role of translating the genetic code during protein synthesis. Beyond solely a passive decoding role, the tRNA pool exerts selection pressures on the codon usage of organisms and the viruses that infect them because processing codons read by rare tRNAs can be slow or even erroneous. To better understand the interactions of codons and anticodons in eukaryotic species, we first investigated whether tRNAs packaged into HIV-1 particles may relate to the poor codon usage of HIV-1 genes. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding poorly adapted codons are overrepresented in HIV-1 virions. Because the affinity of Gag-Pol for all tRNAs is non-specific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Moreover, differences that we found in the codon usage between early and late genes suggest alterations in the tRNA pool are induced late in viral infection. Next, we tested whether a reduced tRNA anticodon pattern, which was called into question by predicted tRNA datasets, is maintained across eukaryotes. tRNA prediction methods are prone to falsely identifying tRNA-derived repetitive sequences as functional tRNA genes. Thus, we proposed and tested a novel approach to identify falsely predicted tRNA genes using phylogenetics. Phylogenetic analysis removed nearly all the genes deviating from the anticodon pattern, therefore the anticodon pattern is reaffirmed across eukaryotes.

Benthic diatoms are often used as indicators of water quality and past environmental conditions. This depends entirely on a reliable taxonomic system. With the advent of DNA techniques, genetic analyses can now be used in tandem with traditional microscopy in order to improve taxonomy and determine evolutionary relationships. This thesis examined a speciose genus of diatoms Neidium (> 300 species) and, using sequence data from molecular markers as well as traditional morphological analyses, investigated phylogenetic relationships. Fresh benthic samples from aquatic ecosystems in Eastern North America were collected; Neidium taxa were examined using light and scanning electron microscopy then compared to the original specimen types. A total of 124 individual cells were retrieved, amplified, and sequenced for four molecular markers (rbcL, 18S, psbA, and psbC). Phylogenetic reconstructions were completed using Maximum likelihood and Bayesian analyses; when compared with morphological analyses this led to the delineation of several novel Neidium species.

Comparing genomes in a computationally efficient manner is a difficult problem. Methods that provide the highest resolution are too inefficient and methods that are efficient are too low resolution. In this thesis, we show that the Colored de Bruijn Graph (CdBG) is a suitable method for comparing genomes because it is efficient while maintaining a useful amount of resolution. To illustrate the usefulness of the CdBG, the phylogenetic tree for 12 species in the Drosophila genus is reconstructed using pseudo-homologous regions of the genome contained in the CdBG.

No description available.

The services that urban trees provide to human society and the natural environment are widely recognized, but urban trees are in jeopardy due to climate change and urban stressors. With drought as a major threat in many areas, it is important for the future of urban forestry to select species composition based upon performance under water stress. Certain leaf functional traits can help horticulturalists more accurately predict water usage of urban trees. Comprehension through rigorous experimentation is lacking, partly due to the thousands of mostly exotic species. Previous studies suggest that species whose leaves have a denser arrangement of smaller stomata and a higher leaf mass per area (LMA) are better adapted to low water availability. We sampled 70 urban tree species California and analyzed their stomatal length, stomatal density, and LMA. We compared the traits with water use data from the Water Use Classification of Landscape Species to assess possible correlations. All pairwise trait comparisons show significant correlation (P < 0.05), and LMA is significantly higher in low water use species compared to medium water use species (P= 0.0045). After using independent contrasts to incorporate phylogenetic relationships, significance was lost, implying that basal divergences are responsible for observed trends. Other potential explanations for differences in species water usage are foliar longevity (deciduous vs. evergreen) and stomatal distribution (amphistomatous vs. hypostomatous). Low water use species are more likely to be evergreen and amphistomatous compared to medium water use species. Consideration of all these traits in combination with good management practices can help ensure future success of urban forests.

Rare, alpine, endemic species are particularly at risk for extinction. Alpine environments are especially vulnerable to climate change and human impacts, such as ski resort development and snowmaking. Draba asterophora Payson is a rare, alpine species that occurs only in three disjunct mountain-top regions surrounding Lake Tahoe. It is currently threatened by human impacts, such as ski resorts, as well as indirect influences of climate change and therefore in need of better understanding for conservation purposes. Draba asterophora may be able to serve as a case study for other similarly vulnerable, rare, alpine, endemic species with conservation needs. We utilized demographic, ecological, phylogenetic, and cytogenetic data to better understand D. asterophora's life history, habitat requirements, and delineate species boundaries. Draba asterophora occurs in three population clusters surrounding Lake Tahoe, segregated into two varieties, variety asterophora in the north (N) and south (S) and variety macrocarpa C. L. Hitchcock in the southwest (Sw). Populations exist on ski resort property in the north and south (variety asterophora) regions and thus face more threats. Therefore, these regions were the focus of long-term monitoring over a four year period. We assessed various morphological traits, survivorship and density estimates in these two population clusters (north and south). We created projection matrices for each population cluster and calculated finite rates of increase (λ), as well as reproductive and survivorship rates. The population projection matrices estimated growth rates close to 1.00 for both clusters (S: λ=0.977; N: λ=1.014), although neither cluster had reached a stable population structure. Plants in the north tended to be more robust, having more rosettes, inflorescences, flowers and fruits than the plants in the south. However, the plants in the northern population cluster did not have significantly higher brood sizes and the southern plants actually had larger seed to ovule ratios than those in the north ((S: x = 0.387l; N: x = 0.346). These results may be in part influenced by habitat differences (e.g. greater water availability in the north), specific site microclimate/microhabitat differences, genetic drift, and/or possibility polyploidy vigor (the northern cluster is tetraploid). However, as an autopolyploid, the NE cluster may have some difficulties with pairing in meiosis which could also contribute to its reduced seed to ovule ratios. Although the populations were found to be fairly stable currently, D. asterophora var. asterophora is potentially quite vulnerable to disturbance. All of the monitored populations in both clusters existed in small populations with low local densities confined to narrow geographic boundaries, and exhibit low fecundity. Because the taxon relies on survivorship of adults for population stability rather than new recruits, it is crucial to maintain stable adult populations in conservation efforts. Draba asterophora is similar to other alpine species tend, exhibiting high adult survivorship with low fecundity. We also examined the habitat requirements of D. asterophora by characterizing the abiotic habitat (soil chemical and texture analysis and site features such as aspect, slope, elevation) and the vegetative communities in D. asterophora sites. Draba asterophora sites all have fairly similar abiotic and biotic habitats despite large geographical separation, although some specific sites have unique characteristics as well. Draba asterophora habitats consist of steep, granitic slopes in the subalpine conifer zone with little understory. Draba asterophora's community may be facilitated by the diversity-stability hypothesis, as D. asterophora abundance (cover and/or frequency) was positively correlated with species richness and diversity, but negatively correlated with total vegetative cover (relative cover). In addition, D. asterophora has greater seed production (both seed/ovule ratio and brood size) in areas with greater species diversity. Draba asterophora does not appear to have many specific soil composition requirements or specific interspecific interactions, but generally occurs in diverse communities, albeit somewhat sparsely populated, in relatively open north-facing alpine habitats on steep granitic slopes. Changes in vegetation, topology and/or snow cover, due to disturbances such as grading, erosion, or snowmaking, may be detrimental to D. asterophora by rendering its habitat unsuitable. Therefore, D. asterophora habitat should be protected from further human impacts. Draba; the largest and most diverse genus in Brassicaceae, the mustard family, has complex phylogenetics due to its high degree of reticulate evolution, polyplodization, rarity and endemism. The D. asterophora complex has not been included in previous phylogenetic analyses. Only he northern population has been examined cytologically (2n=40). Thus, its taxonomy is poorly understood. We utilized one nuclear molecular marker, ITS, as well as two new chloroplast markers, trnS-G and trnH-psbA, to help resolve complex phylogenetic relationships and delimitation species boundaries within the D. asterophora complex. In addition, we examined the cytogenetics of all three population clusters to determine any differences in ploidy levels exist. The D. asterophora complex appears to be composed of three separately evolving trajectories differentiated by separate geographic regions surrounding Lake Tahoe, CA/NV. This is supported by both phylogenetic analyses as well as cytology. The combined DNA concatenated analysis demonstrated that all three regions form separate branches within the D. asterophora clade. Cytologically, chromosome counts were distinct in all three regions, with the southern cluster being a diploid (2n=20), the northern cluster an autotetraploid (2n=40), and the cluster in the southwest ( variety macrocarpa) an autooctoploid (2n=80). Based on these findings, we recommend that the three population clusters be treated as distinct taxonomic entities for conservation purposes. This demonstrates the importance of considering phylogenetics and ploidy levels, even of autopolyploids, in determining taxonomy, especially for rare, endemic species with disjunct habitats. Overall, this research suggests that the three geographic regions of the D. asterophora complex are distinct demographically and on own their evolutionary trajectories. Conservation efforts need to be targeted towards separate management of each population cluster. Maintaining stable adult populations, diverse plant communities, and preventing further destruction of habitat are the key conservation suggestions for D. asterophora.

To understand present patterns of biodiversity, knowledge of a lineage’s past – both evolutionary and geographic – is required. Here I present the first comprehensive phylogenomic study of an Amazonian poison frog genus, Ameerega, as well as the introduction of a new method for characterizing ancestral distributions via phylogenetic niche modeling, which I use to investigate Ameerega’s biogeographic past. I sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. My phylogenetic inference diverged strongly from those of previous studies. I also introduce a new phylogenetic niche modeling method, which accounts for issues of bias in other methods by incorporating knowledge of evolutionary relationships into niche models. Given modern-day and paleoclimatic data, species occurrence data, and a time-calibrated phylogeny, my method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. I demonstrate my method on the Ameerega bassleri group. I also use simulations to show that my method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space.

We have examined phylogenetic relationships of suckers of tribe Moxostomatini (Cypriniformes, Catostomidae) using cytochrome-b and Growth Hormone gene intron sequences. Phylogenies were significantly different from recent estimates of relationships based primarily on morphology (Smith, 1992) and cytochrome-b sequences (Harris et al., 2002). Overall, there was little support for many basal nodes in the phylogeny, however it was clear that Scartomyzon and Moxostoma were not monophyletic, despite morphological evidence provided Robins and Raney (1956, 1957), Jenkins (1970), and Smith (1992). Growth Hormone sequences provided good support for a monophyletic Western Scartomyzon lineage and thus suggested a single ancestral invasion of Scartomyzon-like fishes into drainages of Texas and Mexico. Phylogenetic relationships of Western Scartomyzon are structured geographically and do not conform well to current taxonomy.

abstract: This project was completed to understand the evolution of the ability to digest wood in termite symbiotic protists. Lower termites harbor bacterial and protist symbionts which are essential to the termite ability to use wood as a nutritional source, producing glycoside hydrolases to break down the polysaccharides found in lignocellulose. Yet, only a few molecular studies have been done to confirm the protist species responsible for particular enzymes. By mining publicly available and newly generated genomic and transcriptomic data, including three transcriptomes from isolated protist cells, I identify over 200 new glycoside hydrolase sequences and compute the phylogenies of eight glycoside hydrolase families (GHFs) reported to be expressed by termite hindgut protists. Of those families examined, the results are broadly consistent with Todaka et al. 2010, though none of the GHFs found were expressed in both termite-associated protist and non-termite-associated protist transcriptome data. This suggests that, rather than being inherited from their free-living protist ancestors, GHF genes were acquired by termite protists while within the termite gut, potentially via lateral gene transfer (LGT). For example one family, GHF10, implies a single acquisition of a bacterial xylanase into termite protists. The phylogenies from GHF5 and GHF11 each imply two distinct acquisitions in termite protist ancestors, each from bacteria. In eukaryote-dominated GHFs, GHF7 and GHF45, there are three apparent acquisitions by termite protists. Meanwhile, it appears prior reports of GHF62 in the termite gut may have been misidentified GHF43 sequences. GHF43 was the only GHF found to contain sequences from the protists not found in the termite gut. These findings generally all support the possibility termite-associated protists adapted to a lignocellulosic diet after colonization of the termite hindgut. Nonetheless, the poor resolution of GHF phylogeny and limited termite and protist sampling constrain interpretation. / Dissertation/Thesis / Masters Thesis Biological Design 2019