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In 1975, Elongation Factor P (EF-P) protein was first discovered in the bacterium Escherichia coli. EF-P is believed to facilitate the translation of proteins by stimulating peptide bond synthesis for a number of different aminoacyl-tRNA molecules in conjunction with the 70S ribosome peptidyl transferase. Known eukaryotic homologs, eukaryotic translation initiation factor 5A (eIF-5A) of EF-P exist but with very low sequence conservation. Nevertheless, because of the high sequence similarities seen between bacterial EF-Ps and its low sequence similarity with eIF-5A, there is interest in the pharmaceutical industry of developing a novel antibacterial drug that inhibits EF-P. Of 322 completely sequenced bacterial genomes stored in GenBank, only one organism lacked an EF-P protein. Interestingly, sixty-six genomes were discovered to carry a duplicate copy of efp. The EF-P sequences were then used to construct a protein phylogenetic tree, which provided evidence of horizontal and vertical gene transfer as well as gene duplication. To lend support to these findings, EF-P GC content, codon usage, and nucleotide and amino acid sequences were analyzed with positive and negative controls. The adjacent 10 kb upstream and downstream regions of efp were also retrieved to determine if gene order is conserved in distantly related species. While gene order was not preserved in all species, two interesting trends were seen in some of the distantly related species. The EF-P gene was conserved beside Acetyl-CoA carboxylase genes, accB and accC in certain organisms. In addition, some efp sequences were flanked by two insertion sequence elements. Evidence of gene duplication and horizontal transfers of regions were also observed in the upstream and downstream regions of efp. In combination, phylogenetic, sequence analyses, and gene order conservation confirmed evidence of the complex history of the efp genes, which showed incongruencies relative to the universal phylogenetic tree. To determine how efp is regulated, the upstream regions of efp were used to try to predict motifs in silico. While statistically significant motifs were discovered in the upstream regions of the orthologous efp genes, no conclusive similarities to known binding sites such as the sigma factor binding sites or regulatory protein binding sites were observed. This work may facilitate and enhance the understanding of the regulation, conservation, and role of EF-P in protein translation.

In 1975, Elongation Factor P (EF-P) protein was first discovered in the bacterium Escherichia coli. EF-P is believed to facilitate the translation of proteins by stimulating peptide bond synthesis for a number of different aminoacyl-tRNA molecules in conjunction with the 70S ribosome peptidyl transferase. Known eukaryotic homologs, eukaryotic translation initiation factor 5A (eIF-5A) of EF-P exist but with very low sequence conservation. Nevertheless, because of the high sequence similarities seen between bacterial EF-Ps and its low sequence similarity with eIF-5A, there is interest in the pharmaceutical industry of developing a novel antibacterial drug that inhibits EF-P. Of 322 completely sequenced bacterial genomes stored in GenBank, only one organism lacked an EF-P protein. Interestingly, sixty-six genomes were discovered to carry a duplicate copy of efp. The EF-P sequences were then used to construct a protein phylogenetic tree, which provided evidence of horizontal and vertical gene transfer as well as gene duplication. To lend support to these findings, EF-P GC content, codon usage, and nucleotide and amino acid sequences were analyzed with positive and negative controls. The adjacent 10 kb upstream and downstream regions of efp were also retrieved to determine if gene order is conserved in distantly related species. While gene order was not preserved in all species, two interesting trends were seen in some of the distantly related species. The EF-P gene was conserved beside Acetyl-CoA carboxylase genes, accB and accC in certain organisms. In addition, some efp sequences were flanked by two insertion sequence elements. Evidence of gene duplication and horizontal transfers of regions were also observed in the upstream and downstream regions of efp. In combination, phylogenetic, sequence analyses, and gene order conservation confirmed evidence of the complex history of the efp genes, which showed incongruencies relative to the universal phylogenetic tree. To determine how efp is regulated, the upstream regions of efp were used to try to predict motifs in silico. While statistically significant motifs were discovered in the upstream regions of the orthologous efp genes, no conclusive similarities to known binding sites such as the sigma factor binding sites or regulatory protein binding sites were observed. This work may facilitate and enhance the understanding of the regulation, conservation, and role of EF-P in protein translation.

Random amplified polymorphic DNA (RAPD) markers were used in three genetic studies in lentil (<i>Lens culinaris</i> Medikus). The first study involved development of RAPD markers linked with genes for resistance to ascochyta blight, caused by <i>Ascochyta fabae</i> f. sp. lentis Gossen et al. Seventy F₂-derived F₃ (F_2:3) lines were field screened for ascochyta blight reaction in each of two hybrid populations, Indianhead x Eston and ILL 5588 x Eston, that were segregating for resistance to ascochyta blight. Resistance to ascochyta blight in ILL 5588 lentil was conferred by a single dominant gene (<i>Ral₁</i>), whereas resistance in Indianhead lentil was conferred by a single recessive gene (<i>ral₂</i>). An efficient DNA extraction procedure and a PCR protocol that yielded RAPD markers with high resolution were developed for lentil. Bulked segregant analysis was used to produce four bulks of DNA from resistant vs. susceptible F₂ plants in each of these two populations which were then screened for RAPD markers using 400 random oligonucleotide primers. One RAPD marker, UBC227₁₂₉₀, was linked to the recessive gene, <i>ral₂</i>, in Indianhead lentil in repulsion phase with a map distance of 14.1 ± 4.5 cM. No RAPD marker was linked with the <i>Ral₁</i> gene in ILL 5588 lentil. In the second study, RAPD markers were used to study phylogeny of the genus Lens. DNA, extracted from 23 accessions of all five taxa of the genus Lens (culinaris, orientalis, nigricans, odemensis and ervoides), was screened for RAPD polymorphisms, using 11 random oligonucleotide primers. Two accessions of the differentiated cytotype of L. nigricans were also included. One hundred and forty eight polymorphic RAPD markers were resolved. A dendrogram for these RAPD markers, using the unweighted pair group method, clearly separated all accessions into their supposedly related taxa. Lens orientalis was the undisputed progenitor of the cultivated lentil, <i>Lens culinaris</i>. A low level of RAPD polymorphism was observed in <i>Lens culinaris</i> and L. ervoides. The differentiated cytotype of L. nigricans was well separated from the normal cytotype of L. nigricans and was closely associated with the L. odemensis accessions, indicating its close genetic similarity to L. odemensis. Principal component analysis (PCA) also indicated a similar relationship among these accessions, but resulted in a better resolution of the groupings. In the third study, the genetic polymorphism of seven Canadian lentil cultivars were studied using RAPD markers. Four lentil cultivars, CDC Gold, CDC Matador, Eston and Indianhead each had a unique, cultivar-specific RAPD marker, allowing their identification.

Leptosporangiate ferns, with more than 9000 extant species, are truly exceptional among the non-flowering lineages of vascular plants. However, this rather remarkable diversity was not simply a consequence of being able to "hold on" as flowering plants rose to dominance. Instead, it appears to be the result of an ecological opportunistic response to the establishment of more complex, angiosperm-dominated ecosystems. The proliferation of flowering plants across the landscape undoubtedly resulted in the formation of a plethora of new niches into which leptosporangiate ferns could diversify. Many of these were evidently on shady forest floors, but many others were actually within the new angiosperm-dominated canopies. Today, almost one third of leptosporangiate species grow as epiphytes on angiosperm trees. My dissertation aims to demystify the evolution and diversification of epiphytic ferns in order to more fully understand the leptosporangiate success story. By assembling and analyzing the most inclusive molecular dataset for leptosporangiate ferns to date, I provide unprecedented insight into overall fern relationships and a solid and balanced phylogenetic framework within which the evolution of epiphytism can be examined. By employing this phylogeny and numerous constraints from the fern fossil record, I uncover the timing of epiphytic fern diversification and examine the origin of the modern tropical rain forest biome in which these ferns reside. / Dissertation

<p>Edaphic factors--those pertaining to the substrate or soil--are thought to play an important role in the diversification of flowering plants. Although edaphic factors are widely interpreted as causal agents in plant diversification, little is known about the evolutionary origin of most edaphic endemic plants, preventing inference of potential mechanisms by which substrate properties may influence speciation. The North American plant genus Ceanothus (Rhamnaceae) contains 9 edaphic-endemic species, taxa restricted to soils derived from specific geological materials. The three components of my dissertation research aim to improve understanding of how edaphic ecology has influenced the diversification of Ceanothus. First, I use DNA sequence data from the low-copy nuclear gene nitrate reductase to reconstruct the phylogeny of Ceanothus and elucidate diversification of this group into the California Floristic Province (CFP) of western North America, including the evolution of edaphic endemism. This research indicates that diversification of the two Ceanothus subgenera (Cerastes and Ceanothus) is centered on the CFP and is characterized by shallow divergence and phylogenetic relationships defined predominantly by geography. Divergence time estimation suggests that diversification of both Ceanothus subgenera began approximately 6 Ma. The nine edaphic-endemic taxa are not phylogenetically clustered in my analyses, suggesting that the origin of edaphic endemism has occurred on multiple occasions, including multiple examples of serpentine endemism. The second chapter of my dissertation uses soil chemistry data in combination with a more detailed examination of genetic variation in nitrate reductase to elucidate the evolution of a single edaphic endemic species.</p> / Dissertation

Basioccipital foramen (bof) is found in four acropomatid species, including Apogonops anomalus, Doederleinia berycoides, Neoscombrops annectens, and Synagrops japonicus belonging to four genera. This structure is just near the fish¡¦s inner ear and to which the anterior diverticulae of the swim bladder in the species protrudes. This configuration is though to be closely related to enhance hearing capabilities and an important synapomorphic system to the phylogeny of acropomatids. The structural parameters of the sagittae (i.e., otolith area, otolith sulcus area, ratio of sulcus to area, otolith weight, hair cell density in otolithic macula, and the stereocilia number per hair cell bundle) were estimated, measured, and analyzed. The data of the parameters from the ¡¥bof-possessing¡¦ acropomatids are lower than that of the ¡¥non-bof¡¦ acropomatids. These values infer a probable poorer auditory capability of the ¡¥bof-possessing¡¦ acropomatids. COI, cytochrome b, and rhodopsin sequences of 12 species in five acropomatid genera (i.e., Acropoma, Doederleinia, Malakichthys, Neoscombrops, Synagrops) were analyzed to resolve the issue whether the configuration between ¡¥bof¡¦ and anterior diverticulae of swim bladder representing synapomorphic characters. The constructed Bayesian and maximum parsimony trees indicate that the ¡¥bof-possessing¡¦ acrpomatids do not form a clade. These results suggest that thses specialized structures (¡¥bof¡¦ and anterior swim bladder diverticulae) have developed more than once in Acropomatidae (i.e., a case of convergence).

Batrachoididae, one of the most well-studied soniferous fishes, are typical examples of fish using intrinsic sonic muscles to excite vibration of swim bladder to emit sound. Most fishes possess a single swim bladder including the Batrachoididae. However, the grunting toadfish (Allenbatrachus grunniens) was found to have two separated swim bladders located in the dorsal part of the abdominal cavity; the size of the swim bladders were quite similar. Sonic muscles were firmly attached to the lateral side of each swim bladder. The aims of this study were to (1) investigate the specialized swimbladder morphology and the acoustic signals of the grunting toadfish (A. grunniens), (2) to falsify the hypothesis that this unique form of swim bladder is a synapomorphic character, and species that possess this character are sister groups. The vocal repertoire in grunting toadfish can generally divided into two types ¡V grunt and boatwhistle. Grunts were harmonic signals with shorter call duration, and could be emitted alone as single grunt (i.e., hand-held grunt) or in series (known as grunt train). Boatwhistles were also hamonic but much longer in call duration and usually appeared in succession. A small portion of signals were found to have acoustic beats, which was previously described in the three-spined toadfish (Batrachomoeus trispinosus), which also possess a pair of swim bladders. Therefore, signals with acoustic beats may be a key character for generating sound by two separated swim bladders. Comparing the morphological measurements of swim bladders indicated that there were no significant differences between swim bladders on different sides. However, comparisons between genders showed that the width, thickness, and weight of sonic muscle in females were significantly higher than males. Less wide sonic muscles with shorter sonic muscle fibers may enables the muscle to contract at a higher velocity in male fishes. However, females were found to have thicker sonic muscle, which indicated that the vocal ability in females may be higher than it was expected. The sonic muscle fibers of females have a larger myofibrillar region compared with males, which have a relatively larger central core. These characters may increase the fatigue-resistance of sonic muscle in males, which can contract at a relatively higher rate for a longer duration. Species with two separated swim bladders were found to be sister group in the molecular phylogenetic tree, implying that this specialized morphological character is synapomorphy.

Diapriids (Hymenoptera: Diapriidae) are small parasitic wasps. Though found throughout the world they are relatively unknown. A framework for advancing diapriid systematics is developed by introducing a new web-based application/database capable of storing a broad range of systematic data, and the first molecular phylogeny specifically focused at examining intrafamilial relationships. In addition to these efforts, a description of a new taxon is provided. Several advantages of digital description, including linking descriptions to an ontology of morphological terms, are highlighted. The functionality of the database is further illustrated in the production of a catalog of diapriid host associations. The hosts database currently holds over 450 association records, for over 500 named taxa (parasitoids and hosts), and over 180 references. Diapriids are found to be primarily endoparasitoids of Diptera emerging from the host pupa. Phylogenetic inference for a molecular dataset of 28S and 18S rRNA sequence data, derived from a diverse selection of diapriids, is accomplished with a new suite of tools developed for handling complex rRNA datasets. Several parsimony-based methodologies, including an alignment-free method of analyzing multiple sequences, are reviewed and applied using the new software tools. Diapriid phylogenetic relationships are shown to be broadly congruent with existing morphology-based classifications. Methods for analyzing typically excluded sequence data are shown to recover phylogenetic signal that would otherwise be lost and the alignment-free method performed remarkably well in this regard. Empirically, phylogenetic approaches that incorporate structural data were not notably different than those that did not.

In this thesis, we shall propose heuristic algorithms to construct evolutionary trees under the distance base model. For a distance matrix of any type, the problem of constructing a minimum ultrametric tree (MUT), whose scoring function is the minimum tree size, is NP-hard. Furthermore, the problem of constructing an approximate ultrametric tree with approximation error ratio within $n^{epsilon}, epsilon > 0$, is also NP-hard. When the distance matrix is metric, the problem is called the triangle minimum ultrametric tree problem ($ riangle$MUT). For the $ riangle$MUT, there is a previous approximation algorithm, with error ratio $leq 1.5 ( lceil log n ceil + 1 )$. And we shall propose an improvement, with error ratio $leq lceil log_{alpha} n ceil + 1 cong 1.44 lceil log n ceil + 1$, where $alpha = frac{sqrt{5}+1}{2}$ for solving the $ riangle$MUT problem. We shall also propose a heuristic algorithm to obtain a good leaf node circular order. The heuristic algorithm is based on the clustering scheme. And then we shall design a dynamic programming algorithm to construct the optimal ultrametric tree with some fixed leaf node circular order. The time complexity of the dynamic programming is $O(n^3)$, if the scoring function is the minimum tree size or $L^1$-min increment.