Freshwater sculpins (Cottus) are common throughout temperate regions of the Northern Hemisphere. Their broad distribution in the Western North America makes them a good model for understanding phylogeographic relationships among western fishes. Within much of the interior west three lineages, C. bairdii, C. confusus, and the C. beldingii complex, are most prevalent. The distribution of these three overlap in the Snake River Basin. All occur below Shoshone Falls on the Snake River. However, only two currently reside in the Upper Snake River above the falls. An exception are the Lost River streams of central Idaho. While these streams are technically part of the Upper Snake River Basin, they do not directly connect with the Snake River. Preliminary studies with a single mitochondrial DNA (mtDNA) gene suggested multiple pathways for Cottus introduction into the Lost River stream complex. Here, three mitochondrial and five nuclear genes were examined to investigate the phylogenetic relationships of these three lineages. Sequences were obtained from 71 different populations in the Lost River streams and surrounding basins. Maximum Likelihood (ML) phylogenies were constructed using these data. Our data indicate that relationships among populations within these species are complex and that no single invasion into the Lost River streams and surrounding regions can account for the phylogenetic signals detected. Instead, it appears that multiple invasions in an evolving landscape played a significant role in the modern distribution of species in this region.

Features of the infraorbital region, such as infraorbital surface topography, infraorbital surface orientation, and curvature of the zygomaticoalveolar crest, have long played a prominent role in phylogenetic analyses of Homo. However, there is currently considerable debate regarding the phylogenetic reliability of infraorbital characters, as numerous researchers have questioned the degree to which these features are morphologically independent of one another and facial size. These questions largely stem from methodological limitations for accurately quantifying the curvilinear morphology of the infraorbital surface and zygomaticoalveolar crest, which have significantly impeded the ability to discern patterns of infraorbital integration and allometry. In this study, infraorbital surface and zygomaticoalveolar crest morphology are precisely assessed, through geometric morphometric methodologies well-suited for quantifying complex curvilinear structures, in a large sample of fossil (n = 71) and recent Homo (n = 303). Once quantified, measures of infraorbital surface topography, infraorbital surface orientation and zygomaticoalveolar crest curvature are further evaluated for intercorrelation and allometry in order to more fully evaluate the morphological independence of commonly cited infraorbital characters. The results of this study indicate that most aspects of infraorbital surface topography, infraorbital surface orientation and zygomaticoalveolar crest curvature are significantly correlated with facial size across Homo. Moreover, certain aspects of infraorbital shape, such the degree of infraorbital surface depression and the overall curvature of the zygomaticoalveolar crest, appear to show additional, size-independent, intercorrelations, suggesting they form a singular "infraorbital complex." In light of these results, the use of infraorbital characters as separate independent characters in phylogenetic assessments of Homo is called into question, while the importance of facial size in human craniofacial evolution is further highlighted.

<p>In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix <em>d</em>.</p><p>In this thesis I present a few methods for constructing a phylogenetic tree from <em>d</em>. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a tree. When <em>d</em> does not perfectly match a tree, the resulting graph will instead show the different possible topologies, and how strong support they have from the data.</p><p>Finally I have tested the methods both on real measured data and constructed test cases.</p>

Reticuloendotheliosis virus (REV) is a retrovirus that causes a neoplastic disease in a wide range of avian hosts including chickens, turkeys, and ducks. In 1993, REV was detected in the endangered Attwater's prairie chicken (Tympanachus cupido attwateri), a subspecies of Tympanachus cupido. Subsequent infections of this prairie chicken have been identified at captive breeding facilities throughout Texas. The implications of these infections have severely hindered repopulation efforts by these facilities. This study focused on investigating REV infection of captive Attwater'€™s prairie chicken in order to better understand the disease affecting these endangered birds. The overall objective was to develop a means of eliminating this threat to the repopulation of the Attwater's prairie chicken. Several aspects of virus infection were investigated. Reagents capable of recognizing prairie chicken IgY and viral gag polypeptides were developed for use in assays for detection of antibody responses and titration of viral concentrations. Sequencing data of genomes collected from isolates of Texas prairie chickens and domestic chickens, as well as three REV prototype viruses, were compared to determine relationships among strains and identify the potential origin of the REV infecting Attwater'€™s prairie chicken. Additionally, a flow cytometry technique of segregating the lymphocyte population from peripheral blood mononuclear cells (PBMC) using a pan leukocyte monoclonal antibody was developed to more accurately measure changes within lymphocyte populations. This technique combined with intracellular labeling was used to deduce the target cells of REV infection. A nested polymerase chain reaction (PCR) test was developed for greater sensitivity in detecting infection in birds than the previous method of single amplification PCR. This greater sensitivity results in earlier identification of the virus in infected birds, which allows for earlier removal of infected birds to minimize transmission of the virus throughout the flock. The sensitivity of the nested PCR diagnostic test was determined in a dose response pathogenesis study, which was conducted on hybrid greater/Attwater's prairie chicken to observe the experimental development of disease in these birds. Finally, a vaccine was developed using plasmid DNA with REV encoded genes and tested on naturally infected prairie chickens to determine its efficacy in reducing viral load. Although no reduction in viral load was detected, the vaccine may be effective in providing prophylactic protection in future studies.

Un des buts principaux de la biologie évolutive et de la médecine moléculaire consiste à reconstruire les relations phylogénétiques entre organismes à partir de leurs séquences moléculaires. En littérature, cette question est connue sous le nom d’inférence phylogénétique et a d'importantes applications dans la recherche médicale et pharmaceutique, ainsi que dans l’immunologie, l’épidémiologie, et la dynamique des populations. L’accumulation récente de données de séquences d’ADN dans les bases de données publiques, ainsi que la facilité relative avec laquelle des données nouvelles peuvent être obtenues, rend l’inférence phylogénétique particulièrement difficile (l'inférence phylogénétique est un problème NP-Hard sous tous les critères d’optimalité connus), de telle manière que des nouveaux critères et des algorithmes efficaces doivent être développés. Cette thèse a pour but: (i) d’analyser les limites mathématiques et biologiques des critères utilisés en inférence phylogénétique, (ii) de développer de nouveaux algorithmes efficaces permettant d’analyser de plus grands jeux de données.

In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix d. In this thesis I present a few methods for constructing a phylogenetic tree from d. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a tree. When d does not perfectly match a tree, the resulting graph will instead show the different possible topologies, and how strong support they have from the data. Finally I have tested the methods both on real measured data and constructed test cases.

MicroRNAs are important biomolecules for regulating biological processes. Moreover, the secondary structure of microRNA is important for its activity and has been used previously as a mean for finding unknown microRNAs. A phylogenetic study of the microRNA secondary structure reveals more information than its primary sequence, because the primary sequence can undergo mutations that give rise to different phylogenetic relationships, whereas the secondary structure is more robust against mutations and therefore sometimes  more informative. Here we constructed a phylogenetic tree entirely based on microRNA secondary structures using tools PHYLIP (Felsenstein, 1995) and RNAforester (Matthias Höchsmann, 2003, Hochsmann et al., 2004), and compared the overall topology and clusters with the phylogenetic tree constructed using microRNA sequence. The purpose behind this comparison was to investigate the sequence and structure similarity in phylogenetic context and also to investigate if functionally similar microRNA genes are closer in their structure-derived phylogenetic tree. Our phylogenetic comparison shows that the sequence similarity has hardly any effect on the structure similarity in the phylogenetic tree. MicroRNAs that have similar function are closer in the phylogenetic tree based on secondary structure than its respective sequence phylogeny. Hence, this approach can be very useful in predicting the functions of the new microRNAs whose function is yet to be known, since the function of the miRNAs heavily relies on its secondary structure.

Since Darwin proposed that all species on the earth have evolved from a common ancestor, evolution has played an important role in understanding biology. While the evolutionary relationships/histories of genes are represented using trees, the genomic evolutionary history may not be adequately captured by a tree, as some evolutionary events, such as horizontal gene transfer (HGT), do not fit within the branches of a tree. In this case, phylogenetic networks are more appropriate for modeling evolutionary histories. In this dissertation, we present computational algorithms to reconstruct phylogenetic networks from different types of data. Under the assumption that species have single copies of genes, and HGT and speciation are the only events through the course of evolution, gene sequences can be sampled one copy per species for HGT detection. Given the alignments of the sequences, we propose systematic methods that estimate the significance of detected HGT events under maximum parsimony (MP) and maximum likelihood (ML). The estimated significance aims at addressing the issue of overestimation of both optimization criteria in the search for phylogenetic networks and helps the search identify networks with the ``right" number of HGT edges. We study their performance on both synthetic and biological data sets. While the studies show very promising results in identifying HGT edges, they also highlight the issues that are challenging for each criterion. We also develop algorithms that estimate the amount of HGT events and reconstruct phylogenetic networks by utilizing the pairwise Subtree-Prune-Regraft (SPR) operation from a collection of trees. The methods produce good results in general in terms of quickly estimating the minimum number of HGT events required to reconcile a set of trees. Further, we identify conditions under which the methods do not work well in order to help in the development of new methods in this area. Finally, we extend the assumption for the genetic evolutionary process and allow for duplication and loss. Under this assumption, we analyze gene family trees of proteobacterial strains using a parsimony-based approach to detect evolutionary events. Also we discuss the current issues of parsimony-based approaches in the biological data analysis and propose a way to retrieve significant estimates. The evolutionary history of species is complex with various evolutionary events. As HGT contributes largely to this complexity, accurately identifying HGT will help untangle evolutionary histories and solve important questions. As our algorithms identify significant HGT events in the data and reconstruct accurate phylogenetic networks from them, they can be used to address questions arising in large-scale biological data analyses.

Porifera (sponge) has been considered the earliest branching group of the metazoan crown, it plays an important role of evolution from protist to multicellular organisms. The sponges do not have tissues and organs. There are 15,000 species of sponges in the world. They contain a rich variety of secondary metabolites which may have the potential of becoming anticancer or antivirus drugs. The morphological characteristics of sponges may be affected by the environmental conditions and cause ambiguity and confusion in sponge identification. The complete mitochondrial DNAs of four Demospongiae sponges, Terpios hoshinota, Xestospongia testudinaria, Petrosia corticata, and Suberea clavata in Green Island were determined by PCR and primer walking. The sequences can be used for evolution and phylogenetic analyses. The complete mitochondrial genomes of the four sponges contain 20498 bp, 18988 bp, 18562 bp and 19559 bp, respectively. The genomes encode 2 rRNA genes (rns, rnl), 14 protein-coding genes (atp6, atp8-9, cox1-3, cob, nad1-6, and nad4L) and 25 tRNAs. All the genes of T. hoshinota, X. testudinaria, P. corticata are transcribed on the same strand. Whereas, some of the genes (nad 4L ~ tRNA-SerUGA) of S. clavata are encoded on the complementary strand. The results showed the differences between the mitochondrial DNA sequences of X. testudinaria and the Atlantic sponge, X. muta, are very limited, therefore, they may be reclassified as the same species. Meanwhile, S. clavata and Aplysina fulva are close phylogenetically. The conflict between molecular and morphology taxonomy should be re-examined.

The expressed sequence tags, derived from the developing tilapia brain, were established in our laboratory. An unique gene, high mobility group proteins 2 (HMG2), were investigated. HMG2 is a non-histone chromatin protein. HMG2 cloned from tilapia, Oreochromis mossambicus, is a gene with open reading frame 642bps, and deduced as 213 amino acid protein sequence. NCBI Conserved Domain search, the Gene Ontology, NEBcutter restrict enzyme analysis, NCBI blastx, and neighbor phylogenetic tree were used for the bioinformatic analysis. In the present study, the protein expression of HMG2 in the BL21 E.coli system, a prokaryotic system, and purified with 6X His Tag NI-NTA affinity chromatography.