xiv, 196 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / Establishing homologous (evolutionary) relationships among a set of genes allows us to hypothesize about their histories: how are they related, how have they changed over time, and are those changes the source of novel features? Likewise, aggregating related genes into larger, structurally conserved regions of the genome allows us to infer the evolutionary history of the genome itself: how have the chromosomes changed in number, gene content, and gene order over time? Establishing homology between genes is important for the construction of human disease models in other organisms, such as the zebrafish, by identifying and manipulating the zebrafish copies of genes involved in the human disease. To make such inferences, researchers compare the genomes of extant species. However, the dynamic nature of genomes, in gene content and chromosomal architecture, presents a major technical challenge to correctly identify homologous genes. This thesis presents a system to infer ancient homology between genes that takes into account a major but previously overlooked source of architectural change in genomes: whole-genome duplication. Additionally, the system integrates genomic conservation of synteny (gene order on chromosomes), providing a new source of evidence in homology assignment that complements existing methods. The work applied these algorithms to several genomes to infer the evolutionary history of genes, gene families, and chromosomes in several case studies and to study several unique architectural features of post-duplication genomes, such as Ohnologs gone missing. / Committee in charge: John Conery, Chairperson, Computer & Information Science; Virginia Lo, Member, Computer & Information Science; Arthur Farley, Member, Computer & Information Science; John Postlethwait, Member, Biology; William Cresko, Outside Member, Biology

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La compréhension de la dynamique des réarrangements génomiques est une problématique importante en phylogénie.La phylogénie est l'étude de l'évolution des espèces. Un but majeur est d'établir les relations d'évolution au sein d'un groupe d'espèces, pour déterminer la topologie de l'arbre d'évolution formé par ce groupe et des ancêtres communs à certains sous-ensembles.Pour ce faire, il est naturellement très utile de disposer d'un moyen d'évaluer les distances évolutionnaires relatives entre des espèces, ou encore d'être capable d'inférer à un groupe d'espèces le génome d'un ancêtre commun à celles-ci.Ce travail de thèse, dans la lignée d'autres travaux, consiste à élaborer de tels moyens, ici dans des cas particuliers où les génomes possèdent des gènes en multiples copies, ce qui complique les choses.Plusieurs hypothèse explicatives de la présence de duplications ont été considérées, des formules de distance ainsi que des algorithmes de calcul de scénarios ont été élaborés, accompagnés de preuves de complexité. / Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order to infer the topology of an evolutionary tree formed by this group and common ancestors to some of these species. In this context, having means to evaluate relative evolutionary distances between species, or to infer common ancestor genomes to a group of species would be of great help.This work, in the vein of other studies from the past, aims at designing such means, here in the particular case where genomes present multiple occurrencies of genes, which makes things more complex. Several hypotheses accounting for the presence of duplications were considered. Distances formulae as well as scenario computing algorithms were established, along with their complexity proofs.

Mitosis diploma work is figurative sculpture created by duplication statues. These duplicates to form pairs at each mitotic bind. Couples are composed into complex system, and thus form a spherical object. Against the background of this work is to introduce perspective on the human population and its culture as an independent organic whole.

Order Acipenseriformes (sturgeons and paddlefishes) is an ancient lineage of bony fishes (> 200 million years old) with most extant species at conservation risk. The pallid sturgeon, Scaphirhynchus albus, is a federally endangered species native to the Mississippi and Missouri River basins. Hybridization with sympatric shovelnose sturgeon, S. platorynchus, is one of several threats to pallid sturgeon. Current molecular markers cannot reliably distinguish among pure species and multigenerational backcrosses. This information is critical for implementation of management strategies to increase populations through natural reproduction and artificial propagation. Genotypes from a large panel of unlinked single-nucleotide polymorphisms (SNPs) may provide greater resolution of the two species; however, paralogous sequence variants (PSVs) within individuals resulting from an ancient whole genome duplication event confound SNP development. The aim of this dissertation was to produce unlinked disomic SNPs that would increases resolution between pallid sturgeon and shovelnose sturgeon. This was achieved by producing haploid gynogens, which contain only DNA from the maternal parent, and then producing a reference from these haploid gynogens. Sequence assembly based on haploids informed the presence of multi-locus contigs. More than 11,000 disomic SNP markers were produced that differentiate between the two species by mapping 120 individuals of either species onto the haploid reference. A linkage map, based on three haploid families, was able to resolve some paralogs and can be used to inform which discriminatory SNP markers are linked. Future research should convert the disomic markers derived in this study to an applied form, such as that achieved by genotyping-by-thousands.

By increasing genomic size, whole-genome duplication (WGD) is considered a major source of evolutionary innovation and speciation. We examined sequence evolution and expression divergence following WGD in a tetraploid African clawed frog (\textit{Silurana}). We hypothesized that the redundancy generated by WGD might allow for sex-specific and/or tissue-specific divergence, contributing to sexual dimorphism in this frog, and that such changes could be detected at both the expression and sequence levels. We investigated this hypothesis with a transcriptome-based approach, comparing both sexes across brain, heart and liver. We compared molecular evolution and expression divergence of duplicate gene homeologs to singleton genes and to an extant diploid relative, and identified genes with evidence for sex-biased expression. In doing so, we provide evidence for an allopolyploid mechanism of WGD and speciation in \textit{Silurana}. Additionally, we find that female-biased gene expression is more prevalent among duplicate genes than male-biased expression, particularly in brain where expression levels are highest. We similarly identified antagonistically sex-biased homeologs with indication of positive selection. Our results indicate that divergent evolution at both the sequence and expression levels following WGD favors the co-option of female-biased gene expression and may help resolve sexually antagonistic selection in this frog, thereby facilitating the evolution of sexual dimorphism. / Thesis / Master of Science (MSc) / Whole-genome duplication (WGD) is considered a major source of evolutionary innovation and a driver of speciation. By increasing genetic content and introducing redundancy, selective pressures are reduced and paralogous pairs diverge. We investigate how sex and tissue type contribute to duplicate gene divergence following WGD in a tetraploid African clawed frog. We find evidence for sex-dependent variation in sex-biased expression patterns of duplicate genes in brain, heart and liver, and evaluate how molecular evolution of duplicate genes accounts for expression divergence between sexes. This thesis provides a general framework for investigating sex-biased duplicate gene evolution in an amphibious tetrapod.

<p> The mode of chromosome duplication during meiosis and mitosis in Haplopappus gracilis was investigated. Tritiated thymidine was incorporated into the pollen mother cells during premeiotic interphase, and the cells were allowed to reach the tetrad stage. The autoradiographs prepared from the tetrads showed an unequal distribution of grains over their nuclei, suggesting a conservative mode of chromosome duplication during meiosis. Seedlings were fed with tritiated thymidine for the duration of one cell cycle and also for the duration of several cell cycles. The autoradiographs prepared from the root tip cells, thus treated, showed both labelled and unlabeled chromatids in the anaphases of all the experiments, thus again suggesting a conservative mode of chromosome duplication. A chromosome model to explain the results is discussed. </p> / Thesis / Doctor of Philosophy (PhD)

The substantial difference in ionic concentration and osmotic pressure between marine and freshwater environments creates a barrier to dispersal that relatively few metazoan lineages have been able to cross during the evolution of life on earth. Only about half of animal phyla have representatives in both marine and freshwater environments. Even within the phyla that contain freshwater species there are often large clades that continue to be exclusively marine. Interestingly, though, among some of the clades with freshwater species, this transition has occurred repeated. In order to begin to better understand the mechanisms that have allowed some marine lineages to colonize freshwater environments, I investigated the role of gene duplications in this process. First, using published annelid genomes I compared the gene copy number of the Na+/K+-ATPase alpha subunit gene family, the plasma membrane Ca2+ ATPase (PMCA) gene family, and the sarcoplasmic reticulum Ca2+ (SERCA) gene family between marine and freshwater species. I also used gene tree/species tree reconciliation to infer the time of those duplication events. There was a burst of duplications of the Na+/K+-ATPase alpha subunit gene that coincides with the colonization of freshwater habitats by annelids. The evidence of such a burst of duplications for the PMCA or SERCA gene families is inconclusive. Next, in order to increase the sample size and look for more gene families that were involved in the transition to freshwater habitats I downloaded 11 genomes from spiralian animals. I looked for specific gene families that showed a significant increase in size in freshwater species compared to marine species and identified the Na+/K+-ATPase alpha subunit gene family among others. I also used GO enrichment analysis to determine which GO terms were overrepresented in gene families that expanded along freshwater lineages and found terms related to ion transfer to be most common. Finally, I examined available mollusk genomes to compare size of the gene families of interest from the spiralian analyses between marine and freshwater mollusk species. I again found the Na+/K+-ATPase alpha subunit gene family to show a significant increase in size in the freshwater species. How marine animals were able to colonize freshwater habitats is one of the great questions in metazoan evolution and this work represents an important early step in understand this process.

<p> Gene expression, and its mechanisms of regulation, remains a major area for contemporary research in evolution. With its role connecting specific gene sequences and their protein products, contributing to efforts toward understanding the specific contributions of different mechanisms of gene expression regulation is the goal of this thesis. Through two specific case studies, this thesis examines expression regulatory divergence in two different physiological contexts; the immuno-response rag1 and rag2 genes, and the male upregulated sex differentiation gene dmrt1. </p> / Thesis / Master of Science (MSc)

In the modern software development process, it has become a very mainstream practice to build software projects on top of third-party packages to simplify the development process. In this development method, it is quite common to copy existing code or files in other libraries instead of making regular calls. Although this approach can reduce the project's dependence on other libraries and make the project more streamlined, it also causes difficulties in maintenance and understanding. The ignorance of code duplication by third-party library community can even be exploited for malicious purpose, such as typo-squatting attack. This paper serves as a starting point to analyze the growing code duplication issues surrounding third-party open source packages, and what is the root cause of code duplication. In this paper, I conducted code duplication-related research based on some popular packages in the third-party open source packages community, the NPM community, by using the tokenizer tool and the code comparison tool to compute the code similarity, quantitatively analyzed the prevalence of code duplication in the NPM community, and did some related experiments based on this similarity. In the experiments, I found that code duplication is very common in NPM community: 17.1% of all the files have 1-93 similar file in other package when the threshold of similar file is set to 0.5. 29.3% of all the packages has at least one "similar package" when the threshold of similar package is set to 0.5. In all the 951 similar package pairs, 33.9% of them, 323 package pairs comes from the same domain. The ultimate goal of this paper is to promote the awareness of the commonness and the importance of code duplication in the third-party package community and the reasonable use of code duplication by developers in the project development. / In the modern software development process, developers often call other people's completed code to build their own programs. There are generally two ways to do this: indirectly call other people's code through "import" or similar instructions in the program, or directly copy and paste other people's code and make slight modifications. The second method can make the program more independent and easy to use, but the code duplication problem caused by this method also has great security risks.This paper serves as a starting point to analyze the growing code duplication issues, and what is the root cause of code duplication. In this paper, I conducted code duplication-related research based on some popular code packages in the NPM community.I used some tools to compute a value to define how different codes are similar to each other, quantitatively analyzed the prevalence of code duplication in the NPM community, and did some related experiments based on this similarity. In the experiments, I found that code duplication is very common in the NPM community: 17.1% of all the files have 1-93 similar file in other package, and 29.3% of all the package have at least one "similar package", when the definition of similar files and packages are not that "strict".In all the 951 similar package pairs, 33.9% of them, 323 package pairs comes from the same domain. The ultimate goal of this paper is to promote the awareness of the commonness and the importance of code duplication in the third-party package community and the reasonable use of code duplication by developers in the project development.