The yeast Saccharomyces cerevisiae genome is descendant from a whole genome duplication event approximately 150 million years ago. Following this duplication many genes were lost however, a certain class of genes, termed ohnologs, persist in duplicate. In this thesis we investigate network centrality as it relates to ohnolog re- tention with the goal of determining why only certain genes were retained. With this in mind, we compare physical and genetic interaction networks and genetic and pro- tein sequence data in order to reveal how network characteristics and post-duplication retention are related. We show that there are two subclasses of ohnologs, those that interact with their duplication sister and those that do not and that these two classes have distinct characteristics that provide insight into the evolutionary mechanisms that affected their retention following whole genome duplication. Namely, a very low ratio of non-synonymous mutations per non-synonymous site for ohnologs that retain an interaction with their duplicate. The opposite observation is seen for ohnologs that have lost their interaction with their duplicate. We interpret this in the fol- lowing way: ohnologs that have retained their interaction with their duplicate are functionally constrained to buffer for the other ohnolog. For this reason they are retained; ohnologs that have lost their interaction with their duplicate are retained because they are functionally divergent to the point of being individually essential. Additionally we investigate small scale duplications and show that, generally, the mechanism of duplication (smale scale or whole genomes) does not affect the distri- bution of network characteristics. Nor do these network characteristics correlate to the selective pressure observed by retained paralogous genes, including both ohnologs and small scale duplicates. In contrast, we show that the network characteristics of individual genes, particularly the magnitude of their physical and genetic network centralities, do influence their retention following whole genome duplication. / Graduate / mjrimrie@gmail.com

This paper examines the concept of uploading one’s consciousness on to a computer, and its role in personal identity. I first examine the technology behind uploading, and the likely timeline for that technology to become widespread. Then taking uploading as a given, I examine our intuitions about how we will interact with these uploads on a daily basis. Then, I argue that Derek Parfit’s account of survival and identity is the one best suited for a post-upload world. After explaining the benefits of Parfit’s view in this world, I defend Parfit against criticisms by Eric Olson, and Susan Schneider. Finally, I show why animalism and four-dimensionalism are not as strong of accounts of personal identity as Parfit’s view, in a world where uploading is a reality.

Guppies exhibit color based sexual dimorphism and females generally prefer the most colorful males. It has also recently been found that guppies possess a large opsin repertoire. As opsins are the receptors responsible for color vision, this ten gene repertoire might have contributed to the evolution of extravagant male coloration in this species. My study starts by characterizing the opsin repertoire of Jenynsia onca, a noncolorful relative of the guppy belonging to the family Anablepidae (sister group to Poeciliidae, of which the guppy is a member). A PCR based survey indicated that J. onca had a very similar opsin repertoire to the guppy; J. onca had nine genes including orthologs of all but one of the guppy opsins. To gain further insight into the origin of the guppy repertoire, a bioinformatics based survey of ray-finned fish opsins was undertaken. This revealed that large opsin repertoires are common in ray-finned fish and are the product of gene duplication events, spanning the age of the taxon Teleostei. Given that the large opsin repertoire of the guppy did not appear to be perfectly correlated with the evolution of color based sexual selection in this lineage, I turned to investigating the expression of this opsin repertoire. In situ hybridization was used to characterize the pattern of opsin expression across the surface of the retina of adult male and female guppies. In situ hybridization demonstrated that most opsin genes had distinct expression profiles. These expression patterns also indicated that sensitivity and discrimination in the dorsal retina might differ from the ventral retina; the ventral retina appears to be tuned to middle-wavelength light (green), while the dorsal retina is predicted to have exceptional wavelength discriminatory ability and broad spectral sensitivity. This expression data was then used to evaluate models of sexual selection in the context of the predicted visual capacity of the guppy. / Graduate

The rewrite relation with parameters m and n and with the possible lengthlimit = k or :::; k we denote by w~, =kW~· or ::;kw~ respectively. Theidempotency languages generated from a starting word w by the respectiveoperations are wD<l::', w=kD<l::' and W<;kD<l::'.Also other special cases of idempotency languages besides duplication havecome up in different contexts. The investigations of Ito et al. about insertionand deletion, Le., operations that are also observed in DNA molecules, haveestablished that w5 and w~ both preserve regularity.Our investigations about idempotency relations and languages start out fromthe case of a uniform length bound. For these relations =kW~ the conditionsfor confluence are characterized completely. Also the question of regularity is-k n answered for aH the languages w- D<lm . They are nearly always regular. Onlythe languages wD<lo for n > 1 are more complicated and belong to the class ofcontext-free languages.For a generallength bound, i.e."for the relations :"::kW~, confluence doesnot hold so frequently. This complicatedness of the relations results also inmore complicated languages, which are often non-regular, as for example thelanguages W<;kD<l::' for aH bounds k 2 4. For k :::; 2 they are regular. The case ofk :::; 3, though, remains open. We show, however, that none of these languagesever exceeds the complexity of being context-free.Without any length bound, idempotency relations have a very complicatedstructure. Over alphabets of one or two letters we still characterize the conditionsfor confluence. Over three or more letters, in contrast, only a few casesare solved. We determine the combinations of parameters that result in theregularity of wD<l::', when the alphabet of w contains only two letters. Only thecase of 2 :::; m < n remains open.In a second chapter sorne more involved questions are solved for the specialcase of duplication. First we shed sorne light on the reasons why it is so difficultto determine the context-freeness ofduplication languages. We show that theyfulfiH aH pumping properties and that they are very dense. Therefore aH thestandard tools to prove non-context-freness do not apply here.The concept of root in Formal Language ·Theory is frequently used to describethe reduction of a word to another one, which is in sorne sense elementary.For example, there are primitive roots, periodicity roots, etc. Elementaryin connection with duplication are square-free words, Le., words that do notcontain any repetition. Thus we define the duplication root of w to consist ofaH the square-free words, from which w can be reached via the relation w~.Besides sorne general observations we prove the decidability of the question,whether the duplication root of a language is finite.Then we devise acode, which is robust under duplication of its code words.This would keep the result of a computation from being destroyed by duplications in the code words. We determine the exact conditions, under whichinfinite such codes exist: over an alphabet of two letters they exist for a lengthbound of 2, over three letters already for a length bound of 1.Also we apply duplication to entire languages rather than to single words;then it is interesting to determine, whether regular and context-free languagesare closed under this operation. We show that the regular languages are closedunder uniformly bounded duplication, while they are not closed under duplicationwith a generallength bound. The context-free languages are closed underboth operations.The thesis concludes with a list of open problems related with the thesis'topics.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [111]-128).

Thesis (Ph. D.)--University of Washington, 2004. / Vita. Includes bibliographical references (leaves 146-156).

Understanding the genetics underlying the speciation process has been a long-standing goal of evolutionary biology. Studying inter-population crosses can elucidate the genetic architecture of reproductive isolation and, ultimately, the process of speciation. Hybridization between two species is often maladaptive and results in offspring with decreased fitness compared to the parental forms. Recently, with the development of molecular and genomic tools, it has become possible to understand how and when reproductive isolation arises and what are the underlying mechanisms in the evolution of genetic incompatibilities. Heliconius is a genus of neotropical butterfly best know for their Müllerian mimicry. Here I focus on Heliconius cydno and Heliconius melpomene, two hybridising sympatric species with low levels of inter-specific hybridisation that nonetheless results in genome-wide signatures of admixture. I show that hybrids develop ovarian tissue and, occasionally, oocytes; and use genomic approaches to examine several potential mechanisms underlying post-zygotic isolation between H. cydno and H. melpomene. Firstly, I investigate evolution by gene duplication and identify loci putatively under divergent selection that may play a role in species divergence and speciation. Secondly, I quantify sexually dimorphic expression in H. melpomene, and calculate rates of molecular evolution between H. melpomene and H. erato. Thirdly, I identify differentially expressed genes in the H. cydno x H. melpomene F1 hybrids that may be involved in the species barrier. Finally, investigate whether epigenetic silencing mechanisms could underlie post-zygotic isolation between H. cydno and H. melpomene by quantifying transposable element expression and small RNAs. Overall, I identify loci that merit further investigation for their potential in maintaining reproductive barriers between these two species. I show that different regions of the genome evolve at different molecular rates but there is no faster-Z effect, and consider how might this affect evolution of reproductive isolation. Finally, I show that aberrant epigenetic silencing, a mechanism behind hybrid sterility that is common in other species, is not correlated with post-zygotic isolation between H. cydno and H. melpomene.

ix, 120 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. / Gene duplication underlies the evolution of many protein functions and is a known stimulus for molecular innovation. Many models exist to explain the maintenance of duplicate genes in the genome and the dynamics that drive the evolution of novel protein functions; few if any of these models, however, incorporate knowledge of how protein structures and functions actually evolve. A growing body of work on the historical mechanisms of molecular evolution and the ways in which proteins evolve in the lab has provided profound insights into the ways in which proteins respond to mutation, selection, and drift. Evolutionary models of duplicate gene evolution could greatly benefit from the knowledge gained from these mechanistic studies of protein evolution. My dissertation seeks to address this gap in knowledge by reconstructing the process by which novel steroid signaling pathways evolved after gene duplication. I focus specifically on a class of hormones called corticosteroids--critical regulators of the stress response, metabolism, and immunity--and the mineralocorticoid and glucocorticoid receptors that mediate the steroid response. Both the enzymes that synthesize corticosteroids and the hormone receptors are the result of ancient gene duplication events, and I make use of methods in phylogenetics, molecular biology, and structural biology to reconstruct the mechanisms and dynamics by which they evolved. This dissertation comprises three separate but complementary studies that illuminate the origins of corticosteroid signaling. In the first project, I show how lineage-specific steroid signaling arose in elasmobranchs as a novel hormone exploited the structural promiscuity of preexistent receptors. Next, I describe how degenerative and stabilizing mutations defined the divergence of the glucocorticoid receptor after gene duplication. And finally, I use phylogenetic and functional analyses to reconstruct the origins of corticosteroid synthesis with the duplication of enzymes in the steroid synthesis pathway. Together, I provide a comprehensive reconstruction of the evolution of corticosteroid signaling. This work also highlights specific evolutionary mechanisms--molecular exploitation, structural and functional promiscuity, degenerative mutations, and stabilizing mutations--that could drive the evolution of novel protein functions after gene duplication. This dissertation includes both previously published and unpublished co-authored materials. / Committee in charge: Patrick Phillips, Chairperson, Biology; Joseph Thornton, Advisor, Biology; William Cresko, Member, Biology; John Postlethwait, Member, Biology; Kenneth Prehoda, Outside Member, Chemistry

This thesis focuses on software source code plagiarism. In the theoretical part there is a description of usual plagiarism techniques. The main output in practical part is the program that checks source codes of Java programs, whether these codes are really developed by individual students independently. It detects two or more students with identical source codes by controlling names of methods and variables.

The Hox gene complement of zebrafish, medaka, and fugu differs from that of other gnathostome vertebrates. These fishes have seven to eight Hox clusters compared to the four Hox clusters described in sarcopterygians and shark. The clusters in different teleost lineages are orthologous, implying that a “fish-specific” Hox cluster duplication has occurred in the stem lineage leading to the most recent common ancestor of zebrafish and fugu. The timing of this event, however, is unknown. To address this question, we sequenced four Hox genes from taxa representing basal actinopterygian and teleost lineages and compared them to known sequences from shark, coelacanth, zebrafish, and other teleosts. The resulting gene genealogies suggest that the fish-specific Hox cluster duplication occurred coincident with the origin of crown group teleosts. In addition, we obtained evidence for an independent Hox cluster duplication in the sturgeon lineage (Acipenseriformes). Finally, results from HoxA11 suggest that duplicated Hox genes have experienced diversifying selection immediately after the duplication event. Taken together, these results support the notion that the duplicated Hox genes of teleosts were causally relevant to adaptive evolution during the initial teleost radiation.