HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

A game-theoretic network formation model

We study the dynamics of a game-theoretic network formation model that yields large-scale small-world networks. So far, mostly stochastic frameworks have been utilized to explain the emergence of these networks. On the other hand, it is natural to seek for game-theoretic network formation models in which links are formed due to strategic behaviors of individuals, rather than based on probabilities. Inspired by Even-Dar and Kearns (2007), we consider a more realistic model in which the cost of establishing each link is dynamically determined during the course of the game. Moreover, players are allowed to put transfer payments on the formation of links. Also, they must pay a maintenance cost to sustain their direct links during the game. We show that there is a small diameter of at most 4 in the general set of equilibrium networks in our model. Unlike earlier model, not only the existence of equilibrium networks is guaranteed in our model, but also these networks coincide with the outcomes of pairwise Nash equilibrium in network formation. Furthermore, we provide a network formation simulation that generates small-world networks. We also analyze the impact of locating players in a hierarchical structure by constructing a strategic model, where a complete b-ary tree is the seed network.

When the Beautiful Game Turns Ugly: A Study of Fan Experiences of Perceived Match Fixing in Soccer

Limited academic attention has been given to the nexus between corruption in soccer and its impact on fandom. Consequently, the purpose of this qualitative study was to better understand the lived experiences of highly identified soccer fanatics living through this era of match fixing in the sport. Social networking site Twitter was utilized to recruit participants from three continents – Africa, Europe, and North America – based on submissions to the site in response to a perceived fix from a high-profile March, 2013 match. A total of 12 semi-structured interviews were conducted with highly identified soccer fans in accordance with Funk and James’ (2001) Psychological Continuum Model (PCM). Despite the majority of participants feeling skepticism about the purity of soccer today, half of the participants’ fandom remained unchanged in the face of perceived match fixing. Directions for future research and recommendations are considered and discussed.

Demolishing the Competition: The Association between Competitive Video Game Play and Aggression among Adolescents and Young Adults

The link between video game play and aggression is an important issue as video games The link between video game play and aggression is an important issue as video games are the fastest growing form of entertainment in the world. Past research on this association has been focused primarily on the link between video game violence and aggression; however, this research has confounded the effect of video game violence versus competition on aggression. The main goal of the current dissertation, therefore, was to examine the short- and long-term associations between competitive video game play and aggression. In addition, the longitudinal work on this association to date has been limited to adolescent samples, but not young adults. Thus, the second goal of the dissertation research was to investigate whether video game play predicts aggression in the long-term among young adults in addition to adolescents. To address these goals, three studies were conducted. Study 1 consisted of a series of experiments examining the short-term effect of video game violence versus competition on aggression. Study 2 examined the long-term association between competitive video game play and aggression among adolescents, and Study 3 examined this long-term link among young adults, in addition to adolescents. Taken together, the results of the three dissertation studies converged to suggest that video game competition, rather than violence, may be a stronger predictor of aggression in both the short- and long-term. Overall, the current research represents an important advance in our understanding of the association between video game play and aggression, and leads to a new direction in the video game and aggression literature. are the fastest growing form of entertainment in the world. Past research on this association has been focused primarily on the link between video game violence and aggression; however, this research has confounded the effect of video game violence versus competition on aggression. The main goal of the current dissertation, therefore, was to examine the short- and long-term associations between competitive video game play and aggression. In addition, the longitudinal work on this association to date has been limited to adolescent samples, but not young adults. Thus, the second goal of the dissertation research was to investigate whether video game play predicts aggression in the long-term among young adults in addition to adolescents. To address these goals, three studies were conducted. Study 1 consisted of a series of experiments examining the short-term effect of video game violence versus competition on aggression. Study 2 examined the long-term association between competitive video game play and aggression among adolescents, and Study 3 examined this long-term link among young adults, in addition to adolescents. Taken together, the results of the three dissertation studies converged to suggest that video game competition, rather than violence, may be a stronger predictor of aggression in both the short- and long-term. Overall, the current research represents an important advance in our understanding of the association between video game play and aggression, and leads to a new direction in the video game and aggression literature.

Ontario Game and Fishery Laws 1916

A paperback booklet of the Ontario Game and Fishery Laws 1916. The booklet is 91 pages in length and includes an index. See the full text in the Brock University Special Collections and Archives.

An act to consolidate and amend the laws for protection of game and fur-bearing animals in Ontario

An act to consolidate and amend the laws for protection of game and fur-bearing animals in Ontario (1 double-sided page of printed material), 1871.