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Sexual dimorphism, i.e., differences in morphology, physiology, and behavior between conspecific males and females, is ubiquitous, extensive, and often species-specific, indicative of its rapidly evolving nature. Ever since Darwin first described a general theory of sexual selection to explain the extraordinary differences between males and females of the same species, biologists have proposed a variety of mechanisms ranging from runaway selection to good genes to sexual conflict. While a popular approach is studying the effects of sexual selection on different components of fitness, the results of these studies are generally difficult to interpret and are typically not generalizable across populations, let alone taxa. Recent advances in the “omics” field are transforming the way that we study patterns and processes involved in sexual selection. At the molecular level, sexual dimorphism is present in gene expression differences between the sexes, providing a powerful framework to study sexual selection. By studying genes that are sex-biased in expression, we will better understand the underlying genetic basis of traits that are sexually dimorphic. Alreadly, studies of sex-biased genes in model organisms, particularly Drosophila, have revealed that male-biased genes are among the most rapidly evolving functional classes of genes. However, while a number of intrinsic factors appear to correlate with evolutionary rate (e.g., gene expression level, codon bias), it is unclear whether any of these factors drive the rapid divergence of male-biased genes. Another important discovery is the prevalence of sex-biased gene expression. However, even with widespread sexual dimorphism at the phenotypic level, it remains unknown the extent to which sex-biased gene expression exists in humans and their primate relatives. In fact, studies of sexual dimorphism on a molecular level in primates have been very few, even though understanding this phenomenon in humans could further our knowledge of the nature of sex-biased phenotypes and diseases. In this thesis, I advance our knowledge of the genetic bases and mechanisms that shape sexual dimorphism. First, I review a classic framework that biologists have traditionally applied to define and partition fitness measures between males and females in the model system, Drosophila. Second, I apply a molecular framework to compare the relative roles of intrinsic factors on the evolutionary rate of rapidly evolving male-biased genes in Drosophila. Third, I review the current state of our knowledge of sexual dimorphism and sex-biased gene expression in humans. Fourth, I present a bioinformatics framework to identify the extent of sex-biased expression in primate tissue and to examine the selective forces involved in their evolution. Overall, I demonstrate the effectiveness of using a functional comparative genomics approach in studying the nature of sexual dimorphism at the molecular level across multiple taxa. / Biology

The variation of genome content and structure across the tree of life is astounding and can provide clues to understand the process of evolution. Overall, this helps us understand the history of life and how organisms have fundamentally changed and adapted to their environments. Gene duplication is an important mechanism for molecular evolution because it provides opportunity for functional novelty and molecular innovation. Gene duplication creates new functional gene copies with different selective pressures that allow them to take on new or specialized functions. Throughout this work, I explored the interplay between genetic changes, molecular phenotype, and the selection of duplicate gene copies. I particularly focused on the genetic opportunity, consequences, and selective pressures of the mechanisms for short-term and long-term duplicate copy retention. I modeled the stochastic processes of mutation and selection and their effect on duplicate gene copy retention. Specifically, I modeled the interplay between subfunctionalization and dosage balance and found that selection may cause genes that are sensitive to dosage balance effects to experience delayed subfunctionalization, but ultimately lead to higher levels of subfunctionalization. These findings suggest that subfunctionalization may not occur as a purely neutral process. Next, I used survival analysis methods to model patterns of duplicate gene retention in genomes experiencing consecutive whole genome duplication events. I modeled three hypotheses to explain patterns of duplicate gene retention including the Independence Hypothesis, the Gene Duplicability Hypothesis, and a novel Mutational Opportunity Hypothesis. Under the Gene Duplicability and Mutational Opportunity hypotheses, the expected patterns of duplicate gene retention after consecutive whole genome duplication events are greatly affected by the ages of the whole genome duplication events and the functional properties of the genomic content that influence opportunity and selection. Additionally, I describe how statistical model testing techniques can be applied to investigate which hypothesis is consistent with patterns of retention in real-world phylogenetic datasets. I used these described techniques to explore the hypotheses’ parameter space consistent with a modest dataset of fish and plant lineages. These results suggest that a gene duplicate’s retention after whole genome duplication events may be influenced by its functional properties. Key findings underscore the multifaceted nature of duplicate gene retention, influenced by a myriad of factors including genetic opportunity, selective pressures, and evolutionary context. By dissecting the underlying mechanisms driving duplicate gene retention, this dissertation advances our understanding of the evolutionary dynamics shaping genome evolution and functional diversity across diverse biological systems. / Biology

Doctor of Philosophy / Department of Psychological Sciences / Gary Brase / Although fertility decision-making has been the source of considerable theoretical and empirical investigation, the effect of several contextual variables on individuals’ fertility decision-making processes are not yet understood. For example, are individuals more strongly influenced by social forces that are informational or normative? Also, do individuals change their fertility intentions based on their current and developmental economic conditions? Further, how ‘shared’ are reproductive decisions within a couple, are males or females more likely to get what they want? This 3-study program of research used both experimental and exploratory qualitative methods to elucidate the nature of these unresolved issues within the domain of fertility decision-making. Study 1 (N = 344, M[subscript]age = 23, SD[subscript]age =6.41, 59.3% female) found that highly motivated individuals’ fertility intentions were more susceptible to informational, compared to normative messages (the opposite was true for unmotivated participants). Study 2 (N = 249, M[subscript]age = 24, SD[subscript]age =6.10, 61.4% female) found that exposure to mortality primes up-regulated fertility intentions for individuals with “fast” life history strategies, but facilitated the down-regulation of fertility intentions for individuals with “slow” life history strategies. Interestingly, resource scarcity primes were associated with the postponement of fertility plans in individuals’ with “fast” life history strategies. Study 3 (N = 120, M[subscript]age = 21, SD[subscript]age =4.96, 50% female) found that, contrary to predictions, the similarity of couples’ gender role attitudes, career-orientations, and education levels did not significantly predict the frequency of their use of statements coded as compromise and agreement or persuasion and disagreement in their discussions regarding their future reproductive plans. Findings do suggest that individuals with higher levels of education were more likely to use persuasion and disagreement statements in their child timing and number discussions with their romantic partner, indicative of greater decision-making power in that particular social exchange. Further, men and women in study 3 were equally likely to use statements coded as compromise and agreement, persuasion and disagreement, and concession when discussing both their future fertility plans as well as their future financial plans.

Doctor of Philosophy / Department of Entomology / J.P. Michaud / James R. Nechols / The manner in which organisms allocate reproductive resources for reproduction is a central question with respect to life history theory. The main objectives of this research were to i) examine lifetime patterns of reproductive allocation in the lady beetles Coleomegilla maculata (DeGeer) and Hippodamia convergens (Guérin-Menéville) (Coleoptera: Coccinellidae) while manipulating environmental conditions that affect female body size (i.e., larval food supply), ii) to study the interaction between factors underlying female body size and the resources available during reproduction, and iii) to explore the maternal effects of female size and age on the development and survival of progeny. When different size classes of females were produced and adult females were maintained with unlimited food, there were no differences in egg size across female size in C. maculata, but egg size increased over time in all females. In H. convergens, only larger females increased egg size over time, and they laid larger eggs, on average, than did small females. Maternal body size was positively correlated with the number of eggs laid per day in both species. When three size classes of females were subjected to a fluctuating food supply as adults, female size was again positively correlated with egg and daily fecundity. Whereas both species varied daily fecundity in response to adult food supply, egg size was unaffected and demonstrated a fixed pattern of change with female age and species-specific effects of maternal body size. To observe maternal effects in H. convergens, three female size classes were again produced and progeny were reared from three different periods of each female‟s reproductive life. Offspring from later oviposition days and larger females developed faster and achieved larger adult size than those reared from earlier oviposition days. Egg size showed inconsistent correlations with developmental parameters and adult progeny size, so other, more cryptic, maternal signals were inferred to signal phenotype development in progeny. A fixed program of producing faster-developing offspring that mature to larger sizes late in the oviposition cycle is adaptive for exploiting ephemeral aphid blooms that exhibit predictable dynamics of declining prey abundance and increasing competition. In the case of H. convergens, resource limitation during development constrained not only body size, fecundity and egg size, but also maternal ability to manipulate progeny phenotypes.