<p> The larval nutritional mode of marine invertebrates is an important life history trait that has strong effects on their ecology and evolution. Increases in egg size and transitions from feeding to nonfeeding larvae have happened repeatedly. In Spiralia, a change in cytoplasm allocated to macromeres at the 8-cell stage (that could delay the development of a functional gut) may accompany these transitions. The first part of this thesis describes the development of the gastropod <i>Crepidula williamsi</i> and compares it to the closely related <i>C. fornicata,</i> with a focus on changes in allocation to macromeres and the development of a functional gut. The second part is a phylogenetic comparison of egg size and allocation to macromeres in 44 species of spiralians, which revealed a significant correlation between the two. A phylogenetic comparison like this one has not previously been done on the development of such diverse marine invertebrate taxa.</p>

<p> At its core human evolutionary biology seeks to answer the question of how the defining characteristics of modern humans evolved, such as large-brains, obligatory bipedal gait, extended juvenile period, and increased longevity. Traditional fossil-based research uses morphology to infer behavior and life history and only recently have researchers been able to make predictions regarding the effect of modifications to the DNA and proteins of our forbearers. Using these innovative methods we investigated the molecular evolution of a superfamily of transcription factors called the Nuclear Receptors. The patterns of sequence evolution observed in our bioinformatic analyses suggest a shift in the intensity of selection pressure occurred on <i>NR2C1</i>, a gene that plays a role early in embryonic stem cell proliferation and neuronal differentiation. Methods are now available to reconstruct ancestral DNA and its corresponding protein sequences and thus generate testable hypotheses about the functional evolution of genes on specific lineages. These methods allowed us to analyze how modifications to the modern human version of <i> NR2C1</i> affected the ability of an embryonic stem cell to remain in its proliferative state. We began by creating three different copies of our gene of interest: the human copy, the chimpanzee copy, and the ancestral copy of <i>NR2C1</i> for the inferred last common ancestor of chimpanzee and modern humans. Inserting these three different gene variants into mouse embryonic stem cells that have had NR2C1 knocked down allowed us to quantitatively analyze the transcriptional and regulatory functions of <i>NR2C1</i>. </p>

<p> This study examines how the different behavioral, environmental and physiological factors might be influencing the essential physiological trait of erythrocyte mean cell diameters (MCD). At present no other study has explored the effects of these factors. Erythrocyte MCD for 153 species were collected from recent literary sources and compared to erythrocyte MCDs collected by Gulliver (1875), genome sizes and spleen sizes were also collected from a variety of literary sources. This data was analyzed using R with phylogenetic generalized least square analyses against several different behavioral, environmental and physiological factors. From these analyses, I found that as mammal mass and length increase the erythrocyte MCD also increases and as mammals move into higher elevations and warmer climates erythrocyte MCD decreases. All other behavioral, environmental, and physiological factors did not have an influence on erythrocyte MCD. These data did not support hypotheses previously offered by the other studies done on erythrocytes. Further research needs to be conducted on this topic because other factors that influence erythrocyte MCD may still exist that were not examined in this study.</p><p>

Many laboratory speciation experiments have raised allopatric populations in different environments to determine whether reproductive isolation evolves as a by-product of adaptation. Few, however, have controlled for the effects of genetic drift, addressed the evolution of both pre- and postmating isolation, or investigated the conditions that promote or hamper the process. I present results of a long-term evolution experiment in which 12 replicate populations of Drosophila melanogaster independently evolved for more than 57 generations under alternative desiccation treatments (six control and six desiccation-selected populations). Specifically, I demonstrate the divergence between the desiccation and control populations of cuticular hydrocarbons, key traits that have been implicated in mate choice and sexual isolation in Drosophila. Despite this divergence, there was no detectable pre- or postmating isolation between the desiccation and control populations. Novel environments are generally thought to promote the evolution of reproductive isolation. Understanding the conditions that favour or hamper this remains a key challenge for speciation research.

The taxonomic status of the 16 nominal species of the genus Trinectes (Pleuronectiformes: Achiridae) Rafinesque 1832 was revised based on a morphological study of 647 type and non-type specimens. Nine species were recognized as valid Trinectes inscriptus, T. maculatus, T. microphthalmus, and T. paulistanus are found in the Atlantic Ocean, from the Northern United States to Southern Brazil, whereas T. fimbriatus, T. fluviatilis, T. fonsecensis, T. opercularis, and T. xanthurus are found in the Pacific Ocean, from Mexico to Peru. An identification key to species is provided. The phylogenetic relationships of the species recognized were hypothesized based on a cladistic analysis of 22 morphological, meristic, and osteological characters. The analysis resulted in one most parsimonious tree with a length of 39 steps (CI = 0.69; RI = 0.79). The tree showed that Trinectes is monophyletic on the basis of two synapomorphies: an unpierced interbranchial septum, and seven to nine pterygiophores anterior to the neural spine of the third precaudal vertebra. Trinectes inscriptus is the most plesiomorphic species of the genus, and all other species form a monophyletic group subdivided into two clades. The first contains (from most plesiomorphic to recent): T. paulistanus, T. fonsecensis, and the T. fluviatilis-T. xanthurus clade. The second clade includes (from most plesiomorphic to recent): T. maculatus, T. opercularis, and the T. fimbriatus- T. microphthalmus clade. The resulting cladogram depicts a sequence of speciation events and provides an opportunity to propose a biogeographical hypothesis on the evolution of Trinectes.

The adaptive landscape heuristic can be used to answer the question "how predictable is evolution?" because its topology will impact the repeatability of evolution. In my Masters research I addressed this question in two ways: (1) I reviewed empirical adaptive landscape studies in the fields of directed protein evolution and microbial experimental evolution and (2) I performed a selection experiment to characterize adaptive landscape topology by measuring variance in fitness and metabolic phenotype within and among genetically distinct Pseudomonas fluorescens strains in two environments. Empirical studies have found that protein level landscapes are generally smooth, however, population level landscapes are rugged even in simple environments. Experimentally I found that the pattern of variance in fitness and metabolic phenotype was unique to the selection environment. The response to selection was highly repeatable at the level of fitness, but the underlying genetic routes taken were different for each environment and more variable in xylose than in glucose, suggesting a more rugged underlying landscape. More generally, my research suggests that making statements about the predictability of adaptive evolution at the population level may be challenging and wi11likely depend on the specifics of the environment in which selection occurs.

Experimental evolution was used to independently evolve 12 replicate populations of Drosophila melanogaster for 34+ generations in one of three treatment environments of varying PO2: hypoxia (5.0-10.1 kPa), normoxia (21.3 kPa), and hyperoxia (40.5 kPa). Several traits related to whole animal performance and metabolism were monitored during experimental evolution and several common garden assays were performed at various stages to directly compare evolved and acclimatory differences between treatments. Results clearly demonstrate the evolution of increased anoxia tolerance in hypoxia-evolved populations, suggesting adaptation to this environment. This was correlated with an increase in citrate synthase activity compared to normoxic (control) populations, suggesting an increase in mitochondrial density in these populations. In contrast, no direct evidence of increased performance of the hyperoxia-evolved populations was detected, although an evolutionary cost was observed as a substantial decline in anoxia tolerance. Changes in performance did not result in an increase in any of the fitness components measured, including productivity and longevity, suggesting that these assays failed to capture the components of fitness relevant to adaptation.

Morphology can play a major role in ecological diversification and adaptive radiation when it consistently enhances performance and behavior. Here I investigate how cranial and dental morphology, feeding performance and behavior relate to one another and to the dietary radiation in Neotropical leaf-nosed bats (Family Phyllostomidae). First, I build a 3D biomechanical model to investigate the mechanism connecting cranial morphology and bite performance (bite force) and how bats with different diets vary in biomechanical parameters predicting bite force. The model demonstrates that cranial morphology is a strong predictor of bite force variation, and that bats differ in biomechanical predictors of bite force when they are classified according to dietary hardness. Second, I investigate the relationship between biting behavior and bite force across phyllostomids. My results indicate that bats modulate their performance by changing their biting behaviors to maximize bite force when feeding on hard foods. Using phylogenetic correlations and ancestral state reconstructions, I provide evidence for correlated evolution of behavior and performance, and rapid evolution in these traits that coincided with the use of plant resources. Third, I investigate the trends in molar complexity, chewing behavior and efficiency in breaking down prey across phyllostomids with different diets. My results illustrate that frugivores exhibit a higher dental complexity than insectivores and omnivores, and that the latter groups achieve higher performance in insect breakdown through higher molar complexity and chewing behavior. Finally, I investigate if other behavioral traits relevant to fitness have shaped the evolution of the skull morphology, using roost excavation in Lophostoma silvicolum as a model system. Through finite element analysis, I provide support for the prediction that the skull of L. silvicolum presents adaptations for roost excavation, in the form of a stronger skull. When all my findings are considered there is evidence that, although morphology can strongly predict performance, behavior plays an important role in modulating performance, and selection on this ability could have contributed to the ecological diversification of phyllostomids. Overall, the dietary radiation of phyllostomids, in particular the use of plant resources, was associated with dramatic changes in cranial and dental morphology, feeding performance and behavior.

<p> The sheer complexity of evolutionary systems biology requires us to develop more sophisticated tools for analysis, as well as more probing and biologically relevant representations of the data. My research has focused on three aspects of evolutionary systems biology. I ask whether a gene&rsquo;s position in the human metabolic network affects the degree to which natural selection prunes variation in that gene. Using a novel orthology inference tool that uses both sequence similarity and gene synteny, I inferred orthologous groups of genes for the full genomes of 8 mammals. With these orthologs, I estimated the selective constraint (the ratio of non-synonymous to synonymous nucleotide substitutions) on 1190 (or 80.2%) of the genes in the metabolic network using a maximum likelihood model of codon evolution and compared this value to the betweenness centrality of each enzyme (a measure of that enzyme&rsquo;s relative global position in the network). Second, I have focused on the evolution of metabolic systems in the presence of gene and genome duplication. I show that increases in a particular gene&rsquo;s copy number are correlated with limiting metabolic flux in the reaction associated with that gene. Finally, I have investigated the proliferative cell programs present in 6 different cancers (breast, colorectal, gastrointestinal, lung, oral squamous and prostate cancers). I found an overabundance of genes that share expression between cancer and embryonic tissue and that these genes form modular units within regulatory, proteininteraction, and metabolic networks. This despite the fact that these genes, as well as the proteins they encode and reactions they catalyze show little overlap among cancers, suggesting parallel independent reversion to an embryonic pattern of gene expression.</p>

<p> Sex determination in leatherback sea turtles is directed primarily by the temperatures a clutch experiences during the middle third of development. Warmer temperatures tend to produce females will cooler temperatures yield males. Nest temperatures can vary spatially and temporally. During the 2010 and 2011 nesting seasons, this study estimated the hatchling sex ratio of leatherback sea turtles on Sandy Point National Wildlife Refuge (SPNWR), St. Croix, U.S. Virgin Islands. I measured sand temperatures from May- August and across the spatial range of leatherback nesting habitat. I spatially interpolated those temperatures to create maps that predicted temperatures for all nests incubating on SPWNR. Nest temperatures were also directly measured and compared with predicted nest temperatures to validate the prediction model. Sexes of dead-in-nest hatchlings and full term embryos were used to confirm the sex-temperature response. The model showed that microclimatic variation likely impacts the production of both sexes on SPNWR.</p>