Neotropical coral reef fish communities are species-poor compared to those of the Indo-West Pacific. An exception to that pattern is the blenny clade Chaenopsidae, one of only three coral reef fish families endemic to the Neotropics. Within the chaenopsids, the genus Acanthemblemaria is the most species-rich. To understand the origin and maintenance of genetic and species diversity in these fishes, I characterized the population genetics for two Acanthemblemaria species, reconstructed the phylogeny of the group, and identified suites of correlated morphological characters responsible for the distinctive skull morphology of these fishes. By combining nuclear and mitochondrial sequence data I was able to recover the complex demographic history of two closely related Acanthemblemaria species, A. aspera and A. spinosa. Old population expansions in both species were obscured by a rapid mitochondrial substitution rate, but the mitochondrial DNA allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. However, the older expansions that took place in both species were only recovered using the nuclear markers. Across the genus I found that mitochondrial COI is evolving nearly 100X faster than the nuclear markers and at an absolute rate of nearly 25% pairwise sequence divergence per million years. Replicate Bayesian phylogenetic analyses failed to converge on the same posterior distributions because proposals to update the rate multiplier parameter were rarely accepted, but when the tuning parameter was adjusted, all datasets converged quickly on to the same posterior distribution. When COI was included, posterior probabilities of the species tree were lower and topological estimates were worse than those from the nuclear-only dataset. The species tree that was constructed for the genus conflicted with the morphological phylogeny for the group, primarily due to the convergence of skull bones with spines. By performing phylogenetic analyses on these characters, I resolved some of the conflicts between the morphological and molecular phylogenies. Divergence time estimates recovered a mid-Miocene origin for the genus, with speciation both before and after the closure of the Isthmus of Panama. Some sister taxa were broadly sympatric, but many occur in allopatry.

Species incidence results from a complex interaction among species traits (e.g., mobility and behavior), intra- and inter-specific interactions, quality and configuration of the landscape, and historical events. Determining which factors are most important to incidence is difficult because the multiple processes affecting incidence operate at different temporal and spatial scales. I conducted an empirically-based study relating individual behavior (dispersal, habitat selection, and intra-specific interactions) with hierarchically-organized environmental filters to predict the incidence of Odontotaenius disjunctus (Passalidae), a saproxylic (=decayed wood dependent) beetle common to eastern North American forests, at multiple spatial scales. In dispersal experiments, O. disjunctus movement was faster and more linear in suitable habitat than in unsuitable matrix (non-forest), and O. disjunctus exhibited a strong response to a high-contrast boundary between forest and open-field. A hierarchically-organized (log-section < log < subplot < forest plot) survey of incidence across 22 forest plots in Louisiana showed that patchiness in incidence was greatest at fine-scales (log-section and log), partly in relation to two environmental variables: decay state and log surface area. In fine-scale habitat selection experiments, resettlement distances were usually less than 5-10 meters, and immigration was positively influenced by log size and the presence of conspecifics, although aggregation associated with conspecific attraction did not occur because emigration balanced immigration. Additionally, population growth rate showed negative density dependence in post-settlement experiments. Finally, I developed an individual-based, spatially-explicit simulation model to relate fine-scale response to cues (habitat, mate, and conspecific density) and dispersal limitation to the density-area relationship. Unlike conspecific search, mate search did not result in large aggregations of individuals on large patches, but instead resulted in almost even density among patches. Both habitat and mate search led to high overall incidence even when dispersal limitation was high. I conclude that O. disjunctus is a low-mobility species for which incidence is primarily determined by fine-scale interactions with conspecifics and the environment, and for whom high incidence can be explained in part by efficient use of cues during habitat search. Although sensitivity to large-scale habitat loss is a consistent pattern across taxa, this study emphasizes the overriding importance of fine-scale processes in predicting incidence.

Retrotransposons, a class of mobile elements, generate new copies in host genomes using RNA intermediates and reverse transcribing new copies into new loci. As such, the copy numbers of many active retrotransposon families increase dramatically over time. For example, ~42% of the human genome is comprised of retrotransposon sequences. The insertion activity of these elements, and the high degree of identity existing between the copies, have been shown to significantly impact the structure and stability of genomes, contributing in various ways from exon shuffling to inversions and from non-allelic homologous recombination to altering gene regulation. The two most successful mobile element lineages in primate genomes are LINE-1 (Long Interspersed Element-1) and Alu elements. Full-length LINE-1, or L1, elements are >6,000 bp in length and possess open reading frames encoding their own mobilization enzymes. Alu elements are a primate-specific family of SINEs (Short Interspersed Elements) that are ~300 bp in length and must hijack the enzymatic machinery of L1s for their mobilization. The mechanism by which most L1 and Alu insertions occur is called Target Primed Reverse Transcription (TPRT). The structure of an insertion can be examined to determine if it is the result of TPRT, and many examples exist of loci that inserted in non-canonical fashions. We computationally searched through all assembled primate genomes and identified a group of atypical L1 insertions, all of which were truncated with homopolymeric stretches of thymine at their 5 ends within the target site duplications, but which otherwise showed hallmarks of TPRT. We propose two possible mechanisms whereby these insertions may be explained, a variant of twin priming and a mechanism we term dual priming. Because most retrotransposon insertions are found in non-coding regions of genomes, they are essentially neutral with respect to natural selection. These elements, therefore, can serve as excellent markers for reconstructing phylogenetic relationships. Alu elements, in particular, have been very successful throughout the primate radiation. We computationally screened the complete, unassembled sequence of the Northern white-cheeked gibbon (Nomascus leucogenys leucogenys) to identify 132 gibbon-specific Alu insertions. These insertions were then used to reconstruct a robust genus-level phylogeny of family Hylobatidae.

AEBP2 is a zinc finger protein that has been shown to interact with the mammalian Polycomb Repression Complex 2 (PRC2). I characterized this unknown protein and tested its potential targeting roles for the PRC2. AEBP2 is an evolutionarily well-conserved gene that is found in animals ranging from flying insects to mammals. The transcription of mammalian AEBP2 is driven by two alternative promoters and produces multiple transcripts that give rise to at least two isoforms of the protein. These isoforms show developmental stage-specific expression patterns: the larger adult-specific form (52 kDa) and the smaller embryo-specific form (31 kDa). The AEBP2 protein binds to a DNA-binding motif with an unusual bipartite structure, CTT(N)15-23cagGCC with lower-case base pairs being less critical. A large fraction of AEBP2's target loci also map closely to the known target loci of the PRC2. In fact, many of these loci are co-occupied by the two proteins, AEBP2 and SUZ12. This suggests that AEBP2 is most likely a targeting protein for the mammalian PRC2 complex. To investigate the in vivo roles of this protein, a mutant mouse line with disrupted Aebp2 transcription has been generated. Breeding experiments demonstrated embryonic lethality in the Aebp2-mutant homozygotes, but survival of the heterozygotes to adulthood with fertility. In developing mouse embryos, Aebp2 is expressed mainly within cells of neural crest origin, such as the dorsal root ganglia, and facial cartilages and bones. In addition, many heterozygotes display a set of phenotypes, including enlarged colon and hypopigmentation, similar to those observed in human patients with Hirschsprungs disease and Waardenburg syndrome. These phenotypes are caused by the absence of the neural crest-derived ganglia in hindguts and melanocytes. Additional analyses further confirmed changes in the expression and methylation levels of H3K27me3 on the genes involved in the development of the neural crest cells in the Aebp2 heterozygotes. Overall, these results suggest that Aebp2 may regulate the development of the neural crest cells through the PRC2-mediated epigenetic mechanism.

The sale of eastern oysters (Crassostrea virginica) is a multi-million dollar industry in the United States. Triploid production of oysters helps to alleviate the decline in sales during summer months that normally results from the loss of flavor and texture when diploid oysters are spawning. Research to improve the ease of triploid production is critical for the expansion of oyster hatcheries producing triploids. The goals of this research were to determine the period of time when triploid oysters are most fertile and to determine if prostaglandin E2 (PGE) plays a role in oocyte maturation of C. virginica. The results of this research will assist in creating triploid broodstock for tetraploid production. Triploid oysters were found to reach full gonadal maturity as well as spawn, however at lower percentages than diploid oysters. In this study, diploid oysters peaked in maturity from April 18-May 07. Triploid oysters peaked in maturity in early February and had two smaller peaks in early June and mid August. This suggests that triploid development is shifted from diploid development and should be spawned either earlier or later in the year than diploids. Oysters with oocytes in early development (stage II) continually increased PGE titers through stages III and IV. Once oysters were ready for spawning in stage V, titers decreased in value. This correlation of PGE titers with gonadal stage suggests that PGE plays a role in the early maturation phase of oocytes. PGE titers were not significantly different when compared to 2N and 3N cohorts or amongst gonadal stages. The lack of significance may be due to high variability as a result of random sampling.

Resprouting and reseeding shrubs are predicted to be restricted to habitats with long and short return intervals of natural disturbances, respectively. Nonetheless, resprouters and reseeders co-occur along Gulf of Mexico coastal ecoclines where lightning-ignited fires were historically frequent. In this collection of studies, I examine fire responses, habitat associations, distribution limits, and seedling recruitment of <i>Hypericum</i> species along ecoclines in pine savannas of the St. Joe Bay State Buffer Preserve in Gulf County of Florida. In this area, ecoclines are characterized by topographic, soil moisture, and fire heterogeneity gradients. <i>Hypericum microsepalum</i>, an obligate resprouter, primarily resprouts following disturbances that remove aboveground stems. It is associated with upland, dry habitats that frequently burn, but can survive over a wide range of habitats along ecoclines. <i>Hypericum chapmanii</i>, an obligate reseeder, is killed by fires and recruits with a pulse of seedlings. <i>Hypericum brachyphyllum</i>, a facultative reseeder/resprouter, both reseeds and resprouts after low intensity disturbances, but only reseeds after high intensity disturbances. <i>Hypericum brachyphyllum</i> and <i>H. chapmanii</i> are associated with intermediate, mesic areas along ecoclines where fires become increasingly heterogeneous to rare as they move down slopes. These species have low survival outside of their original habitats. Direct effects of fire, specifically removal of aboveground biomass and litter, increase seedling recruitment of <i>H. brachyphyllum</i> and <i>H. chapmanii</i>. Fires have no direct effect on the growth of <i>H. brachyphyllum</i> to juvenile and reproductive adult stages, but indirectly increase growth of <i>H. chapmanii</i>. This is likely the result of fire facilitating regeneration of associated nurse plants. Therefore, fires are important for seedling recruitment and growth of <i>Hypericum</i> species. Time to reproduction is longer for <i>H. chapmanii</i> (3+ years) and <i>H. brachyphyllum</i> (3 years) than <i>H. microsepalum</i> (2 years). Differences in time to reproduction should cause species to segregate along a fire frequency gradient. I thus conclude that heterogeneous fires within a high fire frequency landscape may increase persistence of <i>Hypericum</i> resprouters and reseeders in higher and lower areas along ecoclines, respectively. It should also allow plants with different life histories to co-occur in intermediate areas along ecoclines where fires are patchy and vary in intensity.

Pine savannas are an endangered ecosystem and cover <2% of their former range. Although often characterized by the presence of a single tree, P. palustris, the groundcover vegetation is extremely species rich. Thus, the groundcover vegetation is the focus of conservation efforts in pine savannas. This dissertation describes how fire, patches of shrubs, winter avian granivores, winter mammalian herbivores, and an introduced climbing fern (Lygodium japonicum) affect pine savanna groundcover. The fieldwork for this dissertation was done at Camp Whispering Pines, a pine savanna that has been undergoing restoration since 1990. Biennial, prescribed fires at the beginning of the growing season are a part of the habitat restoration. Although stem production of all groups of plants except bunchgrasses was stimulated by fire, annuals were found to respond most strongly to fire. Thus frequent fires appear to increase the presence of annuals in the groundcover of pine savannas. Pine savanna vegetation is interspersed with patches of shrubs. Along the margins of shrub patches there were more annual stems and fewer bunchgrass stems. Thus, shrubs appear to increase the heterogeneity of the groundcover. Pine savannas have a diverse group of avian granivores including some rare and endemic species. Avian granivores are probably selective in the seeds that they remove. Thus, they probably change the composition of the pool of seeds available to germinate. By removal of common species or large-seeded competitive dominants, avian granivores were predicted to increase the species richness of pine savanna groundcover vegetation. The White-tailed Deer (Odocoileus virginianus) and the Eastern Cottontail (Sylvilagus virginianus) are mammalian herbivores present at the study site. Mammalian herbivores often affect plant communities by removal of competitive dominants or selective removal of woody species. Mammalian herbivory was found to decrease the numbers of bunchgrasses, but did not affect other components of the plant community. In addition, bunchgrasses showed a large increase through the five seasons of data. There were, however, no subsequent changes as a result of this increase in stem numbers. Thus, bunchgrasses do not appear to competitively exclude other members of the species-rich groundcover community. Lygodium japonicum potentially threatens pine savanna groundcover. I evaluated how shrubs and fire affect its ability to invade pine savannas. Lygodium japonicum was found to occur in many more of the experimental plots along the margins of shrubs, and fire did not decrease its biomass. Presence of shrubs appears to facilitate invasion of pine savannas by L. japonicum, and fire is not an effective method of control.

The geographical range, abundance, and cohesion of populations can track landscape and climatic dynamism in ways that help set (and reset) the evolutionary trajectory of a species. Understanding the nature of this interaction can elucidate both evolutionary and geographical history as well as clarify the parameters that govern diversification. In this study, I apply multilocus genetic data from populations of the North American ground skink, Scincella lateralis, to investigate phylogeographic history as well as the interaction between population genetic and geographical processes that have shaped it. First, I examined the geographic distribution of genetic diversity for S. lateralis and tested whether an interaction between riverine barriers and climate-mediated population contractions have contributed to observed patterns. I found evidence for extensive mtDNA fragmentation resulting in 14 lineages and more moderate fragmentation of nuclear loci resulting in seven populations. The distribution and bounds of diversity are consistent with differentiation in response to riverine barriers that were rendered more isolating in the past when populations likely resided in southern refugia. I next applied multilocus sequence data and several analytical methods to reconstruct hierarchical relationships among S. lateralis populations and determine how dispersal has impacted divergence. In doing so, I explored the robustness of methods to assumption violations inherent when evaluating natural populations that have diversified recently and without complete isolation. Discordant hierarchical structure was recovered when using different methods and estimates of divergence and migration were invoked to evaluate population relationships. Rejection of a model of isolation-with-migration is largely contingent upon whether regions near adjacent populations are sampled, suggesting that recent gene flow following allopatric isolation is the primary mode of divergence. Finally, using mtDNA and microsatellite data I investigated the role of rivers in population genetics in more detail by estimating the current rate of S. lateralis migration across the Mississippi River and testing whether migration can be facilitated by meander loop cutoff, a common feature of major rivers. I found that gene flow across the river is high and largely asymmetrical in the direction predicted by cutoff-mediated dispersal, supporting one mechanism that may intermittently contribute to the permeability of riverine barriers.

Reef-dependent and reef-associated communities found on oil and gas platforms in the Gulf of Mexico occur in high densities and are species rich. Platforms may impact nearby communities through the introduction of benthic primary producers and by altering biological and environmental factors that may create influential gradients associated with these structures. To quantify the presence and effective distance exerted by such gradients, reef-dependent and reef-associated communities were analyzed in two ways: (1) community patterns of abundance and diversity were compared near and far from platforms; and (2) a food-web tracer was used to indentify basal resources from platforms used by consumers. Demersal and benthic communities, along with environmental gradients, were sampled 0.25 and 1.5 km from four operational platforms in the Gulf of Mexico. No distance effects were observed in demersal or benthic communities, metals concentration, organic carbon content of the sediment, or sediment particle size. A distance effect was detected in the abundance of Micropogonius undulatus (Atlantic croaker) and Centropristis philidelphica (rock sea bass). Prey depletion near platforms (i.e., a foraging halo) was not observed for potential demersal prey items of Lutjanus campechanus (red snapper) or in the benthic community. Reef-dependent communities at two platforms were sampled via SCUBA and analyzed using stable isotopes to determine the role of benthic algae from platforms in the diets of reef-dependent and reef-associated communities. Partial contributions of red algae endemic to platforms were observed in the crabs Pseudomedaeus agassizii, Teleophrys pococki, Micropanope nuttingi, stenothoid amphipods, and harpacticoid copepods as well as in the gut contents of L. campechanus and Balistes capriscus (grey triggerfish); however, phytoplankton is likely the dominant basal resource in both reef-associated and reef-dependent communities, contributing to over 78% of the diet of reef-dependent suspension-feeders. Dense suspension feeding communities may capture and process phytoplankton making secondary production and egestia available to reef-dependent and reef-associated consumers. No distance effects of stable isotopes were observed within reef-associated organisms or bulk sediment. Overall, the effects of platforms (both on community structure and food webs) are generally localized to < 250 m with species-specific effects on abundance, diversity, and diet extending to this distance.

Nopp140 is a nucleolar protein with several purported roles in ribosome biogenesis. To further characterize Nopp140 in Drosophila, we used FLP-FRT recombination to delete the Nopp140 gene. Genomic PCR, RT-PCR, and immuno-fluorescence microscopy confirmed the loss of Nopp140 and its products. Compared to embryos bearing the transposons used to generate the deletion, Nopp140-/- embryos displayed similar hatching rates, but resulting larvae died after 8 days, still in the second instar stage. Nucleoli were apparent in Nopp140-/- cells with no observable morphological defects, but the rRNA methyl-transferase, fibrillarin, redistributed partially to the nucleoplasm. BrU-labeling indicated that rDNA transcription is reduced overall in Nopp140-/- larvae, while Northern analysis showed that pre-RNA cleavage was un-affected. Surprisingly, Northern analyses of Nopp140-/- larvae showed an unusually large pre-rRNA bearing the R2 retro-transposon sequence and the processed R2 transcript. The observation suggests a fundamental shift in rDNA chromatin structure and expression upon loss of Nopp140. Transmission electron microscopy of Nopp140-/- cells showed excess nuclear virus-like copia particles, reduced cytoplasmic ribosomes, autophagosome-like structures, and many electron dense cytoplasmic granules that are likely to be stress bodies and proccessing (P) bodies. Because the downstream piggyBac element used to delete Nopp140 resides in CG7145, phenotypes caused by this insertion were compared to those caused by Nopp140 deletion. Delta-1-pyrroline-5-carboxylate dehydrogenase (P5CDh) is a nuclear-encoded mitochondrial enzyme that catalyzes the second step in proline degradation. Mutations in human P5CDh cause type II hyperprolinemia, a complex syndrome displaying increased serum proline and mental disabilities. Conceptual gene CG7145 in Drosophila melanogaster encodes the orthologous DmP5CDh1. The mutant allele, CG7145f04633, contains a piggyBac transposon that truncates the enzyme by 83 residues. Heterozygous (CG7145f04633/TM3) individuals developed normally, while homozygous (CG7145f04633/CG7145f04633) individuals displayed proline levels twice that of normal, swollen mitochondria, and ultimately larval and pupal lethality. These mutants showed normal ribosomal enrichment in cytoplasm, and normal rRNA gene transcription, processing, and pre-rRNA modifications. We conclude that the Nopp140 plays a critical role in ribosomal biosynthesis, and that the phenotypes in Nopp140-/- can be distinguished from the phenotypes caused solely by the CG7145 mutation.