The Diadectomorpha is a central taxon in understanding the origin and early evolution of amniotes. It is considered a sister taxon to Amniota and is so similar to amniotes that some researchers have placed it within the Amniota itself. This group is composed of three families: the Limnoscelidae, the Tseajaiidae, and the Diadectidae. Being the most basal member of this group, the family Limnoscelidae is especially important in these studies.

Stress is a ubiquitous aspect of everyday life. As such, there exists a great deal of variability in the individual response to stress, particularly as a functional cause of depression. The aim of this dissertation is to investigate the mechanisms behind individual differences in response to stressful events in the attempt to explain differing levels of vulnerability to depression and drug addiction following exposure to stress. To accomplish this goal, we examine variations in the stress response using a rodent model of individual differences based on novelty-seeking behavior. Outbred rats can be classified as either High Responders (HR) or Low Responders (LR) depending on their locomotor activity in a novel environment. Previous studies have demonstrated that HR and LR rats differ in key components of the stress response pathway and would thus make a good model of individual differences in response to stress. Of the many types of stressors that one might encounter in their daily activities, the most commonly experienced is social stress. We therefore utilized a rodent model of social stress termed social defeat to investigate whether exposure to social stress might induce depressive-like behaviors. We then examined histone modifications as a potential mechanism behind such behavioral alterations. Our results found that repeated social defeat induces a number of depressive-like behaviors in Sprague- Dawley rats that are correlated with short-term changes in histone acetylation in the hippocampus and the amygdala. We then focused on individual differences in response to social defeat and in histone modifications. We found that HR rats are more susceptible to the effects of social stress, as evidenced by the expression of depressive-like behaviors following exposure to social defeat. Additionally, HR rats differ from LR rats in the levels of hippocampal histone acetylation in both basal conditions and following exposure to social defeat. We investigated potential genes that may be responsible for our observed changes in acetylation. We found basal changes in cyclic-AMP response element binding (CREB) Binding Protein (CBP) mRNA between HR and LR rats. These results indicate a role for epigenetic mechanisms as a potential mechanism for individual differences in responses to stress. We then explored individual susceptibilities in acute versus repeated social defeat exposure. We found that while both HR and LR rats exhibit long-term memories to repeated social defeat, only HR rats display long-term memories of an acute social defeat exposure. We examined histone acetylation levels following an acute exposure to social defeat, and found changes in the timing of acetylation patterns between HR and LR rats in the hippocampus and amygdala. These findings again highlight the importance of considering individual differences in stress responses and uncover the HR/LR model as a potential model for posttraumatic stress disorder. Finally, in a collaborative study, we investigated the role of methionine in depression and drug addiction. We found that systemic injection of methionine, a methyl donor, blocked behavioral sensitization to cocaine and resulted in decreased cocaine self-administration in male Sprague-Dawley rats. We propose several follow-up studies for investigating the role of DNA methylation further, including investigation of specific DNA methyltransferases, such as DNMT3A, and their target genes. This particular enzyme has also been implicated in the pro-depressant behaviors following exposure to social defeat, providing a common mechanism for the fields of depression and addiction. / A Dissertation submitted to the Department of Biomedical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2011. / November 8, 2010. / neurobiology, hippocampus, depression, stress, Novelty-seeking / Includes bibliographical references. / Approved: Mohamed Kabbaj, Professor Directing Dissertation; Zuoxin Wang, University Representative; Akash Gunjan, Committee Member; Carlos Bolanos, Committee Member; James Olcese, Committee Member.

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.

Spiny lobsters (Family Palinuridae) are large, diverse, and abundant marine crustaceans, which have conquered tropical, subtropical, and temperate coastal waters around the globe despite strong predation pressure. The mechanisms and function of antipredation strategies for most species in this highly successful taxon, encompassing behavior, morphology, and life-history characteristics, are poorly understood, particularly against natural predators. I investigate mechanisms of antipredation in spiny lobster Panulirus argus in the open during the day, at night, and while sheltering diurnally in natural dens. I also examine the function of putatively defensive acoustic signals produced by P. argus during diurnal attacks by piscine predators and while escaping octopuses at night. I also compare and contrast the mechanism and survival value of antipredator behavior and morphology between sympatric Panulirus argus and P. guttatus. Finally, I investigate ontogenetic changes in defensive behavior by diurnally sheltered P. argus to chemically-mediated predator cues. Nearly 40 species of spiny lobsters produce a characteristic sound (termed stridulation), speculated to deter predation. The occurrence and efficacy of stridulation has not been documented quantitatively during encounters with natural predators. I examined sound production in the sympatric spiny lobsters Panulirus argus and P. guttatus during attacks by their common predator, gray triggerfish Balistes capriscus, to determine if lobsters produce sound during defense, how stridulation integrates with behavioral and morphological defenses, and how interspecific differences in sound production relate to efficacy in repelling predators. Both lobster species stridulated coincident with specific defensive actions during triggerfish attack. In P. argus, stridulation occurred both during antennal lunging and during escape attempts (rapid retreat by tailflips). Panulirus guttatus stridulated only coincident with tailflips and did not lunge. Same-sized individuals of P. guttatus were subdued ~3 times more quickly on average than P. argus. The two species differed also in the relative size of the primary defensive weapons, the spinose 2nd antennae, which were far more robust in P. argus, particularly at larger body sizes. These results suggest that stridulation is an integral component of aggressive defense and escape behavior in spiny lobsters. The timing of sound production during aggressive, retaliatory defensive behavior (lunging) by P. argus suggests an aposematic role for stridulation against triggerfish. Using staged encounters of P. argus with B. capriscus, I examined whether stridulation, coincident with thrusting spines during aggressive defense, functions aposematically or simply renders a defending lobster more difficult to subdue without playing an aposematic role. I demonstrate, by disabling the stridulating organ in some lobsters (muting), that sound plays a vital role in defense against inexperienced (naïve) triggerfish, resulting in fewer successful attacks in subsequent encounters. Choice experiments with triggerfish that previously bypassed defenses and consumed lobsters show that experienced attackers do not choose muted lobsters over stridulating individuals. I propose that stridulation by P. argus against triggerfish is aposematic, as part of a multi-modal display, advertising the lobster's spiny defenses to predators. It is widely documented that sound production in P. argus and other spiny lobsters accompanies grasping of the carapace or other disturbance by human captors. Additionally, stridulation accompanies tailflip escape attempts during attacks by triggerfish. Although sound production during daytime attacks does not appear to increase survival against triggerfish, stridulating during escape may be more effective against grasping predators like octopus. Here, I investigate P. argus defensive behavior during nighttime encounters with Caribbean reef octopus Octopus briareus to determine whether P. argus stridulate during octopus attacks, how stridulation is used along with other defensive behavior (e.g. tailflips), and whether sound production improves survival in stridulating individuals. Lobsters stridulate both during grasping attacks by octopus and during escape attempts after being captured. Stridulating lobsters are also more likely to escape from attacking octopuses and remain uncaptured longer during encounters. I suggest that improving the efficacy of tailflip escapes against octopus may have been the function for which the stridulating organ initially evolved in the Stridentes clade of the Palinuridae. Benthic stages of P. argus reside in shelters during the day as a primary means of antipredation. However, when an active predator approaches and/or successfully attacks a nearby conspecific, these individuals must decide whether to emigrate quickly from the area or remain in shelter (dens or macroalgae) and rely on crypticity, defensive behavior, or the presence conspecifics to avoid attack, injury, or death. In this study, I examine how the three benthic juvenile phases of Caribbean spiny lobster Panulirus argus respond to exposure to fresh conspecific body fluid and how antipredator behavior, particularly the decision to stay or leave the area, changes during ontogeny. Additionally, I examined how the presence of conspecifics affects the decision to stay or leave in gregarious juvenile stages of P. argus. Although all size classes of P. argus respond to alarm odor, the decision to stay or leave dens changes unexpectedly with increasing body size and in the presence of conspecifics. Once shelters were abandoned, body size was a strong indicator of distance traveled in response to alarm odor. This indicates that Panulirus argus undergo an ontogenetic shift in defensive behavior, more frequently leaving dens in response to alarm odor and traveling across open substrate during the day, but only after reaching a body size at which they can effectively defend against predators. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2006. / October 4, 2006. / Marine Biology, Panulirus argus, Lobster, Triggerfish, Octopus, Aposematism, Bioacoustics, Behavioral Ecology / Includes bibliographical references. / William F. Herrnkind, Professor Directing Dissertation; David E. Thistle, Outside Committee Member; Joseph Travis, Committee Member; Walter R. Tschinkel, Committee Member; Thomas A. Houpt, Committee Member.

Gag grouper, Mycteroperca microlepis, compose an important recreational and commercial fishery along the Gulf coast and Eastern Seaboard of the United States (Coleman et al. 2000, Morris et al. 2000, and Musick et al. 2000). Like many Serranids, gag have a complex life cycle in which juveniles spend each summer developing within inshore structured habitats before joining the adult population offshore (Heemstra and Randall 1993, Koenig et al. 1996, Grover et al. 1998). As is the case with most fisheries, heavy fishing pressures have led to a decline in gag abundance (Renan et al. 1996). The most efficient policies to mitigate for these population have as of yet focused on adult gag preservation; this study, however, attempt to use select juvenile gag population metrics (abundance and date of fertilization) to provide crucial data that may one day assist in providing a juvenile-centric population model. Over the course of a three-year study, juveniles were captured in two regions; near the Florida State University Coastal and Marine Laboratory (Turkey Point Shoal and Lanark Reef sites) and inside of Saint Andrew Bay, Panama City. Otolith analysis was performed to determine age and fertilization date of the juveniles, and abundance statistics were determined for each year. It was found that, consistent with previous literature, average fertilization date varied significantly across years and sampling sites (range = 41.9 to 91.8). The 2009 field season exhibited a significantly earlier fertilization date for both regions, and only one specimen was captured in Saint Andrew Bay. The 2009 Turkey Point Shoal field season was the only occurrence where abundance significantly declined during the course of the field season. Various environmental and physical factors may have been responsible for the enormous interannual variation seen in both abundance and fertilization date, such as large-scale current patterns and predator densities in the two regions. While no concrete conclusions may be drawn from the data, this study was essential in expanding on background knowledge of early juvenile gag population dynamics. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2011. / May 20, 2011. / Juvenile Grouper, Seagrass, Nursery Habitat, Abundance / Includes bibliographical references. / David Thistle, Professor Directing Thesis; Chris Koenig, Professor Co-Directing Thesis; Markus Huettel, Committee Member; Jeff Chanton, Committee Member.

The traditional method for producing taxonomic illustrations requires the preparation of inked copies of pencil originals. These individual figures are then grouped into plates for publication. I describe an alternative, computer-based approach. In a preliminary step, a pencil drawing is digitized and imported into an illustration program. The program's tools are then used to trace the image. Each figure is stored as a separate computer file. To make a plate for publication or a slide for presentation, several figures can be combined. The approach has several advantages. (1) It is easier to master than the pen-and-ink method. (2) Figures can be manipulated electronically, so the size and orientation of a figure is infinitely adjustable, providing great flexibility in the preparation of plates. (3) Multiple "originals" can be printed. (4) Mistakes can be corrected easily. I describe two new species of Diosaccidae (Harpacticoida, Copepoda) from an unvegetated sand at 18 m depth in the northern Gulf of Mexico. One is assigned to the genus Protopsammotopa; the other is assigned to Actopsyllus, and traits in common with Eoschizopera Wells & Rao (1976) are noted. I used the computer-based techniques to produce the figures for these descriptions. The effects of winter storms on the two new diosaccids described here were studied through a reanalysis of data from Thistle et al. (1995a). I found that Actopsyllus sp. nov. did not migrate downward in response to erosive flow. Protopsammotopa sp. nov. males, but not females, did. Protopsammotopa sp. nov. is found at shallower depths in the sediment than Actopsyllus sp. nov., which may explain the difference in response to erosion by two morphologically similar and phylogenetically related species. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2003. / September 3, 2003. / Taxonomy, Benthos, Harpacticoids, Meiofauna, Storms / Includes bibliographical references. / David Thistle, Professor Directing Dissertation; William Herrnkind, Outside Committee Member; Richard Iverson, Committee Member; William Landing, Committee Member; Nancy Marcus, Committee Member.

Gastropods are a highly diverse clade of molluscs that includes limpets, snails and slugs, and the only molluscan lineage with members that have successfully colonized land. Amphibious operculate freshwater gastropods, Ampullariidae, exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying the mechanisms underlying adaptive evolution in gastropods. In the last two decades, there have been interests in the diverse reproductive behaviors of ampullariids: while most genera of apple snails deposit their eggs in a jelly mass underwater, two genera (i.e., Pomacea and Pila) deposit calcareous egg clutches above the waterline. The shift from aquatic to aerial oviposition required the concerted evolution of the adult snail's egg laying behavior as well as the composition of the egg. Today, only limited genomic information is available for this ecologically important family, except in the genus Pomacea, which hinders the investigation of its evolutionary history and mechanism. I have, therefore, developed the publicly accessible transcriptome database, AmpuBase, as molecular resources to support various transcriptomic and proteomic analyses. The database comprise de novo transcriptome assembly of eight species that belong to five representative genera of Ampullariidae. For each species there were 20,730 to 35,828 unigenes with predicted open reading frames, with an N50 ranging from 1,320 to 1,803 bp and 69.7% to 80.2% with functional annotation. Since the ability of laying out-of-water eggs is one of the key steps of terrestrialisation for aquatic snails, I analysed the proteome of perivitelline fluid (PVF) for the eggs of Marisa cornuarietis that were laid underwater. The PVF proteome of P. diffusa also investigated to reveal and compare the biochemical adaptation between P. diffusa clade and P. canaliculata clade. Using LC-MS/MS coupled with transcriptome database, I identified a total of 36 and 32 PVF proteins from M. cornuarietis and P. diffusa, respectively. Comparison of PVF proteomes among the aquatic (M. cornuarietis) and three aerial ovipositing ampullariids (P. diffusa, P. canaliculata and P. maculata) showed that the four species all contain several major perivitellins that are important for the nutrition of the embryos. M. cornuarietis invests heavier in protection against pathogens, whereas the unique presence of calcium binding protein and their high albumen gland expression in three Pomacea, implying the importance of the novel acquisition of this protein for forming the calcareous eggshell of terrestrial eggs. I also found the absence of a neurotoxin (PV2) in M. cornuarietis and P. diffusa PVF, indicating this protein was acquired after the divergence between the ancestors of P. diffusa clade and the P. canaliculata clade, and protects P. canaliculata and P. maculata eggs against terrestrial predators. Evolutionary analyses detected the involvement of gene duplication, positive selection and neofunctionalisation in the formation of several major PVF proteins. With the availability of ampullariid genomes and transcriptomes, I conducted an integrated evolutionary analysis of Pomacea PVF with an aim to understand the molecular adaptations underlying the transition from underwater to terrestrial egg deposition. There were many expanded gene families in the New World ampullariids; some of them may be important for their evolution towards terrestrial egg laying. The PV1 oligomer protein was a novel protein acquired by the common ancestor of New World species to nourishing their terrestrial eggs. Meanwhile, gene duplication followed by neofunctionalisation of MACPF-tachylectin paralogs has contributed to the novel acquisition of the toxic PV2 protein in the P. canaliculata species complex. Overall, using Ampullariidae as an example, my study has demonstrated the power of integrative genomics to address various fundamental questions in evolutionary biology. The findings have enhanced our mechanistic understanding of invasion of terrestrial habitats by aquatic gastropods.

Contemporary biology belongs among the most diversified sciences; yet one of its most fundamental and controversial questions is surprisingly: "What is life?". The aim of this study is to point out that biology is special among other natural sciences because its need of the notion of meaning. Meaning takes the central position in the biological rea-soning. Compared to other sciences, biology has to reflect the dimension of information and its interpretation: language-like properties, communication and interpretation belong to the basic characteristics of life. In spite of the fact, most contemporary theories of evo-lution deny active participation of living beings on the very process - living being come out of its description as puppets or zombies controlled by external forces. As a remedy from such a situation, biology should start with a new model for living entities. A bene-ficial methapor seems to be that of natural languages, i.e. an analogy between a net of historical interactions and conventional ways of interpretation of meaning in (i) living entities and (ii) in system of natural languages. I consider as the most appropriate biolo-gical systems for modeling of such a network of symbiotic interactions, i. e. the pheno-menon of symbiosis and especially symbiogenesis. Keywords: life,...

Due to its great importance, both from the fundamental and from the practical points of view, it is imperative that the concept of entanglement is explored. In this thesis I investigate the connection between information measures, entanglement and the “speed” of quantum evolution. In Chapter 1 a brief review of the different information and entanglement measures as well as of the concept of “speed” of quantum evolution is given. An illustration of the quantum no-cloning theorem in connection with closed timelike curves is also provided. The work leading up to this thesis has resulted in the following three publications and in one conference proceeding: (A) C. Zander and A.R. Plastino, “Composite systems with extensive Sq (power-law) entropies”, Physica A 364, (2006) pp. 145-156 (B) S. Curilef, C. Zander and A.R. Plastino, “Two particles in a double well: illustrating the connection between entanglement and the speed of quantum evolution”, Eur. J. Phys. 27, (2006) pp. 1193-1203 (C) C. Zander, A.R. Plastino, A. Plastino and M. Casas, “Entanglement and the speed of evolution of multi-partite quantum systems”, J. Phys. A: Math. Theor. 40 (11), (2007) pp. 2861-2872 (D) A.R. Plastino and C. Zander, “Would Closed Timelike Curves Help to Do Quantum Cloning?”, AIP Conference Proceedings: A century of relativity physics, ERE 841, (2005) pp. 570-573. Chapter 2 is based on (A) and is an application of the Sq (powerlaw) entropy. A family of models for the probability occupancy of phase space exhibiting an extensive behaviour of Sq and allowing for an explicit analysis of the thermodynamic limit is proposed. Chapter 3 is based on (B). The connection between entanglement and the speed of quantum evolution as measured by the time needed to reach an orthogonal state is discussed in the case of two quantum particles moving in a one-dimensional double well. This illustration is meant to be incorporated into the teaching of quantum entanglement. Chapter 4 is based on (C). The role of entanglement in time evolution is investigated in the cases of two-, three- and N-qubit systems. A clear correlation is seen between entanglement and the speed of evolution. States saturating the speed bound are explored in detail. Chapter 5 summarizes the conclusions drawn in the previous chapters. / Dissertation (MSc)--University of Pretoria, 2007. / Physics / MSc / Unrestricted

This thesis concerns the molecular phylogenetics of three tribes of the family Bovidae, the Antilopini, Neotragini, and Tragelaphini. None of these tribes have been studied extensively with molecular techniques. The tribe Antilopini is one of the most speciose tribes (it includes 6 genera with 20 species) and the classification of several species of the genus Gazella is not clear. The tribe Neotragini is thought to be paraphyletic. Mitochondrial sequences of the cytochrome c oxidase ill and cytochrome b genes totalling 1083 base pairs have been determined for 52 taxa and used to determine phylogenetic relationships using cladistic and distance methods. Karyological analysis identified polymorphisms in several species (especially in Gazella saudiya and G. subgutturosa). Karyotypes of G. dorcas pelzelni and an XXY karyotype of a G. dorcas individual are shown for the first time. The main conclusions are that the Antilopini and the Tragelaphini are monophyletic and that the tribe Neotragini is paraphyletic. There is a lack of phylogenetic resolution between tribes which is probably due to the rapid radiation of the different tribes about 20 million years ago. The genus Taurotragus in the tribe Tragelaphini is shown to be paraphyletic and it would be appropriate to incorporate these taxa in the genus Tragelaphus. The genus Gazella could be paraphyletic, due to the position of Antilope cervicapra, in which case the genus needs to be split into two genera or renamed as Antilope. It is also argued that the use of the subgenus Trachelocele should be discontinued and that its only species, G. subgutturosa should be included in the subgenus Gazella. G. rufifrons and G. thomsonii may be more appropriately considered as conspecific. Cytogenetic and sequence data reveal that the herd of G. saudiya in Al Areen Wildlife Park is hybridised with G. bennettii and it is argued that it is important to identify unhybridised G. saudiya in other collections, since this species is on the brink of extinction. This case study demonstrates the need to genetically screen individuals which are part of a captive breeding program, especially if they are intended for reintroduction into the wild.