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Mathematical models with fixed parameters have a long history of use in describing the dynamics of populations in ecological interactions. However, in many instances, evolutionary changes in species characteristics can have a significant influence on these dynamics. Using evolutionary game theory, we incorporate evolution into population dynamic models and apply the resulting “Darwinian dynamic” models to study the effects that evolutionary changes can have on populations in several ecological scenarios. We start with a single species (Chapter 2), then add a competitor (Chapter 3), and a predator (Chapter 4). In Chapter 2, a rigorous mathematical analysis of the Darwinian logistic model for a single species shows that stable equilibria occur at strategies that maximize population size rather than growth rate. We apply this model to the data obtained from an experimental study on genetically perturbed populations of the flour beetle Tribolium castaneum. In Chapter 3, we apply a Darwinian dynamic modification of the Lotka-Volterra model to investigate circumstances under which evolution will change expected competitive outcomes. We compare the results of our Darwinian Lotka-Volterra model to studies in which unusual observations were made in studies of the flour beetles T. castaneum and T. confusum, including a reversal in the “winner” of competitive exclusion, and evolution from exclusion to coexistence. Chapters 2 and 3 provide one of the few examples in which evolutionary game theory has been successfully applied to empirical data. From a foundation provided by the Darwinian logistic equation, we build Darwinian dynamic models with two and three trophic levels to study effects of evolution on some basic ecological interactions in Chapter 4. We show how a consumer can cause a resource (producer) species to evolve to a mean strategy that increases its growth rate rather than its population size. We also briefly study how predation on the consumer species can affect equilibrium strategies of species lower in the food chain. Our results show how evolutionary game theoretic methods can be useful for studying both theoretical and applied problems that arise due to evolutionary processes, even when they occur on a ecological time scale. They provide a foundation for the future study of evolutionary effects in larger complex networks of interacting species.

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Doctor of Philosophy / Genetics Interdepartmental Program / Susan J. Brown / In Drosophila, all segments form in the blastoderm where morphogen gradients spanning the entire anterior-posterior axis of the embryo provide positional information. However, in the beetle Tribolium castaneum and most other insects, a number of anterior segments form in the blastoderm, and the remaining segments form sequentially from a posterior growth zone during germband elongation. In this work, I show that segmentation at both blastoderm and germband stages of Tribolium is based on a segmentation clock. Specifically, I show that the Tribolium primary pair-rule gene, Tc-even-skipped (Tc-eve), is expressed in waves propagating from the posterior pole and progressively slowing until they freeze into stripes; such dynamics are a hallmark of clock-based segmentation. Phase shifts between Tc-eve transcripts and protein confirm that these waves are due to expression dynamics. Such waves, like their counterparts in vertebrates, are assumed to arise due to the modulation of a molecular clock by a posterior-to-anterior frequency gradient. I provide evidence that the posterior gradient of Tc-caudal (Tc-cad) expression regulates the oscillation frequency of pair-rule gene expression in Tribolium. I show this by correlating the gradient of Tc-cad expression to the spatiotemporal dynamics of Tc-even-skipped expression in WT as well as in different knockdowns of Tc-cad regulators. Specifically, the spatial extent, frequency, and width of Tc-eve waves correlate with the spatial extent, expression level, and slope of Tc-cad gradient, respectively, as predicted by computer modeling. These results pose intriguing evolutionary questions, since Drosophila and Tribolium segment their blastoderms using the same genes but different mechanisms, and highlight the role of frequency gradients in pattern formation.

Doctor of Philosophy / Division of Biology / Susan J. Brown / A segmented body plan is conserved in vertebrates and arthropods. Comparative studies implicate a conserved mode of A-P axis patterning and segmentation among vertebrates: Wnt signaling is involved in fate map patterning along the A-P axis and in segmentation in the posterior region of the embryo. On the other hand, comparative studies in arthropods have revealed distinct modes of development between long and short germ insects, which differ both morphologically and genetically. In the short germ insect Tribolium, a Wnt activity gradient contributes to A-P axis patterning and generates a posterior Tc-cad expression gradient that regulates segmentation through a pair-rule gene clock, forming segments sequentially as in vertebrates. In contrast, instead of Wnt activity, a hierarchy of regulatory genes regionalizes the blastoderm and defines segments simultaneously in the long germ insect Drosophila. In Tribolium, Tc-zen-1, Tc-otd-1 and Tc-cad play key roles in patterning serosa, head and trunk regions, respectively, of the blastoderm fate map, which are impacted by changes in Wnt activity levels. However, interactions between these genetic factors have not been described. My work revealed that cross talk between the Wnt and Dpp signaling pathways regulates the expression of Tc-zen-1 to determine the serosa. Furthermore, mutually repression between Tcotd-1 and Tc-cad defines the head and trunk regions while mutual repression between Tc-zen-1 and cad determines the posterior extent of the dorsal serosa. Analysis of target genes of the posterior Tc-cad gradient indicates that the Tc-cad gradient regulates the serial expression of gap genes, which are predominately regulators of Hox genes. Thus the posterior Tc-cad gradient determines segment formation through regulation of pair-rule genes in the insect segmentation clock, and defines segmental identity through regulation of gap genes. Given its effect on Tc-zen-1 and Tc-cad, the Wnt activity gradient is a key organizer of the Tribolium blastoderm fate map. Since homologs of these genes as well as the Wnt signaling pathway have also been identified in several other short germ band insects, and affect cell fates along the A-P body axis, this work provides a new paradigm for the short germ mode of development to guide studies in other arthropods.

Doctor of Philosophy / Entomology / David C. Margolies / Yoonseong Park / Insect metamorphosis is driven by two major hormones, juvenile hormone (JH) and ecdysone (Ec). The presence of JH with an Ec peak in each stadium results in larval-larval molting whereas in the last larval instar a decline of JH to undetectable level combined with pulses of Ec leads to larval-pupal metamorphosis. Larval-pupal metamorphosis normally occurs after a certain number of larval instar and upon reaching a certain size (critical weight). However, in the flour beetle, Tribolium freemani, under crowded conditions larva continue larval-larval molting (LLC) without pupation for longer than 14 instars (6 months). Previous studies have implicated high JH titer as preventing the metamorphosis leading to supernumerary molts. My investigation of JH roles in LLC started by asking whether suppression of JH would rescue the LLC phenotype and allow pupal metamorphosis. Using RNA interference (RNAi), I found that under crowded conditions RNAi of T. freemani methyltransferase3 (TfMT3), which encodes a crucial enzyme for the final methylation step in the JH biosynthesis, or RNAi of T. freemani Krüppel homolog1 (TfKr-h1), the JH downstream gene, did not rescue the larvae but resulted in prepupal lethality. Surprisingly, under crowded conditions prepupal lethality was rescued by RNAi of both TfMT3 and TfKr-h1 administered together, although developmental arrest occurred at the pharate adult stage; this is also the phenotype of TfKr-h1 RNAi-treated larvae under isolated conditions. In investigations of the role of Ec titer in LLC, lethality of the larvae with RNAi of TfMT3 under crowded conditions was associated with the loss of the major ecdysteroid peak, while TfKr-h1 RNAi-treated larvae under crowded conditions showed a delayed, but normal, Ec peak occurring at prepupal arrest. The pattern of Ec peak in RNAi of both TfMT3 and TfKr-h1 together was similar to that with TfKr-h1 RNAi alone. I suggest that a hormonal imbalance, high JH and high Ec in the prepupal arrest of TfKr-h1 RNAi, was rescued by RNAi of both TfMT3 and TfKr-h1 for low JH and high Ec. These results demonstrate that the signaling pathways for LLC are through at least two independent pathways; JH biosynthesis and TfKr-h1-mediated JH response.

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Made available in DSpace on 2014-10-09T12:37:41Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:00:15Z (GMT). No. of bitstreams: 1 05344.pdf: 2112095 bytes, checksum: b5b5473c9436a1e4d97ff7f054328796 (MD5) / Dissertacao (Mestrado) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN/CNEN-SP

MicroRNAs are short non-protein coding RNAs which negatively regulate gene expression by guiding the RNA-induced silencing complex to complementary target mRNAs. MicroRNA regulation is implicated in essentially all biological processes, and microRNAs have a prominent role in animal development. Several microRNA families are conserved between deuterostomes and protostomes, however the majority of microRNAs in animal species are a result of continuous de novo gene birth processes throughout natural history. The acquisition of novel microRNAs, and changes in existing microRNAs, has been suggested to play a role in animal evolution. However, the constraints on microRNA emergence, evolution and expression are not well understood. We have studied the interplay of microRNA developmental expression and evolutionary dynamics in model insects displaying different modes of embryogenesis. We first determined the evolutionary origins and rates of change of microRNAs in Drosophila melanogaster and Drosophila virilis, and analysed their temporal expression profiles throughout development by deep sequencing. We found a good correlation between microRNA conservation and abundance at most stages except for the early embryo, where fast-evolving microRNAs are highly expressed. We further showed that the temporal expression of orthologous microRNAs is highly similar between species, and the global microRNA profiles across development display an hourglass-like conservation pattern, previously observed for protein-coding genes. We next extended our analyses to the red flour beetle Tribolium castaneum, which develops via the short germband mode of embryogenesis. This developmental mode is ancestral and widespread in arthropods, yet the microRNA complement of a representative species has not been previously characterized. We find a number of conserved features between Drosophila and Tribolium, including microRNA maternal loading and modifications, and microRNA-mediated targeting of maternally deposited transcripts. We also describe an abundant pool of maternally loaded and zygotically expressed piRNAs, which appear to be turned on in response to active transposons. In contrast to the previously observed piRNA profile in flies, beetle piRNAs are abundant throughout the entire embryogenesis. A majority of the newly identified microRNAs in the flour beetle are expressed during a discrete period in the early blastoderm, and also target maternally provided transcripts. The observation that the early embryos of both Drosophila and Tribolium are uniquely characterized with high levels of novel and dynamically evolving microRNAs suggests a conserved phenomenon where the blastoderm stage is a highly permissive environment for microRNA innovations.

No description available.