Studying nonnative species soon after their introduction is critical to understanding their risk of becoming widely invasive and determining effective methods of control. I conducted laboratory and field experiments on the Rasberry crazy ant (Paratrechina sp. nr. pubens), which was introduced to Pasadena, TX in 2002 and has since been spreading rapidly. These experiments focused on intraspecific aggression, as well as individual and colony-level interactions between crazy ants and red imported fire ants (Solenopsis invicta), which are dominant in the crazy ant's introduced range. Crazy ants displayed no intraspecific aggression. In individual aggressive encounters with fire ants, crazy ants had higher mortality than fire ants, but in colony-level clashes, crazy ants had less mortality and better control of food resources. These findings suggest that crazy ant abundance is key to their competitive success, and fire ants may provide biotic resistance to crazy ants in some areas.

<p> Sedentary organisms that inhabit the marine intertidal zone must be adapted to withstand forms of environmental stress that are uncommon in other marine environments. Adaptations to these stressors are apparent in the morphologies, behaviors, life histories, and regulation and products of genes of sedentary intertidal organisms (Lent 1969; Garrity 1984; Schmidt et al 2008). However, for those species that have a planktonic larval stage, evolutionary specialization at the molecular level could be constrained by opposing requirements for larvae and adults that are adapted to very different environments. This constraint would have been removed in lineages that lost the ancestral larval stage, and reinstated in lineages that secondarily reacquired a larval stage. A comparative approach using a group in which the planktonic larval stage has been lost and reacquired could be used to test the hypothesis that adaptive evolution of stress-related genes accompanies these life-history transitions. </p><p> Genes with known roles in physiological stress tolerance include those that encode the family of 70 kilodalton heat shock proteins (<i>hsp70s </i>) (Feder and Hofmann 1999). Statistical tests for departures from selective neutrality were applied to sequence variation in <i>hsp70 </i> genes of calyptraeid gastropods. The Calpytraeidae include both intertidal and subtidal species, as well as species that have lost or secondarily reacquired the ancestral planktonic larval stage (Collin 2003a; Collin et al. 2007). I focused on two species: <i>Crepidula fornicata</i> and <i>C. atrasolea</i>. Both species are found in low intertidal and subtidal habitats in the western tlantic region. However, whereas the eggs of <i>C. fornicata</i> hatch into planktonic veligers, the eggs of <i>C. atrasolea</i> develop directly into crawling juveniles. I tested for selection with statistics that characterize the distribution of sequence variation within and between species, comparing values for each <i> hsp70</i> gene fragment with expectations for selectively neutral loci. </p>

<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>

<p> Plumage color evolution in birds has been the focus of theoretical and empirical research on sexual selection since Darwin. Many of the yellow, orange, and red hues seen in bird plumage are the result of carotenoid pigmentation. While a great number of recent studies have examined the functions of carotenoid-based plumage coloration in a single species, few have examined the evolutionary history of this trait in a comparative phylogenetic context. Using the New World blackbirds as a model clade, I focus on two questions that a comparative phylogenetic approach can uniquely address. First, what is the history of evolutionary change in carotenoid color that led to the colors seen in extant blackbird taxa? Second, by what proximate mechanisms have carotenoid pigments evolved? In Chapter 1, I present an ancestral state reconstruction of carotenoid-based plumage coloration across the Icterid phylogeny, based on reflectance measurements of museum skins. My results show robust evidence that red coloration was gained repeatedly from a yellow common ancestor. In Chapter 2, I used pigment biochemistry of meadowlark (<i>Sturnella</i>) and Cacique (<i>Cacicus</i>) feathers to test whether independent gains of red coloration are the result of parallel or convergent metabolic mechanisms. Meadowlarks have evolved red coloration using a different set of carotenoids than caciques, but the caciques have evolved the same set of carotenoids twice. This suggests that red coloration evolved by convergent evolution among different blackbird clades, but evolved by parallel evolution within the caciques. Lastly, in Chapter 3 I examine the relationship between color and carotenoid pigmentation in orioles, a blackbird clade in which orange has been gained at least twice independently from a yellow common ancestor. I found red-producing keto-carotenoids only in orange species and never in yellow species. This result is a striking contrast to our expectation for a continuous gradient of a carotenoid pigment concentration. These results suggest that repeated gains of C4-oxygenation ability best explain evolutionary changes in orange coloration in orioles. To summarize, I showed using phylogenetic comparative methods that blackbirds have repeatedly evolved towards redder carotenoid coloration. Using HPLC biochemistry, I showed that each of these gains of orange and red coloration is likely the result of a gain of C4-oxygenation ability. The prevalence of gains of orange and red coloration suggests that there may be a directional bias towards evolving longer-wavelength carotenoid plumage. The research presented in these chapters provides the phylogenetic framework necessary for future studies to examine the functional causes underlying the repeated evolution of carotenoid-based coloration.</p>

<p> Adult echinoderms form a mineralized skeleton, but only sea urchins and brittle stars form larval skeletons. In the sea urchin <i>Strongylocentrotus purpuratus</i>, the gene regulatory network (GRN) leading to skeleton formation has been characterized. This <i>S. purpuratus</i> GRN includes several members of the <i>ets</i> family, including <i> Erg, Ets1/2</i> and <i>Gabp</i>. The brittle star <i> Ophiocoma wendtii</i> forms an embryonic skeleton similar to <i> S. purpuratus</i>. The goal of this proposal is to see if expression of the <i>ets</i> family members is conserved as part of the skeletogenic GRN in <i>O. wendtii</i>. Four genes were identified in <i> O. wendtii</i>; homologous to <i>S. purpuratus Erg, Ets1/2, Ets4 </i> and <i>Gabp</i> based on phylogenetic analysis. The coding sequences of these <i>O. wendtii</i> genes were obtained and their temporal expression was determined. These results suggest that sea urchins and brittle stars share a GRN leading to skeleton formation that has been activated in the embryos of both.</p>

<p> <i>Arabidopsis thaliana</i> has undergone three whole genome duplications within its ancestry, and these events have dramatically affected its gene complement. Of the most recent whole genome duplication events (&alpha; event), there remain 11,452 conserved noncoding sequences (CNSs) that have been retained proximal to &alpha; duplicate gene pairs. As functional DNA elements are expected to diverge in sequence at a slower rate than nonfunctional DNA elements, the retained CNSs likely encode gene regulatory function. Within this dissertation I provide evidence for the regulatory role of CNSs within <i> Arabidopsis thaliana</i>. Using a collection of over 5,000 microarray RNA expression profiling datasets, I demonstrate that the presence of CNSs near &alpha; duplicate pairs is correlated with changes in average expression intensity (AEI), &alpha; duplicate pair co-expression, mRNA stability, and breadth of gene expression. The effects of CNSs on AEI, co-expression, and mRNA stability vary relative to their subgene position, because they are located in nontranscribed (5&rsquo;-upstream and 3&rsquo;-downstream) and transcribed (5&rsquo;- UTR, intronic and 3&rsquo;-UTR) regions. Modeling gene interactions through the generation of co-expression networks, I also demonstrate that a portion of CNSs participate in known gene regulatory networks. Collectively, this body of work demonstrates that CNSs regulate steady-state mRNA levels within Arabidopsis thailiana through both transcriptional and post-transcriptional mechanisms.</p>

Software development projects typically involve repeated interactions among several groups of people. This setting seems well suited for an analysis by means of the standard-model of the evolution of cooperation, the Iterated Prisoner's Dilemma. Computer simulations of a population of stochastic reactive strategies show that the existence of intergroup discrimination can be modeled endogeneously as a result of noise due to misperception of the opponent's move. (author's abstract) / Series: Working Papers on Information Systems, Information Business and Operations

<p> This research examines the evolution, phylogenetic distribution, and functional explanations for a peculiar and often overlooked character seen in birds, herein called tracheal and esophageal displacement. Of special interest to this study is examining whether the trait was present in non-avian theropod dinosaurs. This study found that essentially all birds are characterized by a laterally displaced trachea and/or esophagus. The displacement may occur gradually along the neck, or it may happen immediately upon exiting the oropharynx. Displacement of these organs is the result of a heavily modified neck wherein muscles that create mobility restrictions in lizards, alligators, and mammals (e.g., <i>m. episternocleidomastoideus, m. omohyoideus,</i> and <i> m. sternohyoideus</i>) no longer substantially restrict positions in birds. Rather, these muscles are modified, which may assist with making tracheal movements. </p><p> An exceptionally well-preserved fossil theropod, <i>Scipionyx samniticus </i>, proved to be paramount. Its <i>in situ</i> tracheal and esophageal positions and detailed preservation (showing the hallmarks of displacement including rotation, obliquity, a strong angle, and a dorsal position in a caudad region of the neck) demonstrate that at least some theropods were characterized by tracheal and esophageal displacement. Ultimately, the presence of the trait correlates with a highly flexible neck, allowing slack and permitting for the organs to save length as they avoid the long curves of the S-shaped neck.</p>

<p> Flower shape, color and size are extensively studied to both identify and classify different angiosperm taxa. The availability of well-supported molecular phylogenies produced using complex models of sequence evolution, coupled with an understanding of the genes that regulate morphological form in model organisms, and new methods to infer gene expression patterns in diverse species now allow us to understand the genetic basis of morphological differences among closely related species. Studies in Plantaginaceae, Gesneriaceae, Fabaceae and Brassicaceae show the importance of <i>CYCLOIDEA (CYC), RADIALIS (RAD)</i> and <i>DIVARICATA (DIV)</i> in regulating flower shape, but also show divergence in gene function within flowering plants. Previous studies in the zygomorphic model species <i>Antirrhinum majus </i> (snapdragon) have shown that <i>AmCYC</i> is expressed in the adaxial (dorsal) petals of flowers where it activates <i>AmRAD </i>. This expression of <i>AmRAD</i> within adaxial petals represses <i>AmDIV</i> expression causing <i>AmDIV</i> to be restricted to abaxial (ventral) and lateral petals. Like <i>Antirrhinum </i>, traditional <i>Diplacus</i> flowers have distinct dorsal, ventral and lateral petal identities. However, within the clade actinomorphic flowers have evolved independently on two occasions: once in <i>D. pictus </i> and once in <i>D. mohaviensis</i>. mRNA reveal <i> DIV</i> expression to be conserved between <i>D. pictus</i> and snapdragon, whereas <i>CYC</i> and <i>RAD</i> expression, and presumably function, differ between the two species. <i>DpCYC</i> is expressed in a narrow portion on the upper lip of abaxial petals, whereas <i> DpRAD</i> is expressed within both lateral and abaxial petals. <i> D. pictus</i> flowers are characterized by a novel upturned abaxial petal which may be linked to localized <i>CYC</i> expression along the upper surface of the structure. This study sheds new light on the mechanisms regulating flower shape in an endemic Californian monkey flower and shows the importance of testing hypotheses from model species such as <i>Arabidopsis </i> and snapdragon in non-model taxa such as <i>D. pictus</i> to undercover the true variety of mechanisms driving morphological evolution.</p>