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An outstanding question in galaxy evolution research is whether the star formation histories of low mass systems are dominated by global starbursts or modes that are more quiescent and continuous. In this thesis, we quantify the prevalence of global starbursts in dwarf galaxies at the present epoch, and attempt to infer their characteristic durations, frequencies and amplitudes in the past. Our approach is to directly tally the number of bursting dwarfs in a complete local sample, and to compute the fraction of star formation that is concentrated in these systems. The resulting starburst number and mass fractions are then combined with B-V colors from the literature, the H-alpha EWs presented here, and stellar evolutionary synthesis models in order to place constraints on the average starburst duty cycle. The primary dataset used has been put together by the 11 Mpc H-alpha UV Galaxy Survey, who have collected data on an approximately volume-limited, statistical sample of star-forming galaxies within 11 Mpc of the Milky Way.Our main observational results, along with the accumulation of star formation studies of dwarf galaxies over the past three decades, paint a consistent picture where systems that are currently experiencing a massive global burst are just the 6% +/- 3% tip of a low-mass galaxy iceberg. Moreover, bursts are responsible for 22% +/- 10% of the total star formation in the overall dwarf galaxy population, so the majority of stars in low-mass systems do not appear to be formed in this mode today.Over their lifetimes, however, a greater fraction of the stellar mass of a dwarf may be formed in the burst mode. Synthesis modeling suggests that bursts cycles appear to be necessary in order to simultaneously explain the present-day observed blue B-V colors and modest H-alpha EWs of TYPICAL, CURRENTLY NON-BURSTING dwarf irregulars, unless non-standard assumptions concerning the IMF and the escape fractions of Lyman continuum photons are made. The starburst cycle that we converge upon involves burst durations of 50-100 Myrs, cycle frequencies of 1 to 3 per Gyr, and elevated burst SFRs that are a factor of 6-10 higher than the rate in the quiescent state. Galaxies characterized by such a SFH would spend ~10% of their lives in the burst state, and form ~50% of their stellar mass during this time.

<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>

Ontology learning supports ontology engineers in the complex task of creating an ontology. Updating ontologies at regular intervals greatly increases the need for expensive expert contribution. This naturally leads to endeavors to automate the process wherever applicable. This paper presents a model for automated ontology learning and a prototype which demonstrates the feasibility of the proposed approach in learning lightweight domain ontologies. The system learns ontologies from heterogeneous sources periodically and delegates all evaluation processes, eg. the verification of new concept candidates, to a crowdsourcing framework which currently relies on Games with a Purpose. Furthermore, we sketch ontology evolution experiments to trace trends and patterns facilitated by the system.(authors' abstract)

<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>

The majority of typically sized galaxies in the local Universe reside in a common dark matter halo with other similar galaxies known as a galaxy group. However, this was not always the case. Nine billion years ago, when the universe was one third its current age, these galaxies were almost exclusively the only massive galaxy in their dark matter haloes. In this thesis, I use both observational and theoretical methods to attempt to understand the effect these galaxy groups have on the evolution of galaxy properties. I examine the morphological and star formation properties of galaxies in redshift selected samples of galaxy groups at two redshift epochs, z=0 and z=0.4. Galaxy groups contain fewer disk galaxies, as determined by quantitative morphology measures, than similar luminosity field galaxies at both redshift epochs. Furthermore, the difference, at fixed luminosity, grows from 6% at z=0.4 to 19% at z=0. The fraction of passive galaxies, as determined from spectral energy distribution fitting of UV and optical photometry, shows similar behaviour. However, at neither redshift do we find that the disk dominated and star forming galaxies in groups have properties which are significantly different from those in the field. The disks in both environments show similar scaling relations and similar distributions of asymmetry. While both group and field star forming galaxies have similar average star formation rates at fixed stellar mass and redshift. These results argue in favor of a relatively gentle physical mechanism of transformation, like strangulation, which removes the hot halo of a galaxy as it falls into a more massive halo. I use a semi-analytic galaxy formation to understand the accretion histories of galaxies which reside in galaxy groups and clusters at different redshift epochs. The use of a simple model for environmental effects finds that the evolution seen in our observations of passive galaxies can be explained if a galaxy becomes passive 3 Gyrs after falling into a dark matter halo which has a mass of greater than 10E13 Msun. Finally, I use two novel methods for exploring how diffuse stellar mass and dust is distributed in and around galaxy groups. These are important probes of the environmental influence on galaxy evolution. By correlating the positions of hostless type Ia supernovae with galaxy groups, I find that as much as half of a galaxy's stellar mass is in a diffuse form outside of galaxies. These means that processes which shred or harass galaxies must be particularly strong in the group environment. I also find that dust is destroyed by the hot gas contained within groups and clusters. Dust is a necessary component of star formation, and its destruction could be an additional mechanism to suppress the production of stars in galaxy groups.

<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>

This work presents detailed analysis from the GEEC2 spectroscopic survey of galaxy groups at 0.8<z<1. This deep survey, which has a magnitude limit of r_AB<24.75, had previously found a population of intermediate ('green') galaxies between the star-forming ('blue') and quiescent ('red') sequences. GMOS-S spectroscopy for the 11 X-ray selected galaxy groups was obtained and is highly complete ( > 66 per cent) for eight of the eleven groups. Using an optical-NIR colour-colour diagram, the galaxies in the sample are separated with a dust insensitive method into the three categories, star-forming, quiescent, and intermediate. The strongest environmental dependence is observed in the fraction of quiescent galaxies, which is higher inside groups than in the field for all stellar masses. While intermediate galaxies represent ~15-20 per cent of the star-forming population in both the group and field, the average specific star formation rates (sSFR) of the group population is lower by a factor of ~3. The intermediate population also does not show the strong Hδ absorption that is characteristic of starburst galaxies. Inside groups, only 4.4-6.7 per cent of star-forming galaxies are starbursts, which gives additional validity to the assumption that the quenching of star-formation is the primary process in the transition from the star-forming to the quiescent state. With the use of stellar synthesis models, two possible scenarios for the origins of the intermediate population are investigated, including the quenching of star-forming galaxies via environmental processes and the rejuvenation of star formation in early-type galaxies via mixed mergers. To model the quenching scenario, we have tested the use of different exponential quenching timescales (τ_2) and different types of delays between satellite accretion and the onset of quenching. We found that the fraction of intermediate galaxies depends most strongly on the value of τ_2. The relative fractions of galaxies rule out both the no-delay scenario, which would require a long τ_2 that over-produces intermediate galaxies, as well as the constant 3 Gyr delay model, which does not produce a sufficient number of quiescent galaxies. The observed fractions are best matched with a model that includes a dynamical delay time and a τ_2=0.25 Gyr, but this model also predicts intermediate galaxies Hδ strength higher than that observed. For the rejuvenation scenario, we found that the time visible in the intermediate region is directly related to the size of the second 'burst' of star-formation, which can then be further constrained by the Hδ strength for the intermediate population. The observations are best matched to a burst size of ~1 per cent, at a rate of ~3 times per Gyr. In order to properly distinguish between the two scenarios, we will need to both increase the signal-to-noise ratio for the Hδ measurements and conduct a deeper survey of satellite galaxies both inside groups and in the field.