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Fireflies are some of the most captivating organisms on the planet. Because of this, they have a rich history of study, especially concerning their bioluminescent and visual behavior. Among insects, opsin copy number variation has been shown to be quite diverse. However, within the beetles, very little work on opsins has been conducted. Here we look at the visual system of fireflies (Coleoptera: Lampyridae), which offer an elegant system in which to study visual evolution as it relates to their behavior and broader ecology. They are the best-known case of a terrestrial organism that communicates through the use bioluminescence. The molecular basis for this communication is relatively simple: one gene-family (opsins) controls the detection of the signal, and one gene family (luciferase) controls the production of the signal. We use a transcriptomic approach to sample for and investigate opsin evolution in fireflies. We also present the first total evidence approach using both an extensive molecular matrix and a robust morphological matrix to reconstruct the lampyrid phylogeny. We then use this phylogeny to assess the hypothesis that adult use of bioluminescence occurred after the origin of Lampyridae. We find evidence for only two expressed opsin classes in each of the nine firefly species studied, one in the ultra-violet sensitive and one in the long-wavelength sensitive areas of the visible spectrum. Despite the need for most adult fireflies to respond to a clearly sexual and colorful visual signal (bioluminescence) to maximize fitness, their visual system is relatively simple, and does not match the trend for opsin duplication found in other insect groups. All subfamilies except for Lampyrinae are recovered as monophyletic; Pterotinae and Ototretinae are recovered within the Lampyridae. The ancestral state of adult bioluminescence is suggested to be non-bioluminescent, with at least three gains and at least three losses.

Circadian rhythms are outputs of the internal clock that regulates the daily functions of almost all living organisms. Circadian rhythms are typically 24 hours because they are synchronized by external cues such as the natural light/dark cycles of the environment. When external cues are removed, the circadian rhythm “free-runs,” thus revealing the organism’s endogenous circadian period. Recent studies have found that the trashline orbweaving spiders Cyclosa turbinata and Allocyclosa bifurca have abnormally short circadian rhythms of approximately 19 and 18 hours, respectively. Trashline orbweavers construct a line of debris made of prey carcasses in the center of their web and then remain undetectable by being cryptic within their trashline. Despite similar circadian rhythms and web-building behaviors, recent genetic findings indicate that these species actually are not closely related. In fact, both genetic and morphological data now suggest A. bifurca is more closely related to Cyrtophora citricola, the Tropical Tent-web spider. This would suggest that trashline behavior and exceptionally short circadian clocks evolved independently in C. turbinataand A. bifurca. This study analyzed the circadian rhythm of C. citricola and compared it to the circadian rhythm of A. bifurca. If C. citricola has an abnormally short clock like A. bifurca, this would indicate that the evolution of the short clock preceded the divergence of these species’ lineages. However, if C. citricola has a more typical clock, this would suggest that the unusually short clock evolved in the A. bifurca lineage and may be more ecologically linked to the trashline behavior. Thirty-two female C. citricola were collected in Southern Florida and had their locomotor activity measured over four days of 12:12 light/dark cycles followed by complete darkness to determine their circadian free-running periods (FRP). Cyrtophora citricola was found to have a more typical FRP of 24.0 + 0.43 hours. Despite being closely related, C. citricola and A. bifurca differ significantly in their circadian rhythms, suggesting that short circadian rhythms may be ecologically linked with trashline behavior.

Adaptive radiations, or evolutionary diversifications, are the evolutionary divergence of a single lineage into many different adaptive forms. They play a critical role in the history of life as groups of organisms speciate and fill new ecological roles over geologically rapid time intervals. There is currently no agreed upon operational unit, timeframe, or amount of divergence for organisms to be considered to have undergone an adaptive radiation. Additionally, the paucity of both comparative and fossil studies has limited the utility of the adaptive radiation in framing macroevolutionary questions, such as, is ecological and morphological diversification simultaneous? An ideal fossil clade to test this question is the Archosauriformes (crocodylians, birds, and their closest relatives). Archosauriforms radiated following the end-Permian mass extinction and their lineage diversification through the Early to Late Triassic is well documented in the literature. Prior to the end-Permian mass extinction, these reptiles were both species poor and ecologically limited, but by the Late Triassic they dominated terrestrial ecosystems in both species abundance and ecological breadth. However, continued environmental instability following the end-Permian extinction has led to the hypothesis that ecological expansion of archosauriforms lagged behind the diversification of lineages. The first chapter of my dissertation uses a Middle Triassic archosauriform tooth assemblage from Tanzania to reconstruct dietary specialization, estimated by morphological disparity of teeth. In addition to comparing tooth disparity of isolated and in situ teeth, this also provides a lens for comparing the timing of dietary specialization and species diversification. I found the archosauriforms to be faunivorous with little morphological disparity amongst the teeth. The second chapter uses an Early Triassic reptile tooth assemblage from South Africa to reconstruct the dietary specialization of archosauriforms early in their radiation to compare the amount of morphological disparity and lineage diversity. I use methods from Chapter 1 and integrate 3D morphometrics to better capture shape. I described several tooth morphotypes including six new to the locality. The morphological and dietary differences were minimal, indicating a greater species diversity than ecological diversity. The third chapter is a description of a new pseudosuchian archosaur taxon from the Middle Triassic of Tanzania. As species descriptions form the basic data unit of macroevolutionary analyses, this assists future studies of the archosauriform radiation. I recover this new taxon as the oldest known aetosaur. This species provides insights into the evolution of an armored carapace in crocodylian-line archosaurs and shows morphology related to armor evolved prior to the evolution of an herbivorous diet. / Doctor of Philosophy / There is an incredible diversity of life on Earth, but this is a small fraction of the life that once existed on our planet. The fossil record provides us a window into the past to reconstruct the history of life on our planet. Two of the patterns we see in the fossil record are rapid drops in biodiversity called mass extinctions, and rapid increases in biodiversity called biological radiations. Both of these events are often related and mass extinctions are followed by biological radiations throughout earth history. A particularly interesting case is the end-Permian mass extinction, not only because it is the largest extinction event, but also because the subsequent radiation was delayed by continuing environmental instability. An ideal group of animals to study in this time period are the archosaurs, the group of reptiles including crocodylians, birds, and their extinct relatives. Archosaur reptiles went from very few species before the extinction, to dominate ecosystems for the next 200 million years. However, we do not know if the radiation of many archosaur species occurred at the same time as they filled new roles in their communities. The first two chapters of my dissertation focus on using fossil teeth to reconstruct the diets of archosaurs at a single location. My first chapter describes teeth from the Middle Triassic (247-237 million years ago) of Tanzania. I measured the shapes of these teeth and used that to help assign them to diets. Doing this I found there were more species than types of diets indicating the radiation of species may have occurred before specialization of life habits. In the second chapter where I describe a reptile tooth assemblage from the Early Triassic (252-247 million years ago) of South Africa. I added additional methods for measuring tooth shape, found several different types of teeth (likely different species) but mostly similar diets, indicating again a delay in life habit specialization. In my third chapter I name a new species of archosaur reptile from the Middle Triassic of Tanzania. This new species helps us to understand how heavily armored plant eaters evolved in early crocodylian relatives during the archosaur radiation.

Peanuts (<i>A. hypogaea</i>) are an economically important crop, a source of food allergies and a member of the South American genus <i>Arachis</i>. The eighty species of genus <i>Arachis</i> have been divided into nine sections. The largest, section <i>Arachis</i>, has been further subdivided into three genome groups. The current intuitive understanding of the evolutionary relationships among <i>Arachis</i> is based on morphological, geographic and cytogenetic data, but a comprehensive phylogenetic study for the genus is lacking. A total of 48 species representing all nine sections were used to reconstruct a phylogeny based on sequence information from plastid <i>trn</i>T-<i>trn</i>F and nuclear ITS genomic regions. Phylogenetic analysis resolved section <i>Extranervosae</i> at the base, followed by sections <i>Triseminatae</i> and <i>Caulorrhizae</i>. Two major terminal lineages were recovered. One is comprised of sections <i>Erectoides</i>, <i>Heteranthae</i>, <i>Procumbentes</i>, Rhizomatosae</i>, and <i>Trierectoides</i>, referred to here as group erectoides. The other is comprised of two major clades, arachis I (B genome, D genome, and aneuploid species) and arachis II (A genome species). The phylogenetic trees show that sequence data partially agrees with the relationships described in the monograph; however, some further investigation is necessary to clarify relationships within and among species of the two terminal lineages. In addition, the major allergen Ara h 2 from 12 wild species from across the genus was analyzed for mutations that could potentially produce a hypoallergenic ortholog. It was found that the evolution of the allergen mostly reflected the species phylogenies based on ITS and combined. The majority of substitutions and length variations were concentrated in the loop connecting helices H2 and H3. Section <i>Arachis</i> species tended to have larger H2-H3 loops, while those from other sections had shorter loops. The immunodominant epitopes #6 and #7, located within this loop, tended to contain mutations or were truncated among species outside of section <i>Arachis</i>. Dot immunoblots showed reduced IgE-binding to peptides representing portions of the H2-H3 loop from <i>A. guarantica</i> and <i>A. triseminata</i>. Orthologs from wild species have demonstrated that they could potentially contain variations of the allergen Ara h 2 that could be utilized to develop a safer peanut cultivar. / Ph. D.

Comparative DNA sequencing of matK, a maturase-encoding gene located within the intron of the chloroplast trnK gene, was evaluated for phylogenetic utility above the family level and within the grass family (Poaceae). There are three major objectives in the research. The first one is to study the utility of the matK gene in plant evolution. The second objective is to characterize the matK gene in the grass family. The last major goal is to address the phylogenetic questions in the Poaceae using the matK sequences from representatives of different grass groups. In order to study the potential application of matK to plant systematics above the family level, eleven complete sequences from GenBank representing seed plants and liverworts and nine partial sequences generated for genera representing the monocot families Poaceae, Joinvilleaceae, Cyperaceae, and Smilacaceae were analyzed. The study underscored the following useful properties of the matK gene for phylogenetic reconstruction: reasonable size (1500 bp), high rate of substitution, large proportion of variation at the first and the second codon positions, low transition-transversion ratio, and the presence of mutationally-conserved sectors. The use of different sectors of the gene and the cumulative inclusion of informative sites showed that the 3' region was the most useful in resolving phylogeny, and that the topology and robustness of the tree reached a plateau after the inclusion of 100 informative sites. The presence of a relatively conserved 3' region and the less conserved 5' region provides two sets of characters that can be used at different taxonomic levels from the tribal to the division levels. It also has demonstrated the potential of partial sequencing in resolving systematic relationships from the tribe to the division level. The matK gene in the Poaceae was characterized with complete sequences from 11 grass genera, representing 7 subfamilies and 11 tribes, and one outgroup (Joinvillea plicata, Joinvillaceae). The alignment of 1632 base pairs from 14 species yielded a data set of 601 (36.8)% variable sites and 246 (15.1%) informative sites. The variations at nucleic and amino acid levels evenly distributed throughout the entire gene, and the 5' region appears to have more variation than the 3' region. The changes at the third codon position are very low as compared to the total of the first and second positions. This has led to a similar variation pattern at nucleic and at amino acid levels. The average tr/tv ratio generated from 14 entire matK sequences is 1.29. It is intriguing to find that the tr/tv ratios were regionally related. RASA analysis of the alignment data indicated a relatively high phylogenetic signal in the data set of 14 taxa. In the two half analyses, while the tRASA of the 5' half of the matK gene (0.43) is not significant, the 3' of the matK gene showed a significant phylogenetic signal. Among the 5 sections of the 14 entire matK sequences, only the fourth sector contains a statistically significant phylogenetic signal. These results indicate that matK is a phylogenetically valuable gene and that the 3' region of the matK gene contains strong phylogenetic information. A single most parsimonious tree was obtained from the 246 informative sites of the 14 entire matK sequences. Seven major groups were well resolved on the most parsimonious tree, corresponding to the seven commonly recognized subfamilies: Aruninoideae, Bambusoideae, Centothecoideae, Chloridoideae, Panicoideae, Pooideae and Oryzoideae. Approximately 960 base pairs of the matK gene were sequenced from grass species representing 48 genera, 21 tribes, and seven subfamilies to reconstruct a phylogeny for the Poaceae. Joinvillea plicata (Joinvilleaceae) was used as an outgroup species. The aligned sequences showed that 495 nucleotides (51%) were variable and 390 (36%) were phylogenetically informative. RASA indicated that very significant phylogenetic signals exist in this data set. The cumulative addition of informative sites starting at the internal end of the sequences revealed that at 300 sites, tree topology and bootstrap values matched those of the consensus tree based on the entire sequence. Parsimony analyses using PAUP resulted in six most parsimonious trees and a strict consensus tree showing major lineages supported by high bootstrap values. These lineages corresponded to six subfamilies: Bambusoideae, Oryzoideae, Pooideae, Chloridoideae, Panicoideae, and Arundinoideae. The Bambusoideae, including woody and herbaceous taxa, diverged as the most basal lineage, and the monophyletic oryzoid species formed a sister group. The Chloridoideae, Panicoideae, Arundinoideae, and the centothecoid Zeugitis (PACC group) emerged as a monophyletic assemblage with 95% bootstrap support. The Aristideae branched off as a monophyletic line basal to the chloridoid clade. Stipeae appeared as a sister taxon to the Pooideae. The matK-based phylogeny did not reveal a major dichotomy in the family. The matK gene has provided sequence information sufficient for good resolution of the major grass lineages. / Ph. D.

Cereals represent one of the most important food crops in the world. Rice (Oryza sativa) is one of the most commonly consumed cereal grains, and as a result, has considerable economic and agricultural importance, despite their potential as a source of genetic material. The phylogenetic relationships among rice and its wild species are not well understood. The objectives of this study are to evaluate the rate and type of molecular variation present in the gene that encodes the 10 kDa prolamin polypeptide in Oryza (Poaceae), and use this information in understanding the evolution of the Oryza genus. Our principle hypothesis is that genetic diversity exists at the molecular level in wild species of Oryza, and that this diversity can provide useful information regarding the phylogenetic relationships among rice species and permit a more theoretical examination of the evolutionary processes, such as concerted evolution, within Oryza and its nine genomes. A phylogeny of Oryza is presented, and modes of evolution are discussed. / Master of Science

The study focuses on the genus Bothriochloa (Andropogoneae, Poaceae) in Australia. Despite morphological features separating this genus from the closely related two genera Capillipedium and Dichanthium, (the three hereafter will be called BCD), De Wet and Harlan introduced the compilospecies complex to show the interbreeding phenomena that occurred among species of these genera. This study was carried out to assess species/genus relatedness of the BCD complex using different evidences from morphology, molecular information and genomic content. Nineteen morphological characters were observed, three regions (trnT-F, rps16 intron and 3'trnK) of chloroplast genome phylogenetic were used in phylogenetic reconstruction, and chromosome counting as well as flow cytometry for chromosome number and genome size were conducted during the study. Phylogenetic trees were constructed using MP with NJ for morphological data, and MP, RAxML, and BI for molecular data. Based on morphology, all three genera were separated as monophyletic units. Bothriochloa consisted of two clades. However, phylogenetic analyses based on chloroplast genomic regions reveal that Bothriochloa and Dichanthium are paraphyletic clades and only Capillipedium is resolved as a monophyletic clade. The concatenated data set has performed better than individual data sets in terms of resolution and support for clades. Flow-cytometry and chromosome counting only found diploid and tetraploid but not hexaplod species. TCS network reveals that tetraploidization followed different pathways from the ancestral diploid species. This study provided new insight onto the evolution of the chloroplast genome in the compilospecies and empirical evidence of species grouping of the compilospecies based on morphology. / Master of Science

Growing on dry saline soils throughout the Intermountain Region of the United States is a group of herbaceous, perennial species of Atriplex, including A. corrugata, A. cuneata, A. cuneata ssp. Introgressa, A. falcata, A. gardneri, A. tridentata, and A. welshii, designated as the Atriplex gardneri complex. Highly adaptive and competitive in the arid salt deserts, these species are valuable as forage for livestock and wildlife. Because of extensive variation present within this complex, considerable taxonomic confusion has resulted. To clarify taxonomic and phylogenetic relationships, selected populations and plants were analyzed morphologically, cytologically, ecologically, phenologically, and genetically. Polyploidy is common within most of the major taxons. The polyploid species show little morphological variation from that of their diploid ancestors. Diploids occupy well drained soils relatively low in salt and grow in isolated pockets; polyploid derivatives are more widely distributed, growing in the lower valley floors characterized by heavy soils of high sodium content.