Browsing by Subject "Phylogeny"
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Item Algorithms for the analysis of whole genomes(2004) Wyman, Stacia Kathleen; Kuipers, Benjamin; Jansen, Robert K.With the advent of whole genome sequencing, we now have an abundance of whole genomes which have been sequenced and we have entered an era when algorithms can address problems at the whole genome level. In the past, sequencing efforts often focused on a single gene, and therefore, existing algorithms are at the scale of a single gene. With whole genome sequencing, we have access to sequence data for the entire genome of an organism or an organelle and algorithms are needed for whole genome analysis. In this research, we have addressed new computational problems that have arisen out of the availability and abundance of whole genome data. In genome annotation, all of the genes of a genome are located and identified in preparation for publication of the complete genome sequence. We address the problem of genome annotation with a software package that allows researchers to locate and identify all the genes in a genome and prepare the genome for direct submission to GenBank. A difficult problem that arises in the annotation of organellar genomes is the identification of animal mitochondrial transfer RNA genes. We present an experimental evaluation a set of methods (including our own) for identifying tRNAs. The problem of reconstructing phylogenies from gene order data involves recreating the evolutionary history of a set of organisms based on the order and direction of the genes in the genomes. This can give insight into mechanisms of large-scale evolutionary events. We present a new method for gene order phylogeny reconstruction, as well as improvements to an existing method, and evaluate the results on both real and simulated datasets. Finally, we address the problem of identification of regulatory elements. Understanding gene expression is one of the most pressing unsolved problems in molecular biology today because gene expression controls all of the metabolic and developmental processes in an organism. We present a new method which uses a comparative genomics approach which is made possible now that we have access to the complete DNA sequences of many sets of related organisms.Item Emerging epizootic diseases of amphibians and fish : approaches to understanding Ranavirus emergence and spread(2013-12) Abrams McLean, Audrey Jeanine; Cannatella, David C.; Hillis, David M., 1958-Ranaviruses are large dsDNA viruses that are considered emerging pathogens, and they are known to cause mortality events in amphibian and fish populations. This research utilizes experimental and genomic data to elucidate the mechanisms driving the evolution and spread of ranaviruses, with a focus on host switching within the genus. In Chapter 1, we utilize virus challenge assays to examine potential transfer of ranaviruses between cultured juvenile largemouth bass (M. salmoides) and bullfrog tadpoles (Rana catesbeiana). Additionally, a commonly used antiparasitic treatment containing malachite green and formalin (MGF) was utilized to suppress the immune system of largemouth bass to assess the susceptibility of immunocompromised fish to ranaviruses. The results indicate that tadpoles are not susceptible to Largemouth Bass Virus (LMBV), but that bass are susceptible to ranaviruses isolated from amphibians. Furthermore, immunocompromised fish were more susceptible to both LMBV and FV3 infections than immunocompetent fish. In Chapter 2, we used eight sequenced ranavirus genomes and two selection-detection methods (site-based and branch-based) to identify genes that exhibited signatures of positive selection, potentially due to the selective pressures at play during host switching. We found evidence of positive selection acting on four genes via the site-based method, three of which are newly-acquired genes unique to ranavirus genomes. Our results suggest that the group of newly acquired genes in the ranavirus genome may have undergone recent adaptive changes that have facilitated interspecies and interclass host switching. In Chapter 3, we annotated and analyzed the nearly complete genomic sequence of LMBV to determine its taxonomic classification. The available genomic content and phylogenetic evidence suggests that LMBV is more closely related to amphibian-like ranaviruses (ALRVs) than grouper ranaviruses, and this is further supported by greater genomic collinearity between LMBV and ALRVs. This data suggests that the classification of LMBV as a ranavirus is warranted. The results presented here will help to clarify the taxonomic relationships of ranaviruses, and will also be useful in developing management strategies to limit interspecific and intraspecific viral spread. The information garnered from this research will have far-reaching implications in studies of amphibian conservation, disease evolution, and virology.Item Endohelminths from six rare species of turtles (Bataguridae) from Southeast Asia confiscated by international authorities in Hong Kong, China(Texas A&M University, 2004-09-30) Murray, Rebecca AnnSpecimens of 6 species of threatened, vulnerable, and endangered turtles (Cuora amboinensis, Cyclemys dentata, Heosemys grandis, Orlitia borneensis, Pyxidea mouhotii, and Siebenrockiella crassicollis) belonging to family Bataguridae, were confiscated in Hong Kong, China on 11 December 2001 by international authorities. Endohelminth studies on these turtle species are scarce, and this study provided a rare opportunity to examine a limited number of specimens for endohelminths. Ten different parasite species were collected and there were 16 new host records. This is the first record of a parasite from P. mouhotii. The parasite prevalences found in this study provide a basis for a better understanding of the phylogenetic relationships of the family Bataguridae to other families, especially Testudinidae. Based on known life cycles, parasites found provided an indication of food preferences of these 6 turtle species that support previous studies of the turtles' feeding habits. However, the results of the parasite survey from O. borneensis provided additional feeding habit information. The list of endohelminths herein is intended to provide a foundation for future parasite studies of the 6 species of Asian turtles.Item Estimating phylogenetic trees from discrete morphological data(2015-05) Wright, April Marie; Hillis, David M., 1958-; Cannatella, David C; Jansen, Robert K; Linder, Craig R; Smith, Martha KMorphological characters have a long history of use in the estimation of phylogenetic trees. Datasets consisting of morphological characters are most often analyzed using the maximum parsimony criterion, which seeks to minimize the amount of character change across a phylogenetic tree. When combined with molecular data, characters are often analyzed using model-based methods, such as maximum likelihood or, more commonly, Bayesian estimation. The efficacy of likelihood and Bayesian methods using a common model for estimating topology from discrete morphological characters, the Mk model, is poorly-explored. In Chapter One, I explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, I describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity. I further examine the use of the Mk model in Chapter Two. Like any model, the Mk model makes a number of assumptions. One is that transition between character states are symmetric (i.e., there is an equal probability of changing from state 0 to state 1 and from state 1 to state 0). Many characters, including alleged Dollo characters and extremely labile characters, may not fit this assumption. I tested methods for relaxing this assumption in a Bayesian context. Using empirical datasets, I performed model fitting to demonstrate cases in which modelling asymmetric transitions among characters is preferred. I used simulated datasets to demonstrate that choosing the best-fit model of transition state symmetry can improve model fit and phylogenetic estimation. In my final chapter, I looked at the use of partitions to model datasets more appropriately. Common in molecular studies, partitioning breaks up the dataset into pieces that evolve according to similar mechanisms. These pieces, called partitions, are then modeled separately. This practice has not been widely adopted in morphological studies. I extended the PartitionFinder software, which is used in molecular studies to score different possible partition schemes to find the one which best models the dataset. I used empirical datasets to demonstrate the effects of partitioning datasets on model likelihoods and on the phylogenetic trees estimated from those datasets.Item Evolutionary and ecological influences on color pattern variation in the Australian common froglet, Crinia signifera(2009-08) Symula, Rebecca E.; Cannatella, David C.; Hillis, David M., 1958-Elucidation of mechanisms that generate and maintain population-level phenotypic variability provides insight into processes that influence within-species genetic divergence. Historically, color pattern polymorphisms were used to infer population-level genetic variability, but recent approaches directly capture genetic variability using molecular markers. Here, I clarify the relationship between genetic variability and color pattern polymorphism within and among populations using the Australian common froglet, Crinia signifera. To illustrate genetic variability in C. signifera, I used phylogenetic analysis of mitochondrial DNA and uncovered three ancient geographically restricted lineages whose distributions are consistent with other southeastern Australian species. Additional phylogeographic structure was identified within the three ancient lineages and was consistent with geographic variation in male advertisement calls. Natural selection imposed by predators has been hypothesized to act on black-and-white ventral polymorphisms in C. signifera, specifically through mimicry of another Australian frog, Pseudophryne. I used clay replicas of C. signifera to test whether predators avoid black-and-white coloration. In fact, black-and-white replicas were preferentially avoided by predators in some habitats, but not in others, indicating that differential selection among habitats plays a role in maintaining color pattern polymorphism. When black-and-white color patterns in a sample of C. signifera populations were compared with those in sympatric Pseudophryne, several color pattern characteristics were correlated between the species. Furthermore, where C. signifera and Pseudophryne are sympatric, color patterns are more similar compared to those in allopatry. Extensive phylogenetic variability suggests that phylogenetic history and genetic drift may also influence C. signifera color pattern. Fine-scale phylogenetic analysis uncovered additional genetic diversity within lineages and low levels of introgression among previously identified clades. Measures of color pattern displayed low levels of phylogenetic signal, indicating that relationships among individuals only slightly influence color patterns. Finally, simulations of trait evolution under Brownian motion illustrated that the phylogeny alone cannot generate the pattern of variation observed in C. signifera color pattern. Therefore, this indicates a minimal role for genetic drift, but instead supports either the role of stabilizing selection due to mimicry, or diversifying selection due to habitat differences, in color pattern variation in C. signifera.Item Fast and accurate estimation of large-scale phylogenetic alignments and trees(2011-05) Liu, Kevin Jensen; Linder, C. Randal; Warnow, Tandy, 1955-; Maddison, Wayne; Plaxton, C. Gregory; Press, William H.Phylogenetics is the study of evolutionary relationships. Phylogenetic trees and alignments play important roles in a wide range of biological research, including reconstruction of the Tree of Life - the evolutionary history of all organisms on Earth - and the development of vaccines and antibiotics. Today's phylogenetic studies seek to reconstruct trees and alignments on a greater number and variety of organisms than ever before, primarily due to exponential growth in affordable sequencing and computing power. The importance of phylogenetic trees and alignments motivates the need for methods to reconstruct them accurately and efficiently on large-scale datasets. Traditionally, phylogenetic studies proceed in two phases: first, an alignment is produced from biomolecular sequences with differing lengths, and, second, a tree is produced using the alignment. My dissertation presents the first empirical performance study of leading two-phase methods on datasets with up to hundreds of thousands of sequences. Relatively accurate alignments and trees were obtained using methods with high computational requirements on datasets with a few hundred sequences, but as datasets grew past 1000 sequences and up to tens of thousands of sequences, the set of methods capable of analyzing a dataset diminished and only the methods with the lowest computational requirements and lowest accuracy remained. Alternatively, methods have been developed to simultaneously estimate phylogenetic alignments and trees. Methods optimizing the treelength optimization problem - the most widely-used approach for simultaneous estimation - have not been shown to return more accurate trees and alignments than two-phase approaches. I demonstrate that treelength optimization under a particular class of optimization criteria represents a promising means for inferring accurate trees and alignments. The other methods for simultaneous estimation are not known to support analyses of datasets with a few hundred sequences due to their high computational requirements. The main contribution of my dissertation is SATe, the first fast and accurate method for simultaneous estimation of alignments and trees on datasets with up to several thousand nucleotide sequences. SATe improves upon the alignment and topological accuracy of all existing methods, especially on the most difficult-to-align datasets, while retaining reasonable computational requirements.Item Fossils, phylogeny, and anatomical regions : insights exemplified through turtles(2013-08) Burroughs, Robert Wayne; Bell, Christopher J., 1966-There are more than 300 species of extant turtles, the majority of which belong to the Testudinoidea. Here I describe a new box turtle from the Eocene-Oligocene boundary of west Texas. This specimen impacts the phylogeny of Testudinoid turtles by pulling the divergence of extant Testudinoid turtles back in time approximately 25 million years. This results in a need to refocus on paleontological research of Testudinoid turtles into the late Paleogene and early Neogene to identify fossil localities and specimens that can help further elucidate the evolution of the group. New work on the fossil record of turtles also requires a re-evaluation of methods used for identifying and evaluating the evolutionary history of turtles as a group. An implicit assumption over the last 150 years of turtle paleontology was that both turtle shells and turtle heads reveal congruent and complimentary evolutionary relationships. This assumption was never adequately tested. I utilized a series of methods to evaluate the congruency of phylogenetic hypotheses using disparate anatomical regions. Using a dataset of extant Emydid turtles, I evaluated whether turtle shells and turtle heads provided congruent and complimentary phylogenetic hypotheses. My methods employed parsimony-based reconstruction, maximum-likelihood-based reconstruction, and Bayesian-based reconstruction, including Bayesian-partition analyses. My conclusions are that heads and shells do not provide fully congruent topologies, and that in many cases there is a loss of phylogenetic resolution when only turtle sklls are used to generate phylogenies. The implication is that a focus on a robust and complete dataset of anatomical features will provide the best basis for further investigation of fossils. My work also provides a framework for dataset exploration by providing a method to identify the most robust phylogenetic signal found within a dataset. This framework will allow non-turtle paleontologists and systematists the ability to further investigate their own datasets and develop robust hypotheses of evolutionary relationships across the diversity of the tree of Life.Item Genome organization, mobile DNA, and chromosomal evolution in mammals(Texas Tech University, 2003-05) Parish, Deidre ArthurNot availableItem The implementation of phylogenetic structural equation modeling for biological data from variance-covariance matrices, phylogenies, and comparative analyses(2009-12) Santos, Juan Carlos; Wilke, Claus O.; Bryant, JamesOne statistical approach with a long history in the social sciences is a multivariate method called Structural Equation Modeling (SEM). The development of SEM followed the evolution of factor and path analyses, multiple regression analysis and MACOVA. One of the key innovations of factor analysis and SEM is that they group a set of multivariate statistical approaches that condense variability among a set of variables in fewer latent (unobserved) factors. Most biological systems are multivariate, which are not easily dissected into their component parts. However, most biologists use only univariate statistical methods, which have definitive limitations in accounting for more than a few variables simultaneously. Therefore, the implementation of methodologies like SEM into biological research is necessary. However, SEM cannot be applied directly to most biological datasets or generalized across species because of the hierarchical pattern of evolutionary history (i.e., phylogenetic non-independence or signal). This report includes the theoretical grounds for the development of Phylogenetic SEM in preparation of the development of utilitarian algorithms. I have divided this report in six parts: (1) a brief introduction to factor analysis and SEM from historical perspective and a brief description of its utility; (2) a summary of the implications of using biological data and the underlying hierarchical structure due to shared common ancestry or phylogeny; (3) a summary of the two most common comparative methods to incorporate the phylogeny in univariate analyses (i.e., phylogenetic independent contrasts and phylogenetic generalized least squares); (4) I describe how some intermediate output from both comparative methods can be used to estimate the variance–covariance matrix that has been corrected for phylogenetic signal; (5) I describe how to perform a exploratory factor analysis, specifically principal component analysis, with the corrected variance–covariance matrix; and (6) I describe the development of the phylogenetic confirmatory factor analysis and phylogenetic SEM. I hope that this report encourages other researchers to develop adequate multivariate analysis that incorporate the evolutionary principles in its analyses.Item The molecular phylogeny of Pectis L. (Tageteae, Asteraceae), with implications for taxonomy, biogeography, and the evolution of C4 photosynthesis(2012-05) Hansen, Debra Rae; Jansen, Robert K., 1954-; Simpson, Beryl BrintnallThis study examines the evolutionary history of Pectis L., a neotropical genus of ~90 species of xeric-adapted, herbaceous, annuals and perennials. Pectis is rare among the Asteraceae, as it uses C₄ photosynthesis, a complex suite of traits that concentrates carbon around Rubisco. Plants with C₄ photosynthesis do well in environments of high light and high heat, and the C₄ syndrome is thought to have evolved as a response to such environments. Pectis is most diverse in Mexico, the Caribbean Islands, and South America, and its distribution mirrors the disjunctions of patches of desert, thornscrub, coastal plains, savanna, and openings in seasonally-dry tropical forests and oak-pine woodlands. Vicariance and long-distance dispersal theories can explain the patchy distribution of xeric-adapted plants, as well as the origin of Caribbean species. To answer evolutionary questions about a group, one must understand how its members are related. The most comprehensive taxonomic treatment of Pectis is over 100 years old, and includes only North American species. Recent revisions still leave half the species unassigned to section. Molecular studies have found Pectis sister to, or encompassing, the genus Porophyllum. To infer evolutionary relationships between and within Pectis and Porophyllum, DNA from the nuclear and chloroplast genomes of 78 Pectis and 22 Porophyllum species were sampled, sequenced, and analyzed. The molecular phylogeny was used to suggest updated sections based on monophyletic groups. To infer the photosynthetic pathway of Pectis and Porophyllum species, carbon isotope ratios were obtained from 62 Pectis and 18 Porophyllum species. The timing and location of the evolution of Pectis and Porophyllum has implications for the evolution of C₄ photosynthesis. The carbon isotope data were combined with the phylogeny to determine the extent and direction of the evolution of C₄ photosynthesis, and the timing of its evolution was inferred from a fossil-calibrated analysis using chloroplast data from species across the Asteraceae. Distribution data was combined with the Pectis phylogeny to answer questions regarding the biogeographical history of Pectis, including questions regarding its disjuncted distribution, the timing of the evolution of desert species, and the timing and pattern of dispersal to and from the Caribbean Islands.Item Molecular systematics and the origins of gypsophily in Nama L. (Boraginaceae)(2012-05) Taylor, Sarah Elizabeth; Simpson, Beryl Brintnall; Jansen, Robert K.; Levin, Donald A.; Panero, Jose L.; Mueller, Ulrich G.Nama L. is a genus of approximately 50 species of herbs and subshrubs that occurs in habitats ranging from arid deserts to mesic woodlands in the New World and the Hawaiian Islands. The group has historically been divided into five or six subgeneric groups based on habitat as well as on the morphology of the anthers, styles, leaves and seeds. At least 14 species of Nama from the Chihuahuan Desert Region are either facultatively or obligately endemic to gypsum deposits. This dissertation examines interspecies relationships within Nama from a molecular phylogenetic perspective in order to evaluate historic morphology-based subgeneric classification systems of the genus and to examine the origins of facultative and obligate gypsophily within the genus. DNA sequence data from the chloroplast regions matK and ndhF and from the nuclear ribosomal region ITS were collected from 46 species of Nama as well as from four new species and several outgroups. Data were analyzed using maximum likelihood and Bayesian methods. Phylogenetic analyses recover seven strongly supported major lineages within Nama. These lineages do not correspond to traditionally recognized subgenera, although they are largely congruent with an informal system based on ultrastructural observations of seeds. Four of the seven major lineages include gypsophilous species; these range from two lineages that include a single facultative gypsophile each, to one lineage that is almost entirely comprised of gypsophiles. Gypsum endemism in general, as well as facultative and obligate gypsophily in particular, has arisen multiple times in Nama. Parametric bootstrapping rejected the hypothetical monophyly of gypsophiles across the genus as a whole and within each of the two clades that contain multiple gypsophiles. Because approximately 20 species have been described since the last major revision of Nama nearly 80 years ago, detailed morphological observations of herbarium specimens were made in order to produce a comprehensive key to the species of Nama as well as the revision of a lineage comprising eight gypsophiles and one limestone endemic.Item Molecular systematics of neotomine-peromyscine rodents based on nuclear DNA sequences(Texas Tech University, 2003-05) Reeder, Serena AnnNot availableItem Observations on the osteology of scutellosaurus lawleri Colbert, 1981 (Ornithischia: Thyreophora) on the basis on new specimens from the Lower Jurassic Kayenta Formation of Arizona(2016-05) Breeden, Benjamin Thomas, III; Rowe, Timothy, 1953-; Bell, Christopher J; Martindale, Rowan CScutellosaurus lawleri is a basal thyreophoran dinosaur from the Lower Jurassic Kayenta Formation, and it is the most abundantly known ornithischian dinosaur from the Lower Jurassic of North America. Despite its abundance in the fossil record, certain aspects of its anatomy have remained poorly understood due to the incomplete nature of the holotype, paratype, and referred specimens. I report here nearly 30 new specimens of Scutellosaurus lawleri collected along the Adeii Eechii Cliffs of northern Arizona between 1997 and 2000 by field parties from The University of Texas at Austin. Among this new material are two disarticulated associated skeletons, each preserving anatomy that is poorly known or not previously reported for the taxon, including the nasal, maxilla, lacrimal, postorbital, quadratojugal, squamosal, opisthotic, scapula, and ilium. These specimens have both been compressed taphonomically, making their removal from the surrounding matrix in their field jackets difficult without risk of damage to the fossil bone, so the specimens were CT scanned to aid with preparation. A phylogenetic analysis supports the position of Scutellosaurus lawleri as the basalmost member of Thyreophora. New autapomorphies identified include six premaxillary teeth, narrow and elongate frontals, a humerus substantially longer than the scapula, and neural spines of the proximal caudal vertebrae that are greater than 50% taller than the centra.Item Phylogenetic analysis of tribe habrolepidini and revision of Homalopoda and Ceraptroceroideus (Hymenoptera: Encyrtidae)(Texas A&M University, 2006-04-12) Rodriguez Velez, BeatrizA taxonomic and phylogenetic study of the tribe Habrolepidini is described. A cladistic analysis was carried out in order to establish the phylogenetic relationships of the supraspecific taxa of the tribe. An illustrated key for the identification at the level of genera is included. Based on the results of the phylogenetic analysis, the diagnosis and taxonomic descriptions of the recognized taxa are presented. A single most parsimonius parsimony tree was obtained from the cladistic analysis based on 67 morphological characters, generated by a two-step procedure using PAUP. Initially, heuristic searches considering all characters with equal weights resulted in three equally parsimonious trees. Then the method of successive approximation weighting was applied to the three trees. The values of statistic parameters of the most parsimonious tree are: length = 582 steps; consistency index = 0.4966, retention index = 0.5850. The results support the hypothesis that the tribe Habrolepidini is monophyletic. It is defined by the presence of a specialized ventral mandibular tooth that is formed through modification of a seta into a stout socketed spine and three more unambiguous characters, clava length from 2.57 to 3.28, small hexagonal sculpture of scutellum and sensilla in three circles in a straight line. The inclusion of the genera Anthemus, Arrenophagoidea, Arrenophagus, Thomsonisca and Zaomma into Habrolepidini is supported by the presence of the mandibular tooth or by sister group relationships to other taxa with the mandibular tooth. The revision of the genera Ceraptroceroideus and Homalopoda is included; the taxonomic revision of each genus includes a key, diagnosis, descriptions and illustrations for all the species.Item Phylogenetic and ecological significance of the variation in the scleral ring of aquatic forging birds(2014-12) Browne, Katharine Elizabeth; Clarke, Julia A.; Bell, Chris; Kirk, Chris; Schmitz, LarsSDiving birds must accommodate their vision to air and water, two very different optical media. A few species, such as penguins (Sphenisciformes), dive to depths approaching the aphotic zone of the ocean and must accommodate their vision to both the change in media and significant light attenuation. Previous studies show that optical properties of the eye e.g., pupil aperture and focal length, are reflected in the eye’s gross morphology and have a strong positive correlation with osteological proxies from the orbit and scleral ring. This study combines qualitative and quantitative measurements utilized in previous studies to create a larger feature space for classification. A total of 170 species were evaluated for distinct classes of eye shape, 87 of which were newly measured species of Charadriiformes, Procellariiformes, "Pelecaniformes", and Sphenisciformes. Unlike in previous studies of land birds, no pattern was recovered in eye shape based on the light levels where the birds foraged. Aquatic birds are active in a wide range of conditions; foraging both day and night and at varying water depths based on the time of year and available prey. Diverse aquatic bird ecology probably contributes to the lack of distinct eye shape classes based on dive depth. Regression analysis was able to recover prey capture style (i.e., plunge, pursuit, skimming, or wading) based on orbit and scleral ring measurements. Misclassification was most common in taxa that exhibited multiple modes of prey capture such as the albatross (Diomedeidae). The ability to determine foraging style based on osteological eye measurements may have implications for identifying prey capture method in extinct species of aquatic birds.Item Phylogenetic relationships of the Old World nectar-feeding bats (Pteropodidae, Macroglossinae) based on features of the female reproductive tract(Texas Tech University, 1986-05) Hood, Craig SNot availableItem Phylogenetic systematics of the canal raphe bearing orders Surirellales and Rhopalodiales (Bacillariophyta)(2010-08) Ruck, Elizabeth Clare; Theriot, Edward C.(Edward Claiborne), 1953-; Jansen, Robert K.; Simpson, Beryl B.; Cannatella, David C.; La Claire, John W.The class Bacillariophyceae, encompasses all diatoms that possess a raphe. Members of the orders Bacillariales, Rhopalodiales and Surirellales have a canal raphe system. Historically, the possession of this character was considered support for a close evolutionary relationship. To investigate phylogenetic relationships, a three gene dataset was constructed for 49 strains representing 9 of the 11 orders within the Bacillariophyceae. We provide the first formal tests of homology of the canal raphe system and the first demonstration that the Rhopalodiales are nested within the Surirellales. Results strongly reject the monophyly of Bacillariales, Rhopalodiales, and Surirellales thereby discounting the canal raphe as a homologous character. The Surirellales include three families: Surirellaceae, Entomoneideaceae, and Auriculaceae, while Rhopalodiales has only three genera in one family, the Rhopalodiaceae. In order to test familial and generic concepts, I expanded taxon representation and collected DNA sequence data for 125 strains. Taken together, only 5 of the 12 genera (Entomoneis, Stenopterobia, Cymatopleura, Petrodictyon and Epithemia) were found to be monophyletic. Our current concepts of the two most species-rich genera, Surirella and Campylodiscus, are too broad as the analyses resolved taxa from these two genera into multiple independent lineages. The “Robustoid” lineage, comprised of Surirella Robustae, Campylodiscus Robusti, and Stenopterobia, exhibits a high degree of endemism within ancient Lake Ohrid, with 17 species considered endemic or relict taxa. A dataset of three molecular markers and 71 Robustoid taxa from Lake Ohrid, Europe, and North America was used to construct a preliminary phylogeny. The aim was to investigate phylogenetic relationships and test hypotheses of speciation and morphological evolution. The recovered paraphyly of Lake Ohrid taxa eliminates the possibility that the Ohrid Robustoids as a whole are a product of intralacustrine speciation. However, sister relationships between putative Ohrid endemics and unexplored morphological diversity within some species complexes (e.g. Campylodiscus marginatus, Scoliodiscus spp.) leave open the possibility that these lineages may be the result of intralacustrine speciation.Item Phylogeny and evolutionary ecology of thalassiosiroid diatoms(2006-08) Alverson, Andrew James; Theriot, Edward C. (Edward Claiborne), 1953-Salinity is a significant barrier to the distribution of diatoms, and though it is generally understood that diatoms are ancestrally marine, the number of times diatoms independently colonized fresh waters and the adaptations that facilitated these colonizations remain outstanding questions in diatom evolution. Resolving the exact number of freshwater colonizations will require large-scale phylogenetic reconstruction with dense sampling of marine and freshwater taxa. A more tractable approach to understanding the marine--freshwater barrier is to study a group of diatoms with high diversity in each habitat. The "centric" diatom order Thalassiosirales affords an excellent opportunity to study the origin and evolution of diatoms in fresh waters. Thalassiosirales is a well-supported monophyletic group common in marine, brackish, and freshwater habitats. Thalassiosirales species historically are classified into the marine Thalassiosiraceae or freshwater Stephanodiscaceae, reflecting the more generally held hypothesis that diatoms are naturally split along marine--freshwater lines. The fossil record suggests that Stephanodiscaceae traces to a single colonization of freshwater in the mid-Miocene, and in addition, Stephanodiscaceae species share a suite of complex cell wall characters, which has been interpreted as corroborating evidence for their monophyly. I reconstructed the phylogeny of Thalassiosirales and used the phylogeny to test these and other hypotheses and to address a number of other problems related to the marine--freshwater boundary in diatoms. Phylogenetic analyses showed strong evidence for multiple colonizations of freshwater and reject all previous colonization hypotheses. Results further show that part of Stephanodiscaceae is an early diverging lineage within Thalassiosirales, indicating that these two distantly related and separately derived Stephanodiscaceae lineages independently evolved a similar set of complex morphological features upon or shortly after the colonization of fresh waters. Finally, marine and freshwater diatoms, including Thalassiosirales, show several important differences in silicon physiology. In addition to containing an order of magnitude more silica in their cell walls, freshwater diatoms have a drastically lower enzymatic affinity for silicic acid, the dissolved form of silica used by diatoms. I sequenced the silicon transporter genes from marine and freshwater Thalassiosirales and show that physiological differences are not due to differences in the coding sequence.Item Phylogeny and floral host relationships of Callandrena (Hymenoptera : Andrenidae : Andrena)(2002-05) Larkin, Leah laPerle; Simpson, Beryl BrintnallCallandrena, a subgenus of 80 described species of bees in the genus Andrena (Hymenoptera: Andrenidae) is shown, via phylogenetic analysis of both mitochondrial and nuclear DNA sequence data, to be polyphyletic. The characters previously uniting this group have likely arisen by convergent evolution among unrelated lineages that have independently specialized on flowers of the Asteraceae for pollen consumption. At this time, we cannot definitively state whether there are two or three clades of bees formerly ascribed to Callandrena, nor whether one clade may belong to the European subgenus Chrysandrena as has been proposed, so we do not erect a new subgenus of Andrena at this time. The limits of Callandrena sensu stricto are provisionally delimited based on a single morphological character. The phylogenetic relationships of the two groups relative to other Andrena subgenera are discussed in Chapter 2. In Chapter 3, Clade B, as defined for Callandrena in Chapter 2, is used to investigate the evolution of pollen host choice. Diet breadth is determined by analysis of pollen loads of at least 20 individual females per species. The choice of host and degree of specificity are then mapped onto the molecular phylogeny to investigate the evolution of these traits. Oligolecty appears to be the ancestral state in Andrena; polylecty has evolved several times; and reversals to oligolecty within these lineages have also occurred. Within the oligolectic lineage studied, host shifts were not uncommon. During the course of this study, a number of undescribed species were collected. Five are described in Chapter 4.Item Phylogeny of the genus Gossypium and genome origin of its polyploid species inferred from variation in nuclear repetitive DNA sequences(Texas A&M University, 2006-04-12) Rong, YingKnowledge of phylogenetic relationships among taxa is essential for comparative and evolutionary genomic research. Here, we report reconstruction of the phylogenetic tree of the genus Gossypium containing cultivated cottons of importance in agriculture by using variation of nuclear repetitive DNA sequences. Genomic DNA was isolated from 87 available accessions of 35 species representing all eight basic genome groups of the genus Gossypium and analyzed to infer phylogeny of the genus and genome origin of its polyploid species. Twenty-two interspersed repeated sequence clones derived from G. hirsutum, each representing a repeated sequence family, were hybridized to the genomic DNA of the 35 species, respectively. Southern hybridization showed that 15 of the repetitive DNA sequences could be detected in all of the eight diploid genome groups, five were A genome-specific, and two were detected in some of the non D-genome groups. A total of 642 major restriction bands of repeated sequences were used for phylogenetic analysis of the species. A phylogenetic tree of the species was constructed, based on the parsimony method and evaluated by the bootstrap approach. The tree was consistent with those previously constructed with different methods in major clades in which the genealogical lineages of species are largely congruent with genome designations and geographical distribution; but significantly different branching among some of the species was observed. These results not only further confirm the previously phylogenetic analysis of the species and the utility of repetitive DNA sequences for phylogenetic analysis of the genus Gossypium, but also provide new insights into the phylogeny of the genus.