Browsing by Subject "phylogenetics"

Now showing 1 - 11 of 11
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    A Revision of the Leafhopper Genus Xyphon (Hemiptera: Cicadellidae)
    (2012-02-14) Catanach, Therese A.
    The leafhopper genus Xyphon, included in the sharpshooters, is a widely distributed group of insects whose species are vectors for various plant diseases. Xyphon has historically contained up to 9 species. These species have been poorly delimited in the past and their identification has been difficult using published keys. The genus is revised here based on a new species level phylogenetic assessment that incorporates both morphological and molecular data. The genus Xyphon was erected to contain leafhoppers that possessed a reticulated forewing apex but lacked both a median sulcus on the crown and a carinate anterolateral crown-face margin both of which are present in the closely related genus Draeculacephala. Young (1977) revised most of the genera included in Xyphon's containing subfamily. He did not attempt a revision of Carneocephala (the genus that formerly contained most Xyphon species), but noted the need for a revision of its species. This revision of the genus Xyphon is based on the examination of approximately 8,000 specimens and includes a phylogenetic analysis of the genus that includes data from one gene (NDI) and 47 morphological characters. A generalized model of each preliminary taxonomic unit was used to test the monophyly of each species. These tests resulted in the synonomization of 4 former species: Xyphon gillettei to include X. balli; and X. reticulatum to include X. diductum, X. dyeri, and X. sagittiferum. Parsimony and Bayesian techniques were used to infer relationships among species. These analyses resulted in almost identical tree topologies. In all analyses Xyphon was monophyletic and Draeculacephala was its sister genus although clade support for the genus was generally low. The analyses found that X. flaviceps and X. fulgidum form a basal clade within Xyphon, above which X. gillettei and X. n. sp. 1 (new species 1) form a clade that is sister to a third clade containing X. triguttatum, X. nudum, and X. reticulatum.
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    Algorithms for Searching and Analyzing Sets of Evolutionary Trees
    (2014-04-18) Brammer, Grant
    The evolutionary relationships between organisms are represented as phylogenetic trees. These trees have important implications for understanding biodiversity, tracking disease, and designing medicine. Since the evolutionary process that led to modern biodiversity was not directly recorded, phylogenetic trees are inferred from modern observations. Inferring accurate phylogenies is computationally difficult and many inference algorithms produce multiple phylogenetic trees of equal quality. The common method for presenting a set of trees is to summarize their common features into a single consensus tree. Consensus methods make it easy to tell which features are common to a set of trees, but how do you explore the hypotheses that are not the majority of trees? This question is best answered by a search algorithm. We present algorithms to query a set of trees based on their internal structure. Trees can be queried based on their bipartitions, quartets, clades, subtrees, or taxa, and we present a new concept which unifies edge based relationships for search functions. To extend the power of our search functions we provide the ability to combine the results of multiple searches using set operations. We also explore the differences between sets of trees. Clustering algorithms can detect if there are multiple distinct hypotheses within a set of trees. Decision tree depth and distinguishing bipartitions can be used to measure the similarity between sets of trees. For situations where a set of trees is made up of multiple distinct sets, we present p-support which is a measure to quantify the impact of the individual sets on a single consensus tree. The algorithms are presented within the context of TreeHouse. This is my open source platform for querying and analyzing sets of trees. One goal of TreeHouse was to unite query and analysis algorithms under a single user interface. The seamless interaction between fast filtering and analysis algorithms allows users to the explore their data in a way not easily accomplished elsewhere. We believe that the algorithms in this document and in TreeHouse can shed new light on often unexplored territory.
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    Genetic and Phylogenetic Studies of Toll-Like Receptor 5 (TLR5) in River Buffalo (Bubalus Bubalis)
    (2012-08-21) Jones, Brittany
    River buffalo are economically important to many countries and only recently has their genome been explored for the purpose of mapping genetic variation in traits of economic and biologic interest. The purpose of this research is to characterize the genetic and evolutionary profile of Toll-like receptor 5 (TLR5), which mediates the mammalian innate immune response to bacterial flagellin. This study is comprised of three parts: 1) generating a radiation hybrid (RH) map of river buffalo chromosome 5 (BBU5) where the TLR5 gene is located and building a comparative map with homologous cattle chromosomes; 2) conducting a single-nucleotide polymorphism (SNP) survey of the TLR5 gene to reveal variation within river buffalo and other species; and 3) performing an evolutionary study by inferring phylogenetic trees of TLR5 across multiple taxa and determining the possible evolutionary constraints within the TLR5 coding region. River buffalo chromosome 5 is a bi-armed chromosome with arms corresponding to cattle chromosomes 16 and 29. A BBU5 RH map was developed using the previously published river buffalo RH mapping panel and cattle-derived markers. The RH map developed in this study became an integral part of the first river buffalo whole genome RH map. Genetic variation of the TLR5 gene was evaluated in a small domestic herd of river buffalo. Sequencing of the TLR5 coding region and partial associated 5'- and 3'-untranslated regions yielded 16 novel SNPs. Six SNPs were identified as non-synonymous with one predicted to potentially code for a functionally altered product. For the evolutionary study of the TLR5 coding region, phylogenetic trees were inferred based on TLR5 variation across multiple orders and another for artiodactyla. Species that are closely related to river buffalo appear to have undergone negative selection in TLR5 while those that diverged from river buffalo earlier may be retaining alleles that river buffalo are removing from the population. In conclusion, putative chromosomal rearrangements were identified between river buffalo and cattle, the variation that was uncovered in the TLR5 coding region could potentially lead to differential immunity across species, and there appears be some evolutionary flexibility in the DNA sequence of the TLR5 coding region.
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    Journeys within the Leucophoropterini: Revision of the Tribe, Genera and Species, and Description of New Genera and Species from Australia and the Indo-Pacific
    (2012-07-16) Menard, Katrina Louise
    The tribe Leucophoropterini (Miridae: Phylinae) is a diverse assemblage of primarily Indo-Pacific and Australian bugs which are united by simple, small genitalia and a trend towards ant-mimetic body forms. Previous to this work, the relationship of the Leucophoropterini to the other tribes of Phylinae, as well as the generic relationships within the lineage, was unresolved. Further, the characters initially proposed to unite the tribe are brought into question with the addition of several recently discovered taxa from Australia. The Leucophoropterini is first re-evaluated within a phylogenetic analysis of the subfamily Phylinae, using a combined molecular and morphological dataset to test the monophyly of the lineage, re-test the character synapomorphies supporting it, and to determine the closest relatives to the tribe. The molecular dataset includes 4 genes (COII, 16S, 28S, and 18S), and 123 morphological characters for 104 taxa, which is analyzed in a parsimony analysis using Tree analysis using New Technology [TNT], a model-based analysis in RAxML, and a Bayesian analysis in Mr. Bayes. All three methods resulted in phylogenetic trees with nearly identical generic and tribal groupings, and a lineage containing Pseudophylus Yasunaga, Decomia Poppius and Tuxedo Schuh being sister-group to the Leucophoropterini. With the closest relatives to the Leucophoropterini determined for outgroup selection, a generic revision of the tribe including both Australian and Indo-Pacific taxa is accomplished using 137 morphological characters and is analyzed in an un-weighted and implied weighted parsimony analysis using TNT for 86 leucophoropterine taxa. The Indo-Pacific taxa of Leucophoropterini are found to be related to the Australian Leucophoropterini, and at least two genera within the tribe (Sejanus Distant, Leucophoroptera Poppius) were found to be paraphyletic. Lastly, taxa are revised within the context of the generic-level phylogenetic analysis, with new genera and species from Australia and the Indo-Pacific being described.
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    Molecular and Biochemical Characterization of Hydrocarbon Production in the Green Microalga Botryococcus braunii
    (2012-10-19) Weiss, Taylor Leigh
    Botryococcus braunii (Chlorophyta, Botryococcaceae) is a colony-forming green microalga that produces large amounts of liquid hydrocarbons, which can be converted into transportation fuels. While B. braunii has been well studied for the chemistry of the hydrocarbon production, very little is known about the molecular biology of B. braunii. As such, this study developed both apparatus and techniques to culture B. braunii for use in the genetic and biochemical characterization. During genetic studies, the genome size was determined of a representative strain of each of the three races of B. braunii, A, B, and L, that are distinguished based on the type of hydrocarbon each produces. Flow cytometry analysis indicates that the A race, Yamanaka strain, of B. braunii has a genome size of 166.0 +/- 0.4 Mb, which is similar to the B race, Berkeley strain, with a genome size of 166 +/- 2.2 Mb, while the L race, Songkla Nakarin strain, has a substantially larger genome size at 211.3 +/- 1.7 Mb. Phylogenetic analysis with the nuclear small subunit (18S) rRNA and actin genes were used to classify multiple strains of A, B, and L races. These analyses suggest that the evolutionary relationship between B. braunii races is correlated with the type of liquid hydrocarbon they produce. Biochemical studies of B. braunii primarily focused on the B race, because it uniquely produces large amounts of botryococcenes that can be used as a fuel for internal combustion engines. C30 botryococcene is metabolized by methylation to generate intermediates of C31, C32, C33, and C34. Raman spectroscopy was used to characterize the structure of botryococcenes. The spectral region from 1600?1700 cm^-1 showed v(C=C) stretching bands specific for botryococcenes. Distinct botryococcene Raman bands at 1640 and 1647 cm^-1 were assigned to the stretching of the C=C bond in the botryococcene branch and the exomethylene C=C bonds produced by the methylations, respectively. A Raman band at 1670 cm^-1 was assigned to the backbone C=C bond stretching. Finally, confocal Raman microspectroscopy was used to map the presence and location of methylated botryococcenes within a living colony of B. braunii cells.
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    Molecular epidemiology of West Nile virus in North America
    (2005-09-07) Charles Todd Davis; Alan D.T. Barrett; T. Kley Hughes; Robert S. Lanciotti; Robert B. Tesh; Nigel Bourne
    The introduction of West Nile virus (WNV) into the U.S. during the summer of 1999 led to the largest epidemic of arboviral encephalitis ever recorded in the Western Hemisphere during 2002. Over the course of six years, the distribution of WNV has expanded to include each of the contiguous U.S. states and seven Canadian provinces, as well as Mexico, several Caribbean Islands, and Colombia. In order to understand how the virus has evolved since its emergence in North America, this dissertation investigates the genetic and phenotypic variation among WNV isolates collected in various regions of North America during different transmission seasons. The overall objectives of this dissertation were to study the extent to which WNV has evolved since its emergence in North America and to better understand the relationship between viral evolution and phenotypic variation in an emerging viral population. The first aim of this project was to compare nucleotide and deduced amino acid sequences of WNV isolates collected in North America during 2002, 2003, and 2004 to those collected during earlier years. Sequence comparisons of WNV isolates collected throughout North America during different years have identified nucleotide/amino acid substitutions that reveal the emergence of genetically divergent variants of WNV in recent years and support the hypothesis that microevolution of WNV will continue from year to year and as the distribution of the virus expands. In addition, these studies have identified a dominant genotype of North American WNV that has displaced all other known genotypes throughout North America. This research also led to the discovery of several genetic variants with altered phenotypes. Thus, the second aim of this project investigated the phenotypic characteristics of WNV variants collected in 2003 and 2004 by evaluating their small plaque and temperature-sensitive phenotypes, their multiplication kinetics in cell culture, and attenuation in a mouse model. Finally, reverse genetic techniques were used in a third aim in order to precisely identify the mutations responsible for the observed phenotypic changes in WNV and to illustrate novel molecular mechanisms of attenuation of WNV. The results from these aims demonstrate that as WNV has accumulated mutations in its genome, phenotypic variants have emerged with significantly different biological properties when compared to progenitor virus isolates that initiated the epidemic in North America. Also, this study has identified novel molecular determinants of attenuation in WNV that provide valuable insight into the multigenic components of pathogenicity for WNV and possibly other related flaviviruses.
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    Phylogenetic Toric Varieties on Graphs
    (2010-10-12) Buczynska, Weronika J.
    We define the phylogenetic model of a trivalent graph as a generalization of a binary symmetric model of a trivalent phylogenetic tree. If the underlining graph is a tree, the model has a parametrization that can be expressed in terms of the tree. The model is always a polarized projective toric variety. Equivalently, it is a projective spectrum of a semigroup ring. We describe explicitly the generators of this projective coordinate ring for graphs with at most one cycle. We prove that models of graphs with the same topological invariants are deformation equivalent and share the same Hilbert function. We also provide an algorithm to compute the Hilbert function, which uses the structure of the graph as a sum of elementary ones. Also, this Hilbert function of phylogenetic model of a graph with g cycles is meaningful for the theory of connections on a Riemann surface of genus g.
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    Resolution of Phylogenetic Relationships and Characterization of Y-Linked Microsatellites within the Big Cats, Panthera
    (2010-10-12) Davis, Brian W.
    The pantherine lineage of cats diverged from the remainder of modern Felidae less than 11 million years ago. This clade consists of the five big cats of the genus Panthera, the lion, tiger, jaguar, leopard, and snow leopard, as well as the closely related clouded leopard, which diverged from Panthera approximately 6 million years ago. A significant problem exists with respect to the precise phylogeny of these highly threatened great cats. Within the past four years, despite multiple publications on the subject, no two studies have reconstructed the phylogeny of Panthera with the same topology, showing particular discordance with respect to sister-taxa relationships to the lion and the position of the enigmatic snow leopard. The evolutionary relationship among these cats remains unresolved partially due to their recent and rapid radiation 3-5 million years ago, individual speciation events occurring within less than 1 million years, and probable introgression between lineages following their divergence. We assembled a 47.6 kb dataset using novel and published DNA sequence data from the autosomes, both sex chromosomes and the mitochondrial genome. This dataset was analyzed both as a supermatrix and with respect to individual partitions using maximum likelihood and Bayesian phylogeny inference. Since discord may exist among gene segments in a multilocus dataset due to their unique evolutionary histories, inference was also performed using Bayesian estimation of species trees (BEST) to form a robust consensus topology. Incongruent topologies for autosomal loci indicated phylogenetic signal conflict within the corresponding segments. We resequenced four mitochondrial and three nuclear gene segments used in recent attempts to reconstruct felid phylogeny. The newly generated data was combined with available GenBank sequence data from all published studies to highlight phylogenetic disparities stemming either from the amplification of a mitochondrial to nuclear translocation event, or errors in species identification. We provide an alternative, highly supported interpretation of the evolutionary history of the pantherine lineage using 39 single-copy regions of the felid Y chromosome and supportive phylogenetic evidence from a revised mitochondrial partition. These efforts result in a highly corroborated set of species relationships that open up new avenues for the study of speciation genomics and understanding the historical events surrounding the origin of the members of this lineage.
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    Sylvatic dengue: evolution, emergence, and impact on human health
    (2007-10-24) Nikolaos Vasilakis; Scott C. Weaver; Stanley J. Watowich; Robert B. Tesh; Peter W. Mason; Kathryn A. Hanley; D. Mark Estes
    Dengue viruses (DENV) are the most important arboviral pathogens in tropical and subtropical regions throughout the world. Transmission includes a sylvatic, enzootic cycle between nonhuman primates and arboreal mosquitoes of the genus Aedes, and an urban, endemic/epidemic cycle between Aedes aegypti, a mosquito with larval development in peridomestic water containers, and human reservoir hosts. All 4 serotypes of endemic DENV evolved independently from ancestral sylvatic viruses and have become both ecologically and evolutionarily distinct. The independent evolutionary events that resulted in the emergence of DENV were facilitated by the expansion of DENV progenitors’ host range in Asia to new vectors and hosts that occurred gradually over a period of several hundred years. Emerging viral pathogens often become human pathogens by changing their host range from another vertebrate organism. This study assessed the likelihood of current sylvatic DENV-2 strains to emerge into the human transmission cycle by investigating the factors that facilitate their emergence. My analysis of sylvatic and endemic DENV-2 strains’ ability to replicate in two surrogate human model hosts, determined that adaptation to humans is probably not a necessary component of sylvatic dengue emergence. Then, through an analysis of several sylvatic DENV-2, I demonstrated that both endemic and sylvatic DENV-2 share similar rates of evolutionary change and patterns of natural selection. These findings imply that the potential of future DENV re-emergence from the sylvatic cycle is high. Subsequently, phylogenetic analysis of virus genomes isolated from febrile patients in Nigeria during DENV-2 activity, demonstrated that unrecognized outbreaks of sylvatic DENV-2 in humans are possible. However, their re-emergence into the endemic cycle would be limited by homotypic immunity mediated by virus neutralizing antibodies.
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    Web-Integrated Taxonomy and Systematics of the Parasitic Wasp Family Signiphoridae (Hymenoptera, Chalcidoidea)
    (2014-12-09) Dal Molin, Anamaria
    This work focuses on the taxonomy and systematics of parasitic wasps of the family Signiphoridae (Hymenoptera: Chalcidoidea), a relatively small family of chalcidoid wasps, with 79 described valid species in 4 genera: Signiphora Ashmead, Clytina Erd?s, Chartocerus Motschulsky and Thysanus Walker. A phylogenetic analysis of the internal relationships in Signiphoridae, a discussion of its supra-specific classification based on DNA sequences of the 18S rDNA, 28S rDNA and COI genes, and taxonomic studies on the genera Clytina, Thysanus and Chartocerus are presented. In the phylogenetic analyses, all genera except Clytina were recovered as monophyletic. The classification into subfamilies was not supported. Out of the four currently recognized species groups in Signiphora, only the Signiphora flavopalliata species group was supported. The taxonomic work was conducted using advanced digital imaging, content management systems, having in sight the online delivery of taxonomic information. The evolution of changes in the taxonomic workflow and dissemination of results are reviewed and discussed in light of current bioinformatics. The species of Thysanus and Clytina are revised and redescribed, including documentation of type material. Four new species of Thysanus and one of Clytina are described. The taxonomy of Chartocerus is reviewed, including redescriptions of 25 out of 33 currently valid species, most based on type or topotypical material.