tRNA genes have the fundamental role of translating the genetic code during protein synthesis. Beyond solely a passive decoding role, the tRNA pool exerts selection pressures on the codon usage of organisms and the viruses that infect them because processing codons read by rare tRNAs can be slow or even erroneous. To better understand the interactions of codons and anticodons in eukaryotic species, we first investigated whether tRNAs packaged into HIV-1 particles may relate to the poor codon usage of HIV-1 genes. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding poorly adapted codons are overrepresented in HIV-1 virions. Because the affinity of Gag-Pol for all tRNAs is non-specific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Moreover, differences that we found in the codon usage between early and late genes suggest alterations in the tRNA pool are induced late in viral infection. Next, we tested whether a reduced tRNA anticodon pattern, which was called into question by predicted tRNA datasets, is maintained across eukaryotes. tRNA prediction methods are prone to falsely identifying tRNA-derived repetitive sequences as functional tRNA genes. Thus, we proposed and tested a novel approach to identify falsely predicted tRNA genes using phylogenetics. Phylogenetic analysis removed nearly all the genes deviating from the anticodon pattern, therefore the anticodon pattern is reaffirmed across eukaryotes.

Gymnotus, the banded electric knifefish, is a diverse genus with a range that extends from Argentina to southern Mexico and includes species distributed both east (cis-Andean) and west (trans-Andean) of the Andes. Each Gymnotus species exhibits a distinctive electric organ discharge (EOD), used for communication and navigation. Here, I present a new molecular phylogenetic hypothesis for 35 Gymnotus species based on two mitochondrial (cyt b and 16S) and two nuclear genes (RAG2 and Zic1). I found that the trans-Andean species are distributed in four distinct lineages with varying amounts of divergence from their closest cis-Andean sister taxa. I suggest that not all trans-Andean species evolved as a result of the orogeny of the Andes. I evaluate EOD phase number evolution in Gymnotus and find a trend for reduced phase numbers in both cis- and trans-Andean regions. Finally, I suggest hypotheses to account for the patterns of EOD phase number diversification.

Gymnotus, the banded electric knifefish, is a diverse genus with a range that extends from Argentina to southern Mexico and includes species distributed both east (cis-Andean) and west (trans-Andean) of the Andes. Each Gymnotus species exhibits a distinctive electric organ discharge (EOD), used for communication and navigation. Here, I present a new molecular phylogenetic hypothesis for 35 Gymnotus species based on two mitochondrial (cyt b and 16S) and two nuclear genes (RAG2 and Zic1). I found that the trans-Andean species are distributed in four distinct lineages with varying amounts of divergence from their closest cis-Andean sister taxa. I suggest that not all trans-Andean species evolved as a result of the orogeny of the Andes. I evaluate EOD phase number evolution in Gymnotus and find a trend for reduced phase numbers in both cis- and trans-Andean regions. Finally, I suggest hypotheses to account for the patterns of EOD phase number diversification.

CD109 is a 170kD glycosylphosphatidylinositol-anchored protein expressed on subsets of fetal and adult CD34+ haematopoietic stem cells, endothelial cells, activated T cells, and activated platelets. Cloning of the CD109 cDNA by our group identified the molecule as a novel member of the alpha2M/C3/C4/C5 family of thioester containing proteins. Curiously, CD109 bears features of both the alpha2M and complement branches of the gene family. Additionally CD109 carries the antigenic determinant of the Gov alloantigen system, which has been implicated in a subset of immune mediated platelet destruction syndromes. In this thesis, the status of CD109 in the evolution and phylogeny of the A2M family has been clarified. First, I elucidated the evolutionary relationships of CD109, and of the other eight human A2M/C3/C4/C5 proteins, using sequence analysis and a detailed comparison of the organization of the corresponding loci. Extension of this analysis to compare CD109 to related sequences extending back to placazoans, defined CD109 as a member of a distinct and archaic branch of the A2M phylogenetic tree. Second, in conjunction with collaborators, the molecular basis of the Gov alloantigen system was identified as an allele specific A2108C; Y703S polymorphism. Utilizing cDNA and genomic sequence we then developed methods to accurately and precisely genotype the Gov system. Finally, the expression kinetics of platelet CD109 was elucidated, in order to obtain basic information regarding its expression and subcellular localization, and to resolve discrepancies in reported platelet CD109 expression. Quantitative flow cytometry demonstrated that CD109 was expressed on the surface of activated platelets at very low levels in most healthy volunteers. In resting platelets, CD109 was localized to the OCS and intracellular storage granules. CD109 displayed differential agonist induced expression in comparison to GPIIb/IIIa epitope unmasking, and surface expression of CD62P and CD63. CD109 was rapidly expressed on the cell surface in response to low doses of both strong and weak agonists. This early expression is likely the result of CD109’s proximity to the plasma membrane in resting platelets. As such, CD109 is positioned to participate at early stages of primary haemostasis.

CD109 is a 170kD glycosylphosphatidylinositol-anchored protein expressed on subsets of fetal and adult CD34+ haematopoietic stem cells, endothelial cells, activated T cells, and activated platelets. Cloning of the CD109 cDNA by our group identified the molecule as a novel member of the alpha2M/C3/C4/C5 family of thioester containing proteins. Curiously, CD109 bears features of both the alpha2M and complement branches of the gene family. Additionally CD109 carries the antigenic determinant of the Gov alloantigen system, which has been implicated in a subset of immune mediated platelet destruction syndromes. In this thesis, the status of CD109 in the evolution and phylogeny of the A2M family has been clarified. First, I elucidated the evolutionary relationships of CD109, and of the other eight human A2M/C3/C4/C5 proteins, using sequence analysis and a detailed comparison of the organization of the corresponding loci. Extension of this analysis to compare CD109 to related sequences extending back to placazoans, defined CD109 as a member of a distinct and archaic branch of the A2M phylogenetic tree. Second, in conjunction with collaborators, the molecular basis of the Gov alloantigen system was identified as an allele specific A2108C; Y703S polymorphism. Utilizing cDNA and genomic sequence we then developed methods to accurately and precisely genotype the Gov system. Finally, the expression kinetics of platelet CD109 was elucidated, in order to obtain basic information regarding its expression and subcellular localization, and to resolve discrepancies in reported platelet CD109 expression. Quantitative flow cytometry demonstrated that CD109 was expressed on the surface of activated platelets at very low levels in most healthy volunteers. In resting platelets, CD109 was localized to the OCS and intracellular storage granules. CD109 displayed differential agonist induced expression in comparison to GPIIb/IIIa epitope unmasking, and surface expression of CD62P and CD63. CD109 was rapidly expressed on the cell surface in response to low doses of both strong and weak agonists. This early expression is likely the result of CD109’s proximity to the plasma membrane in resting platelets. As such, CD109 is positioned to participate at early stages of primary haemostasis.

tRNA genes have the fundamental role of translating the genetic code during protein synthesis. Beyond solely a passive decoding role, the tRNA pool exerts selection pressures on the codon usage of organisms and the viruses that infect them because processing codons read by rare tRNAs can be slow or even erroneous. To better understand the interactions of codons and anticodons in eukaryotic species, we first investigated whether tRNAs packaged into HIV-1 particles may relate to the poor codon usage of HIV-1 genes. By comparing the codon usage of HIV-1 genes with that of its human host, we found that tRNAs decoding poorly adapted codons are overrepresented in HIV-1 virions. Because the affinity of Gag-Pol for all tRNAs is non-specific, HIV packaging is most likely passive and reflects the tRNA pool at the time of viral particle formation. Moreover, differences that we found in the codon usage between early and late genes suggest alterations in the tRNA pool are induced late in viral infection. Next, we tested whether a reduced tRNA anticodon pattern, which was called into question by predicted tRNA datasets, is maintained across eukaryotes. tRNA prediction methods are prone to falsely identifying tRNA-derived repetitive sequences as functional tRNA genes. Thus, we proposed and tested a novel approach to identify falsely predicted tRNA genes using phylogenetics. Phylogenetic analysis removed nearly all the genes deviating from the anticodon pattern, therefore the anticodon pattern is reaffirmed across eukaryotes.

In this thesis we present a novel algorithm, <I>HyperCleaning*</I>, for effectively inferring phylogenetic trees. The method is based on the quartet method paradigm and is guaranteed to recover the best supported edges of the underlying phylogeny based on the witness quartet set. This is performed efficiently using a collapsing mechanism that employs memory/time tradeoff to ensure no loss of information. This enables <I>HyperCleaning*</I> to solve the relaxed version of the Maximum-Quartet-Consistency problem feasibly, thus providing a valuable tool for inferring phylogenies using quartet based analysis.

In this thesis we present a novel algorithm, <I>HyperCleaning*</I>, for effectively inferring phylogenetic trees. The method is based on the quartet method paradigm and is guaranteed to recover the best supported edges of the underlying phylogeny based on the witness quartet set. This is performed efficiently using a collapsing mechanism that employs memory/time tradeoff to ensure no loss of information. This enables <I>HyperCleaning*</I> to solve the relaxed version of the Maximum-Quartet-Consistency problem feasibly, thus providing a valuable tool for inferring phylogenies using quartet based analysis.

The Rhodophyta (red algae) are an ancient crown group of the Eukarya (ca. 1400-1500 million years), comprised of 5000 - 6000 species. Gametophytes of taxa excluding the speciose Class Florideophyceae are typically of very simple unicellular, filamentous or foliose morphologies. These simple morphologies are often homoplasious (resulting from convergent or parallel evolution) and can be indistinguishable among distinct taxa, leading to cryptic species. As a result, historical morphology-based taxonomy is often not congruent with evolutionary history. Intraspecific genetic variation is not yet characterized for non-Florideophyceae taxa. Here the intraspecific genetic variation was characterized for a locally endemic, morphologically distinct bangiophyte red alga, Bangia maxima Gardner using inter simple sequence repeat (ISSR) patterns from 91 individual filaments across seven local populations. A high degree of genetic variation was observed over very small distances (< 25 cm) and very little genetic exchange was observed between populations. It is possible that B. maxima is a true endemic species and its population dynamics may differ from other Bangia species. Metrics of sequence-based identification rely on genetic divergence among isolates to distinguish taxonomic units independent of morphology. Such metrics are especially useful for morphologically simple or cryptic species. The mitochondrial cytochrome oxidase c subunit 1 gene has been proposed for the Florideophyceae. An evaluation of this gene as a metric for non-Florideophyceae taxa was undertaken and limited utility was demonstrated in most lineages of Rhodophyta due to poor or inconsistent amplification and conflicts with nuclear and plastid phylogenies. Patterns of genetic divergence among taxa are used to infer evolutionary relationships. The nuclear ribosomal small subunit (nSSU rRNA) is the taxonomically broadest pool of gene sequence data for the Rhodophyta. The use of stochastic models of nucleotide evolution is the most common approach to inferring phylogenies using this gene, ignoring much of its evolutionary information as different characters that contribute to secondary structure (e.g. paired nucleotides) are treated independently. The incorporation of structural information leads to more biologically realistic evolutionary models increasing phylogenetic resolution. Parametric models incorporating structural information were used here to more fully resolve phylogenies for all known Rhodophyta lineages. Novel phylogenetic topologies were observed and well supported for each Class within the Rhodophyta resulting in a number of formally proposed or suggested taxonomic revisions. These include phylogenetic resolution of Rhodophyta Classes, support for the introduction of 11 genera within the Bangiales and support for various taxonomic revisions within the Florideophyceae previously proposed but not yet fully adopted. As structure evolves more slowly than its constituent sequence, secondary structure elements can further resolve evolutionary relationships, especially in lineages as old as the Rhodophyta. A novel encoding of secondary structure elements and subsequent multivariate analysis was performed for all known Rhodophyta nSSU rRNA gene sequences, reinforcing phylogenetic results. Computer programs developed for these analyses are publicly available. The analyses presented here significantly advanced understanding of the evolutionary distribution of cryptic species within the Rhodophyta. Furthermore, useful methods for the characterization of such species are presented, as is a demonstration of the utility of biologically realistic sequence models parameterizing nSSU rRNA structure in resolving ambiguous phylogenetic relationships. Most importantly, this work also represents a significant improvement toward taxonomy congruent with evolutionary history for the Rhodophyta.

Invasive species are capable of causing considerable damage to natural ecosystems, agricultures and economies throughout the world. These invasive species must be identified and adequate control measures should be investigated to prevent and reduce the negative effects associated with exotic species. A recent introduction of an exotic ant, Paratrechina sp. nr. pubens, has caused tremendous economic and ecological damage to southern Texas. Morphometric and phylogenetic procedures were used to identify this pest ant, P. sp. nr. pubens, to Southern Texas. The populations in Texas were found to be slightly different but not discriminating from P. pubens populations described in previous literature. Analysis of the distribution and expansion of P. sp. nr. pubens found numerous geographically discrete populations and moderately expanding territories. These expansion rates were determined to be ~20 and ~30 m per mo for a neighborhood and industrial area, respectively. Several laboratory and field control strategies were implemented for control of this intensely pestiferous species. Dinotefuran exhibited high laboratory efficacy against P. sp. nr. pubens, while treatments using novaluron were inconclusive. The use of expanded-use Termidor� demonstrated trends in these data that suggest it as the treatment of choice. Other field treatments, such as Termidor and Top Choice�, Termidor and Advance Carpenter Ant BaitTM, and Transport� and Talstar� G, did not attain the success found in the expanded-use Termidor treatment. Most treatments examined were determined ineffective against high populations of P. sp. nr. pubens. Additional and more intensive population management regimes should be investigated. Abating further P. sp. nr. pubens population proliferation to other regions will only be realized from additional control research supplemented with state and federal interdiction policies.