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Title: The use of chitin synthase gene sequences to study the phylogeny of the oomycete pathogen Pythium insidiosum
Creator: Lin, Chia-Ju
Date: 2005
Collection: Electronic Theses & Dissertations

Title: Phylogeny of North American Aphaenogaster species (Hymenoptera: Formicidae) reconstructed with morphological and DNA data
Creator: DeMarco, Bernice Bacon
Date: 2015
Collection: Electronic Theses & Dissertations
Description: The ant genus Aphaenogaster Mayr is an ecologically diverse group that is common throughout much of North America. Aphaenogaster has a complicated taxonomic history due to variability of taxonomic characters. Novomessor Emery was previously synonymized with Aphaenogaster, which was justified by the partial mesonotal suture observed in A. ensifera Forel. Previous studies using Bayesian phylogenies with molecular data suggest Aphaenogaster is polyphyletic. Convergent evolution and retention of...
Show moreThe ant genus Aphaenogaster Mayr is an ecologically diverse group that is common throughout much of North America. Aphaenogaster has a complicated taxonomic history due to variability of taxonomic characters. Novomessor Emery was previously synonymized with Aphaenogaster, which was justified by the partial mesonotal suture observed in A. ensifera Forel. Previous studies using Bayesian phylogenies with molecular data suggest Aphaenogaster is polyphyletic. Convergent evolution and retention of ancestral similarities are two major factors contributing to non-monophyly of Aphaenogaster. Based on 42 multi-state morphological characters and five genes, we found Novomessor more closely related to Veromessor Forel and that this clade is sister to Aphaenogaster. Our results confirm the validity of Novomessor stat. r. as a separate genus and it is resurrected based on the combination of new DNA, morphological, behavioral and ecological data. Twenty-three Aphaenogaster species (Hymenoptera: Formicidae) occur in North America. While morphology and ecology define most species, the species limits of a group in the Eastern United States are unclear. In particular, the morphological and behavioral characters once thought to define A. carolinensis, A. picea and A. rudis do not associate with their hypothesized species limits. These observations suggest that these species are not monophyletic. We therefore tested the monophyly of Aphaenogaster in the context of molecular phylogenetic analyses. We used DNA data from five genes: CO1, CAD, EF1αF2, Long-wavelength Rhodopsin and Wingless to reconstruct phylogenies for 44 Aphaenogaster and outgroup species. In the resulting trees, reconstructed using parsimony and Bayesian inference, species boundaries associate with well-supported monophyletic clades of individuals collected from multiple locations. For example, A. carolinensis was monophyletic and a missing CAD intron was a diagnostic trait for the clade. However, some clades were unresolved, and A. picea and A. rudis were not monophyletic. Given the short branch lengths, these results suggest that these ants have likely recently radiated, and lack of gene lineage sorting explains the non-monophyly of species. Conversely, these results may indicate that clades of multiple species represent fewer but morphologically varied species. Additional biological information concerning pre- and post-mating barriers is needed before a complete revision of species boundaries for Aphaenogaster.Aphaenogaster Mayr 1853, contains 227 species worldwide (Bolton 2006) with 23 valid North American species, several species of which are hard to separate based on morphology alone (Umphrey 1996). The difficulty in identifying some of these species is due to limited diagnostic characters and to the lack of a comprehensive illustrated key. A recent analysis returned three species from Aphaenogaster to Novomessor, thus making Aphaenogaster in North America monophyletic (DeMarco and Cognato 2015). While many species have easily identifiable morphological characters, some east coast species within the A. rudis clade in North America are difficult to differentiate. Two of these species, A. carolinensis and A. miamiana, can be diagnosed using DNA. The gene CAD was missing an intron in those taxa. Four additional taxa, all identified morphologically as A. rudis, were found to be polyphyletic (DeMarco and Cognato, in prep, or see Chapter 2).
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Title: Phylogenetics of the Scolytini (Coleoptera : curculionidae: Scolytinae) and host-use evolution
Creator: Smith, Sarah Marie
Date: 2013
Collection: Electronic Theses & Dissertations
Description: The Nearctic bark beetle genus Scolytus was revised based in part on a molecular phylogeny. Monophyly of the native species was tested using mitochondrial (COI) and nuclear (28S, CAD, ArgK) genes and 43 morphological characters in parsimony and Bayesian phylogenetic analyses. Parsimony analyses of molecular and combined datasets provided variable results while Bayesian analysis recovered most nodes with posterior probabilities >90%. Native angiosperm and conifer-feeding ...
Show moreThe Nearctic bark beetle genus Scolytus was revised based in part on a molecular phylogeny. Monophyly of the native species was tested using mitochondrial (COI) and nuclear (28S, CAD, ArgK) genes and 43 morphological characters in parsimony and Bayesian phylogenetic analyses. Parsimony analyses of molecular and combined datasets provided variable results while Bayesian analysis recovered most nodes with posterior probabilities >90%. Native angiosperm and conifer-feeding Scolytus spp. were recovered as paraphyletic. Twenty-five species were recognized. Four new synonyms were discovered: Scolytus praeceps LeConte 1868 (= S. abietis Blackman 1934; = S. opacus Blackman 1934), S. reflexus (= S. virgatus Bright 1972; = S. wickhami Blackman 1934). Two species were removed from synonymy: Scolytus fiskei Blackman 1934 and S. silvaticus Bright 1972. Neotypes were designated for the following species: Scolytus aztecus Wood 1967, S. hermosus Wood 1968 and S. mundus Wood 1968. A key, diagnosis, redescription, distribution, host records and images were provided for each species.The influence of plants in the diversification of herbivorous insects, specifically those that utilize moribund and dead hosts, is unclear. Scolytini, a diverse tribe of weevils, specialize on many different plant taxa as a source of food. The phylogenetics of the Scolytini were reconstructed using Bayesian analyses to examine the origin, test the monophyly of Scolytini genera, and illuminate patterns of host-use and feeding habits among the tribe. Analyses were based on COI, 28S, CAD and ArgK. Ancestral host usage was reconstructed using likelihood criteria. Diversification of the Scolytini generally occurred well after host taxa diversified, as a combination of host shifts and lineage tracking. Repeated independent shifts to the same hosts occurred. Diversification occurred on common and widespread hosts, there was a single origination of conifer-feeding from angiosperm-feeding species and evolution of fungus-feeding from phloem-feeding ancestors. Overall, the observed patterns of Scolytini host-use can be explained by a combination of the sequential evolution and host-use oscillation hypotheses. The Neotropical bark beetle genera Cnemonyx Eichhoff 1868 and Scolytus Geoffroy1762 were reviewed as part of ongoing research into the higher-level taxonomy of the Scolytini. Ceratolepsis Chapuis 1869 was removed from synonymy with Cnemonyx and seven new combinations are reported: Ceratolepsis amazonicus Eggers 1929, C. boliviae (Blackman) 1943, C. hylurgoides (Schedl) 1948, C. insignis (Wood) 1969, C. jucundus Chapuis 1869, C. maculicornis Blandford 1896 and C. niger (Eggers) 1929. One new species was described: Scolytus rabagliatus. Cnemonyx setulosus (Eggers) 1929 was removed from synonymy with C. panamensis (Blandford) 1896. Four new synonyms were discovered: Ceratolepsis Chapuis (= Coptosomus Schedl 1952), Cnemonyx setulosus (Eggers) 1929 (= Cnemonyx similis (Eggers) 1929), Scolytus proximus Chapuis 1869 (=Scolytus brevicauda Wichmann 1915) and Scolytus thoracicus Chapuis 1869 (= Scolytus plaumanni Wood 2007). One new distribution record was reported: Scolytus multistriatus in South America (Brazil).
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Title: Systematics of the genus Rhagoletis (Diptera : Tephritidae : new species, phylogeny, and justifications
Creator: Hulbert, Daniel Lloyd
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Flies of Rhagoletis (Diptera: Tephritidae) are economically important fruit pests (infesting specialty fruit crops including apples, blueberries and cherries), which also serve as models for studying modes of speciation and coevolutionary relationships with their hymenopteran parasitoids. There are new species within the genus which have not been previously formally described. One of these species is within the tabellaria species group. I describe the morphology of Rhagoletis bushi Hulbert &...
Show moreFlies of Rhagoletis (Diptera: Tephritidae) are economically important fruit pests (infesting specialty fruit crops including apples, blueberries and cherries), which also serve as models for studying modes of speciation and coevolutionary relationships with their hymenopteran parasitoids. There are new species within the genus which have not been previously formally described. One of these species is within the tabellaria species group. I describe the morphology of Rhagoletis bushi Hulbert & Smith, its geographic distribution, host association, phylogenetic relationships, and identify an associated species of parasitoid wasp. The new species infests the fruit of buffaloberry (Shepherdia argentea) in the Northern Great Plains of North America. There is a suite of morphological characters, and a unique host plant association, that are diagnostic of R. bushi. Further evidence for the validity of R. bushi and its placement within the tabellaria species group comes from DNA sequence data from multiple genetic loci. The phylogenetic relationships among Rhagoletis species groups remain unresolved despite analyses based on morphology, allozymes, and mitochondrial DNA. Most Nearctic Rhagoletis belong to one of five species groups (pomonella, tabellaria, cingulata, suavis , and ribicola groups), with two unplaced species (R. fausta and R. juniperina), all of which appear to be part of a larger monophyletic group that also includes some Palearctic taxa. Regarding the overall phylogeny of the genus, my goals were to 1) resolve phylogenetic relationships using mitochondrial (COI) and nuclear (28S, CAD, period, AATS) DNA sequences, and 2) to identify the monophyletic group containing these Nearctic species. Using Bayesian analysis of a combined dataset with 4399 aligned nucleotides, I inferred a well-supported monophyletic group containing the five Nearctic Rhagoletis species groups, plus R. fausta, R. juniperina, and two Palearctic species: R. batava and R. flavigenualis. Within this larger monophyletic assemblage, the five Nearctic species groups together are monophyletic as are four of the five individual species groups (not ribicola). Palearctic and Neotropical Rhagoletis were resolved into well-supported clades of taxa often sharing closely related host plants. A well-resolved phylogeny of Rhagoletis is a valuable tool for future work addressing questions pertaining to how history, geography and ecology have shaped the phylogenetic patterns we observe in the genus. It is often claimed that systematic biology is fundamental to all other areas of biology. I critically evaluate the acceptance of this claim by entomologists critically as it relates to the field of entomology. I also critically describe the justification and valuations for systematic biology using the framework of Boltanski and Thevenot's realms of worth and the philosophical framework for justification using virtues, desserts and outcomes. In order to accomplish these purposes, I critically analyze and review relevant entomological literature and interview practitioners of entomology and insect systematic biology. I find justification for systematic biology overwhelming takes the form of appeals to utilitarianism (both internally and externally focused) and are most relevant in the Industrial World. Additionally, some justifications given also pertain to the Civic World and to virtue. Evaluation of justification in systematic biology is important, especially as our globe becomes increasingly ecologically and politically unstable.
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Title: Phylogeny and historical biogeography of the Schistosomatidae
Creator: Carmichael, Allan Christopher
Date: 1984
Collection: Electronic Theses & Dissertations

Title: Review of the phylogenetic position of the tree shrew (tupaia glis diard), with new observations on the arteria carotis interna
Creator: Steurwald, Erla Anne
Date: 1969
Collection: Electronic Theses & Dissertations

Title: Phylogeny and evolution of foraging specialization in the tyrant flycatchers
Creator: Birdsley, Jeffrey S.
Date: 1998
Collection: Electronic Theses & Dissertations

Title: Studies in amatoxin-producing genera of fungi : phylogenetics and toxin distribution
Creator: Hallen, Heather E.
Date: 2002
Collection: Electronic Theses & Dissertations

Title: Scalable phylogenetic analysis and functional interpretation of genomes with complex evolutionary histories
Creator: Hejase, Hussein El Abbass
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Phylogenomics involves the inference of a genome-scale phylogeny. A phylogeny is typically inferred using sequences from multiple loci across a set of genomes of multiple organisms by reconstructing gene trees and then reconciling them into a species phylogeny. Many studies have shown that evolutionary processes such as gene flow, incomplete lineage sorting, recombination, selection, gene duplication and loss have shaped our genomes and played a major role in the evolution of a diverse array...
Show more"Phylogenomics involves the inference of a genome-scale phylogeny. A phylogeny is typically inferred using sequences from multiple loci across a set of genomes of multiple organisms by reconstructing gene trees and then reconciling them into a species phylogeny. Many studies have shown that evolutionary processes such as gene flow, incomplete lineage sorting, recombination, selection, gene duplication and loss have shaped our genomes and played a major role in the evolution of a diverse array of metazoans, including humans and ancient hominins, mice, bacteria, and butterflies. The aforementioned evolutionary processes are primary causes of gene tree discordance, which introduce different loci in a genome that exhibit local genealogical variation (i.e. gene trees differing from each other and the species phylogeny in terms of topology and/or branch length). In this dissertation, we develop a method for fast and accurate inference of phylogenetic networks using large-scale sequence data. The advent of high-throughput sequencing technologies has brought about two main scalability challenges: (1) dataset size in terms of the number of taxa and (2) the evolutionary divergence of the taxa in a study. We explore the impact of both dimensions of scale on phylogenetic network inference and then introduce a new phylogenetic divide-and-conquer method which we call FastNet. We show using synthetic and empirical data spanning a range of evolutionary scenarios that FastNet outperforms the state-of-the-art in terms of accuracy and computational requirements. Furthermore, we develop methods that use better and more accurate phylogenies to functionally interpret genomes. One way to study and understand the biological function of genomes is through association mapping, which pinpoints statistical associations between genotypic and phenotypic characters while modeling the relatedness between samples to avoid generating spurious inferences. Many methods have been proposed to perform association mapping while accounting for sample relatedness. However, the state of the art predominantly utilizes the simplifying assumption that sample relatedness is effectively fixed across the genome. Recent studies have shown that sample relatedness can vary greatly across different loci within a genome where gene trees could differ from each other and the species phylogeny. Thus, there is an imminent need for methods to account for local genealogical variation in functional genomic analyses. We address this methodological gap by introducing two methods, Coal-Map and Coal-Miner, which account for sample relatedness locally within loci and globally across the entire genome. We show through simulated and empirical datasets that these newly introduced methods offer comparable or typically better statistical power and type I error control compared to the state-of-the-art."--Pages ii-iii.
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Title: Phylogenetic relationships in Poliomintha and related genera in the Mentheae (Lamiaceae)
Creator: Godden, Grant Thomas
Date: 2009
Collection: Electronic Theses & Dissertations

Title: Molecular systematics and biogeography of some New World Microtus (Mammalia: Arvicolidae)
Creator: DeBry, Ronald Wayne
Date: 1989
Collection: Electronic Theses & Dissertations

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