Biology Theses and Dissertations

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    Elucidating the Macro- and Micro-evolutionary Relationships of the Federally Listed Endangered Species Agalinis acuta (Orobanchaceae)
    (2010) Pettengill, James Beaton; Neel, Maile C; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Agalinis acuta (Orobanchaceae) is a federally listed endangered plant species native to the mid-Atlantic and northeastern coastal plains of the United States. Due to morphological ambiguity and molecular similarity between A. acuta and Agalinis tenella and Agalinis decemloba a conservation priority is to determine whether A. acuta represents an evolutionarily distinct entity worthy of protection under the Endangered Species Act. To resolve this question, a phylogenetic study was first conducted based on seven chloroplast DNA loci and the nuclear DNA locus ITS from 79 individuals representing 29 Agalinis species. A study evaluating the utility of those cpDNA loci and three analytical techniques for the purpose of DNA barcoding was also conducted. The phylogenetic study indicated that A. acuta was perhaps evolutionarily indistinct from A. decemloba and A. tenella. Based on the results of subsequent analyses of 21 microsatellite loci and morphological data evaluated under myriad species concepts, A. acuta, A. decemloba, and A. tenella best represent a single species with two subspecies; the former two putative species would constitute a subspecies called A. decemloba ssp. decemloba and A. tenella would be A. decemloba ssp. tenella. With evolutionary distinct entities described, a phylogeographic study was conducted to determine the extent to which historical processes rather than contemporaneous events can explain extant patterns of genetic and phenotypic diversity within A. decemloba. The dispersal of a few individuals out of southern refugial populations likely represents the process through which northern populations were established; however, recent anthropogenic effects that disproportionately affected northern populations may have also contributed to extant patterns of diversity. Neutral or adaptive explanations for phenotypic variation among populations are also investigated. The conservation implications of population genetic analyses were assessed for members of A. decemloba ssp. decemloba. Despite the evidence that this taxon is self-compatible, the high levels of inbreeding and low levels of heterozygosity are of such a magnitude in certain populations that genetic factors may be negatively impacting fitness. Because of the small effective population sizes and degree of isolation, all populations should be managed to reduce the risk of extinction associated with demographic and environmental stochasticity.
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    USE OF MOLECULAR TECHNIQUES TO ADDRESS THE EVOLUTION OF DISPLAY TRAITS IN THE PTILONORHYNCHIDAE AND OTHER PASSERIFORM SPECIES
    (2009) Zwiers, Paul; Borgia, Gerald; Fleischer, Robert; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Tests of hypotheses addressing the evolution of complex traits have greatly benefited from advances in the field of molecular genetics. Current molecular techniques allow for the identification of genetic variability, useful in estimating genetic relatedness and potentially explaining phenotypic variation. Here I use molecular data to address the evolution of complex traits within the Ptilonorhynchidae and other Passeriformes. My estimation of a bowerbird molecular phylogeny suggests two highly unlikely scenarios of complex trait evolution (i.e. polygyny, bower construction, decoration use, etc.); either polygyny and complex display traits evolved in parallel, or monogamy evolved from non-resource based polygyny, a transition for which no unambiguous examples could be found, and complex traits evolved once and were lost. Molecular evidence also supports the existence of four Sericulus species, dating the radiation to coincide with the upheaval of the central New Guinea mountain range, and suggests plumage coloration may be a labile trait within this group and therefore a poor indicator of species relatedness. Use of ultraviolet (UV) signals in birds is hypothesized to associate with the ability to see UV wavelengths, a trait with a well-documented genetic basis (replacements at key amino acid positions in the short-wavelength-sensitive 1 (SWS1) opsin pigment influence pigment sensitivity and potentially color discrimination). UV signal use may alternatively evolve to match the local light environment. Results from bowerbirds suggest extreme differences in UV reflectance are due to light availability and not differences in UV vision because amino acid sequences in the bowerbirds were nearly identical. Expanding upon this study, I compared SWS1 opsin gene sequences from 134 passeriform species and plumage UV reflectance measurements from 91 of these species. Results from the molecular data are unprecedented; replacements at five amino acid positions are predicted to have occurred nearly simultaneously, suggesting a constraint on UV vision evolution. Additionally, species reflect most intensely in wavelengths to which they are predicted to be sensitive. These results suggest a constraint on UV vision may also constrain the evolution of UV signals in the Passeriformes. These studies highlight the usefulness of molecular data when testing hypothesis of species and trait evolution.
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    PHYLOGENETIC RELATIONSHIP AMONG POLYMORPHIC OLIGOHYMENOPHOREAN CILIATES, WITH GENE EXPRESSION IN LIFE-HISTORY STAGES OF MIAMIENSIS AVIDUS (CILIOPHORA, OLIGOHYMENOPHOREA)
    (2007-11-29) Gebler, Glenn Frederick; Small, Eugene B.; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The Class Oligohymenophorea is a monophyletic group possessing polymorphic taxa. Thus far, relationships within subclasses of oligohymenophorean ciliates and between polymorphic taxa within families are not well resolved. Here, nuclear small subunit rRNA (SSU rRNA) gene sequences from 63 representative taxa, including several polymorphic species, were used to construct phylogenies and test monophyly of the subclass Scuticociliatia and of the polymorphic taxa within the Oligohymenophorea. In addition, suppression subtraction hybridization (SSH) was used to test the hypothesis that genes are differentially expressed during microstome-to-macrostome and tomite-to-microstome transformation in the polymorphic scuticociliate Miamiensis avidus. Phylogenetic analyses confirmed monophyly of the subclasses Peritrichia and Hymenostomatia. The monophyletic scuticociliates encompassed most, but not all, taxa included in this study. The conditional acceptance of the hypothesis supporting monophyly of the Scuticociliatia was due to the ambiguous placement of three taxa, the apostome Anoplophrya marylandensis, the scuticociliate Dexitrichides pangi, and the peniculine Urocentrum turbo. The polymorphic trait most likely arose on at least four, and perhaps on as many as six, separate occasions within the oligohymenophorean ciliates. Several genes previously implicated in morphogenetic processes in eukaryotes were upregulated during microstome-to-macrostome transformation in M. avidus. Those genes were, elongation factor-1 alpha (Ef-1α), Constans, Constans-like TOC1 (CCT) transcription factor, a disulfide isomerase, heat shock protein 70, step II splicing factor (Slu7), U1 zinc finger protein, and WD40-16 repeat protein. A similar analysis for M. avidus undergoing tomite-to-microstome transformation identified genes previously linked to transformation processes in other protists: two cysteine protease genes lacking formal description (papain-family and XCP1 cysteine protease), two described cysteine protease genes, cathepsin B and cathepsin L, and one cysteine protease inhibitor (cystatin-1) gene. The roles of candidate genes for regulation of M. avidus life-history stages (Ef-1α for microstome-to-macrostome transformation; cathepsin B and cathepsin L for tomite-to-microstome transformation) were examined using pharmacological inhibition experiments. Drug treatments significantly reduced transformation of M. avidus microstomes into macrostomes within 6 h and prevented tomite-to-microstome transformation after 2.5 h. Results indicated that genes specifically linked to oral transformation in M. avidus are differentially expressed during microstome-macrostome and tomite-microstome transformation. Thus, this study used molecular techniques to understand the evolutionary history and development of polymorphism within the Oligohymenophorean ciliates.