Browsing by Subject "mtDNA"
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Item Host Plant Influences on Performance and Haplotype Diversity of Dalbulus maidis, a Specialist Herbivore of Zea(2012-12-06) Davila-Flores, AmandaIn one study, a suite of plants from the maize genus Zea L. (Poaceae) and the specialist herbivore Dalbulus maidis (DeLong and Wolcott, 1923) (Hemiptera: Cicadellidae) were used to test the hypotheses that anti-herbivore defenses are affected by plant life-history evolution and human intervention through domestication and breeding for high yield. The suite of Zea host plants included one Mexican commercial hybrid maize Zea mays ssp. mays L., a landrace variety of maize, two populations of Balsas teosinte (Zea mays ssp. parviglumis Iltis & Doebley), and perennial teosinte (Z. diploperennis Iltis, Doebley & Guzman). This suite of host plants includes three Transitions evident within the genus Zea: life history form perennial to annual life cycle evident between perennial teosinte and Balsas teosinte, domestication transition from wild annual to domesticated annual evident between Balsas teosinte and landrace maize, and; breeding transition from landrace cultivar to a hybrid cultivar. The transitions were correlated with differences in plant defenses, as indicated by corn leafhopper performance. Results showed a performance gradient, suggesting a pattern in which plant defense is stronger in perennial than annual plants, Balsas teosinte than landrace maize, and in landraces than in hybrid maize. Furthermore, results suggested that domesticated maize would be the least defended, most suitable host for corn leafhopper. In a second study, haplotype diversity was assessed to address structuring and interconnectedness among samples of corn leafhopper collected in the southwestern region of Mexico to address microevolution. The geographic focus of the study was maintained within an area encompassing the presumed centers of radiation of Dalbulus and its host genus Zea, and of maize domestication. Samples were complemented with samples of corn leafhopper sequences available at GenBank. Results revealed seven haplotypes from three host plants within Zea: perennial teosinte, Balsas teosinte, and maize. Furthermore, genetic differentiation was present and haplotype diversity appears to correlate with differences in genetic structure between perennial teosinte and maize. One haplotype was found to be present throughout all sites, which appears to parallel the spread of maize cultivation. As maize cultivation spread beyond its area of domestication, corn leafhoppers colonized perennial teosinte, further suggesting that subsequent decreases in maize cultivation in perennial teosinte habitat created a refuge where perennial teosinte- adapted haplotypes could persist. Altogether, my research suggests that the combination of historical expansion of maize cultivation expansion and the weaker anti-herbivore defenses associated within maize domestication appears to have favored genotypes particularly adapted for exploiting maize.Item Insights into relationships among rodent lineages based on mitochondrial genome sequence data(Texas A&M University, 2006-04-12) Frabotta, Laurence JohnThis dissertation has two major sections. In Chapter II, complete mitochondrial (mt DNA) genome sequences were used to construct a hypothesis for affinities of most major lineages of rodents that arose quickly in the Eocene and were well established by the end of the Oligocene. Determining the relationships among extant members of such old lineages can be difficult. Two traditional schemes on subordinal classification of rodents have persisted for over a century, dividing rodents into either two or three suborders, with relationships among families or superfamilies remaining problematic. The mtDNA sequences for four new rodent taxa (Aplodontia, Cratogeomys, Erethizon, and Hystrix), along with previously published Euarchontoglires taxa, were analyzed under parsimony, likelihood, and Bayesian criteria. Likelihood and Bayesian analyses of the protein-coding genes converged on a single topology that weakly supported rodent monophyly and was significantly better than the parsimony trees. Analysis of the tRNAs failed to recover a monophyletic Rodentia and did not reach convergence on a stationary distribution after fifty million generations. Most relationships hypothesized in the likelihood topology have support from previous data. Mt tRNAs have been largely ignored with respect to molecular evolution or phylogenetic utility. In Chapter III, the mt tRNAs from 141 mammals were used to refine secondary structure models and examine their molecular evolution. Both H- and L-encoded tRNAs are AT-rich with different %G and GC-skew and a difference in skew between H- and L-strand stems. Proportion of W-C pairs is higher in the H-strand and GU/UG pairs are higher in the L-strand, suggesting increased mismatch compensation in L-strand tRNAs. Among rodents, the number of variable stem base-pairs was nearly 75% of that observed across all mammals combined. Compensatory base changes were present only at divergences of 4% or greater. Neither loop reduction nor an accumulation of deleterious mutations, both suggestive of mutational meltdown (Muller's ratchet), was observed. Mutations associated with human pathologies are correlated only with the coding strand, with H-strand tRNAs being linked to substantially more of these mutations.Item Structural and functional studies of the human mitochondrial DNA polymerase(2010-08) Lee, Young-Sam; Yin, Yuhui Whitney; Molineux, Ian J.; Johnson, Kenneth A.; Paull, Tanya T.; Robertus, Jon D.The human mitochondrial DNA polymerase (Pol γ) catalyzes mitochondrial DNA synthesis, and thus is essential for the integrity of the organelle. Mutations of Pol γ have been implicated in more than 150 human diseases. Reduced Pol γ activity caused by inhibition of anti-HIV drugs targeted to HIV reverse transcriptase confers major drug toxicity. To illustrate the structural basis for mtDNA replication and facilitate rational design of antiviral drugs, I have determined the crystal structure of human Pol γ holoenzyme. The structure reveals heterotrimer architecture of Pol γ holoenzyme with a monomeric catalytic subunit Pol γA, and a dimeric processivity factor Pol γB. While the polymerase and exonuclease domains in Pol γA present high structural homology with the other members of the DNA Pol I family, the spacer between the two functional domains shows a unique fold, and constitutes the subunit interface. The structure suggests a novel mechanism for Pol γ’s high processivity of DNA replication. Furthermore, the structure reveals dissimilarity in the active sites between Pol γ and HIV RT, thereby indicating an exploitable space for design of less toxic anti-HIV drugs. Interestingly, the structure shows an asymmetric subunit interaction, that is, one monomer of dimeric Pol γB primarily participates in interactions with Pol γA. To understand the roles of each Pol γB monomer, I generated a monomeric human Pol γB variant by disrupting the dimeric interface of the subunit. Comparative studies of this variant and dimeric wild-type Pol γB reveal that each monomer in the dimeric Pol γB makes a distinct contribution to processivity: one monomer (proximal to Pol γA) increases DNA binding affinity whereas the other monomer (distal to Pol γA) enhances the rate of polymerization. The pol γ holoenzyme structure also gives a rationale to establish the genotypic-phenotypic relationship of many disease-implicated mutations, especially for those located outside of the conserved pol or exo domains. Using the structure as a guide, I characterized a substitution of Pol γA residue R232 that is located at the subunit interface but far from either active sites. Kinetic analyses reveal that the mutation has no effect on intrinsic Pol γA activity, but shows functional defects in the holoenzyme, including decreased polymerase activity and increased exonuclease activity, as well as reduced discrimination between mismatched and corrected base pair. Results provide a molecular rationale for the Pol γA-R232 substitution mediated mitochondrial diseases.Item Temporal genetic structure of feral honey bees (Hymenoptera: Apidae) in a coastal prairie habitat of southern Texas: impact of Africanization(Texas A&M University, 2004-09-30) Pinto, Maria AliceThe goal of this study was to examine the impact of Africanization on the genetic structure of the Welder Wildlife Refuge feral honey bee population by scoring mtDNA and microsatellite polymorphisms. Adult honey bee workers, collected between 1991 and 2001, were screened for mtDNA using the cytochrome b/BglII, ls rRNA/EcoRI, and COI/HinfI PCR-based assays. The procedure allowed identification of four mitotypes: eastern European, western European, A. m. lamarckii, and A. m. scutellata. The relative frequencies of the four mitotypes changed radically during the 11-year period. Prior to immigration of Africanized honey bees, the resident population was essentially of eastern European maternal ancestry. The first colony of A. m. scutellata mitotype was detected in 1993. Between 1995 and 1996 there was a mitotype turnover in the population from predominantly eastern European to predominantly A. m. scutellata. From 1997 onward, most colonies (69 %) were of A. m. scutellata mitotype. The temporal change in mtDNA was paralleled by nuclear DNA. The 12 microsatellite loci analyzed indicated (1) the mechanism of Africanization of the Welder population involved both maternal and paternal bi-directional gene flow (hybridization) between European and Africanized honey bees; and (2) the resident panmitic European population was replaced by panmitic asymmetrical admixtures of A. m. scutellata and European genes. The steepest increase in the proportion of introgressed A. m. scutellata nuclear alleles occurred between 1994 and 1997. The post-Africanization gene pool was composed of a diverse array of recombinant classes with a substantial European genetic contribution (mean proportion of European-derived alleles was 37 % as given by mR estimator or 25 % as given by mY estimator, for 1998-2001). If European genes continue to be retained at moderate frequencies, then the Africanized population is best viewed as a "hybrid swarm" instead of "pure African". The most radical change in the genetic structure of the Welder Wildlife Refuge feral honey bee population (observed between 1995 and 1997) coincided with arrival of the parasitic Varroa mite. We suggest that Varroa likely hastened the demise of European honey bees and had a major role in restructuring the Welder Wildlife Refuge feral honey bee population.Item Variation of mitochondrial control region sequences of Steller sea lions: the three-stock hypothesis(Texas A&M University, 2004-09-30) Baker, Alyson ReneeSequence variation of a 238 bp segment of the mitochondrial control region was analyzed for 1,568 Steller sea lions (2.8% of the estimated species population) sampled from 50 rookeries representing nearly every locality at which Steller sea lions are known to breed in significant numbers. Haplotype diversity (H = 0.9164 ? 0.0035) was high and nucleotide diversity (? = 0.00967 ? 0.00586) was moderate. No evidence was observed for significant genetic bottleneck effects. Rookeries were grouped into regions and stocks to examine structure at different spatial scales. F- and ?-statistics were computed for all pairwise comparisons of rookeries, regions and stocks. Significant (P<0.05) divergence of eastern stock (southeastern Alaska to California) animals from western stock animals was supported in analyses at all spatial scales. Likewise, rookeries and regions from Asia were found to be significantly different from all other western stock rookeries. This was most clearly demonstrated using ?-statistics at the regional level. The Commander Islands clearly associate with Alaskan western stock rookeries, not with the Asian rookeries. Within each of the three stocks there is significant isolation by distance among rookeries. This relationship does not hold for inter-stock comparisons indicating that there are important barriers to gene flow among stocks. Mitochondrial DNA analysis supports the recognition of three stocks for appropriate conservation of the species. The currently recognized eastern stock is unaffected, but the western stock is now partitioned west of the Commander Islands yielding a western stock which ranges from Prince William Sound west to the Commander Islands, and an Asian stock including rookeries from the Kamchatka Peninsula, Kuril Islands, and Sea of Okhtosk.