Browsing by Subject "Rodentia"
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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 Population Genetic Analyses of the Baird's Pocket Gopher, Geomys breviceps(2012-10-19) Welborn, SarahThe Baird?s pocket gopher (Geomys breviceps) is a solitary, fossorial rodent found throughout areas of Texas, Arkansas, Oklahoma, and Louisiana. Research focusing on the population genetics of pocket gophers and other species with limited vagility and isolated populations is lacking. Through the use of mitochondrial and microsatellite data, a series of population genetic analyses were completed to better understand the population structure and gene flow among a series of G. breviceps localities. Pocket gophers were captured from five localities in the Brazos Valley and used in this study. Due to the lack of microsatellite loci available for G. breviceps, 10 loci were created for use in this study. Overall estimates from the population genetic analyses showed high levels of gene flow amongst nearby localities with decreasing levels as distance between localities increased. Findings suggest that 2-3 localities located within 2 km of each other function as one genetic cluster thus showing 3-4 total genetic clusters total in this study. Results also suggest that the Baird?s pocket gopher is capable of moving at least 2 km, but further analyses should be completed to better understand dispersal distance.Item The evolution of nuclear microsatellite DNA markers and their flanking regions using reciprocal comparisons within the African mole-rats (Rodentia: Bathyergidae)(Texas A&M University, 2006-10-30) Ingram, Colleen MarieMicrosatellites are repetitive DNA characterized by tandem repeats of short motifs (2 ?????? 5 bp). High mutation rates make them ideal for population level studies. Microsatellite allele genesis is generally attributed to strand slippage, and it is assumed that alleles are caused only by changes in repeat number. Most analyses are limited to alleles (electromorphs) scored by mobility only, and models of evolution rarely account for homoplasy in allele length. Additionally, insertion/deletion events (indels) in the flanking region or interruptions in the repeat can obfuscate the accuracy of genotyping. Many investigators use microsatellites, designed for a focal species, to screen for genetic variation in non-focal species. Comparative studies have shown different mutation rates of microsatellites in different species, and even individuals. Recent studies have used reciprocal comparisons to assess the level of polymorphism of microsatellites between pairs of taxa. In this study, I investigated the evolution of microsatellites within a phylogenetic context, using comparisons within the rodent family Bathyergidae. Bathyergidae represents a monophyletic group endemic to sub-Saharan Africa and relationships are well supported by morphological and molecular data. Using mitochondrial and nuclear DNA, a robust phylogeny was generated for the Bathyergidae. From my results, I proposed the new genus, Coetomys. I designed species-specific genotyping and microsatellite flanking sequence (MFS) primers for each genus. Sequencing of the MFS provided direct evidence of the evolutionary dynamics of the repeat motifs and their flanking sequence, including rampant electromorphic homoplasy, null alleles, and indels. This adds to the growing body of evidence regarding problems with genotype scores from fragment analysis. A number of the loci isolated were linked with repetitive elements (LTRs and SINEs), characterized as robust phylogenetic characters. Results suggest that cryptic variation in microsatellite loci are not trivial and should be assessed in all studies. The phylogenetic utility of the nucleotide variation of the MFS was compared to the well-resolved relationships of this family based on the 12S/TTR phylogeny. Variation observed in MFS generated robust phylogenies, congruent with results from 12S/TTR. Finally, a number of the indels within the MFS provided a suite of suitable phylogenetic characters.