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dc.contributor.advisorHoneycutt, Rodney L.en_US
dc.creatorIngram, Colleen Marieen_US
dc.date.accessioned2006-10-30T23:31:22Z
dc.date.available2006-10-30T23:31:22Z
dc.date.created2005-08en_US
dc.date.issued2006-10-30
dc.identifier.urihttp://hdl.handle.net/1969.1/4370
dc.description.abstractMicrosatellites 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.en_US
dc.format.extent9714925 bytes
dc.format.mediumelectronicen_US
dc.format.mimetypeapplication/pdf
dc.language.isoen_USen_US
dc.publisherTexas A&M Universityen_US
dc.subjectMicrosatellite DNAen_US
dc.subjectMolecular Evolutionen_US
dc.subjectMicrosatellite Flanking Sequencesen_US
dc.subjectMFSen_US
dc.subjectAscertainment Biasen_US
dc.subjectNull Allelesen_US
dc.subjectElectromorphic Homoplasyen_US
dc.subjectMicrosatellite Indelsen_US
dc.subjectPhylogeneticsen_US
dc.subjectFragment Analysisen_US
dc.subjectAfricaen_US
dc.subjectMole-Ratsen_US
dc.subjectBathyergidaeen_US
dc.subjectRodentiaen_US
dc.subjectCoetomysen_US
dc.subjectCryptomysen_US
dc.subjectBathyergusen_US
dc.subjectGeorychusen_US
dc.subjectHeliophobiusen_US
dc.subjectHeterocephalusen_US
dc.subjectMammaliaen_US
dc.titleThe evolution of nuclear microsatellite DNA markers and their flanking regions using reciprocal comparisons within the African mole-rats (Rodentia: Bathyergidae)en_US
dc.typeBooken
dc.typeThesisen
thesis.degree.departmentWildlife and Fisheries Sciencesen_US
thesis.degree.disciplineGeneticsen_US
thesis.degree.grantorTexas A&M Universityen_US
thesis.degree.nameDoctor of Philosophyen_US
thesis.degree.levelDoctoralen_US
dc.contributor.committeeMemberBickham, John W.en_US
dc.contributor.committeeMemberGill, Clare A.en_US
dc.contributor.committeeMemberWoolley, James B.en_US
dc.type.genreElectronic Dissertationen_US
dc.type.materialtexten_US
dc.format.digitalOriginborn digitalen_US


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