Publication Date


Document Type


First Advisor

Duvall, Melvin R.

Degree Name

M.S. (Master of Science)

Legacy Department

Department of Biological Sciences


Grasses--Varieties--Analysis; Plastids; Microstructure; Mutation (Biology)


Basis for the study: Complete plastome analysis of grasses belonging to the subfamily Chlorodoideae was used as a model for identifying microstructural mutations as a means to produce high-resolution phylogenomic trees. Compared to nucleotide substitutions, microstructural mutations are not as well understood. Methods: High-throughput NextGen Illumina and Sanger sequencing methods were used to obtain chloroplast genomes for nine species (Distichlis spicata, Bouteloua curtipendula, Hilaria cenchroides, Sporobolus heterolepis, Spartina pectinata, Zoysia macrantha, Eragrostis minor, Eragrostis tef and Centropodia glauca ). An exhaustive search of these plastomes produced a binary matrix that was used for phylogenomic analyses. Key results: Notable contradictions for the hypothesis that indel size is inversely correlated with frequency were observed. Microstructural mutation results are at odds with nucleotide sequence phylogenomic results and weaken bootstrap values in phylogenomic trees. Conclusions: Plastome-scale analyses produced phylogenies that are congruent with previous work with relatively strong support values and should be considered the most reliable type of dataset when conducting these analyses. Five bp indels seem to occur or be retained by the DNA repair complexes with greater frequency than indels of both larger and smaller size classes across all taxa.


Advisors: Melvin R. Duvall.||Committee members: Thomas L. Sims; Joel P. Stafstrom.||Includes bibliographical references.


xi, 58 pages




Northern Illinois University

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