Theses and Dissertations

Issuing Body

Mississippi State University


Diehl, Walter J.

Committee Member

Wise, Dwayne A.

Committee Member

Wallace, Lisa

Committee Member

Bridges, Susan M.

Committee Member

Pharr, G. Todd

Date of Degree


Document Type

Dissertation - Open Access


Biological Sciences

Degree Name

Doctor of Philosophy (Ph.D)


College of Arts and Sciences


Department of Biological Sciences


The bacterial species belonging to the order Mycoplasmatales have highly truncated genomes, and are thus ideal for studying genome evolution patterns. Fourteen members (twelve species) of this order were selected for study of genome evolution based on gene function and phylogeny. A database was constructed that consisting of the set of genes that are common to all of these species, and these genes were further subdivided based on their functions. A Bayesian phylogenetic tree was also constructed from the 16 S ribosomal DNA sequences from these species and robust clades were identified for testing the influence of selection on gene evolution, from which the clades were selected and tested for evidence of natural selection. Two separate statistical techniques, namely the codon substitution models and McDonald-Kreitman tests were used to analyze the presence or absence of selection for genes in different functional categories. The studies demonstrated that the set of genes associated with cellular processes show the highest percentage of selection and are likely to play a crucial role in Mycoplasma evolution (for example, by altering the arrangement of antigens on the cell surface and thus enabling a particular Mycoplasma species to expand its host range). The presence of selection could only be identified at the earliest divisions of the phylogeny. Tests were also performed to detect the presence of a number of neutral genetic processes that can potentially confound detection of patterns of selection. None of these processes were found to affect the results of the analyses. The study has the potential to identify genes, gene complexes or even pathways that may be involved directly or indirectly in speciation.