Open Access
Leopold, Ian Stuart
Area of Honors:
Bachelor of Science
Document Type:
Thesis Supervisors:
  • Stephen Wade Schaeffer, Thesis Supervisor
  • Bernhard Luscher, Honors Advisor
  • Drosophila pseudoobscura
  • cline
  • inversion mutation
  • third chromosome
The genetic forces that establish chromosomal rearrangements in natural populations are not clearly understood. An analysis of nucleotide and amino acid variation of genes in a Drosophila chromosome that is naturally polymorphic for different gene arrangements generated by a series of paracentric inversions is used to investigate the molecular genomic mechanisms that establish chromosomal rearrangements in natural populations. Cytogenetic analysis is used to identify the different gene orders using the banding and puffing patterns of the polytene chromosomes isolated from the salivary glands of D. pseudoobscura larvae. The different gene arrangements or gene orders are named for the location where the chromosomes were originally collected. Chromosomes of 50 D. pseudoobscura strains collected from the southwestern United States and Mexico were classified via cytogenetic analysis. A subset of these strains was collected from Pablo Etla in Oaxaca, Mexico. The initial analysis identified two gene arrangements in this sample, Tree Line and Cuernavaca. The Cuernavaca arrangement is derived from the Santa Cruz arrangement by a single inversion step and should generate a single large inversion loop in a Santa Cruz/Cuernavaca heterozygote. Cytogenetic analysis of Santa Cruz/Cuernavaca heterozygotes revealed that the putative Cuernavaca strain produced a looping pattern consistent with two rather than one inversion differences between the strains. The strains carrying the putative Cuernavaca arrangement were determined to carry the Paxtepec arrangement. After the cytogenetic identifications were complete, the genomic sequences of the 50 flies from five different gene arrangements of D. pseudoobscura were generated using NextGen sequencing. Using this extensive data set, the pattern and organization of nucleotide and amino acid variation can be examined to determine the evolutionary forces responsible for the origin and establishment of the chromosomal rearrangements. An analysis of variable amino acid sites in the coding sequences of genes from the third chromosome inferred the ancestral and mutation-derived changes to the amino acid sequences. The analysis wished to detect amino acid changed chemical classes that were at high frequency within particular gene arrangements, which might be associated with an adaptive event acting on the chromosomal variants. The majority of amino acid substitutions changed stayed within chemical class (non-polar, polar, acidic, or basis). Of the amino acid changes that went between chemical classes, polar to nonpolar mutations were the most common type. A gene ontology (GO) analysis on proteins with a high frequency of non-conservative chemical changes to identify any functions of the genes or their homologues in Drosophila melanogaster that might help to explain the stable clinal pattern formed by the third chromosome arrangements found in the southwestern United States.