Date of Graduation

Spring 5-2015

Degree Name

Bachelor of Arts

Department or Program

Environmental Studies

Number of Pages


First Advisor

Donald Dearborn


The major histocompatibility complex (MHC) is a highly polymorphic genetic region, encoding both immune and immune and non-immune receptors found on the surface of cells. The characterization of MHC loci provides a basis for the understanding of population ecology and evolutionary biology. Previous genetic analysis of the Great Frigatebird MHC Class II B exon 2 region revealed a maximum number of 4 alleles revealing the possibility that these alleles can be divided into 2 loci. The goal for this investigation was to determine if we could classify the previously determined alleles of the Great Frigatebird into 2 loci using phylogenetic tree analysis. The methods and results are divided into two sections. In Approach I, we used phylogenetic methods to determine if sequence similarity could create two clusters of alleles, consistent with the haplotype distribution across all 92 birds. This failed due to the incompatibility between haplotype cluster locations and haplotype identities for each individual bird. Approach II used logic-based criteria to group the alleles into 2 loci based upon the patterns of the co-occurrence of individual birds’ haplotypes. Only 26 of the 44 haplotypes were successfully classified into a locus, and further nucleotide sequence analysis prevented definitive placement of the remainder of the 18 haplotypes. The results from both approaches reveal that there could be gene conversion and recombination acting upon the sequences in the loci, to prevent the successful classification of alleles into 2 loci. Future studies on the MHC exon 3 region, known to have more homogenized sequences, could reveal a more definitive allele placement.

Components of Thesis

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