Department or Program
Environmental Studies
Abstract
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.
Level of Access
Restricted: Campus/Bates Community Only Access
First Advisor
Donald Dearborn
Date of Graduation
Spring 5-2015
Degree Name
Bachelor of Arts
Recommended Citation
Agyare, Yaa Asantewaa, "Phylogenetic Analysis fails to sort MHC Class II B Exon 2 Alleles by Locus in the Great Frigatebird (Fregata minor)" (2015). Standard Theses. 80.
https://scarab.bates.edu/envr_studies_theses/80
Number of Pages
42
Components of Thesis
1 pdf file
Restricted
Available to Bates community via local IP address or Bates login.