Optimization Techniques for Deriving Genetic Sequences of Ancestral Species Within Phylogenetic Trees
Ilya Vasey
Department of Mathematics
Faculty Supervisor: Serkan Hosten
Reconstructions of the DNA sequences of ancestral species reveal useful information about the stability of genomes during rapid evolutionary transition, identification of genes responsible for certain traits, and tracking disease mutations. Maximum parsimony is a method of phylogenetic tree reconstruction that works off the assumption that the least amount of genetic mutations between a parent specie and its descendant specie will occur. Integer Programming is an effective method for reconstructing the DNA sequences of ancestral species using the mapped genomes of their descendants. My program is a mathematical model of a phylogenetic tree that reads the known nucleotide base-pair sequences of select genes from the descendant’s genomes, and reconstructs the likely nucleotide base-pair sequences of ancestral species, using the method of maximum parsimony, in the form of an optimal solution to an Integer Program. My model is tested on several species of flies within the order Diptera using the mapped sequences of shared genes.