Molecular Phylogenetic Tree using Three Different Methods based on p-distance Model

Abstract

Phylogenetic inference is needed in describing the relationship between proteins, genes or species. In phylogeny, the object is assumed to be evolutionary related. The evolutionary tree is used to show the evolutionary relationship among the organisms. However, to build reliable evolutionary tree, reliable set of data is needed to find the best model. In this paper, the data is obtained from D-loop region in mitochondrion DNA (mtDNA) that is available in Gen Bank. Five different species of animals were used, those were: Bison bison, Bos taurus, Bos indicus, Bubalus bubalis, and Capra hircus. The objective was to obtain the most reliable method, measured by its stability among UPGMA, Minimum Evolution, and Neighbor-Joining. To build the cases, five species were grouped into seven classes that have different characters. P-distance model was used to build the distance matrices. The reliability of each method was measured using the Felsentein’s bootstrap method. The whole bootstrap process for each method will be repeated 100, 1000, and 10000 times to detect its reliability. Almost all methods do not have the misclassified problems in reconstructing the evolutionary tree. However, Minimum Evolution failed to reconstruct a reliable evolutionary tree compared to UPGMA and Neighbor-Joining.