Basic Applied Bioinformatics

CHAPTER 22Construction of Phylogenetic Tree: Fitch Margoliash (FM) Algorithm

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

22.1 INTRODUCTION

This is the first algorithm based on least squares principle for phylogenetic tree reconstruction. It was developed by Walter Fitch and Emanuel Margoliash in 1967 (Fitch and Margoliash, 1967; Fitch, 1970, 1971). The evolutionary distances between the taxa are determined by the Jukes–Cantor model when DNA sequences (instead of distances) of the same length are entered.

22.1.1 Principle

The algorithm is based on optimality criteria that select the tree with a minimum amount of residual (difference between actual and expected summed evolutionary distance). The algorithm estimates the total branch length (distance) and clusters in accordance to taxa pair in order to determine the unrooted tree with minimum distance.

1. The FM algorithm does not assume a constant rate of evolution, which is quite realistic.
2. Optimized tree can be selected out of a number of possible trees.
3. Its demerit is underestimation of very long evolutionary distances, because it ignore homoplasies (absence of a character in the common ancestor, though it is being shared by a group of related species originating from the common ancestor).
4. It ignores the role of intermediate ancestor(s); hence, consistency of evolution is not the basic assumption.
5. Outgroup is added to the sequences in order to generate a rooted tree using the FM method. ...