Estimating Phylogenetic Trees

Abstract

The third chapter covers a probability model of molecular evolution in a way designed to engage the readers with little interest in mathematics. That is accomplished by stating the model in terms of a competitive game rather than mathematical formulas: one team rolls dice to simulate molecular evolution, and the other team then uses the resulting simulated sequence data to estimate the phylogenetic tree. The description of the game rules gradually eases the readers into some simple mathematical formulas needed to understand how evolutionary distances are corrected for multiple substitutions. Exercises provided at the end of the chapter give the readers hands-on experience with the sequence simulation and tree reconstruction methods.

What is dismembered and torn in pieces through extreme analysis is to be linked again in thought, in a total context of life that cannot be gathered through construction or reconstruction, not in intuition or in an irrational way, but rhetorically arranged, in the medium of history, philosophy, and poetry, and in the logic of the image and of thought.

– Johann Georg Hamann¹

As quoted by Oswald Bayer, A Contemporary in Dissent: Johann Georg Hamann as Radical Enlightener (Wm. B. Eerdmans Publishing) [9].