Refined Buneman Trees

Chapter 3
Evolution and
Bioinformatics
The theory of evolution is accredited to Charles Darwin and his work On the
Origin of Species by Means of Natural Selection, or the Preservation of Favoured
Races in the Struggle for Life from 1859. At the time, the theory challenged
many established beliefs, particularly religious beliefs. Before Darwin the origins
of life were credited to so-called “Creation Science” and other superstitions,
and even today small pockets of resistance to Darwins theories exist, notably in
Alabama, USA.
Evolution was hinted at before Darwin, for example by Jean Baptiste de
Lamarck, who suggested that life was governed by two principles: the principle
of use and disuse - individuals lose characteristics they do not require and
develop those which are useful. And inheritance of acquired traits - individuals
inherit the acquired traits of their ancestors. Even in ancient Greece the, Anaximander
fostered ideas similar to evolution. But not until Darwin were these
theories supported by any real scientific evidence.
3.1 The Tree of Life and the language of DNA
After Darwin introduced his theory, biologists started working on reconstructing
the evolutionary history of all organisms on earth, and expressing it in the form
of a phylogenetic tree, the Tree of Life, illustrated in Figure 3.1. This work
was carried out on fossils and living species, using comparative morphology and
comparative physiology. These methods are however rather imprecise, and the
trees thus constructed have been somewhat controversial.
All of this changed when Watson and Crick discovered the ability of deoxyribonucleic
acid (DNA) to encode and replicate hereditary information. Suddenly,
scientists were able to read the recipe for a species in its DNA, which is basically
a string over the alphabet Σ = {A, C, G, T }. It became possible to readily compare
two organisms just by comparing their DNA in a precise and systematic
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