Evolution Between Species: Phylogeny

Abstract

In 1834 Charles Darwin (1809–1882) wrote in his notebook “I think”—but instead of writing down what he was thinking, he drew a phylogeny. When he published his thinking in 1859, The Origin of Species contained a single figure: a phylogeny. We already saw that phylogenies in the form of guide trees are useful for computing multiple sequence alignments. But beyond clever computing, phylogenetic trees embody biologists’ thinking, taxonomies are trees and evolution is pictured as a tree. Trees consist of trees, and this hierarchical structure is explored further in the following section. Phylogenetic trees may or may not have a root, and we show the distinct methods to calculate rooted and unrooted trees in two later sections.