Introduction to Character-Based Phylogeny
Before the modern genetics revolution, phylogenies were constructed from physical characters resulting from direct structural comparison of taxa. A great deal of analysis relied on the fossil record, as fossils provided the only concrete framework for studying the appearance of extinct species and for inferring how they could have evolved into present-day organisms.
A classic case illustrating the utility of the fossil record is the case of dinosaur pelvic bones. In 1887, Harry Seeley proposed a new classification of dinosaurs into two orders, Saurischia and Ornithischia: the former possessed hip bones shaped like those found in reptiles, whereas the latter had a much different hip shape that resembled birds. Seeley's pelvic classification has survived to the present day as the principal division of dinosaurs.
The key point is that hip bone shape is a physical character that separates all dinosaurs into two different groups. Our hope is to construct a phylogeny solely from a collection of characters. Throughout character-based phylogeny, our two-part assumption is that all taxa possessing a character must have evolved from a single ancestor that introduced this character, and conversely, any taxon not possessing the character cannot be descended from this ancestor.
Given a collection of
At the same time, observe that the removal of an edge from an unrooted binary tree produces two
separate trees, each one containing a subset of the original taxa. So each edge may also be
encoded by a split
A trivial character isolates a single taxon into a group of its own. The corresponding split
A character table is a matrix
Given: An unrooted binary tree
Return: A character table having the same splits as the edge splits of