Phylogenetic reconstruction — Intro
One important part of evolutionary biology is determining the ways in which different species are related to each other. This is done by building an evolutionary tree (or “phylogeny”) for a collection of species, a process called phylogenetic reconstruction. Morphological, behavioral, and molecular data can all be used to construct a phylogeny; it’s even possible to combine different types of data in the same tree.
In these exercises, we will build phylogenies using distance-based methods, which group species together on the basis of how many differences exist between them. Another class of tree-building techniques, character-based methods, focuses on evolutionary innovations shared by more than one species. [In general, distance-based methods try to make use of all the available data, while character-based methods use only the part of the data most likely to yield an accurate evolutionary signal.]
Ultrametric trees — Intro
A phylogenetic tree is called ultrametric if each tip is exactly the same distance from the root. A tree that is not ultrametric is termed an additive tree. Examples of an ultrametric and an additive tree are drawn below.
Figure 1A:
An ultrametric tree.
Figure 1B:
An additive tree.
Excel worksheet: “Ultrametric trees”
Summary: This worksheet generates a pairwise distance matrix for an ultrametric tree containing a user-specified number of species (taxa). From this matrix, the user can reconstruct the ultrametric tree using pencil and paper.
In the cell outlined in red, enter the number of species or other taxa for which you want to build a phylogenetic tree. (Ignore the row of dark gray cells to the right). The program will then generate a pairwise distance matrix indicating the number of differences between each pair of taxa. This matrix contains enough information to let you construct an ultrametric tree. It’s best to start with only 6-8 taxa until you get the hang of it.
Points to note:
• The program can at present handle at most 20 taxa. This capacity can easily be expanded if required.
• The gray and white lines have no special significance: they’re present just to make the matrix easier to read.
• A quick way to generate a new distance matrix without changing the number of taxa is to click the “Calculate Now” button in the toolbar at the top of the page. Alternatively, open the Edit menu, go to Preferences, choose the Calculation tab, and note the keyboard shortcut for “Calc Now.”