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.”
Excel worksheet: “Additive trees”
Summary: This worksheet is analogous to “Ultrametric trees,” except that the tree
generated is additive rather than ultrametric. This introduces some new challenges in
reconstructing the phylogeny.
As before, enter the number of taxa in the red-lined cell. The program will then generate
a distance matrix for both an ultrametric tree (which, having done previously, we can
ignore) and an additive tree. Remember that the tips of an additive tree will not all be
the same distance from the tree’s root, which means that reconstruction becomes a little
bit trickier.
Points to note:
• The additive tree was derived by just adding random branchlengths on to the end of the
terminal branches of the associated ultrametric tree. As a result, the additive tree will
always be longer than the ultrametric tree; this is NOT necessarily true for real
phylogenies.