Rooted trees
A rooted tree is a tree diagram where the branches are ordered descending from a ‘root point’
The root is the oldest part of the tree and tells us the direction of evolution, with the flow of information moving from the root (from the past), towards the tips or ‘leaves’ (to the present).
For example, In the diagram below the circle coloured in black was chosen as the root, when reordering the tree based on this root we can see that the direction of change now flows away from the black circle down towards the others.
Below is another example where we can see how the relationships in the tree change based on how we define the root.
E.g When we pick edge 1 as the root we see that 2 and 3 become sister taxa that share a most recent common ancestor.
If we choose edge 2 as the root, 1 and 3 become sister taxa, now these leaves share a most recent common ancestor.
And if we choose edge 3 as the root, 1 and 2 become sister taxa, again the relationship in the tree has changed, now 1 and 2 share a most recent common ancestor.
Rooting methods
There are two general rooting methods:
1.Out group rooting.
2.Mid point rooting.
Out group rooting
In out group rooting the tree is rooted by the edge that represents an ancestral lineage which is related to, but sits outside, the in group.
This lineage, or out group will be the data point that, to the best of your knowledge, represents a common ancestor to all of the leaves in your tree.
Rooting in this way gives a tree the direction of time and an order of descent, ultimately turning the tree into a directed graph.
Rooting is not always straight forward and choosing the right root point can require some thought (this will be explored in more detail in another post).
Mid point rooting
In mid point rooting the distances between tips are first calculated. The root is then placed at the centre of the two longest branches (or in biology speak, between the two most divergent taxa).
Mid point rooting relies on the assumption that all of your sequences are evolving at the same rate (usually this assumption is not true with real data and so out group rooting is often preferred).