What is a Quagga?

Interpreting the Phylogenetic Trees and Assessing the Relatives of the Quagga

Allan Wilson and his colleagues constructed phylogenetic trees for two gene regions. From the placement of the quagga on these trees, they inferred the quagga's relationship with other animals.
Recall that evolutionary close relatives have a common ancestor that is less deep in a phylogenetic tree than is the common ancestor of two distantly related organisms. When branch lengths are proportional to evolutionary change they will indicate whether two organisms differ by a large or small amount from one another, or from their common ancestor.

The Quagga's Relatives

Have a look at the topologies of the two trees that you estimated. What is the quagga's closest relative? Is it the same species for each gene region? Is it a horse or a zebra? If a zebra, then which species?

Recent or Ancient?

In general, evolutionary change accumulates at a roughly constant rate. So, the lengths of branches indicate not only how much change has occurred since an ancestor, but also how much time has elapsed. The branch lengths can give a clue to the age of the quagga.
Now look at the untransformed trees. Consider the difference between the quagga and its closest relative. Has there been a comparatively large or small amount of change, in comparison with the amount of change since its second, or third closest relative? Do you think that the quagga diverged from its closest relative recently or in the distant past?

Give some thought to these questions before moving on to the Conclusions.