There are a couple different answers to this, none of which are exactly what you want but I'll explain them for completeness's sake.
- Truly "dead end" species that never produce any subspecies and fall under a moving population threshold are automatically pruned from the tree
- There is a "purge tree" button to delete all historical data and start the tree over, but that would lose you the ancestry line of the currently extant species.
A "prune" option could probably be worked up.