What is represented by the base root of a phylogenetic tree?

The common ancestor.

A phylogenetic tree shows how a species originates (by evolution) other species. It’s very similar a genealogic tree. If you want your family tree, you should write down your name and the names of all your brothers and sisters and then draw a line from all those names to the names of your parents, and then draw a line from the name of your father to the names of your gramma and grampa, and then do the same with the names of your aunts and uncles. If you repeat the process with many, many generations, you will have the common ancestor to all of those relatives. You can do the same with species: for example, humans are supposed to have a common ancestor with monkeys, so their lines will end together in the same point in the graph. Then you have to draw a line from that point to another point that will be shared with other mammalians, then Mammalians share a point with other vertebrates, and so on… If you keep on going, you will get to LUCA someday.

a motor homunculus represents a map of brain areas dedicated to motor processing for different anatomical divisions of the body.

homunculus represents the importance of various parts of your body as seen by your brain. as a result, they take up a lot of brain space. although the cortical homunculus is a curiosity, penfield's work in mapping the brain's relationship to the body was invaluable.

the answer to your question is tooth decay.