There are gaps in terms of missing proofs in the theory of evolution but the theory is largely valid. It actually accounts quite well for all bio diversity. In fact, there are islands where due to unique conditions evolution is taking place at a fairly rapid pace.
It is difficult to prove in every case conclusively what organism exactly came from where. However, there is a vast preponderence of evidence for a lot of plants and animals.
In humans the evolutionary line from apes is mostly clear. There are gaps though. But if you go over the entire evolutionary theory on apes, you will find it accounts quite well for the differences among various ape families in terms of evolutionary origin and the evolutionary end.
Just because there are gaps in the proofs, it does not discount the entire theory.
