Are Point Mutations problematic for ToE?

Let’s say there was a large population of one type of species and there was a stream running down the middle until eventually it became a wide river that separated the population in half. Wouldn’t this create a reduction in gene flow for both sides of the river? What is observed is that each population changes over time until they have little resemblance to each other and are classified under a new name. How did they obtain these new genes?