Final answer:
If the isthmus formed gradually, a greater percentage of DNA sequence differences would be seen in deep water species due to more isolation and less gene flow, promoting greater genetic divergence and speciation compared to species in shallow water.
Step-by-step explanation:
If the isthmus formed gradually rather than suddenly, we would expect to see a greater percentage of difference in DNA sequence between species that inhabit deep water than between those that inhabit shallow water. This pattern of genetic divergence is because deepwater habitats are more isolated, reducing gene flow and allowing species to diverge more extensively over time. In shallower waters, there is typically more opportunity for gene flow between different populations, which can reduce the rate at which genetic differences accumulate.
Looking at the evolutionary processes at play, we can understand that when two populations become geographically isolated, such as by a gradually forming isthmus, they can start to evolve independently of each other. Over time, the genetic differences can be profound, especially if they are facing different environmental pressures, as would be the case for species in deep versus shallow waters. This concept is supported by the observation that increased distance promotes speciation, and the marine environment offers unique challenges that amplify isolation in deeper water habitats.