To present evidence that red panda populations were becoming less diverse over time, you want to show how diversity changes across different generations.
The correct identification of independent and dependent variables would be:
Independent = Generation and Dependent = Nucleotide Diversity
This means you would look at how nucleotide diversity (a measure of genetic diversity) changes as you examine different generations of red pandas.
So the best choice is:
Independent = Generation and Dependent = Nucleotide Diversity