To present evidence that red panda populations are becoming less diverse over time, you would want to show how the measure of diversity (nucleotide diversity) changes as the generations progress. In this case, the independent variable would be the generation (which you manipulate or track over time), and the dependent variable would be the nucleotide diversity (which is expected to change in response to the different generations).
Thus, the correct choice would be:
Independent = Generation and Dependent = Nucleotide Diversity