Final answer:
On a cladogram, two organisms that are further apart are likely to have fewer amino acids in common, reflecting a more distant common ancestor and greater evolutionary divergence over time. The amino acid sequences and structures of proteins help illustrate these differences and relationships.
Step-by-step explanation:
The cladogram is a graphical representation used to show the evolutionary relationships between different organisms. When two organisms are far apart on a cladogram, they generally have less in common with regard to their amino acid sequences. This is because a cladogram reflects the evolutionary history of organisms, such as the common ancestor, and over time evolutionary changes accumulate causing more differences in the amino acid sequences of distantly related organisms. For instance, a mammal and a bird, being from different classes, would have more molecular differences compared to a mammal and an amphibian (like a frog), or a mammal and a fish, with the mammal and bird having the longest evolutionary separation.
Specifically looking at proteins, the sequence of amino acids can differ substantially between distantly related species. This difference in sequence reflects the evolutionary distance and time since the last common ancestor. For example, human cytochrome c, which contains 104 amino acids, is identical in sequence to that of chimpanzees, indicating a very recent common ancestor; however, when compared to yeast, there are significant differences, indicating a much more distant common ancestor. Similarly, protein structure can be conserved despite changes in the sequence, which also indicates evolutionary relationships, but as structure changes more slowly, it can reflect deeper evolutionary history.