When comparing two species, the presence of which type of structures indicates descent through modification from a common ancestor

Homologous characters indicate descent through modification from a common ancestor.

Explanation:

Homologous characters have the same fundamental structures. They also share the same relations with adjacent structures, and they have the same embryological development.    

These structures might show variations between organisms exhibiting them, according to their function and to the environment in which the organism lives.  

These homologous characters are common in organisms related and that share a common ancestor.  

For example, whales, humans, and horses all have the same bones in the same order, but they matured differently in later embryological development. This is an example of homologous characters.

the principles and empirical processes of discovery and demonstration considered characteristic of or necessary for scientific investigation, generally involving the observation of phenomena, the formulation of a hypothesis concerning the phenomena, experimentation to test the hypothesis, and development of a conclusion that confirms, rejects, or modifies the hypothesis.