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Lines of evidence: The science of evolution :

Homologies: comparative anatomy

Organisms that are closely related to one another share many anatomical similarities. Sometimes the similarities are conspicuous, as between crocodiles and alligators, but in other cases considerable study is needed for a full appreciation of relationships.

Modification of the tetrapod skeleton
Whales and hummingbirds have tetrapod skeletons inherited from a common ancestor. Their bodies have been modified and parts have been lost through natural selection, resulting in adaptation to their respective lifestyles over millions of years. On the surface, these animals look very different, but the relationship between them is easy to demonstrate. Except for those bones that have been lost over time, nearly every bone in each corresponds to an equivalent bone in the other.

Whale/hummingbird comparison

Lines of Evidence
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Read more about recognizing homologies.