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In Evolutionary Biology (or, more often, Paleontology), this refers to an individual somewhere between two extremes that are believed to be related. For example, Whales are Mammals, and presumably evolved on land -- but several adaptations were needed for life underwater. Where are the species that had only some of these adaptations, or had early partial versions of some of these changes. (For whales, some have been found in Pakistan.)

Humans are similar to chimpanzees, but also very different -- if we are really related, then how come there aren't other species in between? (They are believed to be extinct, but we have found fossils of some, such as the Australopithicines.)