The existence of similar but unrelated species was a puzzle to Darwin. Later, he realized that similar animals in different locations were the product of different lines of evolutionary descent.
For example, the beaver and the capybara are similar species that inhabit similar environments of North America and South America. The South American coypu also shares many characteristics with the North American muskrat.
Reference: http://animals.nationalgeographic.com/animals/mammals/beaver/
Reference: http://www.rebsig.com/capybara/
Reference: http://www.animalspot.net/coypu.html
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