1650s "give variety to," from Late Latin variegatus "made of various sorts or colors," past participle of variegare "diversify with different colors," from varius "spotted, changing, varying" (see vary) + root of agere "to do, perform" (from PIE root *ag- "to drive, draw out or forth, move"). Meaning "mark with different colors" is from 1660s (implied in Variegated). Related: vareiegating.
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