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Jumjum, a Western Nilotic language, has an eight-vowel system divided into two sets by the feature [ATR] (Advanced Tongue Root), which is the basis of vowel harmony. A comparison with other Western Nilotic languages shows that (i) this vowel system goes back to a ten-vowel system in Proto-Western Nilotic (PWN), (ii) PWN high [−ATR] vowels have become high [+ATR] vowels in Jumjum, and (iii) conversely, PWN high [+ATR] vowels have become high [−ATR] vowels in Jumjum. The sequence of changes that resulted in this [ATR] reversal in Jumjum relative to PWN provides a historical explanation of synchronically odd, grammatically conditioned vowel-quality alternations in this language.