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Cranial neural crest cells generate the distinctive bone and connective tissues in the vertebrate head. Classical models of craniofacial development argue that the neural crest is prepatterned or preprogrammed to make specific head structures before its migration from the neural tube. In contrast, recent studies in several vertebrates have provided evidence for plasticity in patterning neural crest populations. Using tissue transposition and molecular analyses in avian embryos, we reconcile these findings by demonstrating that classical manipulation experiments, which form the basis of the prepatterning model, involved transplantation of a local signaling center, the isthmic organizer. FGF8 signaling from the isthmus altersHoxa2 expression and consequently branchial arch patterning, demonstrating that neural crest cells are patterned by environmental signals.