Abstract The threespine stickleback (Gasterosteus aculeatus) is primitively an anadromous or resident marine species but has repeatedly colonized fresh water, where predictable phenotypic divergence usually occurs rapidly. A conspicuous element of this divergence is change of the number and position of lateral armor plates from about 33 that cover the entire flank (complete) to <10 anterior plates (low). This difference is caused primarily by variation at the Ectodysplasin (Eda) locus. The low Eda allele appears to be rarer in two geographically adjacent anadromous populations from Cook Inlet, Alaska than in most marine or anadromous populations reported from elsewhere, and there is no evidence of elevated gene flow for Eda between anadromous and resident lake threespine stickleback populations that breed in sympatry. However, the two anadromous populations are divergent for the frequencies of two complete Eda alleles. It is not clear how monomorphic low-plated freshwater populations in Cook Inlet have almost invariably acquired ancestral low Eda alleles from anadromous ancestors in which this allele appears to be extremely rare
