Anadromous species occupy multiple freshwater, estuarine, and marine habitats, which poses special challenges in wildlife management. In particular, the level of immigration between drainages can be a critical factor in the definition of management units and the design of population-specific stocking programs. The semi-anadromous shortnose sturgeon (Acipenser brevirostrum) is listed as an endangered species under the Endangered Species Act in the United States. To assess population structure in this species as a guide to effective management, tissue samples were collected from adult specimens (N = 198) from five river systems in the southeastern U.S., and augmented with a sample from New Brunswick, Canada (N = 13), the extreme northern end of the species' range. Comparisons of mtDNA control region sequences reveal a shallow gene genealogy and modest, but significant, population structuring (φ st = 4.3% or φ st = 17.7% when Canadian samples are included). Popula-tions inhabiting river systems in the southeastern U.S. are closely related, a pattern consistent with more recent divergences along evolutionary timeframes. Haplotype diversity is moderate to high in most drainages (h = 0.383– 1.000), except for the Savannah and Edisto rivers, indicating that historical levels of mtDNA diversity might be largely intact outside of these drainages. Low mtDNA diversity in the Savannah and neighboring Edisto drain-ages might stem from an experimental stocking effort during 1984–1992 that depressed overall genetic diversity in the Savannah and established or augmented the Edisto River population with a relatively limited number of matrilines.
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