Delineation of discrete population segments of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequence analysis

Shortnose sturgeon Acipenser brevirostrum is federally listed as ‘‘an endangered species threatened with extinction’’ in the U.S. but its listing status is currently under review. As part of this process, the U.S. National Marine Fisheries Service will determine if shortnose sturgeon are divided into Distinct Population Segments (DPS) across its distribution. In this regard, we sought to determine if shortnose sturgeon occur in genetically “discrete population segments,” and if so, the boundaries of each. We used mitochondrial DNA (mtDNA) control region sequence analysis to assess the genetic discreteness of 14 of 19 river populations that were recommended as DPS in the 1998 Final Recovery Plan for Shortnose Sturgeon. Nine of the 14 proposed DPS proved significantly discrete ( P < 0.05 after Bonferoni correction) from both of their bracketing populations, the exceptions being those in the Penobscot River, Chesapeake Bay, Cooper River, and Ogeechee River (our sample from the Cape Fear River was insufficient to statistically analyze). Haplotype frequencies in the newly “rediscovered” Penobscot River collection were almost identical to those in the proximal Kennebec River system. Genetic data in combination with tagging results suggest that shortnose sturgeon in the Penobscot River are probably migrants from the Kennebec. Likewise, shortnose sturgeon found today within the Chesapeake Bay appear to be migrants from the Delaware River. While haplotype frequencies in the remnant Santee River population in Lake Marion differed significantly from those in nearby Winyah Bay, they did not differ significantly from those in the Cooper River. This suggests that the Cooper River harbors descendants of the Santee River population that are unable to access their historical spawning locales. The Ogeechee River collection was not genetically distinct from that in the nearby Savannah River, suggesting that it may host descendants of hatchery-reared individuals of Savannah River ancestry. Our genetic results indicate that most, but not all, rivers with shortnose sturgeon host genetically discrete populations, constituting important information in the consideration of DPS designations. However, shortnose sturgeon migrations through coastal waters to proximal rivers and release of hatchery-reared fish may confound results from genetic studies such as ours and lead to the possible misidentification of discrete population segments.