Genetic Structure of Northeastern US American Shad Populations

American shad (Alosa sapidissima) are an important component of the diadromous fish community.  Evaluation of the genetic structure of American shad stocks, with particular focus on northeastern and Maine drainages can be used to understand the genetic relationships among drainages and provide information for management.  Samples were obtained between 2008 and 2012 from six drainages in Maine, as well as the Merrimack, Connecticut, Delaware, Hudson, and Susquehanna rivers, and results obtained from 15 variable microsatellite loci were compared to estimate genetic diversity.  Out of basin stocking has been a commonly used management action to restore American shad populations throughout New England. American shad from both the Connecticut and Merrimack Rivers have been widely distributed to other New England rivers, including the Kennebec, Androscoggin, and Saco rivers.  Similarly, American shad from the Hudson and Delaware have been used to supplement the Susquehanna River. Comparisons of differences in allele frequencies among all rivers sampled indicated that samples obtained from the Narraguagus River and Delaware River were significantly different (P<0.01) from all rivers analyzed, both of which have received limited to no out of basin stocking.  Samples from the Connecticut and Merrimack Rivers, a historical source for American shad stocking in New England did not differ significantly in allele frequencies from the Androscoggin, Kennebec, Penobscot, Saco, or Sheepscot drainages, but did significantly differ in allele frequencies from the Narraguagus River (P<0.01), which received little to no stocking.  Pairwise differences in allele frequencies from American shad sampled from the Hudson, Susquehanna, and Delaware rivers generally were significantly different from the Connecticut, Merrimack, and Maine rivers (P<0.01).  Resulting information about the genetic structure of American shad populations and knowledge of the history of stock transfer can be used to evaluate past and current reintroduction efforts, and to assist ongoing management and conservation efforts for American shad in the northeastern US.