Fine-scale population structure in Atlantic salmon from Maine's Penobscot River drainage

We report a survey of microsatellite DNAvariation in Atlantic salmon from theunimpounded lower reaches of Maine's PenobscotRiver. Our analysis indicates that Atlanticsalmon in the Penobscot River are distinct fromother populations that have little or nohistory of human-mediated repopulation,including two of its tributaries, Cove Brookand Kenduskeag Stream, another Maine river, theDucktrap, and Canada's Miramichi and Ganderrivers. Significant heterogeneity was detectedin allele frequency among all threesubpopulations sampled in the Penobscotdrainage. The high resolution of the 12-locussuite was quantified using maximum likelihoodassignment tests, which correctly identifiedthe source of 90.4–96.1% of individuals fromwithin the Penobscot drainage. Currentpopulations are clearly isolated from eachother, however we are unable to determine fromthe present data whether the populations inCove Brook and Kenduskeag Stream are recentlydiverged from populations stocked into thePenobscot River over the last century, or areaboriginal in origin. The degree of populationstructure identified in the Penobscot drainageis noteworthy in light of its lengthy historyof systematic restocking, the geographicproximity of the subpopulations, and the extentof the differentiation. Similar populationstructure on this extremely limited geographicscale could exist among Atlantic salmon runselsewhere in Maine and throughout the species'range and should be taken into account forfuture management decisions.