Population structure of Atlantic salmon in Maine with reference to populations from Atlantic Canada

Anadromous Atlantic salmon Salmo salar from 12 rivers in Maine, 3 rivers in New Brunswick, and 2 rivers each in Nova Scotia, Quebec, Newfoundland, and Labrador as well as 2 landlocked strains in Maine (N = 3,863) were genotyped at 11 microsatellite loci. Fish in the drainages of Maine's Kennebec and Penobscot rivers were genetically similar to those sampled from the 8 rivers recently listed as containing an endangered distinct population segment under the United States' Endangered Species Act. Genetic distance estimates confirm that Maine's Atlantic salmon, both landlocked and anadromous, represent a discrete population unit, genetically as independent from any Canadian population as the Canadian populations are from each other. Within Maine, the anadromous and landlocked populations were statistically distinct. Anadromous Atlantic salmon were more genetically similar among year-classes within rivers than among rivers, as would be expected if the river is the unit of population. The effective number of breeders estimated within each river is larger than the number of adults estimated from samples and redd counts over the 10-year period from 1991 to 2000.