Mitochondrial DNA diversity in North American and European Atlantic salmonwith emphasis on the Downeast rivers of Maine

The displacement loop and NADH-I dehydrogenase regions of mitochondrial DNA (mtDNA) were amplified by the polymerase chain reaction in 954 Atlantic sa lmon and digested with 40 restriction endonucleases. Variation was detected with 10 enzymes, resulting in 21 composite haplotypes which were strongly patterned geographically with a major discontinuity observed between most N orth American (NA) and European salmon. Significant heterogeneity of haplot ype frequencies was found within and among all classification levels (conti nent, country, and river). Haplotype frequencies were significantly differe nt across continents, within European samples, within NA samples, within Ca nadian samples, within wild Maine samples, within captive Maine strains, an d between captive and wild Maine strains. Nine haplotypes occurred only in NA, seven in Maine, three only in Maine, and 11 occurred only in Europe. So me Maine rivers had only a single haplotype, suggesting that effective popu lation sizes may be low. The second most frequent European haplotype: occur red in tributaries to one Newfoundland river. Gene trees based on parsimony and generic distance suggest that the haplotypes are monophyletic within e ach continent, and that the haplotype found on both continents is intermedi ate between those of Europe and NA, suggesting common ancestry of all haplo types.