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    Atlantic salmon aquaculture is a major industry in downeast Maine and has grown steadily since its inception in the early 1980’s.  As the industry has grown, so has concern about its environmental impacts.  Concerns have arisen from the practice of rearing salmon in net pens in the bays and estuaries of downeast rivers that have their own runs of sea-run hatchery-supported Atlantic salmon.  Some of these concerns are disease transmission from farm to sea-run fish, competitive exclusion, and the resultant genetic swamping of sea-run stocks in the rivers by net pen escapees.  To date, there is no evidence that any of these concerns have ever been realized.

    Regarding the genetics issues, management officials have made the assumption that the farm raised fish are somehow genetically inferior to the sea-run fish they are producing for river stocking programs.  This assumption is based on conservative fisheries management theory and conservation biology.  It is also based on the “hatchery effect”, which is the loss of genetic variation over time in hatchery-supported fish stocks, and has been observed in several different species.  Genetic variation is lost in these stocks over time due to inbreeding and genetic drift at a rate roughly proportional to the number of broodstock used.  Thus, as the number of broodstock used to make the next generation decreases, so does genetic variability, and ultimately reduces the ability of the population to adapt to a changing environment.  Maintaining genetic variation is considered paramount in species management programs, thus it would be prudent to avoid mixing the sea-run stocks with other stocks that have reduced levels of genetic variation.  However the amount of genetic differentiation (here meaning the gain or loss of variability, and the presence of unique genetic markers in the aquaculture stocks) between sea-run and farm fish populations of specific concern to downeast Maine has never been tested in any scientific manner.  The study presented herein addresses the question of genetic differences between Penobscot River sea-run fish and three of the Atlantic salmon strains used in commercial aquaculture in coastal downeast waters.

    There have been several “strains” of Atlantic salmon and their hybrid crosses used for culture in the offshore net pens.  The primary strains used are descendants of Penobscot and St John River sea-run fish and the Scottish Landcatch.  The Scottish Landcatch was imported from northern Europe and have gone through several generations of domestication and selection.  The Penobscot and St John strains, on the other hand, are supplemented with gametes collected from the broodstock used to maintain their namesake sea-run populations.  This would be expected to reduce the amount of differentiation between the wild and aquaculture stocks and to prevent or slow the loss of genetic variation from the aquaculture stocks.  Again, this can only be answered by directly measuring the amount of genetic variation in the stocks of interest.

    The method used to address the degree of genetic similarity between the Penobscot sea-run and the aquaculture stocks was allozyme analysis.  Briefly, allozymes are enzymes whose chemical activity can be easily assayed in the lab using colorimetric tests.  The colorimetric tests are highly efficient in resolving alternate forms of the enzymes that are the direct result of genetic differences.  Their use in fisheries management and genetics dates back to the late 1960’s, and their patterns of inheritance and expression are very well documented and established in salmon and trout.  Tissue samples used for allozyme analysis were taken from Penobscot sea-run broodstock held at Craig Brook NFH (Orland, Maine) and from three aquaculture strains during processing at DE Salmon Co. (Lubec, Maine).  Samples taken from the Penobscot sea-run broodstock represent the Maine – New Brunswick sea-run populations collectively (the Maine – New Brunswick metapopulation), as it is known that the individual rivers do not differ genetically from one another and are largely derived from the Penobscot sea-run stock.

    Genetic differentiation can be measured in a variety of ways.  Three of the most common are via Wright’s F-statistics, contingency tables (Fisher’s Exact Test), and dendrograms produced from Nei’s Unbiased Genetic Distances.  All three are calculated independent of each other and are used extensively in genetics studies addressing the type of questions pertinent to this study.  To avoid biasing the results of this study, all three methods were used to analyze the data, which allowed the conclusions to be more robust.

    The results of this study demonstrate the genetic variation within the Penobscot and St. John aquaculture stocks is not significantly different from the Maine / New Brunswick metapopulation.  Furthermore, the amount of genetic variation (heterozygosity) in the Penobscot and St. John aquaculture stocks is no less than the levels found in the wild populations.  Thus the concern of farm fish reducing the level of genetic variation in the sea-run stock is not a significant issue.  This may have resulted from the fact that the rivers themselves are hatchery supported, often from broodstock sizes of fewer than 50 individuals, and do not differ significantly from one another.  However, the Scottish landcatch fish do differ significantly from the sea-run stock and have a very low level of genetic variation compared to the Maine - New Brunswick metapopulation.  Regarding unique genetic markers, the Penobscot and St John aquaculture strains shared the same markers as those found in the sea-run stocks they were derived from. While the Scottish Landcatch did not possess any unique markers either, they were missing some that are found in high frequency in the metapopulation.  From a pure genetics standpoint, it would be in the best interest of the sea-run stocks to prevent introgression between the Scottish landcatch and those of the rivers, as successful introgression may reduce the level of genetic variation currently found in the sea-run stocks.

    In conclusion, it must be noted the purpose of this study was to address the question of whether or not the aquaculture stocks are different from the metapopulation as far as the presence of unique genetic markers and the loss of genetic variation due to hatchery effect.  In the Penobscot and St John stocks, the aquaculture stocks actually had higher levels of genetic variation than the sea-run stocks from which they originated.  This suggests the hatchery-supported sea-run stocks are loosing variation faster than the aquaculture stocks and is opposite of the assumption made by management officials.  From the gestalt of the data in this study, the low level of differentiation between the Penobscot and St John aquaculture strains and the sea-run stocks does not support any “uniqueness” of these stocks from one another.  The Scottish Landcatch, however, could be easily regarded as unique from the North American stocks, and it would be in the best interest of the sea-run stocks to avoid introgression between the Landcatch and sea-run stocks.

    Studies reporting the differences between aquaculture stocks and their source populations are virtually nonexistant in the mainstream literature, hampering comparisons of the results of this study to similar situations in other parts of the geographic range of the Atlantic salmon.  As a final caveat, two other major factors of concern regarding interaction between aquaculture stocks and sea-run river stocks are disease transmission from domestic to sea-run stocks and behavioral differences that may exclude sea-run stocks from vital resources.  The genetic data of this study cannot be extrapolated to either question, as both of these other issues must be resolved independently of the genetics and of each other.

About the authors

Jeff Rodzen holds a B.S. in Marine Ecology from University of Maine at Machias and a PhD in Animal Genetics from the University of California – Davis, where he worked in the Genomic Variation Laboratory under Dr. Bernie May.  His background is in fisheries / population genetics and animal breeding.  Dr Eric Kindahl holds a PhD in Genetics from Cornell University with a strong background in conservation and population genetics.  He is a former assistant professor of biology at University of Maine at Machias and currently is an assistant professor of biology at Hood College, Frederick, Maryland.
 

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