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COSEWIC assessment and status report on the Atlantic Salmon (Inner Bay of Fundy populations) in Canada

Limiting Factors and Threats

The causes of the marked decline of Atlantic salmon throughout much of their range (WWF 2001), and the collapse in some locations, such as the iBoF, are not well understood.  Several major reviews have attempted to identify and prioritize causes, but there is currently no consensus.  For example, a group of experts discussed 62 factors potentially threatening the survival of Atlantic salmon in eastern North America (Cairns 2001).  Of the 12 leading factors, five are related to predation, five to life history, one to fisheries, and one to physical/biological environment.   Furthermore, two were related to freshwater life stages, nine were related to marine life stages, and one was related to a freshwater cause that manifested in the marine stage. 

The Research Technical Committee of the iBoF Atlantic Salmon Recovery Team identified 49 possible threats but found that there is insufficient information to support conclusions as to the actual threat posed by any of these factors (National Recovery Team 2002).  They recognize that some river populations will suffer from both local threats (e.g., dams) and the regional threats that all iBoF populations apparently share.  Their leading freshwater considerations are: depressed population phenomena (abnormal behaviour due to low abundance; inbreeding depression), and changes in environmental conditions (climate changes leading to premature smolt emigration and decreased freshwater productivity; atmospheric changes increasing ultraviolet radiation).  Leading marine considerations are: interactions with farmed and hatchery salmon (competition with escapees; parasite and disease epidemics), ecological community shifts (increased predation by native species; lack of forage species), depressed population phenomena (lack of recruits to form effective shoals), environmental shifts (regime shift depressing ocean productivity; altered migration routes leading to depressed survival), fisheries (excessive illegal and/or incidental catch), and the possibility of cumulative interactions among these or more factors.  There are considerable research needs if the causes of the mortality of iBoF Atlantic salmon are to be understood.

Since the publication of the National Recovery Team’s report in 2002, there has been increasing concern that pesticides and endocrine-disrupting environmental contaminants may affect the survival of Atlantic salmon in fresh water (e.g., NMFS 2005).  A number of recent studies have provided experimental evidence that suggests a negative association between exposure to various contaminants in fresh water and subsequent survival at sea.  Moore et al. (2003), for example, found that exposure of Atlantic salmon smolts to the oestrogenic chemical 4-nonylphenol (a product found in many products, including pesticide formulations) and the pesticide atrazine (a commonly used herbicide) significantly increased the mortality of smolts when transferred to sea water.  Similar results were reported by Waring and Moore (2004).  Notwithstanding the increased general concern about the potential effects of contaminants of salmon smolt survival, it is not known whether the level of pesticides and other contaminants in those iBoF rivers where these chemicals exist are sufficiently high to significantly influence salmon smolt survival.

A challenge to interpreting the current declines is the partitioning of historic impacts from those currently at play, as Atlantic salmon in the iBoF have experienced a long history of fishing (commercial, recreational and bycatch), habitat modification (e.g., forestry), chemical use in watersheds (e.g., agriculture), and other threats that have contributed to their decline and current status.  Historically (since the mid-19th century), barriers to salmon migration, such as dams, dykes and causeways, have also impacted many iBoF rivers.  For example, many rivers now have tidal barriers that have reduced the habitat available for salmon.  In 1968, the construction of the Petitcodiac River causeway itself impacted about 20% of iBoF salmon production (National Recovery Team 2002; DFO 2003).  It is possible that the impact on such a large component of production may have affected the sustainability of iBoF Atlantic salmon today (Hutchings 2003).  For instance, gene flow from this relatively large population into neighbouring smaller populations may have been important for their genetic ‘health’ (e.g., diversity) and local persistence.  Another possibility is that the iBoF Atlantic salmon are part of one or more metapopulations in which local extinctions and recoveries are characteristic natural histories.  The loss of a major source-population may require several decades before its effects are seen on a metapopulation.  Other habitat losses are known through forestry, agriculture and road-building activity in the iBoF region.  The Recovery Team has decided to focus on threats that coincide temporally with the current declines in wild numbers, and the extent to which historic declines are relevant to the current collapse remains uncertain.

Reduced survival from smolt to adulthood in the marine environment is believed to be a principal limiting factor (National Recovery Team 2002, Amiro 2003).  For example, the survival of tagged iBoF hatchery smolts to first spawning, while variable, is thought to have decreased from an average of 6% (range 1-10%, Big Salmon River 1966-1991, Ritter 1989) to 0.3% for the Big Salmon River (2002 smolt class; Gibson et al. 2004) and between 0.02 and 0.42% for the Stewiacke River (1991-1993; Amiro and Jefferson 1996, see also Amiro 2003).  Hatchery smolt returns in the nearby Saint John River (oBoF) were less than 0.5% in 2002 (DFO 2003).  Reddin et al. (2000) demonstrated at least a 50% decline in smolt-to-adult survival for two rivers in Newfoundland between the 1970s and the 1990s.  For rivers in Maine, Baum (1997) reports that smolt-to-adult survival has declined from 3-15% in the 1950s and 1960s, to 0.5-1.5% in the 1990s.  For Europe, Potter and Crozier (2000) report wide-scale declines in marine survival, beginning in the late 1980s.  These and other studies suggest that decreases in marine survival, which began in the late 1980s, are a significant factor in Atlantic salmon population decline.

What is the population impact of this reduced marine survival?  Amiro (2003) suggests that marine (smolt-to-adult) survival on the order of 3.57% is necessary to provide population stability for iBoF populations.  This is calculated from an assumed freshwater production rate of 28 smolts per spawning salmon, which is derived from the DFO conservation requirement of 2.4 eggs per m2 (DFO 2003).  Following this logic, we can show here that marine survivals of, for example, 0.1%, 1% and 3% would decrease the population size by 97%, 72% and 16% per generation.  Using the decline rate data for Big Salmon and Stewiacke rivers (Gibson and Amiro 2003, Gibson et al. 2003c), the 11 year (3-generation) decline rates of 94.1% and 99%, respectively, give 83% and 97% declines per generation (4-years).  Assuming 28 smolts are produced per spawner, and attributing the declines solely to decreased marine survival, the marine survival rates for these rivers would be 0.6% and 0.1%, respectively.  These rates are consistent with estimates of recent marine survival of iBoF salmon (e.g., 0.3% in 2002 for the Big Salmon River in Gibson et al. 2004; 0.08% for the Stewiacke in Amiro 2003).  The decrease in marine survival may therefore be driving the collapse of iBoF salmon, despite maintained freshwater survival.  Only limited research has been put into resolving the cause of elevated marine mortality (e.g., Cairns 2001).

There is, however, another factor of note, and that is the potential impact of the fish farming industry.  At about the time that iBoF wild salmon were declining, the fish farming industry for Atlantic salmon was rapidly growing in the Bay of Fundy (Amiro 1998, Chang 1998), and escapes of farmed Atlantic salmon into wild rivers began to be recorded (e.g., Carr et al 1997, Stokesbury and Lacroix 1997).  For example, in the Magaguadavic River of the outer Bay of Fundy, adult returns in 1996 consisted of 57% farmed fish that escaped from sea cages, 34% progeny of naturally spawned fish, and 9% farmed fish that had escaped as juveniles from hatcheries (Lacroix and Stokesbury 2004).  Recent genetic assessments in the Upper Salmon River by P. O’Reilly (DFO, personal communication, 9 September 2004) indicate that up to 10% of juveniles in this iBoF river have genetic markers consistent with European aquaculture.  Since only about 10% of the Bay of Fundy farmed stock is of European ancestry, this finding suggests that a much larger proportion of wild fish are at least partially descended from aquaculture fish.  There have been many reviews and studies showing that the presence of farmed salmon results in reduced survival and fitness of wild Atlantic salmon, through competition, interbreeding and disease (e.g., Gross 1998; Fleming et al. 2000; NRC 2002, 2004; McGinnity et al. 2003).  For iBoF Atlantic salmon, an experimental cross between 4th-generation farmed Atlantic salmon of the Saint John River, and wild individuals from the Stewiacke River, showed a significant decrease in F1 survival to the pre-eyed embryonic stage relative to pure crosses (Lawlor 2003).  The magnitude of the impacts of fish farming on iBoF Atlantic salmon remain to be determined, but may be among the leading causes of their decline.