The Uncertain Future of Fraser River Sockeye - Publications du ...

Cohen Commission of Inquiry into the Decline of Sockeye Salmon in the Fraser River • Volume 2
lower probability of spawning. A similar pattern
was found for returning adults tagged in the lower
river and on the spawning grounds, although with
not as high a difference in probability of spawning
success between fish with and without the
mortality-related signature. 132
Dr. Miller also testified that in the 2006 study
she found an association of the mortality-related
signature with more rapid entry into the river and
faster migration to the spawning grounds. 133
In a paper prepared for the June 2010 Pacific
Salmon Commission (PSC) workshop (PSC
workshop paper), she reported that approximately
50 percent of the returning adults tested in 2006
carried this mortality-related signature. 134 Salmon
with the signature in the ocean carried a fourtimes-lower
probability of reaching the spawning
grounds, while those carrying the signature at
the spawning grounds were twice as likely to die
prematurely as those without this signature. 135
Dr. Miller’s paper concluded:
This study showed unequivocally that Fraser
River sockeye salmon are entering the river in
a compromised state, that survivorship was
somewhat predictable based on gene expression
[greater than] 200 km before salmon
reach the river, that stocks may be affected
differently, and that the freshwater environment
alone may not be the sole source of the
highly fluctuating mortalities of salmon in
the river. 136
This PSC workshop paper also reported that
Dr. Miller’s team has since observed this same
mortality-related signature in brain, liver, and
gill tissue (but not muscle) of adult sockeye in all
years over the past decade where available (2003,
2005–2009), with the proportion of affected fish
varying in different years. 137
On the subject of smolts leaving the Fraser
River, Dr. Miller’s PSC workshop paper reported
that the same mortality-related signature was
observed in all years where samples are available
(2007, 2008, and 2009). In 2008, 60 percent of
smolts left the river with the unhealthy signature in
the brain, and 40 percent with the signature in the
liver. Overall, 82 percent of fish were affected in at
least one tissue. There was a 30 percent reduction
in brain prevalence of the signature from summer
to fall in the ocean, and a 50 percent reduction in
the liver. Overall, there were 2.4 times as many fish
with the signature in the fall as in the summer. The
paper concluded: “If these decreases in prevalence
were due to mortality, and if we assume that
120 million smolts left the river in 2008 (there may
have been more), we could account for the loss of
[more than] 27 million salmon in 2008 associated
with the unhealthy signature alone.” 138
Dr. Miller testified that 82 percent of outmigrating
smolts have the mortality-related signature in at
least one tissue, while the proportion of returning
adults affected is much less, for the two years of
available data. 139
In an April 15, 2011, update to DFO scientists,
Dr. Miller reported that, in June 2007 and June 2008,
smolts were sampled in the marine environment.
140 Nine out of 10 from 2007 contained this
mortality-related signature in liver tissue, whereas
in 2008 only 40 percent of liver tissues contained
it. 141 She testified that “[w]here we’re looking
to go is to establish whether or not it’s simply
the prevalence of the signature in the ocean, or
whether it’s the shift in prevalence that we observe
over time that’s more important in terms of being
a predictor.” 142 Dr. Miller speculated that if fish
enter the ocean in poor condition, and the ocean
is additionally stressed, those factors may have a
more profound effect on their survivorship than if
they enter, in good condition, an ocean that is in
good condition. 143
Dr. Miller stated that when a genomic signature
is obtained, one can then compare the similarities
with signatures observed in other controlled studies.
144 From this kind of functional analysis, the most
likely explanation for this signature is that it is virally
mediated (i.e., it is a response to a viral infection). 145
In addition, the fact that the signature was found in
other tissues fits well with a pathogen model, but
does not fit well with a general stressor or toxicant
exposure. 146 In the 2011 Science article, Dr. Miller
and her colleagues stated their hypothesis “that the
genomic signal associated with elevated mortality is
in response to a virus infecting fish before river entry
that persists to the spawning areas.” 147
Dr. Miller stated that her finding that the fish
are already conditionally challenged before they
enter the river during the return migration is
consistent with work done by her colleagues
Dr. Scott Hinch and Dr. Tony Farrell into stress and
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