4.2 | Genome environment association
Fish employing broadcast spawning strategies characterized by larval and
juvenile pelagic drift in ocean currents are subject to large
interannual variability in oceanic conditions (Stockhausen et al.,
2018). Stockhausen et al. (2018) refers to this as “running the
gauntlet”, as it is during this critical life stage that these fish are
most vulnerable, experiencing the highest rates of mortality. This
vulnerability is not only due to the vagaries of physical transport, but
also due to their physiological condition where they must meet energetic
demands of acquiring sufficient lipid reserves in order to move to
inshore nursery areas.
During years favorable ocean conditions with ample food availability,
such as 2014 for POP, mortality may be low and selection weak, allowing
most phenotypes to survive through the pelagic phase and into nearshore
settlement. However, during years of unfavorable ocean conditions, such
as the unusual warming, low primary productivity, and low food
availability in 2015 for POP, mortality may be high. If this increase in
mortality is especially high for certain phenotypes, the selection may
be strong, with only the most favorable phenotypes surviving to
settlement.
Our results show consistent selective forces along the sampling
date/latitude gradient in both 2014 and 2015 for POP with 10 of the 381
putative selective loci being in common in both years (Table 4). The
LFMM analysis was done independently for each of the years and finding
the same putative selected loci in both years is surprising. And
although the LFMM method purportedly accounts for demographic factors
such as population mixtures, the date/latitude gradient association
could be due adult spawning populations being differentiated at these
loci. Based on timing and location of spawning, their progeny may follow
the spatio-temporal pattern identified by GEA. This is further supported
by the distribution of the sNMF identified genetic clusters in relation
to their distribution as seen in Figure 3. Alternatively, this may
indicate that the spawning adult populations contain a high proportion
of alleles at those loci that in 2014 and 2015 years were deleterious to
the YOY progeny encountering the environmental conditions during their
pelagic developmental stage. Since POP are very long-lived and may even
spawn into their 100th year (Conrath and Knoth, 2013; Hulson et al.,
2017; Heppell et al., 2010), some of the alleles in the parental
population are expected to have been selectively advantageous during
their respective first year at sea; therefore, the alleles that were
advantageous when the parents were YOY may be deleterious in some
oceanic conditions encountered by their progeny decades later. It is
then expected that patterns of selection as displayed by the subsets of
selected alleles would be cohort-specific.
Interannual differences in the strength of selection pressure was
evident when comparing the 2014 and 2015 YOY POP fish. Due to the larger
sample size in 2014 (321) than in 2015 (77), we would expect more
putative selected loci in 2014 just due to the increase in statistical
power, but that was not the case. In 2014, the oceanic conditions were
typical (Cavole et al., 2016), with large YOY abundances in the ocean,
and no putative selected loci were identified aside from those
associated with collection date/latitude. However, in 2015, the oceanic
conditions were abnormal with warmer sea surface temperatures (Gentemann
et al., 2017) and were marked by large seabird die-off (Jones et al.
2018). This likely resulted in stronger selective pressure on YOY in
2015 and this is supported by the greater number of putative selected
alleles. Therefore by the time the 2014 and 2015 cohorts settled out in
the nearshore, we expect that most individuals have gene variants that
were most favorable and selected for by the conditions encountered in
that year.
The difference in the change in condition index indicates different
growth conditions between the two years. In 2015, the smaller fish had
less mass than in 2014, but the larger fish had equivalent mass in both
years (Figure 4). This indicates that in 2015, a much warmer year than
in 2014, the smaller fish were unable to gain weight as compared to the
same sized fish in 2014. If the temperatures were still within optima
for POP YOY growth, then smaller size suggests smaller-sized prey items
were either unavailable or of insufficient nutritional value to support
the higher growth rates predicted by the higher temperature in 2015.
However the larger fish in both years were equally successful at gaining
mass. This suggests that the environment in 2015 imposed a larger
variance in fitness and therefore much stronger selection pressure, and
this is consistent with the greater number of putative selected loci in
2015 than in 2014. This is further supported by the recruitment
estimates in the 2017 stock assessment with 2014 cohort being 87.5
million and 38.2 million in 2015 (Hulson et al., 2017).