Hutchings, Jeffrey A.

Permanent URI for this collectionhttps://hdl.handle.net/10222/22300

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Open Access
Jeffrey Hutchings CV
(2013-08-29) Hutchings, Jeffrey
Open Access
Population-specific gene expression responses to hybridization between farm and wild Atlantic salmon
(2009-11) Normandeau, Eric; Hutchings, Jeffrey Alexander; Fraser, Dylan J.; Bernatchez, Louis
Because of intrinsic differences in their genetic architectures, wild populations invaded by domesticated individuals could experience population-specific consequences following introgression by genetic material of domesticated origin. Expression levels of 16 000 transcripts were quantified by microarrays in liver tissue from farm, wild, and farm-wild backcross (i.e. F(1) farm-wild hybrid x wild; total n = 50) Atlantic salmon (Salmo salar) raised under common environmental conditions. The wild populations and farm strain originated from three North American rivers in eastern Canada (Stewiacke, Tusket, and Saint John rivers, respectively). Analysis of variance revealed 177 transcripts with different expression levels among the five strains compared. Five times more of these transcripts were differentiated between farmed parents and Tusket backcrosses (n = 53) than between Stewiacke backcrosses and their farmed parents (n = 11). Altered biological processes in backcrosses also differed between populations both in number and in the type of processes impacted (metabolism vs immunity). Over-dominant gene expression regulation in backcrosses varied considerably between populations (23% in Stewiacke vs 44% in Tusket). Hence, the consequences of introgression of farm genetic material on gene expression depended on population-specific genetic architectures. These results support the need to evaluate impacts of farm-wild genetic interactions at the population scale.
Open Access
Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish
(2013-04) Bradbury, Ian R.; Hubert, Sophie; Higgins, Brent; Bowman, Sharen; Borza, Tudor; Paterson, Ian G.; Snelgrove, Paul V. R.; Morris, Corey J.; Gregory, Robert S.; Hardie, David; Hutchings, Jeffrey Alexander; Ruzzante, Daniel E.; Taggart, Christopher T.; Bentzen, Paul
As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one-third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine-scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation.
Open Access
The relationship between offspring size and fitness: integrating theory and empiricism
(2013-02) Rollinson, Njal; Hutchings, Jeffrey Alexander
How parents divide the energy available for reproduction between size and number of offspring has a profound effect on parental reproductive success. Theory indicates that the relationship between offspring size and offspring fitness is of fundamental importance to the evolution of parental reproductive strategies: this relationship predicts the optimal division of resources between size and number of offspring, it describes the fitness consequences for parents that deviate from optimality, and its shape can predict the most viable type of investment strategy in a given environment (e. g., conservative vs. diversified bet-hedging). Many previous attempts to estimate this relationship and the corresponding value of optimal offspring size have been frustrated by a lack of integration between theory and empiricism. In the present study, we draw from C. Smith and S. Fretwell's classic model to explain how a sound estimate of the offspring size-fitness relationship can be derived with empirical data. We evaluate what measures of fitness can be used to model the offspring size-fitness curve and optimal size, as well as which statistical models should and should not be used to estimate offspring size-fitness relationships. To construct the fitness curve, we recommend that offspring fitness be measured as survival up to the age at which the instantaneous rate of offspring mortality becomes random with respect to initial investment. Parental fitness is then expressed in ecologically meaningful, theoretically defensible, and broadly comparable units: the number of offspring surviving to independence. Although logistic and asymptotic regression have been widely used to estimate offspring size-fitness relationships, the former provides relatively unreliable estimates of optimal size when offspring survival and sample sizes are low, and the latter is unreliable under all conditions. We recommend that the Weibull-1 model be used to estimate this curve because it provides modest improvements in prediction accuracy under experimentally relevant conditions.
Open Access
Why do fish stocks collapse? The example of cod in Atlantic Canada
(1997-02) Myers, RA; Hutchings, JA; Barrowman, NJ
In 1993, six Canadian populations of Atlantic cod (Gadus morhua) had collapsed to the point where a moratorium was declared on fishing. It has been argued that the collapses were caused by poor recruitment of cod to the fishery. Yet we are unable to detect a difference between the recruitment of year classes that should have contributed most to the spawning stock at the time of the collapse and recruitment levels in earlier years. A power analysis shows that we would have almost certainly detected an overall reduction of recruitment of 20%. There are considerable differences in the abundance trends as determined by research surveys and reconstructed from the commercial catch at age data (called ''virtual population analysis'' [VPA]) for each stock. VPA-based abundances consistently depict lower recruitment levels than do survey-based estimates in recent years. More important is the observation that from the early 1980s the VPA-based trend shows a decline where none is apparent in the survey-based trend. One explanation of these differences would be an increase in discarding of young fish as fishing mortality increased. We test the hypothesis that the mortality for young cod is unrelated to the fully recruited fishing mortality. This hypothesis is rejected; in each of the six stocks, high juvenile mortality was associated with high adult mortality. This is consistent with the discarding hypothesis. We suggest that age-specific abundance trends estimated from research surveys and VPA should be compared for all stocks where such data exist, and that high priority should, be given to the measurement of discarding levels and the extent to which catch misreporting is related to changes in fishing mortality.
Open Access
Hybridization effects on phenotypic plasticity: experimental compensatory growth in farmed-wild Atlantic salmon
(2011-05) Morris, Matthew R. J.; Fraser, Dylan J.; Eddington, James; Hutchings, Jeffrey Alexander
Compensatory growth (CG) is a means by which organisms can increase their growth rate above their routine growth rate after a period of environmentally induced growth depression. Despite a focus on the implications of CG for aquaculture, little research has evaluated the effect of domesticated-wild hybridization on CG. Any deviation in the mean compensatory ability of hybrids relative to their wild progenitors, or any notable costs to compensation in terms of body morphology, could affect the ability of hybrids to persist in changing environments. We compared CG of farmed, wild and hybrid (F1, F2, wild backcross) juvenile Atlantic salmon (Salmo salar). Wild salmon experienced both lower routine and CG rates relative to farmed salmon, while hybrids were intermediate. However, the compensatory responses (slopes of the reaction norms) for each cross were parallel, indicating that hybridization did not affect the CG response itself. Morphological costs to compensation were not detected. In addition to contributing to risk assessments of the consequences of interbreeding between wild and escaped domesticated organisms, we conclude that plasticity studies on domesticated-wild hybrids and their progenitors are useful for testing basic predictions about the evolution of phenotypic plasticity, as well as understanding the evolutionary significance of hybrids.
Open Access
Evolutionary and ecological feedbacks of the survival cost of reproduction
(2012-04) Kuparinen, Anna; Hardie, David C.; Hutchings, Jeffrey Alexander
Arguably the most fundamental of trade-offs in life-history evolution is the increase in natural mortality resulting from sexual maturity and reproduction. Despite its central importance, this increase in mortality, a survival cost, garners surprisingly little attention in fish and fisheries modeling studies. We undertook an exploratory analysis to evaluate the consequences of this omission for life-history projections. To this end, we developed a simulation approach that integrates quantitative genetics into the ecological dynamics of a fish population and parameterized the model for Atlantic cod (Gadus morhua, L.). When compared to simulations in which the mortality of immature and mature individuals is equal, the inclusion of a survival cost results in larger asymptotic body size, older age at maturity, and larger size at maturity. We also find that measures of population productivity (spawning stock biomass, recruits-per-spawner) are overestimated if the survival cost is excluded. This sensitivity of key metrics of population growth rate and reproductive capacity to the magnitude of the survival cost of reproduction underscores the need to explicitly account for this trade-off in projections of fish population responses to natural and anthropogenic environmental change, including fisheries.
Open Access
Individual variation in Atlantic salmon fertilization success: Implications for effective population size
(2002-02) Jones, MW; Hutchings, Jeffrey Alexander
Mating structure can influence the variance in individual reproductive success, which in turn has important implications for a population's effective size. Atlantic salmon (Salmo salar) males are characterized by alternative reproductive strategies, maturing as small parr in fresh water and/or as considerably larger anadromous males following a migration to sea. The potential for significant variation in individual reproductive success L in both sexes is high. We established two experimental crosses each involving four anadromous females, four anadromous males, and 20 mature male parr in a seminatural spawning environment. We used hyper-variable microsatellite loci to identify the parents of 755 embryos and to quantify the variance in individual fertilization success. Anadromous males generally dominated fertilization success, with a mean individual fertilization success of 15.7% and 19.3% in replicates A and B, respectively, as compared with 1.9% and 1.2% for the mature male part. There was no relationship between individual mature male parr size and individual fertilization success in any individual nest, nor was there any relationship between anadromous male size and individual fertilization success in either replicate. There was some evidence of size being an important determinant of both the frequency of spawning and the overall individual parr fertilization success among those parr identified as having spawned, although these relationships were not always significant. Both anadromous males and females were identified as having spawned with multiple partners, although the frequency of multiple anadromous males spawning simultaneously with a female was low. Fertilization of eggs by parr can significantly increase the effective number of males on a nest-by-nest basis; however, the variance in individual anadromous male fertilization success appears to have the greatest overall influence on effective population size.
Open Access
Consequences of sexual selection for fisheries-induced evolution: an exploratory analysis
(2008-02) Hutchings, Jeffrey Alexander; Rowe, Sherrylynn
Reproductive behaviour and mating system complexity may influence fisheries-induced evolution. Mate choice and intrasexual competition might favour late-, large-maturing genotypes in contrast to the selection imposed by many fisheries. Here, we simulate changes to the mean and variance in body size of Atlantic cod (Gadus morhua) concomitant with increased fishing intensity. Comparing selection differentials (S) for length under the assumptions that size does and does not affect reproductive success, we find that the strength of selection for smaller body size associated with increased fishing pressure depends on: (i) the initial variance in body size; (ii) changes to the variance in size with increasing fishing intensity; and (iii) the influence of size on reproductive success. If the initial variability in length is sufficiently high and its coefficient of variation (CV) increases with fishing intensity, the predicted evolutionary shift towards smaller size generated by fishing is less than that expected under the assumption that reproductive success is independent of size. However, if size influences reproduction and if the CV in body size declines as fishing pressure increases, a trend that may be characteristic of many intensively exploited populations, the strength of selection for smaller size is predicted to be comparatively rapid. We conclude that fisheries-induced evolution can be influenced by changes to the mean and variance of traits under sexual selection, and that the benefits of maintaining broad phenotypic variability in traits such as body size may be greater than previously thought.
Open Access
Life-history correlates of extinction risk and recovery potential
(2012-06) Hutchings, Jeffrey Alexander; Myers, Ransom A.; Garcia, Veronica B.; Lucifora, Luis O.; Kuparinen, Anna
Extinction risk is inversely associated with maximum per capita population growth rate (r(max)). However, this parameter is not known for most threatened species, underscoring the value in identifying correlates of r(max) that, in the absence of demographic data, would indirectly allow one to identify species and populations at elevated risk of extinction and their associated recovery potential. We undertook a comparative life-history analysis of 199 species from three taxonomic classes: Chondrichthyes (e. g., sharks; n = 82), Actinopterygii (teleost or bony fishes; n 47), and Mammalia (n 70, including 16 marine species). Median r(max) was highest for (and similar between) terrestrial mammals (0.71) and teleosts (0.43), significantly lower among chondrichthyans (0.26), and lower still in marine mammals (0.07). Age at maturity was the primary (and negative) correlate of r(max). In contrast, although body size was negatively correlated with r(max) in chondrichthyans and mammals, evidence of an association in teleosts was equivocal, and fecundity was not related to r(max) in fishes, despite recurring assertions to the contrary. Our analyses suggest that age at maturity can serve as a universal predictor of extinction risk in fishes and mammals when r(max) itself is unknown. Moreover, in contrast to what is generally expected, the recovery potential of teleost fishes does not differ from that of terrestrial mammals. Our findings are supportive of the application of extinction-risk criteria that are based on generation time and that are independent of taxonomic affinity.
Open Access
Response: on the consequences of sexual selection for fisheries-induced evolution
(2008-11) Hutchings, Jeffrey Alexander; Rowe, Sherrylynn
No abstract available.
Open Access
Avoidance of fisheries-induced evolution: management implications for catch selectivity and limit reference points
(2009-08) Hutchings, Jeffrey Alexander
I examined how the fitness (r) associated with early-and late-maturing genotypes varies with fishing mortality (F) and age-/size-specific probability of capture. Life-history data on Newfoundland's northern Atlantic cod (Gadus morhua) allowed for the estimation of r for individuals maturing at 4 and 7 year in the absence of fishing. Catch selectivity data associated with four types of fishing gear (trap, gillnet, handline, otter trawl) were then incorporated to examine how r varied with gear type and with F. The resulting fitness functions were then used to estimate the F above which selection would favour early (4 year) rather than delayed (7 year) maturity. This evolutionarily-sensitive threshold, F(evol), identifies a limit reference point somewhat similar to those used to define overfishing (e. g., F(msy), F(0.1)). Over-exploitation of northern cod resulted in fishing mortalities considerably greater than those required to effect evolutionary change. Selection for early maturity is reduced by the domeshaped selectivities characteristic of fixed gears such as handlines (the greater the leptokurtosis, the lower the probability of a selection response) and enhanced by the knife-edged selectivities of bottom trawls. Strategies to minimize genetic change are consistent with traditional management objectives (e. g., yield maximization, population increase). Compliance with harvest control rules guided by evolutionarily-sensitive limit reference points, which may be achieved by adherence to traditional reference points such as F(msy) and F(0.1), should be sufficient to minimize the probability of fisheries-induced evolution for commercially exploited species.
Open Access
Concurrent habitat and life history influences on effective/census population size ratios in stream-dwelling trout
(2012-03) Belmar-Lucero, Sebastian; Wood, Jacquelyn L. A.; Scott, Sherylyne; Harbicht, Andrew B.; Hutchings, Jeffrey Alexander; Fraser, Dylan J.
Lower effective sizes (Ne) than census sizes (N) are routinely documented in natural populations, but knowledge of how multiple factors interact to lower N-e/N ratios is often limited. We show how combined habitat and life-history influences drive a 2.4- to 6.1-fold difference in N-e/N ratios between two pristine brook trout (Salvelinus fontinalis) populations occupying streams separated by only 750 m. Local habitat features, particularly drainage area and stream depth, govern trout biomass produced in each stream. They also generate higher trout densities in the shallower stream by favoring smaller body size and earlier age-at-maturity. The combination of higher densities and reduced breeding site availability in the shallower stream likely leads to more competition among breeding trout, which results in greater variance in individual reproductive success and a greater reduction in Ne relative to N. A similar disparity between juvenile or adult densities and breeding habitat availability is reported for other species and hence may also result in divergent N-e/N ratios elsewhere. These divergent N-e/N ratios between adjacent populations are also an instructive reminder for species conservation programs that genetic and demographic parameters may differ dramatically within species.
Open Access
Relative risks of inbreeding and outbreeding depression in the wild in endangered salmon
(2011-09) Houde, Aimee L. S.; Fraser, Dylan J.; O'Reilly, Patrick; Hutchings, Jeffrey Alexander
Conservation biologists routinely face the dilemma of keeping small, fragmented populations isolated, wherein inbreeding depression may ensue, or mixing such populations, which may exacerbate population declines via outbreeding depression. The joint evaluation of inbreeding and outbreeding risks in the wild cannot be readily conducted in endangered species, so a suggested 'safe' strategy is to mix ecologically and genetically similar populations. To evaluate this strategy, we carried out a reciprocal transplant experiment involving three neighboring populations of endangered Atlantic salmon (Salmo salar) now bred in captivity and maintained in captive and wild environments. Pure, inbred, and outbred (first and second generation) cross types were released and recaptured in the wild to simultaneously test for local adaptation, inbreeding depression, and outbreeding depression. We found little evidence of inbreeding depression after one generation of inbreeding and little evidence of either heterosis or outbreeding depression via genetic incompatibilities after one or two generations of outbreeding. A trend for outbreeding depression via the loss of local adaptation was documented in one of three populations. The effects of inbreeding were not significantly different from the effects of outbreeding. Hence, at the geographic scale evaluated (34-50 km), inbreeding for one generation and outbreeding over two generations may have similar effects on the persistence of small populations. The results further suggested that outbreeding outcomes may be highly variable or unpredictable at small genetic distances. Our work highlights the necessity of evaluating the relative costs of inbreeding and outbreeding in the conservation and management of endangered species on a case-by-case basis.
Open Access
The Ecology of Atlantic Cod (Gadus morhua) in Canadian Arctic Lakes
(2011-06) Hardie, David C.; Hutchings, Jeffrey Alexander
The range of limnological conditions that support Atlantic cod populations in meromictic Arctic lakes is known to be relatively restricted. The degree to which differences in these features, particularly in the availability of allochthonous and autochthonous prey, affect the condition and growth of cod in these populations is unknown. We compared measures of condition among three Atlantic cod populations on Baffin Island, Nunavut, to assess their relationship to differences in potentially important habitat parameters. We also compared data spanning two decades (Ogac Lake) to five decades (Qasigialiminiq) to assess the degree to which natural and anthropogenic factors may have affected these populations. In general, growth rate and asymptotic length tend to be high under situations of intense cannibalism and when alternative prey species are relatively abundant. Biotic and abiotic habitat features in Ogac Lake appear to have been relatively stable since the 1950s, although the abundance of sea urchins appears to have decreased, which may explain the observation that the incidence of cannibalism has doubled. The mean size of angled cod in Qasigialiminiq has decreased by about 10 cm over the past 20 years.
Open Access
Consequences of farmed-wild hybridization across divergent wild populations and multiple traits in salmon
(2010-06) Fraser, Dylan J.; Houde, Aimee Lee S.; Debes, Paul V.; O'Reilly, Patrick; Eddington, James D.; Hutchings, Jeffrey Alexander
Theory predicts that hybrid fitness should decrease as population divergence increases. This suggests that the effects of human-induced hybridization might be adequately predicted from the known divergence among parental populations. We tested this prediction by quantifying trait differentiation between multigenerational crosses of farmed Atlantic salmon (Salmo salar) and divergent wild populations from the Northwest Atlantic; the former escape repeatedly into the wild, while the latter are severely depleted. Under common environmental conditions and at the spatiotemporal scale considered (340 km, 12 000 years of divergence), substantial cross differentiation had a largely additive genetic basis at behavioral, life history, and morphological traits. Wild backcrossing did not completely restore hybrid trait distributions to presumably more optimal wild states. Consistent with theory, the degree to which hybrids deviated in absolute terms from their parental populations increased with increasing parental divergence (i.e., the collective environmental and life history differentiation, genetic divergence, and geographic distance between parents). Nevertheless, while these differences were predictable, their implications for risk assessment were not: wild populations that were equally divergent from farmed salmon in the total amount of divergence differed in the specific traits at which this divergence occurred. Combined with ecological data on the rate of farmed escapes and wild population trends, we thus suggest that the greatest utility of hybridization data for risk assessment may be through their incorporation into demographic modeling of the short- and long-term consequences to wild population persistence. In this regard, our work demonstrates that detailed hybridization data are essential to account for life-stage-specific changes in phenotype or fitness within divergent but interrelated groups of wild populations. The approach employed here will be relevant to risk assessments in a range of wild species where hybridization with domesticated relatives is a concern, especially where the conservation status of the wild species may preclude direct fitness comparisons in the wild.
Open Access
The Influence of Operational Sex Ratio on the Intensity of Competition for Mates
(2011-02) Weir, Laura K.; Grant, James W. A.; Hutchings, Jeffrey Alexander
The evolution and maintenance of secondary sexual characteristics and behavior are heavily influenced by the variance in mating success among individuals in a population. The operational sex ratio (OSR) is often used as a predictor of the intensity of competition for mates, as it describes the relative number of males and females who are ready to mate. We investigate changes in aggression, courtship, mate guarding, and sperm release as a function of changes in the OSR using meta-analytic techniques. As the OSR becomes increasingly biased, aggression increases as competitors attempt to defend mates, but this aggression begins to decrease at an OSR of 1.99, presumably due to the increased costs of competition as rivals become more numerous. Sperm release follows a similar but not significant trend. By contrast, courtship rate decreases as the OSR becomes increasingly biased, whereas mate guarding and copulation duration increase. Overall, predictable behavioral changes occur in response to OSR, although the nature of the change is dependent on the type of mating behavior. These results suggest considerable flexibility of mating system structure within species, which can be predicted by OSR and likely results in variation in the strength of sexual selection.
Open Access
Mixed evidence for reduced local adaptation in wild salmon resulting from interbreeding with escaped farmed salmon: complexities in hybrid fitness
(2008-08) Fraser, Dylan J.; Cook, Adam M.; Eddington, James D.; Bentzen, Paul; Hutchings, Jeffrey Alexander
Interbreeding between artificially-selected and wild organisms can have negative fitness consequences for the latter. In the Northwest Atlantic, farmed Atlantic salmon recurrently escape into the wild and enter rivers where small, declining populations of wild salmon breed. Most farmed salmon in the region derive from an ancestral source population that occupies a nonacidified river (pH 6.0-6.5). Yet many wild populations with which escaped farmed salmon might interbreed inhabit acidified rivers (pH 4.6-5.2). Using common garden experimentation, and examining two early-life history stages across two generations of interbreeding, we showed that wild salmon populations inhabiting acidified rivers had higher survival at acidified pH than farmed salmon or F(1) farmed-wild hybrids. In contrast, however, there was limited evidence for reduced performance in backcrosses, and F(2) farmed-wild hybrids performed better or equally well to wild salmon. Wild salmon also survived or grew better at nonacidified than acidified pH, and wild and farmed salmon survived equally well at nonacidified pH. Thus, for acid tolerance and the stages examined, we found some evidence both for and against the theory that repeated farmed-wild interbreeding may reduce adaptive genetic variation in the wild and thereby negatively affect the persistence of depleted wild populations.
Open Access
Potential for anthropogenic disturbances to influence evolutionary change in the life history of a threatened salmonid
(2008-05) Williams, John G.; Zabel, Richard W.; Waples, Robin S.; Hutchings, Jeffrey Alexander; Connor, William P.
Although evolutionary change within most species is thought to occur slowly, recent studies have identified cases where evolutionary change has apparently occurred over a few generations. Anthropogenically altered environments appear particularly open to rapid evolutionary change over comparatively short time scales. Here, we consider a Pacific salmon population that may have experienced life-history evolution, in response to habitat alteration, within a few generations. Historically, juvenile fall Chinook salmon (Oncorhynchus tshawytscha) from the Snake River migrated as subyearlings to the ocean. With changed riverine conditions that resulted from hydropower dam construction, some juveniles now migrate as yearlings, but more interestingly, the yearling migration tactic has made a large contribution to adult returns over the last decade. Optimal life-history models suggest that yearling juvenile migrants currently have a higher fitness than subyearling migrants. Although phenotypic plasticity likely accounts for some of the change in migration tactics, we suggest that evolution also plays a significant role. Evolutionary change prompted by anthropogenic alterations to the environment has general implications for the recovery of endangered species. The case study we present herein illustrates the importance of integrating evolutionary considerations into conservation planning for species at risk.

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