Changes in Size and Age of Chinook Salmon Oncorhynchus tshawytscha Returning to Alaska

Body length changes for Atlantic salmon (Salmo salar) over five decades exhibit weak spatial synchrony over a broad latitudinal gradient

Understanding the factors that drive spatial synchrony among populations or species is important for management and recovery of populations. The range-wide declines in Atlantic salmon (Salmo salar) populations may be the result of broad-scale changes in the marine environment. Salmon undergo rapid growth in the ocean; therefore changing marine conditions may affect body size and fecundity estimates used to evaluate whether stock reference points are met. Using a dataset that spanned five decades, 172,268 individuals, and 19 rivers throughout Eastern Canada, we investigated the occurrence of spatial synchrony in changes in the body size of returning wild adult Atlantic salmon. Body size was then related to conditions in the marine environment (i.e., climate indices, thermal habitat availability, food availability, density-dependence, and fisheries exploitation rates) that may act on all populations during the ocean feeding phase of their life cycle. Body size increased during the 1980s and 1990s for salmon that returned to rivers after one (1SW) or two winters at sea (2SW); however, significant changes were only observed for 1SW and/or 2SW in some mid-latitude and northern rivers (10/13 rivers with 10 of more years of data during these decades) and not in southern rivers (0/2), suggesting weak spatial synchrony across Eastern Canada. For 1SW salmon in nine rivers, body size was longer when fisheries exploitation rates were lower. For 2SW salmon, body size was longer when suitable thermal habitat was more abundant (significant for 3/8 rivers) and the Atlantic Multidecadal Oscillation was higher (i.e., warmer sea surface temperatures; significant for 4/8 rivers). Overall, the weak spatial synchrony and variable effects of covariates on body size across rivers suggest that changes in Atlantic salmon body size may not be solely driven by shared conditions in the marine environment. Regardless, body size changes may have consequences for population management and recovery through the relationship between size and fecundity.

Sex-specific heritabilities for length at maturity among Pacific salmonids and their consequences for evolution in response to artificial selection

Artificial selection, whether intentional or coincidental, is a common result of conservation policies and natural resource management. To reduce unintended consequences of artificial selection, conservation practitioners must understand both artificial selection gradients on traits of interest and how those traits are correlated with others that may affect population growth and resilience. We investigate how artificial selection on male body size in Pacific salmon (Oncorhynchus spp.) may influence the evolution of female body size and female fitness. While salmon hatchery managers often assume that selection for large males will also produce large females, this may not be the case-in fact, because the fastest-growing males mature earliest and at the smallest size, and because female age at maturity varies little, small males may produce larger females if the genetic architecture of growth rate is the same in both sexes. We explored this possibility by estimating sex-specific heritability values of and natural and artificial selection gradients on length at maturity in four populations representing three species of Pacific salmon. We then used the multivariate breeder's equation to project how artificial selection against small males may affect the evolution of female length and fecundity. Our results indicate that the heritability of length at maturity is greater within than between the sexes and that sire-daughter heritability values are especially small. Salmon hatchery policies should consider these sex-specific quantitative genetic parameters to avoid potential unintended consequences of artificial selection.

Shrinking body size and climate warming: Many freshwater salmonids do not follow the rule

Declining body size is believed to be a universal response to climate warming and has been documented in numerous studies of marine and anadromous fishes. The Salmonidae are a family of coldwater fishes considered to be among the most sensitive species to climate warming; however, whether the shrinking body size response holds true for freshwater salmonids has yet to be examined at a broad spatial scale. We compiled observations of individual fish lengths from long-term surveys across the Northern Hemisphere for 12 species of freshwater salmonids and used linear mixed models to test for spatial and temporal trends in body size (fish length) spanning recent decades. Contrary to expectations, we found a significant increase in length overall but with high variability in trends among populations and species. More than two-thirds of the populations we examined increased in length over time. Secondary regressions revealed larger-bodied populations are experiencing greater increases in length than smaller-bodied populations. Mean water temperature was weakly predictive of changes in body length but overall minimal influences of environmental variables suggest that it is difficult to predict an organism's response to changing temperatures by solely looking at climatic factors. Our results suggest that declining body size is not universal, and the response of fishes to climate change may be largely influenced by local factors. It is important to know that we cannot assume the effects of climate change are predictable and negative at a large spatial scale.

The social-ecological system of the Kenai River Fishery (Alaska, USA)

We present a collaboratively developed social-ecological model of the Kenai River Fishery. We developed the model through iterative interviews with stakeholders throughout the Kenai Peninsula using a novel participatory Fuzzy Cognitive Mapping process grounded in Ostrom's social-ecological systems framework. Individual social-ecological models, developed one-on-one with stakeholders, were combined into a single aggregated model representing the system's structure and function. We validated this aggregated model through subsequent interviews with stakeholders and focused literature reviews. The result is a model that can: 1) illustrate the breadth and interconnectedness of the Kenai River Fishery's social-ecological system; 2) be used to facilitate discussions around management of the fishery; and 3) be used to explore the components and interactions that move the system toward or away from sustainability. Using the model, we identify how the nature of salmon (migratory) and their habitat (large and unpredictable) leads to uncertainty about effective management strategies. This uncertainty, in addition to a large and diverse set of resource users, creates conflicting management goals that ultimately limit the governance system in making decisions that might increase the sustainability of the fishery.

Declines in body size of sockeye salmon associated with increased competition in the ocean

Declining body sizes have been documented for several species of Pacific salmon; however, whether size declines are caused mainly by ocean warming or other ecological factors, and whether they result primarily from trends in age at maturation or changing growth rates remain poorly understood. We quantified changes in mean body size and contributions from shifting size-at-age and age structure of mature sockeye salmon returning to Bristol Bay, Alaska, over the past 60 years. Mean length declined by 3%, corresponding to a 10% decline in mean body mass, since the early 1960s, though much of this decline occurred since the early 2000s. Changes in size-at-age were the dominant cause of body size declines and were more consistent than trends in age structure among the major rivers that flow into Bristol Bay. Annual variation in size-at-age was largely explained by competition among Bristol Bay sockeye salmon and interspecific competition with other salmon in the North Pacific Ocean. Warm winters were associated with better growth of sockeye salmon, whereas warm summers were associated with reduced growth. Our findings point to competition at sea as the main driver of sockeye salmon size declines, and emphasize the trade-off between fish abundance and body size.

Climate Change Shrinks and Fragments Salmon Habitats in a Snow-Dependent Region

Climate change threatens biodiversity through global alteration of habitats, but efficient conservation responses are often hindered by imprecise downscaling of impacts. Besides thermal effects, warming also drives important ancillary environmental changes, such as when river hydrology evolves in response to climate forcing. Earlier snowmelt runoff and summer flow declines are broadly manifested in snow-dependent regions and relevant to socioeconomically important cold-water fishes. Here, we mechanistically quantify how climate-induced summer flow declines during historical and future periods cause complex local changes in Chinook salmon (Oncorhynchus tshawytscha) habitats for juveniles and spawning adults. Changes consisted of large reductions in useable habitat area and connectivity between the main channel and adjacent off-channel habitats. These reductions decrease the capacity of freshwater habitats to support historical salmon abundances and could pose risks to population persistence in some areas.

Heterogeneous genetic basis of age at maturity in salmonid fishes

Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 × 10^-9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.

Can late stage marine mortality explain observed shifts in age structure of Chinook salmon?

Chinook salmon (Oncorhynchus tshawytscha) populations have experienced widespread declines in abundance and abrupt shifts toward younger and smaller adults returning to spawn in rivers. The causal agents underpinning these shifts are largely unknown. Here we investigate the potential role of late-stage marine mortality, defined as occurring after the first winter at sea, in driving this species’ changing age structure. Simulations using a stage-based life cycle model that included additional mortality during after the first winter at sea better reflected observed changes in the age structure of a well-studied and representative population of Chinook salmon from the Yukon River drainage, compared with a model estimating environmentally-driven variation in age-specific survival alone. Although the specific agents of late-stage mortality are not known, our finding is consistent with work reporting predation by salmon sharks (Lamna ditropis) and marine mammals including killer whales (Orcinus orca). Taken as a whole, this work suggests that Pacific salmon mortality after the first winter at sea is likely to be higher than previously thought and highlights the need to investigate selective sources of mortality, such as predation, as major contributors to rapidly changing age structure of spawning adult Chinook salmon.

The Gill-Oxygen Limitation Theory and size at maturity/maximum size relationships for salmonid populations occupying flowing waters

The slowing of growth as fish age has long been believed to be related to energy expenditure for maturation, and this rationalization has been used to explain why, across nearly all fish species, the relationship between size at first maturity (L_m ) and maximum (L_max ) or asymptotic length (L_∞ ) is relatively constant. In contrast, the Gill-Oxygen Limitation Theory (GOLT) postulates that (a) fish growth slows because as they grow, their two-dimensional ability to extract oxygen from the water diminishes relative to their three-dimensional weight gain, and (b) they can only invest energy for maturation if oxygen supply at their size at first maturity (Q_m ) exceeds that needed for maintenance metabolism (Q_∞ ). It has been reported previously across dozens of marine fish species that the relationship between Q_m and Q_∞ is linear and, further, it can be mathematically converted to L_m vs. L_∞ by raising both terms to the power of D (the gill surface factor), resulting in a slope of 1.36. If the GOLT is universal, a similar slope should exist for L_m ^D vs. L_∞ ^D relationships for freshwater species across multiple individual populations that reside in disparate habitats, although to our knowledge this has never been evaluated. For analysis, we used existing data from previous studies conducted on 51 stream-dwelling populations of redband trout Oncorhynchus mykiss gairdneri, Yellowstone cutthroat trout O. clarkii bouvieri and mountain whitefish Prosopium williamsoni. The resulting L_m ^D vs. L_∞ ^D slopes combining all data points (1.35) or for all species considered separately (range = 1.29-1.40) were indeed equivalent to the slope originally produced for the marine species from which the GOLT-derived relationship was first reported. We briefly discuss select papers both supporting and resisting various aspects of the GOLT, note that it could potentially explain shrinking sizes of marine fish, and call for more concerted research efforts combining laboratory and field expertise in fish growth research.

Y-chromosome haplotypes are associated with variation in size and age at maturity in male Chinook salmon

Variation in size and age at maturity is an important component of life history that is influenced by both environmental and genetic factors. In salmonids, large size confers a direct reproductive advantage through increased fecundity and egg quality in females, while larger males gain a reproductive advantage by monopolizing access to females. In addition, variation in size and age at maturity in males can be associated with different reproductive strategies; younger smaller males may gain reproductive success by sneaking among mating pairs. In both sexes, there is a trade-off between older age and increased reproductive success and increased risk of mortality by delaying reproduction. We identified four Y-chromosome haplogroups that showed regional- and population-specific variation in frequency using RADseq data for 21 populations of Alaska Chinook salmon. We then characterized the range-wide distribution of these haplogroups using GT-seq assays. These haplogroups exhibited associations with size at maturity in multiple populations, suggesting that lack of recombination between X and Y-chromosomes has allowed Y-chromosome haplogroups to capture different alleles that influence size at maturity. Ultimately, conservation of life history diversity in Chinook salmon may require conservation of Y-chromosome haplotype diversity.

A mobile sex-determining region, male-specific haplotypes and rearing environment influence age at maturity in Chinook salmon

Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males influenced by large (up to 20 Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex determination in this species and Pacific salmon in general.

Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey

High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations probably explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent data sets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.

Recent declines in salmon body size impact ecosystems and fisheries

Declines in animal body sizes are widely reported and likely impact ecological interactions and ecosystem services. For harvested species subject to multiple stressors, limited understanding of the causes and consequences of size declines impedes prediction, prevention, and mitigation. We highlight widespread declines in Pacific salmon size based on 60 years of measurements from 12.5 million fish across Alaska, the last largely pristine North American salmon-producing region. Declines in salmon size, primarily resulting from shifting age structure, are associated with climate and competition at sea. Compared to salmon maturing before 1990, the reduced size of adult salmon after 2010 has potentially resulted in substantial losses to ecosystems and people; for Chinook salmon we estimated average per-fish reductions in egg production (-16%), nutrient transport (-28%), fisheries value (-21%), and meals for rural people (-26%). Downsizing of organisms is a global concern, and current trends may pose substantial risks for nature and people.

Population Trends for Chinook and Summer Chum Salmon in Two Yukon River Tributaries in Alaska

An essential management objective of the Yukon Delta and Koyukuk National Wildlife Refuges in Alaska is to conserve fish and wildlife populations and habitats in their natural diversity. In keeping with this objective, the U.S. Fish and Wildlife Service installed weirs in two tributaries of the Yukon River, the East Fork Andreafsky and Gisasa rivers, in 1994 to collect information on salmon populations that used them. The weirs have been in operation for >23 y. Chinook Oncorhynchus tshawytscha and summer Chum Salmon O. keta were counted and sampled for various demographic data each year as they migrated through the weirs to upstream spawning areas. Here we examine this record of population data to describe and compare long-term variation in run abundance, run timing, length and age structure, sex composition, and production for these salmon populations. Fishery managers often look to multiple monitoring projects in-season seeking corroboration of observed run qualities; therefore, we also considered whether Yukon River main-stem indicators of abundance were correlated with these tributary escapements. Our analyses suggest long-term stability of these populations despite large annual variations in most metrics we examined. Annual escapements have varied by factors of 3–5 for Chinook Salmon and >23 for summer Chum Salmon, yet only the Chinook Salmon population in the Gisasa River appears to be declining. Main-stem abundance indicators were not correlated with Chinook Salmon escapements but were strongly correlated with summer Chum Salmon escapements. Run timing has varied annually by as much as a week earlier or later than average for all four populations with no trend over time. Mean age of the Chinook Salmon populations declined over time but remained stable for the summer Chum Salmon populations. Chinook Salmon populations in the East Fork Andreafsky and Gisasa rivers averaged 35% and 28% female, respectively. Both summer Chum Salmon populations averaged close to 50% female. Length at age has been stable or slightly declining for all four populations. Production over time was strongly correlated within species for populations in the two rivers, and averaged >1 recruit/spawner for all populations except Chinook Salmon from the Gisasa River. We discuss these findings in the context of major changes in the fishery and the environments these populations experience.

The geometry of reaction norms yields insights on classical fitness functions for Great Lakes salmon

Life history theory examines how characteristics of organisms, such as age and size at maturity, may vary through natural selection as evolutionary responses that optimize fitness. Here we ask how predictions of age and size at maturity differ for the three classical fitness functions–intrinsic rate of natural increase r, net reproductive rate R₀, and reproductive value V_x−for semelparous species. We show that different choices of fitness functions can lead to very different predictions of species behavior. In one’s efforts to understand an organism’s behavior and to develop effective conservation and management policies, the choice of fitness function matters. The central ingredient of our approach is the maturation reaction norm (MRN), which describes how optimal age and size at maturation vary with growth rate or mortality rate. We develop a practical geometric construction of MRNs that allows us to include different growth functions (linear growth and nonlinear von Bertalanffy growth in length) and develop two-dimensional MRNs useful for quantifying growth-mortality trade-offs. We relate our approach to Beverton-Holt life history invariants and to the Stearns-Koella categorization of MRNs. We conclude with a detailed discussion of life history parameters for Great Lakes Chinook Salmon and demonstrate that age and size at maturity are consistent with predictions using R₀ (but not r or V_x) as the underlying fitness function.

Resurgence of an apex marine predator and the decline in prey body size

Recent recoveries of marine mammal populations worldwide have heightened concerns for their potential impacts on global fisheries. While predator-induced reductions in prey abundance have been documented, trait-mediated changes in life-history characteristics are rarely considered. Here we provide a striking example of the impact of a resurging apex marine predator on a commercially important fish species through changes in prey life-history traits. We find that widespread declines in the body size of Chinook salmon over the past 50 y can be explained by intensified predation by growing populations of resident killer whales that selectively feed on large Chinook salmon, thus revealing a potential conflict between salmon fisheries and marine mammal conservation objectives.

In light of recent recoveries of marine mammal populations worldwide and heightened concern about their impacts on marine food webs and global fisheries, it has become increasingly important to understand the potential impacts of large marine mammal predators on prey populations and their life-history traits. In coastal waters of the northeast Pacific Ocean, marine mammals have increased in abundance over the past 40 to 50 y, including fish-eating killer whales that feed primarily on Chinook salmon. Chinook salmon, a species of high cultural and economic value, have exhibited marked declines in average size and age throughout most of their North American range. This raises the question of whether size-selective predation by marine mammals is generating these trends in life-history characteristics. Here we show that increased predation since the 1970s, but not fishery selection alone, can explain the changes in age and size structure observed for Chinook salmon populations along the west coast of North America. Simulations suggest that the decline in mean size results from the selective removal of large fish and an evolutionary shift toward faster growth and earlier maturation caused by selection. Our conclusion that intensifying predation by fish-eating killer whales contributes to the continuing decline in Chinook salmon body size points to conflicting management and conservation objectives for these two iconic species.

Tracking the Movements of Juvenile Chinook Salmon using an Autonomous Underwater Vehicle under Payload Control

An autonomous underwater vehicle (AUV) under payload control (PC) was used to map the movements of juvenile Chinook salmon (Oncorhynchus tshawytscha) tagged with acoustic transmitters. After detecting a tag, the AUV deviated from its pre-programmed route and performed a maneuver designed to enhance the location estimate of the fish and to move closer to collect proximal environmental data. Nineteen fish were released into marine waters of southeastern Alaska. Seven missions with concurrent AUV and vessel-based surveys were conducted with two to nine fish present in the area per mission. The AUV was able to repeatedly detect and estimate the location of the fish, even when multiple individuals were present. Although less effective at detecting the fish, location estimates from the vessel-based surveys helped verify the veracity of the AUV data. All of the fish left the area within 48 h of release. Most fish exhibited localized movements (milling behavior) before leaving the area. Dispersal rates calculated for the fish suggest that error associated with the location estimates was minimal. The average movement rate was 0.62 body length per second and was comparable to marine movement rates reported for other Chinook salmon stocks. These results suggest that AUV-based payload control can provide an effective method for mapping the movements of marine fish.

Catalog of Chinook Salmon Spawning Areas in Yukon River Basin in Canada and United States

Chinook Salmon Oncorhynchus tshawytscha return to the Yukon River in northwestern North America each summer, migrating to spawning destinations from the lower river to more than 3,000 km upstream. These returns support numerous fisheries throughout the basin. Despite a long history of fisheries research and management, there is no comprehensive account of Chinook Salmon spawning areas in the basin. To address this issue, we cataloged, summarized, and mapped the known spawning areas of Yukon River Chinook Salmon by using a variety of sources including published articles, gray literature, and information archived in agency databases. Most of our sources were published within the past 30 y, but some refer to observations that were recorded as long ago as the late 1800s. We classified spawning areas as major or minor producers with three indicators of abundance: 1) quantitative estimates of escapement (major producer if ≥500 fish, minor producer if <500 fish), 2) radiotelemetry-based proportions of annual production (major producer if ≥1% of the run, minor producer if <1% of the run), and 3) aerial survey index counts (major producer if ≥165 fish observed, minor producer if <165 fish observed). We documented 183 spawning areas in the Yukon River basin, 79 in the United States, and 104 in Canada. Most spawning areas were in tributary streams, but some were in main-stem reaches as well. We classified 32 spawning areas as major producers and 151 as minor producers. The Chinook Salmon spawning areas cataloged here provide a baseline that makes it possible to strategically direct abundance, biological sampling, and genetics projects for maximum effect and to assess both spatial and temporal changes within the basin.

Correction: Changes in Size and Age of Chinook Salmon Oncorhynchus tshawytscha Returning to Alaska

[This corrects the article DOI: 10.1371/journal.pone.0130184.].