The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad‐scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad‐scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin‐wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.     

Reproductive investment patterns,sperm characteristics,and seminal plasma physiology in alternative reproductive tactics of Chinook salmon (Oncorhynchus tshawytscha)

Although alternative reproductive tactics (ARTs) are common across a range of taxa, little is known about whether the different tactics have adapted to sperm competition risk. Chinook salmon, Oncorhynchus tshawytscha, have two ARTs: large males that participate in dominance‐based hierarchies for access to spawning females, known as hooknoses, and small males that attempt to sneak fertilizations during spawning events from peripheral positions, known as jacks. Jacks continually face sperm competition risk because they always spawn in the presence of another male, whereas hooknoses face relatively low sperm competition risk because other males are not always present during spawning events. Based on the sneak‐guard model of sperm competition this asymmetry in sperm competition risk predicts that jacks ought to invest significantly more into sperm‐related traits important for sperm competition success relative to hooknoses. In the present study we report on reproductive investment patterns, sperm characteristics, and seminal plasma physiology of males that exhibit ARTs in Chinook salmon. We found that jacks invest significantly more of their somatic tissue into gonads compared with hooknoses. Sperm velocity also varied significantly between the ARTs, with jacks having significantly faster sperm than hooknoses. No significant differences in seminal plasma physiology metrics related to sperm quality were detected between the ARTs. We interpret these sperm investment patterns in light of the sneak‐guard model of sperm competition that is based on differences in sperm competition risk and alternative investment possibilities among ARTs. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Survival of captured and relocated adult spring-run Chinook salmon Oncorhynchus tshawytscha in a Sacramento River tributary after cessation of migration

We studied the efficacy of the process for capture and upstream relocation of 26 adult spring-run Chinook salmon in Butte Creek, California in 2009. These fish had ceased volitional upstream migration prior to reaching their summer holding habitat. The purpose of the relocation was to move fish upstream of two water diversion dams and release them in a part of the stream from which they could presumably swim to cool summer holding habitat, then spawn in the fall. Fish were netted, transported by truck, given an esophageal radio tag/temperature tag, and released. Radio tagging proved to be a useful technique for determining the survival and movement of relocated fish and temperature tags provide useful information to determine thermal exposure and time of death. Twenty-three tags (88 %) were recovered, compared with a 10 % tag recovery rate for an earlier study using fin clips. Most tags were recovered within 3.5 km upstream and 1 km downstream of the release site. A single tag was recovered 6 km upstream. No fish were determined to have survived to spawn. Temperature tag data indicate that most of the salmon died within 2–6 days after the relocation operation. After preventative measures have been exhausted, future relocations efforts, in any setting, should consider (1) intervention as soon as fish cease volitional migration but before they are exposed to further deleterious conditions (2) monitoring environmental conditions to choose appropriate release sites (3) evaluation of disease transmission risk, and (4) handling practices that minimize potential stress due to air immersion and thermal shock.     

Seasonal changes in the body composition of young riverine Atlantic salmon and brown trout

The body composition of protein and fat in Atlantic salmon Salmo salar and brown trout Salmo trutta before and after winter was investigated in a temperate, small river, normally ice covered from the middle of November until the end of March. Fat, protein and specific energy declined greatly in winter but were replenished rapidly in spring. Rates of decline were slower for the smallest fish, which also had the lowest specific content of fat, protein, and energy, while the differences in absolute amounts were greatest for the largest fish. The mean specific fat content was reduced by 45–70% during winter, relative to the pre-winter period (September). Mean daily reductions in specific enegy of the larger size groups of brown trout (3·7 × 10⁻³ kJ g⁻¹ day⁻¹) were almost half of the corresponding values for the largest Atlantic salmon (6·3 × 10⁻³ kJ g⁻¹ day⁻¹) during winter. A minor reduction in protein content was found during winter, with mean reductions of 6–10% in comparison to those in September. During spring the fat content was replenished rapidly, particularly for the smallest salmon fry (a threefold increase from April to June). Fat content in the larger salmon and trout increased by about 1·8 times. Based on estimated metabolic rates, digested energy during wintertime may contribute about two-thirds of the brown trout fry's energy demand. For Atlantic salmon, the corresponding value is about 50%. The winter period put considerable stress on the young salmonids living in lotic environments, in particular for the smallest fry with the lowest energy content before winter and the largest losses during winter. This should make the fry more vulnerable to adverse abiotic and biotic factors.     

Thermal biology and bioenergetics of different upriver migration strategies in a stock of summer-run Chinook salmon

By combining biotelemetry with animal-borne thermal loggers, we re-created the thermal histories of 21 summer-run Chinook salmon (Oncorhynchus tshawytscha) migrating in the Puntledge River, a hydropower impacted river system on Vancouver Island, British Columbia, Canada. Daily maximum water temperatures in the Puntledge River during the summer-run adult Chinook salmon migration and residency period frequently exceeded 21 °C, a value that has been observed to elicit behavioral thermoregulation in other Chinook salmon populations. We therefore compared river temperatures to body temperatures of 16 fish that migrated through the river to understand if cool-water refuge was available and being used by migrants. In addition, we used thermal histories from fish and thermal loggers distributed in the river to model the effect of thermal habitat on energy density using a bioenergetics model. In general, we found no evidence that cool-water refuge existed in the river, suggesting that there is no opportunity for fish to behaviorally thermoregulate during upriver migration through the regulated portion of the river. Of the thermal histories used in the bioenergetics model, fish that reached an upstream lake were able to access cooler, deeper waters, which would have reduced energy consumption compared to fish that only spent time in the warmer river. Consequently, the Puntledge River water temperatures are likely approaching and in some cases exceeding the thermal limits of the summer-run Chinook salmon during the spawning migration. Further warming may cause more declines in the stock.     

Self-sustaining populations, population sinks or aggregates of strays: chum (Oncorhynchus keta) and Chinook salmon (Oncorhynchus tshawytscha) in the Wood River system, Alaska

Small populations can provide insights into ecological and evolutionary aspects of species distributions over space and time. In the Wood River system in Alaska, USA, small aggregates of Chinook (Oncorhynchus tshawytscha) and chum salmon (O. keta) spawn in an area dominated by sockeye salmon (O. nerka). Our objective was to determine whether these Chinook and chum salmon are reproductively isolated, self-sustaining populations, population sinks that produce returning adults but receive immigration, or strays from other systems that do not produce returning adults. DNA samples collected from adult chum salmon from 16 streams and Chinook salmon from four streams in the Wood River system over 3 years were compared to samples from large populations in the nearby Nushagak River system, a likely source of strays. For both species, microsatellite markers indicated no significant genetic differentiation between the two systems. Simulations of microsatellite data in a large source and a smaller sink population suggested that considerable immigration would be required to counteract the diverging effects of genetic drift and produce genetic distances as small as those observed, considering the small census sizes of the two species in the Wood River system. Thus, the Wood River system likely receives substantial immigration from neighbouring watersheds, such as the Nushagak River system, which supports highly productive runs. Although no data on population productivity in the Wood River system exist, our results suggest source-sink dynamics for the two species, a finding relevant to other systems where salmonid population sizes are limited by habitat factors.     

Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared with the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome–environment associations (GEA) to understand the relationship between landscape and environmental conditions driving selection in seven populations of the anadromous Chinook salmon (Oncorhynchus tshawytscha)—a species of important economic, social, cultural, and ecological value—in the Columbia River basin. We extracted environmental variables for the shared migration corridors and at distinct spawning sites for each population, and used a Pool‐seq approach to perform whole genome resequencing. Bayesian and univariate GEA tests with migration‐specific and spawning site‐specific environmental variables indicated many more candidate SNPs associated with environmental conditions at the migration corridor compared with spawning sites. Specifically, temperature, precipitation, terrain roughness, and elevation variables of the migration corridor were the most significant drivers of environmental selection. Additional analyses of neutral loci revealed two distinct clusters representing populations from different geographic regions of the drainage that also exhibit differences in adult migration timing (summer vs. fall). Tests for genomic regions under selection revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1 region that has been identified previously in salmonids as a region associated with adult migration timing. Our results show that environmental variation experienced throughout migration corridors imposed a greater selective pressure on Chinook salmon than environmental conditions at spawning sites.     

Reproductive cycle of vendace (Coregonus albula L.) in relation to some chemical and biochemical changes in the body

Analysis of the body constituents of vendace indicated that considerable depletion of muscle lipid reserves occurred during gonad formation. Annual changes in total body chemical composition, in the evolution of protein, cholesterol and GPT and GOT activities in the blood, were monitored in both sexes. Significant differences were found in muscle free amino acids between the sexes. Cholesterol level in blood of males was found to be double the amount of that in females. This may explain the earlier mortality of males in coregonid populations when based on atherosclerosis development.     

Finish with a sprint: Evidence for time‐selected last leg of migration in a long‐distance migratory songbird

Under time‐selected migration, birds should choose a strategy for outcompeting rivals over securing access to prime resources at the final destination. Thus, migration can be viewed as a race among individuals where winners are arriving first when conditions are suitable. The sprint migration hypothesis predicts that individuals shift from maximum sustained speed to a final burst of sprint to shorten the transition from migration to breeding (Alerstam, 2006). In this study, we test the hypothesis of a final sprint migration in a long‐distance Afro‐Palearctic migrant, the collared flycatcher Ficedula albicollis, during autumn and spring, and compare migration strategies between the seasons. In both seasons, collared flycatchers evidently exhibited sprint migration by increasing their overall speed over the last leg of migration after the Sahara crossing. This phenomenon was more pronounced in spring, contributing to overall faster spring migration and possibly highlighting higher importance for early arrival at the breeding grounds. In both seasons and particularly in spring, late departing individuals flew at a faster rate, partially being able to catch up with their early departing conspecifics. Differential fueling strategies may play an important role in determining migration speed, especially during the early stages of the migration, and might explain the observed differences in migration speeds between late and early departing individuals. Our findings suggest competition for early arrival at the breeding and at the nonbreeding destinations alike. Sprint migration might be an appropriate strategy to gain advantage over conspecifics and settle in prime territories as well as to cope with the increasingly earlier springs at high latitudes.     

Low cardiac and aerobic scope in a coastal population of sockeye salmon Oncorhynchus nerka with a short upriver migration

This study showed that a coastal population (Harrison) of Fraser River sockeye salmon Oncorhynchus nerka had a lower aerobic and cardiac scope compared with interior populations with more challenging upriver spawning migrations, providing additional support to the idea that Fraser River O. nerka populations have adapted physiologically to their local migratory environment.     

Quantitative genetic and translocation experiments reveal genotype‐by‐environment effects on juvenile life‐history traits in two populations of Chinook salmon (Oncorhynchus tshawytscha)

Understanding the genetic architecture of phenotypic plasticity is required to assess how populations might respond to heterogeneous or changing environments. Although several studies have examined population‐level patterns in environmental heterogeneity and plasticity, few studies have examined individual‐level variation in plasticity. Here, we use the North Carolina II breeding design and translocation experiments between two populations of Chinook salmon to detail the genetic architecture and plasticity of offspring survival and growth. We followed the survival of 50 800 offspring through the larval stage and used parentage analysis to examine survival and growth through freshwater rearing. In one population, we found that additive genetic, nonadditive genetic and maternal effects explained 25%, 34% and 55% of the variance in larvae survival, respectively. In the second population, these effects explained 0%, 24% and 61% of the variance in larvae survival. In contrast, fry survival was regulated primarily by additive genetic effects, which indicates a shift from maternal to genetic effects as development proceeds. Fry growth also showed strong additive genetic effects. Translocations between populations revealed that offspring survival and growth varied between environments, the degree of which differed among families. These results indicate genetic differences among individuals in their degree of plasticity and consequently their ability to respond to environmental variation.     

Integration of Random Forest with population‐based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

Anadromous Chinook salmon populations vary in the period of river entry at the initiation of adult freshwater migration, facilitating optimal arrival at natal spawning. Run timing is a polygenic trait that shows evidence of rapid parallel evolution in some lineages, signifying a key role for this phenotype in the ecological divergence between populations. Studying the genetic basis of local adaptation in quantitative traits is often impractical in wild populations. Therefore, we used a novel approach, Random Forest, to detect markers linked to run timing across 14 populations from contrasting environments in the Columbia River and Puget Sound, USA. The approach permits detection of loci of small effect on the phenotype. Divergence between populations at these loci was then examined using both principle component analysis and F_ST outlier analyses, to determine whether shared genetic changes resulted in similar phenotypes across different lineages. Sequencing of 9107 RAD markers in 414 individuals identified 33 predictor loci explaining 79.2% of trait variance. Discriminant analysis of principal components of the predictors revealed both shared and unique evolutionary pathways in the trait across different lineages, characterized by minor allele frequency changes. However, genome mapping of predictor loci also identified positional overlap with two genomic outlier regions, consistent with selection on loci of large effect. Therefore, the results suggest selective sweeps on few loci and minor changes in loci that were detected by this study. Use of a polygenic framework has provided initial insight into how divergence in a trait has occurred in the wild.     

Annual cycle of energy and time expenditure in a golden-mantled ground squirrel population

Summary We have analyzed seasonal shifts of energy and time allocation in a population of golden-mantled ground squirrels (Spermophilus saturatus) by directly measuring total daily energy expenditure (DEE) with an isotopic technique (doubly labeled water=dlw), and by estimating components of total DEE through an integration of field behavioral observations with laboratory-measured rates of energy expenditure (oxygen consumption) associated with major behavioral and physiological states. Hibernation laster about 7 1/2 months, and the 4 1/2-month activity season consisted of mating, a 28-d gestation of 3–5 young, 5 1/2 weeks of postnatal growth building to a peak in lactation just before the young emerged above ground, an additional 2–3-week period of maternal care before dispersal, and finally restoration of body mass preceding hibernation. Although the hibernation season comprised nearly two-thirds of the year, it involved only 13–17% of annual energy expenditure, leaving about 85% of energy expenditure for the active season. Ground squirrels were actually present on the surface for only about 11% of the year's time, and the foraging time required to obtain the total annual energy supply amounted to only about 2% of the year's time. The squirrels fed mainly on herbs in the early season and hypogeous fungi later; both were used extensively during peak lactation when female energy expenditure and demand were maximal. Average daily foraging time increased steadily throughout the season to a maximum of 28% of aboveground time as availability of greens diminished and fungus predominated in the diet; time availability did not limit foraging since the animals sat on average for 65% of the daily surface time of about 7 h. Timing of reproduction is apparently optimized such that peak reproductive energy demands are matched with maximal food availability and moderate thermal conditions that minimize energy demand. Despite the greater body mass of males, the greatest total DEE (measured by dlw) of any squirrels at any time of year was that of females during peak lactation. For production of young and lactation through above-ground emergence of an average litter of 2.7, females required a total energy increase of 24% above annual nonreproductive metabolism. Yearling females all bred and performed similarly to older females, yet some costs were greater because the yearlings began and ended hibernation at smaller mass, compensated by giving birth later, and finally showed a greater absolute increase in body mass over the active season than older females. Annual metabolic energy expenditure of breeding males was about 18% greater than that of females, due to greater male body mass. Yet the annual energy intake requirement for both sexes was essentially identical (about 42MJ) due to the greater reproductive export by females in the form of newborn and milk. During the mating season males showed wide-ranging exploratory behavior and social interactions, including aggression, that involved considerable locomotory energy expenditures. Although we did not directly account for the energetics of these specific reproductive behaviors, they are critical to male reproductive success and on a daily basis they probably involved much greater energy expenditure than sperm production. Some yearling males avoided these costs by foregoing testicular development, yet they allocated four times as much energy to growth as older males, thereby increasing somatic condition for the future.     

Repeatability of individual migration routes,wintering sites,and timing in a long‐distance migrant bird

Migratory birds are often faithful to wintering (nonbreeding) sites, and also migration timing is usually remarkably consistent, that is, highly repeatable. Spatiotemporal repeatability can be of advantage for multiple reasons, including familiarity with local resources and predators as well as avoiding the costs of finding a new place, for example, nesting grounds. However, when the environment is variable in space and time, variable site selection and timing might be more rewarding. To date, studies on spatial and temporal repeatability in short‐lived long‐distance migrants are scarce, most notably of first‐time and subsequent migrations. Here, we investigated repeatability in autumn migration directions, wintering sites, and annual migration timing in Hoopoes (Upupa epops), a long‐distance migrant, using repeated tracks of adult and first‐time migrants. Even though autumn migration directions were mostly the same, individual wintering sites often changed from year to year with distances between wintering sites exceeding 1,000 km. The timing of migration was repeatable within an individual during autumn, but not during spring migration. We suggest that Hoopoes respond to variable environmental conditions such as north–south shifts in rainfall during winter and differing onset of the food availability during spring migration.     

Anadromous red-spotted masu salmon (Oncorhynchus masou ishikawae), a southernmost sea-migration form of salmonid,displays low variation in both age at seaward migration and sea age

We examined variations in age at seaward migration and sea age for the anadromous form of red-spotted masu salmon (Oncorhynchus masou ishikawae) in two Japanese rivers. The anadromous form of red-spotted masu salmon expressed only two sea migration patterns in the two rivers: (a) the majority of the salmon (95%, n = 81) were of age-0, and age-1 migrants were rare (n = 4); and (b) all the salmon examined (n = 22) made a return migration within a year, with 23% of the salmon exhibiting potamodromy in the river. Owing to low variation in their sea migratory patterns, the anadromous form of red-spotted masu salmon is likely vulnerable to environmental fluctuations.     

Thermal heterogeneity,migration, and consequences for spawning potential of female bull trout in a river–reservoir system

The likelihood that fish will initiate spawning, spawn successfully, or skip spawning in a given year is conditioned in part on availability of energy reserves. We evaluated the consequences of spatial heterogeneity in thermal conditions on the energy accumulation and spawning potential of migratory bull trout (Salvelinus confluentus) in a regulated river–reservoir system. Based on existing data, we identified a portfolio of thermal exposures and migratory patterns and then estimated their influence on energy reserves of female bull trout with a bioenergetics model. Spawning by females was assumed to be possible if postspawning energy reserves equaled or exceeded 4 kJ/g. Given this assumption, results suggested up to 70% of the simulated fish could spawn each year. Fish that moved seasonally between a cold river segment and a warmer reservoir downstream had a greater growth rate and higher propensity to spawn in a given year (range: 40%–70%) compared with fish that resided solely in the cold river segment (25%–40%). On average, fish that spawned lost 30% of their energy content relative to their prespawn energy. In contrast, fish that skipped spawning accumulated, on average, 16% energy gains that could be used toward future gamete production. Skipped spawning occurred when water temperatures were relatively low or high, and if upstream migration occurred relatively late (mid‐July or later) or early (early‐May or earlier). Overall, our modeling effort suggests the configuration of thermal exposures, and the ability of bull trout to exploit this spatially and temporally variable thermal conditions can strongly influence energy reserves and likelihood of successful spawning.     

Bimodal run distribution in a northern population of sockeye salmon (Oncorhynchus nerka): life history and genetic analysis on a temporal scale

Life history variation and genetic differentiation were analysed in sockeye salmon in Klukshu River, Yukon Canada over 7 years (1994-2000). Sockeye salmon return to the Klukshu River in two distinct runs, with a small 'early run' in June-August, and a larger 'late run' in August-September. A maximum likelihood test for clusters indicated that the return frequency distribution was bimodal in all the years analysed. Life history differences (fork length, sex ratio, age at maturity, fresh- and saltwater residency times) were found between the early and late runs; however, inconsistent patterns suggest that environmental effects outweigh, or strongly interact with, genetic effects for the life history characters evaluated. Analysis of variation at eight microsatellite loci showed that the early and late runs are genetically differentiated in all years examined (exact test). FST estimates between runs within years were significantly greater than zero (range: 0.018-0.041) for all years except one (0.004). The genetic variance explained by early vs. late runs (2.27%) was twice the variance among years (1.16%) based on analysis of molecular variance. Our neighbour-joining tree showed early and late runs generally clustering separately, indicating higher gene flow among the early or late run fish across years relative to between-run gene flow. Two years did not fit the general clustering pattern; although the early and late runs in 1995 and 2000 were genetically differentiated, they clustered separately from the rest of the groups. We cannot offer a definitive explanation for these anomalies; however, an analysis of possible cryptic population structure in early and late runs indicated that at least a few fish strayed between the runs in each year, and the highest rate of mixing was in 1995 and 2000. Our data indicate that the runs are at least partially reproductively isolated as a result of temporal and/or spatial isolating mechanisms. Such reproductive isolation has important implications for conservation and management of the Klukshu sockeye salmon, and make them an evolutionarily interesting group because of parallels with incipient speciation.     

Foraging conditions ‘at the end of the world’ in the context of long‐distance migration and population declines in red knots

The long‐distance migrant red knot (Calidris canutus ssp. rufa– Scolopacidae) alternates between the northern and southern ends of the New World, one of the longest yearly migrations of any bird and paradoxically overflying apparently suitable habitat at lower latitudes. This subspecies is sharply declining, with a major mortality event following 2000, attributed to commercial overharvesting of food resources at its Delaware Bay (USA) stop‐over site. A full understanding of this peculiar migrant requires an assessment of the foraging conditions at its southern hemisphere wintering sites. Here, for a major wintering site in Argentinean Tierra del Fuego (Río Grande), we describe and compare food abundance, diet and intake rates during January–February in 1995, 2000 and 2008. The two main prey types were the burrowing clam Darina solenoides and three species of epibenthic mussels Mytilidae. In the year 2000, food availability and intake rate were higher than those recorded at other sites used by knots anywhere else in the world, contributing to the explanation of why red knots carry out this impressive migration. Intake rate in 2008 on the two main prey types was dramatically reduced as a result of birds eating smaller prey and strongly increased human disturbance; the same year we also found a high prevalence of a digenean parasite in Darina. We suggest that during the strongly enhanced winter mortality in 2000, knots did not yet face ecological problems in their southernmost wintering area, consistent with the previous evidence that problems at northern stop‐overs negatively affected their numbers. However, in 2008 the ecological conditions at Río Grande were such that they would have facilitated a further decline, emphasizing the importance of a hemispheric approach to research and management.