Timothy Copeland

Spatial variation buffers temporal fluctuations in early juvenile survival for an endangered Pacific salmon.

Spatial, phenotypic and genetic diversity at relatively small scales can buffer species against large-scale processes such as climate change that tend to synchronize populations and increase temporal variability in overall abundance or production. This portfolio effect generally results in improved biological and economic outcomes for managed species. Previous evidence for the portfolio effect in salmonids has arisen from examinations of time series of adult abundance, but we lack evidence of spatial buffering of temporal variability in demographic rates such as survival of juveniles during their first year of life. We therefore use density-dependent population models with multiple random effects to represent synchronous (similar among populations) and asynchronous (different among populations) temporal variability as well as spatial variability in survival. These are fitted to 25 years of survey data for breeding adults and surviving juveniles from 15 demographically distinct populations of Chinook salmon (Oncorhynchus tshawytscha) within a single metapopulation in the Snake River in Idaho, USA. Model selection identifies the most support for the model that included both synchronous and asynchronous temporal variability, in addition to spatial variability. Asynchronous variability (log-SD = 0·55) is approximately equal in magnitude to synchronous temporal variability (log-SD = 0·67), but much lower than spatial variability (log-SD = 1·11). We also show that the pairwise correlation coefficient, a common measure of population synchrony, is approximated by the estimated ratio of shared and total variance, where both approaches yield a synchrony estimate of 0·59. We therefore find evidence for spatial buffering of temporal variability in early juvenile survival, although between-population variability that persists over time is also large. We conclude that spatial variation decreases interannual changes in overall juvenile production, which suggests that conservation and restoration of spatial diversity will improve population persistence for this metapopulation. However, the exact magnitude of spatial buffering depends upon demographic parameters such as adult survival that may vary among populations and is proposed as an area of future research using hierarchical life cycle models. We recommend that future sampling of this metapopulation employ a repeated-measure sampling design to improve estimation of early juvenile carrying capacity.

Contribution of three life history types to smolt production in a Chinook salmon (Oncorhynchus tshawytscha) population

The most productive juvenile life history in the Pahsimeroi River Chinook salmon (Oncorhynchus tshawytscha; Idaho, USA) population (in terms of smolt production) is being eliminated. Length at emigration and survival from spawn- ing areas to Lower Granite Dam within each of three juvenile phenotypes (age-0 smolts, fall parr, age-1 smolts) were in- fluenced by initial cohort abundance. The proportion of age-1 emigrants reaching Lower Granite Dam was dome-shaped with respect to initial cohort abundance. As initial abundance increased, higher proportions of juveniles adopted the age-1 smolt phenotype or emigrated as fall parr. The age-0 smolt phenotype had the highest relative survival, and the fall parr phenotype, the lowest. The contributions of each emigrant type to cohort smolt production varied with circumstances; hence, the full expression of phenotypic diversity is important to the study population. However, there were no records of tagged age-0 smolts surviving to return from the Pacific Ocean. Given the potential productivity of this life history, man- agement and recovery efforts should be directed at the age-0 smolt phenotype.

Interspecies Synchrony in Salmonid Densities Associated with Large-Scale Bioclimatic Conditions in Central Idaho

Abstract The abundance of lotic salmonids varies substantially through time, but the extent to which several sympatric species respond coherently to large-scale bioclimatic conditions has rarely been investigated for freshwater fishes. We compared correlations in salmonid density in central Idaho and examined the relationships between changes in salmonid density and the variation in large-scale bioclimatic conditions as indexed by stream flow, air temperature, drought, coastal upwelling, and the number of Chinook salmon Oncorhynchus tshawytscha redds (a surrogate for nutrient influx and therefore increased stream productivity). The average densities of six stream-dwelling salmonid fishes were highly synchronous, with declines from the mid-1980s to the mid-1990s followed by a rebound through 2003. All pairwise correlations were positive and 8 of 15 were statistically significant. Stream flow and Chinook salmon redds were correlated with fish densities as a group, but the importance of bioclimatic indices d...

Estimating Abundance and Life History Characteristics of Threatened Wild Snake River Steelhead Stocks by Using Genetic Stock Identification

Abstract Assessments of threatened wild Snake River steelhead Oncorhynchus mykiss have historically been limited due to a lack of stock-specific information and difficulties in field sampling efforts. We used genetic stock identification (GSI) to estimate the composition of wild adult steelhead migrating past Lower Granite Dam on the Snake River between August 24 and November 25, 2008. Further, we combined genetic data with information on sex, length, age, and run timing to examine for differences in life history or demography among stocks. In total, 1,087 samples collected at the dam were genotyped with 13 standardized steelhead microsatellite loci and a new modified Y-chromosome-specific assay that differentiates sex. A genetic baseline of 66 populations was used to complete GSI of unknown-origin samples from Lower Granite Dam. Large differences in reporting group (stock) contributions were observed for the run as a whole; the Snake River–lower Clearwater River reporting group had the largest single con...

The Importance of Juvenile Migration Tactics to Adult Recruitment in Stream-Type Chinook Salmon Populations

AbstractThe existence of multiple migration tactics within a population has been observed for several fish species, and they may contribute differentially to adult recruitment. Relative contribution by juveniles using the same habitats on different schedules is variable; therefore, understanding and conserving this diversity should be important to fisheries managers. We investigated adult recruitment by two distinct juvenile migration tactics in several spawning populations of stream-type Chinook Salmon Oncorhynchus tshawytscha in Idaho: those leaving the spawning grounds as subyearlings during June through November (downstream rearing, or DSR, type) and those emigrating from natal areas 1 year after emergence (natal reach rearing, or NRR, type). The DSR type had greater juvenile abundance in all populations, although the NRR type exhibited better survival from the natal reach to the migratory corridor. The DSR type had greater survival from smoltification to adult return to freshwater compared with the N...

Comparison of Methods Used to Age Spring–Summer Chinook Salmon in Idaho: Validation and Simulated Effects on Estimated Age Composition

Abstract Validation of aging methods with known-age individuals is rarely done with wild fish. We used samples collected from carcasses of adult Chinook salmon Oncorhynchus tshawytscha that were tagged as juveniles to (1) compare accuracy and precision of ocean ages determined from scales and fin rays and (2) simulate the effects of aging errors on run reconstruction (assignment to migratory cohort) under two age composition scenarios. Scale age had an overall accuracy of 81.8% and was biased high (χ2 = 8.67; P = 0.014). Fin ray age had an overall accuracy of 98.6% and was unbiased (χ2 = 2.00; P = 0.34). Precision of fin ray readings was higher than that of scale readings (coefficient of variation = 2.1% versus 7.8%, respectively). Accuracy of fin ray ages was greater than that of scale ages (Z = 2.198; P = 0.03). For two age composition scenarios, age classification errors were greatest when using scales and least when using fin rays. Aging errors inflated the size of weak cohorts in simulated run recons...

Quantitative Assessment of Scale Resorption in Migrating and Spawning Steelhead of the Snake River Basin

AbstractScales have been used for decades as a tool to interpret life histories in steelhead Oncorhynchus mykiss. Resorption can affect the accuracy of life history interpretations based on scale patterns, depending on the amount of material resorbed. For example, resorption can affect the distinctiveness and characteristics of spawn checks. Spawn checks have been reported in iteroparous salmonids, but no published experimental studies have established the precise relationship between reproduction and scale features. Our objectives were (1) to quantify scale resorption, and (2) to identify contributing factors to the observed resorption in migrating and spawning Snake River steelhead. Prespawn and postspawn scale samples from 72 fish were paired for analysis. We found considerable individual variability in the amount of material resorbed between prespawn and postspawn samples (mean, 26%; SD, 13.7%). Most resorption occurred during the winter as gonads matured and secondary sex characteristics were formed....

Life History Diversity of Snake River Steelhead Populations between and within Management Categories

AbstractGrouping populations for management may overlook the fine-scale diversity underpinning the stability and resilience of meta-populations and fisheries. A bimodal timing distribution of summer-run steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) historically was observed at Bonneville Dam (BON), the first barrier to upstream migration in the Columbia River basin. Early mode fish (A-run) tended to be younger and smaller (<78 cm) than later fish (B-run). While A-run fish spawn throughout the Columbia River basin, B-run fish spawn primarily in the Snake River basin. Managers used indices of these modes to make fishery decisions, and later these criteria were adopted for conservation. It is still unclear how life history and body size differences among wild Snake River populations are related to the categories at BON. We examined population parameters characterizing the two categories (date of passage at BON, length) and parameters directly affecting population dynamics (age composition, sex rat...

Do Dead Fish Tell Tales? DNA Degradation in Chinook Salmon (Oncorhynchus tshawytscha) Carcasses

Abstract Carcasses are potentially a valuable source of DNA for genetic studies of Pacific salmon (Oncorhynchus sp.). They can be collected at spawning grounds across a wide geographic area and include populations in streams in which it is logistically difficult or too intrusive to sample spawning fish. However, the quality and quantity of DNA from salmon carcasses is highly variable. Using a standardized set of microsatellite loci, we investigated the relationship of amplification success and genotyping errors to time since death and locus size in Chinook salmon (O. tshawytscha) carcasses. Amplification success declined rapidly from death, smaller loci had greater amplification success than larger loci, and genotyping errors were present in 5% of scored samples. Salmon carcasses can be a valuable source of genetic information; however, the level of effort needed to produce accurate and reliable data with microsatellite loci is considerable. Ideally, field collections should be frequent and focus on fresh carcasses. Data replication should also be incorporated into analyses to reduce amplification failures and genotyping errors. New techniques and markers should improve future cost-effectiveness when analyzing degraded tissue samples. However, we recommend that an evaluation of cost and time be performed at the onset of any population genetic study using salmon carcass tissues, regardless of the technique used.

Parr Production from Adult Hatchery Steelhead Outplanted in Two Tributaries to the Headwaters of the Salmon River, Idaho

Abstract Supplementation is a widespread response to the declining runs of anadromous salmonids in the Pacific Northwest. A common type of supplementation is the intentional release of adult hatchery fish to spawn naturally (outplanting) but this method has seldom been evaluated. Our objective was to quantify the juvenile steelhead (Oncorhynchus mykiss) produc tion from the adult outplants during a 14 year period in two streams. Although densities of juvenile steelhead were highly variable, outplanting status (supplemented versus not supplemented) explained a significant proportion of the variance for the age-1 densities but not for the age-2+densities. We used a simulation model to predict smolt production and adult returns given the observed juvenile age-1 densities from each adult cohort we outplanted. In general, predicted smolt production was greater during the mid 1990s and lower after 1999, despite the fact that more females were stocked into the study streams after 1999. Given the SAR rates measured during the study period and plausible over-winter survival rates in the study streams, we predicted that the observed juvenile production would produce few adults and would not result in a self-sustaining population. This conclusion was corroborated by adult return data. VVe found no evidence that adult outplanting increased wild population levels, i.e., there was no demographic boost in adult spawners. Further, the differences between lire two study streams showed that supplementation programs should carefully assess each target stream.