For salmon populations in the Columbia River and Snake River basins, many of which are listed under the U.S. Endangered Species Act of 1973, reliable estimates of the proportion of hatchery‐origin adults in spawning areas (p) are needed to assess population status and the genetic and demographic interactions of hatchery‐ and natural‐origin fish. Some hatchery fish receive visible marks, coded wire tags (CWTs), parentage‐based tags (PBTs), or all three. This allows one to identify whether fish recovered after release are of hatchery origin. Parentage‐based tagging involves genotyping hatchery broodstock and uses parentage assignments as “tags” that identify the origin and brood year of their progeny. We derived a maximum likelihood estimator of p and applied it to the 2012 and 2013 carcass survey data for spring–summer Chinook Salmon Oncorhynchus tshawytscha in the South Fork Salmon River, Idaho. Maximum likelihood estimation was also applied to CWT data and, for investigating the importance of expected tag recoveries on precision, to simulated PBT data for fall Chinook Salmon spawning in the Hanford Reach of the Columbia River. Precision of p from maximum likelihood estimation increased with the expected number of tag recoveries in a carcass survey, whether CWTs or PBTs. In the South Fork Salmon River application, there were 340% more PBT recoveries than CWT recoveries, leading to greater precision in release‐specific values of p from maximum likelihood estimation. The maximum likelihood estimation procedure provides fisheries managers a method to design a tagging and sampling program aimed at estimating p, a valuable measure of the potential for interaction of wild‐ and hatchery‐origin fish on the spawning grounds. To design a program for estimating p, we recommend selecting a target level of precision and then choosing a tagging fraction and sampling rate that delivers that precision in the most cost‐effective way. Received August 21, 2015; accepted January 19, 2016 Published online April 27, 2016

A climate shift is imminent in the northeast Pacific Ocean, research suggests, and may have a major impact on marine resources, particularly Pacific salmon. Scientists anticipate that the shift, driven by large‐scale changes in the Earth's atmospheric wave pattern, will become evident in the next few years. The most recent shift, characterized by a switch from cold and wet conditions to warm and dry conditions in the Pacific northwest of the United States, occurred in 1977 [e.g., Trenberth and Hurell, 1994]. The expected climate shift is suggested by studies of oscillations in ocean surface water drift and in treering records. Drift trajectories, derived from a new measure of decadal variability, showed well‐defined oscillations in the 20th century, but researchers were concerned that this decadal nature might not be as evident over a considerably longer time. Thus because of the possible rarity of the 30‐year interval since the last climate shift, treering width data was scrutinized for the western juniper for the period from 1500 to 1900 A.D.

Ecologists have become increasingly aware of the combined effects of habitat disturbance and climate change on the establishment and proliferation of invasive species. Long‐term data on the population of the invasive American Shad Alosa sapidissima in the U.S. portion of the Columbia River basin provide an opportunity to examine how habitat disturbances affect the abundance and spatial distribution of an invasive species in a heavily modified environment. After the establishment of American Shad in the Columbia River in the late 1800s, the drainage was transformed from its natural lotic state to a series of reservoirs, with concomitant changes to discharge and temperature regimes, which are confounded by climate change. As the Columbia River was dammed, American Shad extended its range and increased in abundance. A large and rapid increase in spawning population abundance (recruits per spawner = 63) followed completion of The Dalles Dam in 1957, which inundated Celilo Falls, a natural barrier to upriver American Shad migration. Regressions revealed that the annual percentage of American Shad migrating upstream from McNary Dam varied with water temperature and discharge (R2 = 0.72), but not population density. When Atlantic coast rivers were dammed, however, American Shad lost spawning habitat and declined in abundance. Understanding the rapid colonization of the Columbia River by American Shad may reveal ways to help American Shad recolonize rivers where they are native. Understanding the roles of water temperature and discharge may allow us to project effects of climate change on the future distribution and abundance of American Shad in the Columbia River basin. Our results suggest that dam construction and alterations to the temperature and discharge regimes of the Columbia River have contributed to the increase in abundance and spatial distribution of American Shad. These changes might have improved the reproductive success of American Shad by providing access to additional spawning grounds and creating suitable juvenile rearing conditions.

The rapid decline of some salmonid populations in the Columbia River Basin led investigators to analyze spawner-recruit (SR) data in order to understand the potential gains of improving main-stem passage conditions and quantify the effectiveness of the juvenile transportation program. Direct measurements of passage survival and transportation were not always available, so instead, the researchers attempted to tease out the passage or transportation effects by using trends in production estimated from SR models. Small subsets of data, or even single observations, highly influenced the estimates of passage survival and transportation effectiveness derived from these models. For stream-type chinook salmon, deleting 1 of 13 stocks changed the estimate of main-stem passage survival from 11 to 34%. For ocean-type chinook salmon, the conclusion that transportation should be immediately halted hinged on a single observation. The Snake River salmon SR models starkly illustrate the importance of using influence diagnostics to temper inferences.

For salmon populations in the Columbia River basin, many of which are listed under the U.S. Endangered Species Act of 1973, reliable estimation of the proportion of hatchery‐origin spawners in spawning areas (p) is needed to make inferences about their status and potential for interbreeding with wild‐origin adults, which may reduce the genetic fitness of subsequent generations. Despite its importance, accurate and precise techniques for estimating p are lacking, especially when there are spawner inputs from multiple hatcheries in a single spawning area. To identify hatchery‐origin spawners, some hatchery releases are given visible marks, some are tagged with coded wire tags (CWTs), and some are marked in both ways. However, different marking fractions are used at different hatcheries and this complicates the problem of estimating p. To handle this situation, we derived a new generalized least‐squares estimator (GLSE) of p and another, less computationally intensive estimator that uses CWT recoveries alone (SMME). We conducted Monte Carlo simulations using both estimators to compare their precision and statistical accuracy. We then applied the estimators to 2010 carcass survey data for fall Chinook salmon Oncorhynchus tshawytscha in the Hanford Reach of the Columbia River. An incremental change away from identical marking fractions for all source hatchery releases reduced precision, increased bias, and complicated estimation. The GLSE had greater precision than the SMME. Statistical bias shrank as the true spawning population size, the fraction of hatchery‐origin fish, or the CWT fraction increased. The GLSE estimate of p in the Hanford Reach was 0.077, while the SMME estimate was 0.041. To maximize the accuracy and precision of the estimates of p, we recommend that identical marking fractions (preferably 100%) be used for all hatchery releases; barring this, we recommend that the CWT fractions be as large as possible.

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An a priori power analysis was conducted to aid the design of experiments aimed at estimating the reproductive success of hatchery-born spawners relative to wild-born spawners using parentage assignment. Power was defined as the probability of rejecting the null hypothesis of equal reproductive contributions of hatchery- and wild-born spawners. A maximum likelihood estimator of relative reproductive success and its variance were derived. The estimator allowed multiple brood years of data, which was an extension of current approaches. Power increased with stock productivity, initial spawner abundance, fraction of recruits and spawners sampled, and the number of brood years examined. Power decreased with error variance used in the production function. Assuming a fixed total number of spawners, power was a concave-down function of the fraction of hatchery-born spawners. Using nominal values of productivity, error variance, and fraction of hatchery-born spawners, an experiment could achieve 0.8 power if it was run for at least 5 years or if it was applied to a stock with high initial female spawners (>200) and run for at least 2 years.

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