Hatcheries in the U.S. Pacific Northwest are increasingly implementing programs that use an adipose fin clip and coded wire tag to mark a large number of juvenile salmonids Oncorhynchus spp. Traditionally, fin‐clipping and tagging were done by hand, but the need to mass‐mark large numbers of fish has led to the development of an automated tagging trailer system (Northwest Marine Technology, Inc.). We compared the adipose fin clip quality, coded wire tag retention, and injury rates of juvenile stream‐type spring Chinook salmon O. tshawytscha marked and tagged at automated and manual tagging trailers at Warm Springs National Fish Hatchery (NFH) and Carson NFH, two hatcheries located in the Columbia River basin. Clip quality (99% good clips), tag retention (>98%), and injury rates (<7%) were similar between the two types of trailers at Carson NFH, where the manual markers had several years' experience clipping and tagging fish. At Warm Springs NFH, where the majority of manual markers had no previous experience, injury rates were similar (<14%) but the fish marked and tagged in the automated trailer had significantly higher clip quality (95% good clips) and tag retention (98%) than those marked and tagged in the manual trailer (70% good clips, 87% retention), where the clip quality and tag retention were poorest during the first day of tagging. Our results show that automated and manual trailers can perform similarly with regard to fin clip quality, tag retention rate, and injury rate when staffed by experienced markers. We recommend focusing efforts on training and quality control during the initial days of tagging and incorporating postmarking clip quality and coded wire tag retention sampling into all marking programs.

Removal of fish passage barriers provides Pacific salmon Oncorhynchus spp. and steelhead O. mykiss the opportunity to recolonize previously accessible habitat, though the time scale of natural recolonization may not be sufficient for management or conservation goals. One strategy for accelerating recolonization is to outplant hatchery‐origin adults into newly restored habitats. In this paper, we describe how genetic parentage analysis was used to determine the reproductive success of adult stream‐type spring Chinook salmon O. tshawytscha taken from two localized hatchery stocks and outplanted into a stream. We defined reproductive success as the production of migratory juveniles. In 2002 and 2003, 83 and 265 adult hatchery salmon, respectively, were outplanted into Shitike Creek, Oregon, a tributary to the Deschutes River. Using 11 microsatellite markers, 799 and 827 migratory juveniles from the two brood years were genotyped and matched back to potential outplanted parents using genetic parentage analyses. Successful spawning of outplant–outplant, outplant–wild, and wild–wild fish occurred in Shitike Creek in both years. Adults outplanted in 2002 showed far fewer matches (18%) to sampled juveniles than those from 2003 (88%). Additionally, only 1% of juveniles had both parents identified as outplants in 2002, compared with almost 61% in 2003. Differences in the number of females outplanted each year appeared to account for the differential productivity. The number of offspring attributed to an individual outplant was variable, ranging from 1 to more than 10. Multiple outplant × outplant matings were identified for each sex as males mated with up to seven females and females mated with up to four males. This study shows that, under the right conditions, outplanted adult hatchery fish taken from localized hatchery stocks can contribute to the overall juvenile production in a natural stream.

Partial barriers to migration can affect migratory fish population dynamics and be influenced by many biotic, abiotic, and anthropogenic factors, including nutritional deficiencies. We investigated how such variables (including a thiamine deficiency) impact fine-scale movement of landlocked Atlantic salmon (Salmo salar) by treating returning spawners with thiamine and observing their attempts to climb a human-altered, high velocity stretch of river using fine-scale radio telemetry. Multiple re-entries into a river section, along with water temperature, strongly influenced movement rates. High or increasing discharge encouraged downstream movement; males abandoned migratory attempts at a higher rate than females. Although thiamine-injected salmon exhibited greater migratory duration, this did not produce a measurable improvement in passage performance, possibly due to the difficulty associated with this section of river — among 24 tagged salmon staging 10.9 attempts each and lasting 1.5 days per attempt on average, only three traversed the entire reach. This study provides new insights into how biotic and abiotic variables affect fish movement, while suggesting limits to the potential for human intervention (thiamine injections) to assist passage through partial migratory barriers.

Balancing the disparate objectives of fishery augmentation and conservation of an endemic fish population presents a substantial challenge. In the case of Warm Springs National Fish Hatchery (Warm Springs Hatchery), strategies for achieving both objectives included incorporation of natural fish into the hatchery broodstock and restricting proportions of hatchery fish on the spawning grounds. The hatchery has been more successful in implementing the latter than the former. We analyzed 76 single nucleotide polymorphism markers in Spring Chinook Salmon Oncorhynchus tshawytscha collected from the Warm Springs River in 1976-1977 (prior to hatchery production) and 2001-2011 (posthatchery) to examine whether the genetic characteristics of the endemic population had changed during that time. Pre-and posthatchery collections clustered together when compared with those from Round Butte Hatchery, which has a nearby segregated program, and other Columbia River populations. The difference between pre-and posthatchery collections was nonsignificant, but posthatchery samples exhibited significantly lower expected heterozygosity. We observed some evidence of reduced effective size and increased genetic drift in fish produced at Warm Springs Hatchery (relative to natural-origin fish) and even stronger evidence of this in fish produced at Round Butte Hatchery. We conclude that natural-origin Chinook Salmon returning to the Warm Springs River form a distinct group within the interior Columbia Basin spring-run lineage and have changed very little over the past eight generations. We further speculate that differences between hatchery-and natural-origin fish at Warm Springs Hatchery are expected to increase if hatchery operations remain static (i.e., little integration of natural-origin fish and incorporation of Round Butte Hatchery fish in the broodstock).

Marking and tagging fish is a critical component of many hatchery monitoring and evaluation programs, and coded wire tags are part of the foundation for managing Pacific salmon Oncorhynchus spp. Fin‐clipping and coded‐wire‐tagging large numbers of juvenile salmonids is done either by hand or by using an automated tagging trailer system. We compared the hatchery adult recovery rate of spring Chinook Salmon O. tshawytscha marked and tagged as juveniles by manual and automated tagging trailers at Warm Springs National Fish Hatchery (NFH) and Carson NFH. At Warm Springs NFH, the adult recovery rate for fish marked in the automated trailer was 0.16%, compared with a recovery rate of 0.14% for fish marked in the manual trailer. A fish was 1.17 times more likely to be recovered as an adult at the hatchery if marked in an automated trailer. Coded wire tag retention rates were more variable for manually marked fish. At Carson NFH, there was no difference in recovery rate or coded wire tag retention rate between marking trailers. These data suggest that the automated marking procedure does not reduce adult recovery rates from the time of marking to adult return when compared with manual marking. The lower recovery rate of manually marked fish at Warm Springs NFH may have been due to manual marker inexperience, use of anesthetic, or other factors. Additional information on the implications of differential coded wire tag retention and adult survival related to marking methods is necessary for hatchery managers to make decisions on how to mark and tag their fish.