Priest Rapids Hatchery Monitoring and Evaluation Annual Report for 2012-13 Steven P. Richards Paul A. Hoffarth Washington Department of Fish & Wildlife And Todd N. Pearsons Public Utility District Number 2 of Grant County, Washington August 7, 2013 Executive Summary This report is the third annual report dedicated to monitoring and evaluating the Priest Rapids Hatchery (PRH) production of fall Chinook salmon. The PRH is located below Priest Rapids Dam adjacent to the Columbia River and has been in operation since 1963. The Monitoring and Evaluation program associated with PRH consists of nine objectives and is intended to evaluate the performance of the program in meeting hatchery and natural production goals. This report is intended to be cumulative, but also focus attention on the most recent year of data collection and production (2012-2013). The PRH was originally built to mitigate for the loss of fall Chinook salmon that occurred from inundation of spawning grounds caused by the Priest Rapids Project. The hatchery is operated as an integrated program for the purpose of increasing harvest. The hatchery produces 5 million subyearling fall Chinook salmon for mitigation of inundation of spawning grounds caused by the Priest Rapids and Wanapum dams and 1.7 million subyearling fall Chinook salmon under contract with the United States Army Corps of Engineers for mitigation for John Day Dam. The fall Chinook salmon produced at the PRH continue to have high survival before and after release from the hatchery. These fish contribute significantly to a variety of fisheries, such as fisheries off the coasts of Alaska and Canada and fisheries in the Columbia River. The 2012 returns to PRH for both jacks (9,152) and adult fall Chinook salmon (18,785) were the highest on record. A total of 7,677 fish that returned to the volunteer trap at PRH were ponded for broodstock and 4,946 were spawned to meet egg take goals for multiple hatchery programs. The mortality rate of ponded adult fish was 36% which is the highest on record. The cause for the elevated mortality is uncertain; however, high densities of fish in the PRH volunteer trap may have been a contributing factor. All ages except age-6 PRH origin fall Chinook salmon returning in 2012 were otolith marked. We used a combination of marks (e.g., otoliths, adipose clips, and coded-wire tags), to determine origin which is likely more accurate than the expansion of coded-wire recoveries to determine origin. The hatchery origin fish return at a younger age than natural origin fish. PRH origin fish are larger than natural origin fish at age-2 and 3, but smaller at older ages. Hatchery origin fish released from PRH spawn throughout the Hanford Reach, but in 2012 were concentrated in the river reach downstream of Island #2 (River km 605), approximately 56 kilometers downriver of Priest Rapids Dam. Stray rates into other populations appear to be low based upon coded-wire tag (CWT) recoveries. PRH origin fish were estimated to make up 7% of the spawning population in the Hanford Reach during 2012. All hatchery fish combined (including fish released from Ringold Hatchery and strays from outside the Hanford Reach) comprised 13% of the fall Chinook salmon on the spawning grounds. Otolith recoveries at PRH indicate that a very high percentage of hatchery broodstock are of PRH origin. There appears to be a strong negative bias in coded-wire tag based estimates that were previously used to estimate this variable. The proportion of natural influence (PNI) for Hanford Reach fall Chinook salmon including all hatcheries is estimated at 48%. An alternative estimated PNI specific to the contribution of PRH origin fall Chinook salmon is 63%. Both estimates for PNI are lower than optimum for an integrated harvest program (i.e. > 0.67), however the PNI has increased dramatically during the past few years. Low numbers of natural origin broodstock at PRH contributes to difficulty reaching the PNI target. Additional natural origin broodstock for PRH was collected at the Priest Rapids Dam off ladder adult fish trap and © 2013, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS. i from a pilot project in which anglers fishing in the Hanford Reach captured fish by hook and line. These additional fish increased the natural origin component of the broodstock from 6% to 12%. An alternative estimate for the proportion natural origin broodstock (pNOB) was developed for return year 2012 to account for the genetic influence on pNOB resulting from the PRH spawning protocol of mating one male with two females. It is intended to represent actual gene flow to the progeny instead of just the origin and number of parents used in spawning. The alternative pNOB for return year 2012 resulted in an estimate of 14% which corresponded to a PRH origin fall Chinook salmon PNI of 67%. © 2013, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS. ii Table of Contents 1.0 Introduction ......................................................................................................................... 1 2.0 Objectives ........................................................................................................................... 2 3.0 Current Operation of Priest Rapids Hatchery ..................................................................... 3 4.0 Tagging and Marking .......................................................................................................... 5 5.0 Life History – Hanford Reach Fall Chinook Salmon ......................................................... 7 6.0 Project Coordination ........................................................................................................... 7 7.0 Sample Size Considerations ................................................................................................ 7 8.0 Evaluation of Bias ............................................................................................................... 8 9.0 Origin of Adult Returns to Priest Rapids Hatchery ............................................................ 9 9.1 Origin Based on Otolith Recoveries ..................................................................... 10 9.2 Origin Based on Coded-Wire Tag Recoveries...................................................... 11 10.0 Broodstock Collection and Sampling ............................................................................... 12 10.1 Origin of Broodstock ............................................................................................ 12 10.2 Influence of Additional Otolith Samples on Origin .............................................. 13 10.3 Broodstock Age Composition ............................................................................... 14 10.4 Length by Age Class of Broodstock ..................................................................... 16 10.5 Gender Ratios........................................................................................................ 17 10.6 Fecundity............................................................................................................... 19 11.0 Hatchery Rearing .............................................................................................................. 20 11.1 Number of eggs taken ........................................................................................... 20 11.2 Number of acclimation days ................................................................................. 21 11.3 Number released ................................................................................................... 21 11.4 Fish Size and Condition at Release ....................................................................... 21 11.5 Survival Estimates ................................................................................................ 22 11.6 Juvenile PIT Tag Detections at the Priest Rapids Hatchery Array ....................... 23 12.0 Adult Fish Pathogen Monitoring ...................................................................................... 24 13.0 Juvenile Fish Health Inspections ...................................................................................... 25 14.0 Redd Surveys .................................................................................................................... 25 14.1 Hanford Reach Aerial Redd Counts ..................................................................... 26 14.2 Redd Distribution .................................................................................................. 26 14.3 Spawn Timing ....................................................................................................... 27 14.4 Spawning Escapement .......................................................................................... 28 © 2013, PUBLIC UTILITY DISTRICT NO. 2 OF GRANT COUNTY, WASHINGTON. ALL RIGHTS RESERVED UNDER U.S. AND FOREIGN LAW, TREATIES AND CONVENTIONS. iii 14.5 Hatchery Discharge Channel Redd Counts........................................................... 29 15.0 Carcass Surveys ................................................................................................................ 29 15.1 Hanford Reach Carcass Survey: Section 1 – 5 ..................................................... 30 15.1.1 Numbers Sampled: Sections 1 – 5 ...........................................................