Assessing the relative contribution of genetic sub-stocks to the lower Kuskokwim River subsistence fishery

Salmonid Research, Monitoring, and Evaluation (RM&E)

Research
Project ID1603
Recovery Domains -
Start Date07/01/2016
End Date03/30/2018
Year2015
StatusCompleted
Last Edited07/28/2021
 
1 - 1

Description    


Objective 1. Enhance the existing Kuskokwim River Chinook salmon genetic baseline to identify the upper Kuskokwim River sub-stock in mixed stock fisheries.
During the period of July 23–28, 2017, collection efforts were focused on five headwater tributaries: Blackwater River; Big River; and Middle Fork River, Pitka Fork, and Tonzona River. Sampling occurred with 2–3 person teams based out of McGrath using an R44 helicopter to access Chinook salmon spawning locations. All samples were collected using rod and reel methods. All sampled fish were returned alive to the location of capture. A total of 61 samples were collected from the Blackwater River, 93 samples from the Big River, 123 samples from the Middle Fork River, 153 samples from the Pitka Fork, and 121 samples from Tonzona Rivers. Genotyping of these samples at 45 SNP markers was completed in December 2017. Statistical analysis of these and existing baseline samples was completed in March 2018.

Objective 2. Determine the relative contribution of the upper Kuskokwim River stock to the subsistence fishery executed in lower portion of the Kuskokwim River.
Stock composition was estimated using archived scale samples collected from the lower Kuskokwim River subsistence fishery in 2003–2007. A total of 1,900 archived scales were selected for analysis (380 samples for each year 2003–2007) and submitted to the ADF&G Gene Conservation Laboratory in February 2017. DNA extraction was completed in June 2017, and laboratory analysis was completed in July 2017. Estimation of stock composition was conducted following the completion of the genetic baseline (objective 1) and was completed in April 2018.

Objective 3. Determine if the upper Kuskokwim River sub-stock has been exploited at a higher rate compared to fish returning to other areas of the Kuskokwim River.
Activities associated with this objective occurred following completion of objectives 2 and 3, and was completed in May 2018.

Draft results were presented in an oral presentation at the Western Division American Fisheries Society conference in Anchorage, May 2018.

A no-cost extension was considered but was not able to be done due to contracting timelines at the Alaska Department of Fish and Game.

Project Benefit    


Chinook salmon stocks throughout Western Alaska have experienced low runs in recent years. Within the Kuskokwim River, Chinook salmon abundance has declined substantially since 2007, with the lowest run on record occurring in 2012. Early season fisheries closures have been discussed by the Alaska Department of Fish and Game (ADF&G) as the preferred strategy for achieving Chinook salmon escapement goals and addressing harvest distribution throughout the Kuskokwim River during years of low run abundance. While the potential for disproportionate harvest of upper river sub-stocks has been acknowledged, until recently the ADF&G assumed the potential for disproportionate harvest was low. Telemetry studies conducted from 2003—2007 suggested that upper river stocks represented a small (<10%) component of the spawning escapement; however, when similar studies were conducted in 2014—2015, the upper river stocks were a larger (nearly 25%) component of fish tagged. The notable differences between the earlier and more recent studies were higher relative run size and exploitation rates during the earlier time period, leading managers to speculate that upper river sub-stocks may have been harvested at higher rates than previously thought. In order to obtain better estimates of sub-stock representation in Kuskokwim River Chinook salmon harvests, this project enhanced the existing baseline by collecting additional samples from unrepresented populations in the middle and upper river tributaries, and then used genetic mixed stock analysis (MSA) techniques to evaluate the proportion of upper river sub-stocks captured in the 2003—2007 Kuskokwim River Chinook salmon subsistence harvests. MSA results were compared to results from tagging studies to determine if upper river stock components were subjected to higher exploitation compared to lower river stock components. Results indicated a consistent low contribution of upper river sub-stocks in the 2003—2007 subsistence harvest. The harvest was slightly enriched for upper Kuskokwim River stocks for those years compared to telemetry studies, but the subsistence harvest alone did not explain the relatively large proportions of upper river fish observed in 2014—2015 telemetry results. Results support the potential for disproportionate harvest of upper Kuskokwim River stocks in subsistence fisheries, but do not indicate severe effects.

Accomplishments

Metric Completed Originally
Proposed

Funding Details

SourceFunds
PCSRF$111,881
Report Total:$111,881


Project Map



Worksites

41616438    


  • Worksite Identifier: 41616438
  • Start Date:
  • End Date:
Area Description
Kuskokwim River

Location Information

  • Basin: Lower Kuskokwim River
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Alaska
  • Recovery Domain:
  • Latitude: 60.78079469952146
  • Longitude: -161.76296580348458

ESU

  • Un-Named ESU Chinook

Map

Photos

Metrics

Metrics
  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding 111,881.00
    •      . . E.0.b
      Complement habitat restoration project
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
    •      . . E.0.d.1 Number of Cooperating Organizations 0
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
      None
    •      . . E.0.e.1 Number of reports prepared 4
    •      . . E.0.e.2
      Name Of Report
      Gilk-Baumer, Sara, September 20, 2018, AYK SSI Semiannual Progress Report, Alaska Department of Fish and Game Dann, Tyler, December 31, 2017, AYK SSI Semiannual Progress Report, Alaska Department of Fish and Game Liller, Zachary, July 31, 2017, AYK SSI Semiannual Progress Report, Alaska Department of Fish and Game Prince Daniel, Liller Zachary, Gilk-Baumer Sara, 2019, Assessing the Relative Contribution of Genetic Sub-Stocks to the Lower Kuskokwim River Subsistence Fishery
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding 111,881.00
      •      . . . . E.2.b.3 Genetic analysisY (Y/N)
        •      . . . . . . E.2.b.3.a
          Key issues addressed by genetic analysis research
          In 2016 and 2017, baseline genetic collections for Kuskokwim River Chinook salmon occurred in the Hoholitna, Blackwater, Big, Middle Fork, Pitka Fork, and Tonzona rivers. A total of 181 samples were collected from the Hoholitna River, 151 samples were collected from the Blackwater River, 147 samples from the Big River, 135 samples from the Middle Fork River, 153 samples from the Pitka Fork, and 121 samples from Tonzona Rivers. Laboratory analysis of 2016 baseline samples was completed in May 2017. Laboratory analysis of retrospective scale samples was completed in July 2017. The quality of scale samples was high, and of 1,900 fish analyzed only 30 fish were dropped due to poor DNA quality (1.58% over all samples). Laboratory analysis of 554 baseline samples collected in July 2017 was completed in December 2017. Statistical analyses indicate that two groups (Upper Kuskokwim and Lower Kuskokwim) are evident, with the new collections clustering as expected relative to existing samples. These groups performed well in 100% proof tests, with an average 96.8% correct allocation to reporting group over repeated tests. Genetic mixed stock analysis of subsistence harvest samples to these two reporting groups (Upper Kuskokwim and Lower Kuskokwim) was completed from samples randomly selected from each year 2003-2007 Results from this study were compared to contributions of stocks from the upper Kuskokwim River drainage as documented by telemetry studies conducted in 2002-2007 and 2014-2016 (Schaberg et al. 2012; Head, Smith, and Liller 2017; Smith and Liller 2017). Our expectation, if the upper Kuskokwim River stocks have been exploited at a much higher rate than those in the lower Kuskokwim, would be to see a considerably higher proportion of fish from the Upper Kuskokwim reporting group in the subsistence mixtures in 2003-2007 compared to the telemetry results. In 2002-2007, less than 7% of tags each year migrated above McGrath (Schaberg et al. 2012). Results indicate that the subsistence harvest is only slightly enriched for the Upper Kuskokwim stock, and the subsistence harvest alone cannot fully explain any differences in results between tagging studies in 2002-2007 versus 2014-2016. For management, while there is potential for disproportional harvest of upper Kuskokwim River stocks, there is no evidence for severe effects.