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

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.

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.