Genetic Characterization of Chinook Salmon (Onchorhynchus tshawytscha) populations

While two independent Chinook populations have been identified within WRIA 8 by the PSTRT, Marshall (2000) indicated that there might be enough difference between the North Lake Washington Chinook (Bear/Cottage Lake creeks) and fish returning to Issaquah Creek to consider them separate from one another. WRIA 8 would then contain three distinct Chinook populations (Cedar River, Bear/Cottage Lake creeks, and Issaquah Creek) instead of two. In addition to these genetic data, there are other differences among the Chinook from these areas that may reflect genetic differences between Bear/Cottage Lake creeks and Issaquah Creek. For example, the Bear/Cottage Chinook run commences earlier than Issaquah Hatchery returns, peaks at approximately the same time, and tails off over a longer period, although these timing differences maybe more an artifact of broodstock collection practices in the hatchery than genetic differences. As such, the WRIA 8 technical committee has indicated plans to manage for three independent populations in WRIA 8, instead of the two identified by the PSTRT, understanding that there are uncertainties about the population structure within the basin (Lake Washington/Cedar/ Sammamish Watershed Steering Committee 2004). In 2003, the first brood year of 100% adipose-clipped hatchery Chinook returned to hatcheries within WRIA 8 (and other hatcheries out-of-basin). Stray rates in 2003 indicated that there were more hatchery-origin (i.e., ad-clipped) Chinook on the spawning grounds in WRIA 8 than expected (Figure 1). While straying is known to occur (Candy and Beacham 2000; Schroeder et al. 2001; Hayes and Carmichael 2002), the large releases of hatchery fish (e.g., 2.1 million Chinook fry annually from the Issaquah Hatchery) combined with small populations of naturally-spawning Chinook in WRIA 8 (Cedar River adult escapement (redd count base) averaged 694 between 1999 and 2004; Burton et al., 2005) may present a scenario in which the hatchery-origin fish may affect the genetic integrity of the remaining native-origin spawning Chinook populations in the area. These objectives are: 1) Determine if the naturally spawning Chinook in WRIA 8 consist of multiple, independent populations (i.e., stocks). a) Genetically characterize the current natural spawning Cedar River and Bear/Cottage Lake creeks populations, test for population differentiation (i.e., one or two stocks), and determine interrelationships. H o : All naturally spawning aggregations of Chinook in WRIA 8 are part of the same genetic population (panmixia). H a : There is more than one genetically distinct, reproductively isolated "population" in WRIA 8. hatchery stock or more? 2) Test …