Population genetic analysis of Chehalis River watershed winter steelhead (Oncorhynchus mykiss)

Understanding the population structure wild salmon and steelhead (Oncorhynchus spp.) in the Chehalis River is an important part of the Chehalis Flood and Aquatic Species Project and contributes to the Chehalis Basin Flood Hazard Project and Aquatic Species Enhancement Plan. Current predictive models (Ecosystem Diagnostic Treatment, NOAA Watershed Assessment) partition species into geospatial units that have an unknown relationship to actual population structure. Here, we examined the genetic population structure of wild (natural-origin) winter-run steelhead (O. mykiss) in the Chehalis River basin. Specifically, our objectives were to determine the genetic relationship of Chehalis River steelhead with other O. mykiss in Washington State and to examine the genetic structure of O. mykiss within the Chehalis River basin.

Genetic data revealed that Chehalis Basin O. mykiss are of the same Coastal lineage as nearby baseline collections. Similar to the previous study, Chehalis O. mykiss were found to be more closely related to O. mykiss in nearby watersheds (Willapa River, Quinault River) than to more geographically distant populations. Within the Chehalis Basin, Chehalis steelhead were structured hierarchically. At the least inclusive hierarchical level, O. mykiss populations in the Chehalis were structured by spawning tributary, and this structure was temporally stable. At the most inclusive hierarchical level, spawning tributaries were clustered by headwater geography. The lower Chehalis group was represented by the collections from the Humptulips River, Wishkah River, Wynoochee River, and Satsop River and drains the Olympic Mountain Range. The middle Chehalis group was represented by the collections from the Skookumchuck and Newaukum rivers and drains the Cascade Mountain Range. The upper Chehalis group, represented by the South Fork and upper Chehalis collections, drains the Willapa Hills. Similar population structure among major spawning tributaries has been seen in other genetic studies of O. mykiss in Washington, including in the nearby Cowlitz River and in Canada and California.

Genetic diversity of lower Chehalis River O. mykiss was similar to what is typical for other similar-sized wild O. mykiss populations in Washington. The upper Chehalis River populations had slightly lowered diversity, possibly due to impacts from a hatchery program. The Skookumchuck River collections had the reduced diversity typically seen in WDFWs hatchery rainbow trout and steelhead populations. Reduced diversity is an indication of a small population size, however the number of steelhead returning to the Skookumchuck is comparable to other tributaries of the Chehalis River, suggesting the reduced diversity may be due to a population bottleneck, likely due to hatchery propagation. The Newaukum collection significantly deviated from Hardy-Weinberg expectations (HWE). The deviation was not due to excessive sampling of family members, which can cause deviations of this type. Instead, the Newaukum collection appeared to be composed of members of several different populations, which also can cause deviations from HWE (i.e., a Wahlund effect). Skookumchuck hatchery steelhead are released in the Newaukum River, but given the hierarchical genetic relationships in the Chehalis Basin, it is impossible to distinguish a Newaukum genetic signal from planted Skookumchuck hatchery steelhead. Additional replicate collections in future years will be required to accurately characterize a Newaukum O. mykiss population.

This study represents a comprehensive survey and genetic analysis of Chehalis River O. mykiss populations, but some minor holes still exist. The Hoquiam River, Cloquallum Creek, and Black River may also have steelhead populations, but were not sampled. Additional sampling and analysis would shed light on their genetic relationships with other Chehalis River O. mykiss. In particular, the Black River may be interesting given its location in the transition zone from Olympic Mountains to Cascade Mountains headwaters. Samples from the Wynoochee and Skookumchuck rivers were collected downstream of dams. In the Wynoochee River, steelhead are transported upstream of the dam, but the Skookumchuck Dam has no fish passage. Samples of rainbow trout from upstream of the dam may provide additional insights into the genetic diversity issues of the Skookumchuck River collections.