Eliminating Variation in Age at Spawning Leads to Genetic Divergence Within a Single Salmon Population

Abstract

Most coho salmon Oncorhynchus kisutch in Washington state spawn at 3 y of age, creating the potential for three temporal populations or “broodlines” at each spawning site. This is generally prevented by a portion of males in each site that mature and reproduce at 2 y of age, resulting in population structure in which the geographic component is stronger than the temporal component. The Quilcene National Fish Hatchery, located on Big Quilcene River in the Hood Canal region of Washington state, selected against late returning coho salmon by excluding all but the earliest returning fish from its broodstock for an unknown number of generations, and restricted gene flow among broodlines by excluding 2-y-old males for 27 generations. The resulting hatchery population exhibited three distinct broodlines that returned in alternating years: an “early” broodline that arrived 1 mo before the wild fish, a “late” broodline that arrived at the same time as the wild fish, and a “middle” broodline that arrived in between these two broodlines. We evaluated temporal and geographic components of population genetic structure in coho salmon from the Quilcene National Fish Hatchery and nine other sites from Puget Sound and the Strait of Juan de Fuca using 10 microsatellite loci. Genetic diversity at the Quilcene National Fish Hatchery was lowest in the early broodline and highest in the late broodline. Divergence among broodlines at the Quilcene National Fish Hatchery was greater than that observed at any other site, and was also greater than that observed between any of the sites. This apparent reversal of the relative magnitudes of temporal and geographic components for this species emphasizes the importance of variable age-at-maturity in shaping population genetic structure.

Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia River

“…However, distinct temporal structure persisted among broodlines in the Wenatchee River over subsequent generations despite increased potential for gene flow from jacks through natural spawning and inclusion in the local broodstock program. Broodline "B" was the most distinct from the other two broodlines and may have trait characteristics (e.g., differential run-timing) that maintains isolation among broodlines as has been observed in other studies of this species (Smith et al, 2015). However, run-timing and other trait characteristics were not available for individuals in this study.…”

“…Each cluster corresponded to a broodline from one of the initial return years (2000, 2001, and 2002) and their descendants. This was likely the result of genetic drift between year classes within source stocks due to a lack of intergenerational gene flow (i.e., spawning is limited to the 3‐year‐old age class) as has been observed previously in hatchery‐reared stocks of Coho salmon (Smith et al., ). Broodline “B” was the most distinct from the other two broodlines in the PCA plot (Figure ).…”

“…Throughout their natural range, Coho salmon typically have overlapping generation times as adults return to spawn primarily as three year olds, but two-year-old jacks (early maturing males) are also common and provide gene flow across generations (Beacham, Wetklo, Deng, & MacConnachie, 2011;Sandercock, 1991). However, hatchery programs of Coho salmon often limit the use of jacks within broodstock and distinct broodlines that follow three-year intervals can develop (Conrad, Gilbert-horvath, & Carlos, 2013;Smith et al, 2015). This phenomenon of distinct temporal structure between broodlines was apparent at the initiation of the reintroduction program in the Wenatchee River and reflects spawning practices from source hatcheries used for reintroduction.…”

Genomic Characterization of Coho Salmon Spawning Populations from the Hood Canal

“…This has resulted in a series of three genetically distinct broodlines that return to the hatchery on a 3‐year cycle (Smith et al. ). Beginning in the late 2000s, jack inclusion rates were increased from 10% to 20% of the male broodstock.…”

“…Since the broodlines differ slightly in their return timing and are referred to by the hatchery program as “early,” “middle,” and “late” (see Smith et al. ), we used this terminology for consistency. Samples from jacks were also included.…”