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Federal Register / Vol. 86, No. 156 / Tuesday, August 17, 2021 / Notices reproductive isolation. This conclusion was due in part to the observed patterns of genetic variation, in which spring-run and fall-run fish spawning in the same or nearby rivers were genetically similar to each other and more similar to each other than to populations of either run type spawning in geographically distant rivers Myers et al. 1998; Busby et al.
1999. The Panel reviewed subsequent genetic studies and found that they clearly confirm the earlier findings that, as a group, coastal spring-run Chinook salmon are not a distinct evolutionary lineage within the species, but rather share their evolutionary history and most of their genetic variation with the fall-run Chinook salmon spawning in the same and nearby rivers. In other words, the patterns of genetic variation coastwide indicate that spring-run Chinook salmon spawning in different rivers are generally more differentiated from each other than they are to cooccurring fall-run Chinook salmon.
Although this pattern is apparent when viewed on a coastwide scale, it is important to note that most of the coastwide Chinook salmon genetic studies conducted over the past two decades had few samples from the OC
and SONCC areas. The Oregon Department of Fish and Wildlife identified up to nine rivers in the currently defined OC Chinook salmon ESU as having either spring-run populations or a spring-run or summerrun component to a population, but no genetics study has included more than three spring-run or summer-run population samples, and spring-run or summer-run samples have only been analyzed for a total of four OC river systems: Nehalem, Trask, Siletz, and Umpqua rivers. Following a review of the available information, the Panel found that some of the samples from cooccurring spring-run and fall-run populations in the OC areas do not necessarily seem to be closely genetically related. In particular, Umpqua River spring-run sampled from the Rock Creek hatchery tend to cluster with SONCC samples of both run types in a number of studies rather than with Umpqua fall-run samples or other OC fall-run samples Myers et al. 1998;
Waples et al. 2004; Seeb et al. 2007;
Narum et al. 2008; Clemento et al. 2014;
Hecht et al. 2015; note that some studies used the same set of samples so these data are not all independent. This pattern could indicate that Umpqua River spring-run Chinook salmon are in fact historically more closely related to SONCC Chinook salmon, or could be a result of past broodstock transfers from the Rogue River and elsewhere into the
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Rock Creek Hatchery as summarized by Myers et al. 1998, Appendix D. In addition, fall-run samples from the Trask River Hatchery were more closely related to other OC fall-run samples than to Trask River Hatchery spring-run samples Beacham et al. 2006. A
similar pattern was seen in wild fall-run and spring-run Chinook salmon from the Siletz River Davis et al. 2017.
Extensive out-of-basin spring-run and fall-run Chinook salmon hatchery releases in the Trask River may be an explanation for this pattern. Similarly, although relatively few spring-run Chinook salmon hatchery releases have occurred in the Siletz River, that basin did receive more than 2 million Columbia River hatchery Chinook salmon releases between 1934 and 1952
Myers et al. 1998, Appendix D.
Additional sampling and genetic analysis of natural-origin fish across the range of return timing in multiple OC
and SONCC rivers would help improve our understanding of the genetic relationships among OC and SONCC
Chinook salmon populations. However, the available data does not indicate that spring-run Chinook salmon spawning in rivers on the Oregon Coast, as a group, form a distinct lineage separate from OC
fall-run Chinook salmon.
The SONCC area is more thoroughly sampled, particularly with respect to the Rogue River basin. Within the SONCC
ESU, it is apparent that the close genetic relationship between geographically proximate spring-run and fall-run Chinook salmon continues to be true when viewed at the within-ESU scale.
In particular, in several studies, springrun and fall-run samples from the Rogue River are more genetically related to each other than either are to samples from other rivers in the SONCC ESU. In other words, within the currently delineated SONCC Chinook salmon ESU, spring-run and fall-run fish spawning in the Rogue River appear to reproduce more with each other than with fall-run fish spawning in other rivers in the ESU. The Panel found that this pattern is similar to what has been reported in the Upper Klamath and Trinity Rivers Anderson and Garza 2018, and is also apparent in the Puget Sound and Lower Columbia Chinook ESUs.
In addition to neutral genetic variation, adaptive genetic variation has been used to identify differences between individual fish or groups of fish. An example is the gene-region that has been associated with run-timing in Chinook salmon and steelhead, the GREB1L gene otherwise referred to as the GREB1L region of the genome. Hess et al. 2016, Prince et al. 2017 and
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Thompson et al. 2019a characterized the GREB1L region as two alleles different forms and three genotypes different combinations of the two alleles: Individuals with two early runtiming alleles early run homozygotes, individuals with two late run-timing alleles late run homozygotes, and individuals with one allele for the early and one for the late run-timing heterozygotes. There are five recent studies that have examined run-timeassociated variants in the GREB1L
region in OC and SONCC Chinook samples Prince et al. 2017; Anderson &
Garza 2018; Thompson et al. 2019a;
OMalley et al. 2020a; OMalley et al.
2020b. These studies have found that heterozygotes are common, indicating that interbreeding between fish homozygous for the spring-run and fallrun variants is commonly occurring.
This pattern has been extensively studied in the Rogue River basin of the SONCC ESU Thompson et al. 2019;
OMalley et al. 2020a; OMalley et al.
2020b, where researchers have obtained relatively large sample sizes of fish based on carcass surveys and surveys of captured live fish conducted throughout the run. For the OC, the only river that has been sampled using the GREB1L
markers is the Siletz River Anderson and Garza 2018; Thompson et al. 2020.
That study also found substantial proportions of heterozygotes, particularly among fish that returned to the river early and were identified as spring-run 29 percent. A similarly high proportion of GREB1L region heterozygotes have been found in other coastal Chinook salmon ESUs Upper Klamath River, Anderson and Garza 2018; Rogue River, Thompson et al.
2019a; Washington Coast, Thompson et al. 2019b.
The GREB1L region has been demonstrated to be highly associated with run timing in multiple populations of coastal Chinook salmon i.e., coastal spring-run Chinook salmon are homozygous for the early alleles, and fall-run Chinook are homozygous for the late allelesAnderson and Garza 2018, Thompson et al. 2019a,b, OMalley et al.
2020, Thompson et al. 2020. The finding of substantial proportions of heterozygotes provides evidence of contemporary interbreeding between alternative homozygotes at the GREB1L
region. This, in turn, implies that mating among spring-run and fall-run and likely intermediate timed fish is common in multiple watersheds reviewed by Ford et al. 2020. Analysis of recombination events Anderson and Garza 2018, Thompson et al. 2020 also indicates that at least in the Upper
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