Willamette BiOp - Genetic Diversity of Willamette River Spring Chinook Salmon Populations

Identification Information

Citation

Originator: ODFW

Publish Date: July 2013

Online Link: None

BPA Project #:

Contact Information

Agency: Oregon Department of Fish and Wildlife

Name: Jeremy Romer

Job Position: Assistant Project Leader

Telephone: 541-757-4113

E-Mail Address: jeremy.d.romer@odfw.oregon.gov

Description

Abstract: In this study, we used multilocus microsatellite genotype data from 813 spring Chinook salmon Oncorhynchus tshawytscha to investigate patterns of genetic diversity within and among wild and hatchery populations from the Willamette River and Catherine Creek (Grande Ronde River, Oregon). We found that hatchery populations from the Willamette River presented higher heterozygosities than local wild populations, though no pattern was found for allelic richness. An analysis of genetic divergence (?) revealed little or no differentiation between hatchery and local wild populations within Willamette River subbasins. However, we observed weak but statistically significant structure among most Willamette River subbasins. Phylogenetic analyses of Willamette River populations further indicated that hatchery populations are most similar to local wild populations, though no inference could be made for wild Middle Fork Willamette Chinook due to an inadequate sample size. Genetic population structure did not closely reflect geographic structure of the Willamette River, as North Santiam River populations clustered with McKenzie River populations and South Santiam River populations formed a clade with hatchery Chinook from the Middle Fork Willamette River. Structure was particularly weak among populations from the Middle Fork Willamette and South Santiam rivers. We evaluated the accuracy of genetic stock identification for Willamette River spring Chinook, based on 13 GAPS (Genetic Analysis of Pacific Salmon) microsatellite markers. We found that with the GAPS baseline, individuals could be assigned to their population of origin (subbasin) with 43% - 64% accuracy. We estimated 100% assignment accuracy to the Catherine Creek Hatchery population, reflecting the distinctiveness of Willamette River Chinook relative to that population. We observed no measurable increase in assignment accuracy by adding four gene-linked markers to the GAPS baseline. We tested for signals of positive selection on both GAPS microsatellites and four gene-linked markers by examining inter-locus patterns of genetic differentiation. Although we found no evidence for locus-specific selection among Willamette River populations, one GAPS microsatellite and an immune-relevant marker presented aberrantly large genetic diversity index (FST) values between Willamette River populations and the Catherine Creek population. This result suggests that these loci may be linked to genes under positive selection that has generated markedly different allele frequencies in Catherine Creek and Willamette River spring Chinook. Lastly we used our empirical genotypic data from the McKenzie River hatchery and wild populations to perform forward-time simulations, modeling changes in ?, mean heterozygosity and total allele count over 30 generations. We use the term “migration” to describe the interaction of hatchery and wild fish in these simulations; namely the proportion of natural-origin fish spawned in the hatchery as broodstock and the proportion of hatchery fish present on natural spawning grounds. Our findings indicated that migration rates of at least 5% resulted in <2% decline in heterozygosity and an asymptotic FST value of 0.005 or less. No migration from one or both populations resulted in markedly higher rates of population divergence, loss of heterozygosity and reduction in alleles present. The mean number of alleles present (per locus) in the hatchery and wild populations was more sensitive to differences in migration rate than heterozygosity, whereby low levels of hatchery straying and natural-origin broodstock integration best conserved genetic diversity.

Purpose: Given previously identified uncertainties related to the extent of genetic structure among Willamette River spring Chinook populations and the effects that alternate broodstock management practices could have over Chinook genetic diversity, our research carried the following objectives: 1. Collect tissue samples from natural and hatchery origin adult spring Chinook from major eastern subbasins of the Willamette River. 2. Genotype a representative sample of each hatchery and wild population using a suite of polymorphic microsatellite loci. 3. Estimate genetic diversity within and among sampled populations, using conventional population genetics measures. 4. Evaluate potential genetic effects of management actions, including integration of natural-origin broodstock.

Time Period of Content:

Geographic Extent: Clackamas, Molalla, North Santiam, South Santiam, Calapooia, McKenzie, Middle Fork Willamette, and Grande Ronde Rivers

Status: Final

Use Constraints:

Format: PDF

Data Quality Information

Lineage-Source: Task Order Number: W9127N-11-2-0002-0004 Work Completed for Compliance with the 2008 Willamette Project Biological Opinion, USACE funding: 2011-2012

Data Information

No data information was supplied.

Entity and Attribute Information

Attributes Description: Field attribute information is available in the database table field descriptions.

Is a physical copy maintained for reference at Headquarters? No