Hatchery spring Chinook salmon populations in the Willamette River basin have higher genetic diversity than wild populations. Genetic structure exists between subbasins but is weak. Hatchery populations are genetically most similar to the local wild populations they were founded from. Simulations show that migration rates of 5% between hatchery and wild populations can preserve genetic diversity levels similar to a 10% migration rate over multiple generations.

1. The genetic structure of steelhead and
spring Chinook salmon in the upper
Willamette River, Oregon
Marc A. Johnson1, Thomas A. Friesen1,
David J. Teel2, Donald M. Van Doornik2
1Oregon Department of Fish and Wildlife,Corvallis Research
Laboratory, 28655 Highway 34, Corvallis, OR 97333
2NOAA Fisheries, Northwest Fisheries Science Center, Manchester
Research Laboratory, PO Box 130, Manchester, WA 98353

2. Upper Willamette River Chinook and Steelhead
Chinook salmon
•Spring Chinook are
native to the basin
•Hatchery stocks founded
from local, wild stocks
•Integrated hatcheries
•Minimize genetic
divergence
•Reduce consequences
of HxW interactions
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Steelhead
•Winter steelhead are native
to some subbasins
•Hatchery summer steelhead
are not a native UWR stock
•Segregated hatcheries
•Reduce frequency of HxW
interactions
•Minimize natural production
and interbreeding
“One of the most serious problems faced by wild and hatchery populations is the permanent
loss of genetic material. Not only can such losses affect the immediate performance of a
stock, but they also limit its flexibility to respond to changing conditions in the future.”
-Waples et al. 1990. Fisheries 15:19-25

3. Willamette River Spring Chinook
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4. Objectives
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Describe how genetic diversity is distributed within and
among hatchery and wild spring Chinook populations
Evaluate how alternate wild integration and hatchery
straying (migration) rates could affect genetic diversity

5. Sampling
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Fin tissue collected from adult
hatchery and wild spring Chinook
•MF Willamette (H & W)
•McKenzie (H & W)
•Calapooia (W)
•South Santiam (H & W)
•North Santiam (H & W)
•Molalla (W)
•Clackamas (H & W)
•Catherine Cr., Grande Ronde (H)
“Wild” determined by
adipose fin and no
otolith thermal mark

6. In the Lab
Isolated genomic DNA
Amplified and scored 17 microsatellites
• 13 GAPS markers
• 4 “immune-relevant” markers*
An electrophoretogram for a single microsatellite locus from a Willamette River Chinook salmon. This individual is a
heterozygote, with two major “peaks” representing the two different alleles, or character states, for this marker.
*Tonteri et al. (2008) Molecular Ecology Resources 8:1486-1490
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7. Data Analyses
Describe how genetic diversity is distributed within and among hatchery and wild spring
Chinook populations
Estimated
• Mean heterozygosity1
• Allelic richness2
• Pairwise θ1
Inferred
• Phylogenetic relationships among hatchery and wild populations3
Tested
• Locus-specific signatures of selection with FST outlier4
Evaluate how alternate wild integration and hatchery straying (migration) rates could affect
genetic diversity
Simulated
• Effects of alternate migration rates on heterozygosity, θ, total allele
count5
1 GENETIX – Belkhir et al. 2004. Available at http://kimura.univ-montp2.fr/genetix/
2 FSTAT – Goudet. 1995.Journal of Heredity 86:485-486
3 CONTML – Felsenstein. 2009. Available at http://evolution.genetics.washington.edu/phylip/doc/
4 LOSITAN – Antao et al. 2008. Bioinformatics 9: 323
5 NEMO – Guillaume & Rougemont. 2006. Bioinformatics 22:2556-2557
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8. Samples
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Subbasin n wild n hatchery
Clackamas 51 80
Molalla 8 -
North Santiam 72 95
South Santiam 62 94
Calapooia - -
McKenzie 67 95
Middle Fork Willamette 12 144
Catherine Creek - 33
Total 272 541
Total of 813 samples included in statistical analyses

9. Heterozygosity & Allelic Richness
• Higher heterozygosities in hatchery
populations
• No pattern of difference for allelic richness
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Subbasin Wild Ho Hatchery Ho
Clackamas 0.752 0.815
Molalla 0.823
North Santiam 0.777 0.820
South Santiam 0.746 0.813
McKenzie 0.788 0.805
Middle Fork Willamette 0.620 0.818
Catherine Creek 0.735

10. Heterozygosity
and
Allelic Richness
RANK Population He Ho AR
1Lewis Hatchery (spring) 0.866 0.87 15.2
2Cowlitz Hatchery (spring) 0.861 0.853 14.9
3Klickitat River (spring) 0.864 0.846 15.9
4Kalama Hatchery (spring) 0.865 0.837 15.1
5McKenzie Hatchery (spring) 0.817 0.812 12.9
6North Santiam Hatchery (spring) 0.82 0.812 13.1
7Winthrop Hatchery, Carson stock (spring) 0.792 0.809 12.5
8Wenatchee River (spring) 0.795 0.803 13.4
9Tucannon River (spring)a 0.791 0.803 11.6
10Battle Creek (spring) 0.841 0.801 15
11Cle Elum Hatchery (spring) 0.816 0.796 13.2
12Red River (spring)a 0.795 0.795 13
13Entiat Hatchery (spring) 0.782 0.793 11.7
14Imnaha River (spring)a 0.783 0.793 12.7
15Sawtooth Hatchery (spring)a 0.79 0.793 13
16Dworshak Hatchery (spring)a 0.793 0.792 13.5
17Pahsimeroi River (spring)a 0.78 0.79 11.5
18Lochsa River–Powell Trap (spring)a 0.788 0.789 13.1
19Methow River (spring) 0.793 0.788 13.4
20Minam River (spring)a 0.79 0.788 13.5
21South Fork Clearwater (spring)a 0.785 0.782 12.8
22Big Creek-b (spring)a 0.76 0.782 11.3
23West Fork Yankee Fork (spring)a 0.758 0.779 10.3
24Marsh Creek (spring) 0.782 0.777 12.1
25Catherine Creek (spring)a 0.775 0.776 12.7
26Johnson Creek supplementation (spring)a 0.779 0.776 12.2
27Johnson Creek (spring)a 0.776 0.775 11.9
28Lolo Creek (spring)a 0.787 0.767 13.6
29Rapid River Hatchery (spring)a 0.762 0.767 11.3
30Big Creek-a (spring)a 0.754 0.764 11.7
31Lostine River (spring)a 0.754 0.763 11
32Secesh River (spring)a 0.773 0.763 12.1
33Newsome Creek (spring)a 0.765 0.76 12
34Shitike Creek (spring) 0.763 0.757 12.2
35East Fork Salmon River (spring)a 0.769 0.757 12
36John Day River (spring) 0.78 0.755 13.5
37Warm Springs Hatchery (spring) 0.725 0.728 10.9
Narum et al. 2010. Transactions of the
American Fisheries Society 139:1465-1477
RANK Population He Ho AR
1Klickitat River (spring) 0.864 0.846 15.9
2Lewis Hatchery (spring) 0.866 0.87 15.2
3Kalama Hatchery (spring) 0.865 0.837 15.1
4Battle Creek (spring) 0.841 0.801 15
5Cowlitz Hatchery (spring) 0.861 0.853 14.9
6Lolo Creek (spring)a 0.787 0.767 13.6
7Dworshak Hatchery (spring)a 0.793 0.792 13.5
8Minam River (spring)a 0.79 0.788 13.5
9John Day River (spring) 0.78 0.755 13.5
10Wenatchee River (spring) 0.795 0.803 13.4
11Methow River (spring) 0.793 0.788 13.4
12Cle Elum Hatchery (spring) 0.816 0.796 13.2
13North Santiam Hatchery (spring) 0.82 0.812 13.1
14Lochsa River–Powell Trap (spring)a 0.788 0.789 13.1
15Red River (spring)a 0.795 0.795 13
16Sawtooth Hatchery (spring)a 0.79 0.793 13
17McKenzie Hatchery (spring) 0.817 0.812 12.9
18South Fork Clearwater (spring)a 0.785 0.782 12.8
19Imnaha River (spring)a 0.783 0.793 12.7
20Catherine Creek (spring)a 0.775 0.776 12.7
21Winthrop Hatchery, Carson stock (spring) 0.792 0.809 12.5
22Johnson Creek supplementation (spring)a 0.779 0.776 12.2
23Shitike Creek (spring) 0.763 0.757 12.2
24Marsh Creek (spring) 0.782 0.777 12.1
25Secesh River (spring)a 0.773 0.763 12.1
26Newsome Creek (spring)a 0.765 0.76 12
27East Fork Salmon River (spring)a 0.769 0.757 12
28Johnson Creek (spring)a 0.776 0.775 11.9
29Entiat Hatchery (spring) 0.782 0.793 11.7
30Big Creek-a (spring)a 0.754 0.764 11.7
31Tucannon River (spring)a 0.791 0.803 11.6
32Pahsimeroi River (spring)a 0.78 0.79 11.5
33Big Creek-b (spring)a 0.76 0.782 11.3
34Rapid River Hatchery (spring)a 0.762 0.767 11.3
35Lostine River (spring)a 0.754 0.763 11
36Warm Springs Hatchery (spring) 0.725 0.728 10.9
37West Fork Yankee Fork (spring)a 0.758 0.779 10.3

11. Pairwise θ Values
Small but significant values among subbasins
Pairwise θ values among hatchery (H) and wild (W) origin spring Chinook populations from the Willamette River and
Catherine Creek Hatchery (Grande Ronde River), estimated from genotypic data for 13 GAPS microsatellite loci. Values
not significantly different from zero (p > 0.05) are indicated in bold.
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Clackamas
Hatchery
Clackamas
Wild
Willamette
Hatchery
McKenzie
Hatchery
McKenzie
Wild
N.Santiam
Hatchery
N. Santiam
Wild
S. Santiam
Hatchery
S. Santiam
Wild
Catherine Cr. H 0.111 0.106 0.106 0.107 0.102 0.100 0.110 0.099 0.104
Clackamas H 0.007 0.012 0.013 0.013 0.010 0.012 0.010 0.009
Clackamas W 0.004 0.003 0.003 0.004 0.005 0.002 0.001
Willamette H 0.007 0.006 0.008 0.009 0.003 0.004
McKenzie H 0.000 0.003 0.006 0.004 0.005
McKenzie W 0.004 0.006 0.004 0.003
N. Santiam H 0.002 0.005 0.005
N. Santiam W 0.005 0.005
S. Santiam H 0.000

12. Phylogenetic Relationships
Hatchery populations most similar to local wild populations
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Maximum likelihood trees depicting genetic relationships among hatchery (H) and wild origin (W) spring Chinook populations
from the Willamette River and (right) Catherine Creek Hatchery population. Phylogeny inferred from genotypic data for 13
microsatellite loci. Branch lengths represent Cavalli-Sforza chord measures of genetic distances (Cavalli-Sforza and Edwards
1967). Bootstrap values are indicated for nodes with >50% support (left tree only). Branch lengths of the South Santiam H-
South Santiam W-MF Willamette H clade are not significantly different from zero (95% confidence interval).

13. Evidence of Selection
• Among UWR populations: NO
• UWR populations & Catherine Cr: YES
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Overall FST values for 17 microsatellite loci (markers) plotted against heterozygosity, as characterized from the
Catherine Creek hatchery and nine Willamette River spring Chinook populations. Gray shaded area defines the
99.5% CI of expected FST values for all possible heterozygosities, constructed from 50,000 data simulations.
Shaded areas indicate regions associated with positive (red) and balancing (yellow) selection.

14. Simulations of Migration and Diversity
Migration: Represents symmetrical pHOS and pNOB
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Generation
0 5 10 15 20 25 30 35
Heterozygosity
0.94
0.95
0.96
0.97
0.98
m = 0.00
m = 0.02
m = 0.05
m = 0.10
Generation
0 5 10 15 20 25 30 35
Theta
-0.005
0.000
0.005
0.010
0.015
0.020
0.025
0.030
0.035
m = 0.00
m = 0.02
m = 0.05
m = 0.10
Migration of 5% preserves similar level of diversity as 10%
Simulated change in mean heterozygosity and theta for 17 neutral microsatellite loci in hatchery and wild populations of
McKenzie River spring Chinook. Data were simulated under four migration rates (m) across 30 generations.

15. Simulations of Migration and Diversity
Migration: Represents symmetrical pHOS and pNOB
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Migration of 5% preserves similar level of diversity as 10%
Generation
0 5 10 15 20 25 30 35
MeanNumberofAlleles
29
30
31
32
33
34
35
36
37
m = 0.00
m = 0.02
m = 0.05
m = 0.10
Simulated change in total allele count for 17 neutral microsatellite loci in hatchery and
wild populations of McKenzie River spring Chinook. Data were simulated under four
migration rates (m) across 30 generations.

16. introduction methods results summary questions
Key Points
• Heterozygosity in hatchery populations higher than in wilds
• Genetic structure is weak but present among subbasins
• Hatchery populations are genetically most similar to local
wild populations
• No evidence for locus-specific selection among Willamette
populations
• Selection appears to drive divergence between UWR and Catherine
Creek populations at two of the loci examined
• Symmetrical migration of 5% appeared to preserve most
(neutral) genetic diversity – nearly as well as 10%

17. Willamette River Steelhead
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18. Objectives
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Describe genetic structure among Oncorhynchus mykiss
populations
Estimate the proportion of summer steelhead among natural
origin O. mykiss smolts sampled at Willamette Falls and other
locations (subbasins) of the upper Willamette River
Estimate the proportion of summer steelhead hybrids among
natural origin O. mykiss smolts sampled at Willamette Falls and
various locations (subbasins) of the upper Willamette River

19. Sampling and Data Collection
Sample Collections
• Samples of known type– baseline and phylogeny
• Unmarked juvenile and some adult O. mykiss
• Juveniles
• Willamette Falls (2009-2011)
• Subbasins (2011; McKenzie 2005 & 2011)
Data Collection
• All samples genotyped at 15 GAPS microsatellite loci
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20. Analyses
Describe genetic structure among Oncorhynchus mykiss populations
Estimate the proportion of summer steelhead among natural origin O. mykiss smolts sampled at
Willamette Falls and other locations (subbasins) of the upper Willamette River
Genetic Stock Identification (GSI)
• Constructed phylogeny to identify reporting groups1
• Unknown samples assigned with a Bayesian GSI approach2
Estimate the proportion of summer steelhead hybrids among natural origin O. mykiss smolts
sampled at Willamette Falls and various locations (subbasins) of the upper Willamette River
Introgression Analysis
• Bayesian clustering method3
• Samples classified to group or hybrid group
1PHYLIP - Felsenstein. 2009. Available at http://evolution.genetics.washington.edu/phylip/doc/
2ONCOR – Kalinowski. 2007. Available at http://www.montana.edu/kalinowski/Software/ONCOR.htm
3STRUCTURE – Pritchard et al. 2000. Genetics 155: 945-959.
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21. Introgression Analyses (continued)
Introgression Analysis
Based on a four-group stock
structure, we estimated the
proportion (q) of each
individual’s genome
descended from each group
We then used q values to
classify individual samples
into the following general
categories:
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Pure: q > 0.50 for a single population and q < 0.20 for all other populations
Two-way hybrid: 0.20 < q < 0.80 for exactly two populations
Three-way hybrid: 0.20 < q < 0.80 for exactly three populations
S EW RB WW SxEW SxRB
Percentq
0
20
40
60
80
100
SUMMER
EAST-SIDE WINTER
WEST-SIDE WINTER
RAINBOW

22. Willamette Oncorhynchus mykiss
Van Doornik & Teel 2010
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Neighbor-joining dendrogram of Cavalli-Sforza Edwards genetic distances
among Willamette River steelhead populations. Bootstrap values (%) greater
than 50% are shown. The last two digits of the brood year for the earliest
samples are included in the sample names. Major groupings, which also
correspond to the reporting groups used for GSI analyses, are circled.

23. GSI of unmarked juvenile Oncorhynchus
mykiss: Willamette Falls
VanDoornik & Teel 2010, 2011, 2012
Location Year n EW S WW RB
Willamette Falls 2009 240 88.3% 7.5% 4.2% 0.0%
Willamette Falls 2010 287 78.0% 13.2% 8.7% 0.0%
Willamette Falls 2011 56 89.3% 5.4% 5.4% 0.0%
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24. GSI of unmarked juvenile Oncorhynchus
mykiss: Willamette River subbasins
VanDoornik & Teel 2010, 2011, 2012
Location Year n EW S WW RB
Willamette R., various mainstem 2011 29 58.6% 13.8% 0.0% 27.6%
Santiam R., mouth 2011 11 90.9% 9.1% 0.0% 0.0%
North Santiam R. 2011 36 94.4% 2.8% 0.0% 2.8%
South Santiam R. 2011 27 100.0% 0.0% 0.0% 0.0%
McKenzie R., Leaburg Bypass 2005 72 25.0% 75.0% 0.0% 0.0%
McKenzie R., Leaburg Bypass 2011 91 27.5% 68.1% 0.0% 4.4%
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25. Genetic introgression
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KnownsUnknowns
East-side
Winter Rainbow Summer
West-side
Winter

26. Genetic introgression:
Juveniles
Year Location n S EW RB WW SxWW SxEW SxRB WWxEW WWxRB EWxRB 3x Hybrid
2009 Willamette Falls 240 19 126 1 34 1 23 1 31 0 1 3
2010 Willamette Falls 287 39 144 1 37 4 29 0 25 0 3 5
2011 Willamette Falls 56 3 29 0 13 1 3 0 5 0 0 2
Percent of Total 10.5 51.3 0.3 14.4 1.0 9.4 0.2 10.5 0.0 0.7 1.7
2005 McKenzie R., Leaburg 72 56 1 0 0 1 11 1 1 0 0 1
2011 McKenzie R., Leaburg 91 63 2 4 0 1 11 6 0 0 2 2
Percent of Total 73.0 1.8 2.5 0.0 1.2 13.5 4.3 0.6 0.0 1.2 1.8
2010 Mainstem Willamette R. 30 3 10 10 0 1 1 0 0 0 5 0
Percent of Total 10.0 33.3 33.3 0.0 3.3 3.3 0.0 0.0 0.0 16.7 0.0
2011 N. Santiam R. 36 0 25 0 1 0 4 0 4 0 1 1
Percent of Total 0.0 69.4 0.0 2.8 0.0 11.1 0.0 11.1 0.0 2.8 2.8
2011 Santiam R., Mouth 11 0 6 2 0 0 1 0 1 0 0 1
Percent of Total 0.0 54.5 18.2 0.0 0.0 9.1 0.0 9.1 0.0 0.0 9.1
2011 S. Santiam R. 27 0 20 0 1 0 4 0 2 0 0 0
Percent of Total 0.0 74.1 0.0 3.7 0.0 14.8 0.0 7.4 0.0 0.0 0.0
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27. Summer steelhead introgression
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q
0.0 0.2 0.4 0.6 0.8 1.0
Proportion
0.0
0.2
0.4
0.6
0.8
1.0
Willamette Falls 2009
n = 240
q
0.0 0.2 0.4 0.6 0.8 1.0
Proportion
0.0
0.2
0.4
0.6
0.8
1.0
Willamette Falls 2011
n = 56

28. Summer steelhead introgression
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q
0.0 0.2 0.4 0.6 0.8 1.0
Proportion
0.0
0.2
0.4
0.6
0.8
1.0
North Santiam 2011
n = 36
q
0.0 0.2 0.4 0.6 0.8 1.0
Proportion
0.0
0.2
0.4
0.6
0.8
1.0
South Santiam 2011
n = 27
q
0.0 0.2 0.4 0.6 0.8 1.0
Proportion
0.0
0.2
0.4
0.6
0.8
1.0
McKenzie 2011
n = 91
q
0.0 0.2 0.4 0.6 0.8 1.0
Proportion
0.0
0.2
0.4
0.6
0.8
1.0
McKenzie 2005
n = 72

29. introduction methods results summary questions
Key Points
• About ~10% of naturally produced juvenile steelhead
sampled at Willamette Falls were summer-run type
• Little evidence for natural production of pure summer
steelhead in the Santiam rivers, but most juveniles from
the McKenzie River were summer steelhead
• Evidence for some genetic introgression from summer
steelhead detected at all locations

30. Questions?
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Acknowledgments
ODFW Rich Carmichael,
Hatchery managers,
Field crews et al.
Sample collections
WDFW Jeffrey Grimm Otolith analyses
OSU Michael Banks,
Kathleen O’Malley,
Amelia Whitcomb,
Dave Jacobson et al.
Genetic laboratory
services
USACE David Griffith,
Rich Piaskowski,
David Leonhardt et al.
Funding

32. Genetic introgression:
Adults
Year Location n S EW RB WW SxWW SxEW SxRB WWxEW WWxRB EWxRB 3x Hybrid
2009 S. Santiam R., Foster 50 0 42 0 0 0 5 0 2 0 1 0
Percent of Total 0.0 84.0 0.0 0.0 0.0 10.0 0.0 4.0 0.0 2.0 0.0
2004 N. Santiam R., Bennett 28 2 7 0 0 0 16 0 1 0 1 1
2009 N. Santiam R., Minto 11 0 8 0 0 0 2 0 1 0 0 0
2010 N. Santiam R., Minto 1 0 1 0 0 0 0 0 0 0 0 0
Percent of Total 5.0 40.0 0.0 0.0 0.0 45.0 0.0 5.0 0.0 2.5 2.5
2005 Mainstem Willamette R. 1 0 1 0 0 0 0 0 0 0 0 0
2010 Willamette R., Fall Cr. 19 0 16 0 0 0 0 0 0 0 3 0
2011 Willamette R., Fall Cr. 16 0 16 0 0 0 0 0 0 0 0 0
Percent of Total 0.0 91.7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 8.3 0.0
2005 McKenzie R., Mohawk R. 1 0 1 0 0 0 0 0 0 0 0 0
2011 McKenzie R., Leaburg 6 3 0 1 0 0 1 1 0 0 0 0
Percent of Total 42.9 14.3 14.3 0.0 0.0 14.3 14.3 0.0 0.0 0.0 0.0
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