1. Effects of supportive breeding on loci underlying fitness traits in Chinook salmon
Charles D. Waters
Yakima Basin Science and Management Conference
June 15, 2016

2. Patterns: Fitness Studies
Relative reproductive success
Male Female Unknown
Given these results, we need to determine why hatchery fish are not reproductively successful. Specifically,
What’s the mechanism behind the reduced fitness? One thing or many? Which fitness traits may be targeted by domestication?
How does the hatchery environment affect genetic diversity and genetic variation at fitness-related traits? Variation is the foundation for future adaptation. What’s the relative importance of domestication vs drift and inbreeding
Can hatchery management be improved? If so, potential alternative solutions need to be tested to determine their effectiveness.
4) How long can hatcheries operate before increased genetic risks? What’s the long term impacts of hatchery fish on wild populations?
Christie et al. 2014
*Fish born in hatcheries do not produce as many offspring in the wild as wild-born fish*

3. Unresolved Questions
Mechanisms underlying reduced fitness? Which fitness traits are most affected by the hatchery?
Relative importance of domestication vs. genetic drift and inbreeding?
Effects on genetic variation?
Long-term impacts of hatchery fish on wild populations?
Effectiveness of possible solutions?
Given these results, we need to determine why hatchery fish are not reproductively successful. Specifically,
What’s the mechanism behind the reduced fitness? One thing or many? Which fitness traits may be targeted by domestication?
How does the hatchery environment affect genetic diversity and genetic variation at fitness-related traits? Variation is the foundation for future adaptation. What’s the relative importance of domestication vs drift and inbreeding
Can hatchery management be improved? If so, potential alternative solutions need to be tested to determine their effectiveness.
4) How long can hatcheries operate before increased genetic risks? What’s the long term impacts of hatchery fish on wild populations?

4. Applications of Genomics
spawn time
return time
Traits
affected?
Rate of
genetic change
weight
length
age
other?
Informing Hatchery Management
Test
solutions
Genetic tools
for
monitoring
Make sure I specify that, even though the traits may be changing phenotypically, they may not be changing genetically. So it’s important to monitor the genetic variation underlying these traits.

5. Segregated Line Integrated Line
Cle Elum Supplementation and Research Facility Spring Chinook salmon
1998
P1-wild founders
2002
F1 adults-1st gen hatchery
F1 adults-wild founders (no hatchery influence)
2006
F2 adults-2nd gen hatchery
F2 adults-natural origin (possible hatchery influence)
2010
F3 adults-3rd gen hatchery
F3 adults-natural origin (possible hatchery influence)
2014
F4 adults-4th gen hatchery
F4 adults-natural origin (possible hatchery influence)
Segregated Line
Integrated Line
Hatchery Fish
Wild Fish
Hatchery Fish
Wild Fish
Hatchery Fish
Wild Fish

6. Temporal Change in Genetic Variation
P1 Founders
F1 Wild
F1 Hatchery
F2 INT
F2 SEG
0.6
F3 INT
F3 SEG
F4 INT
F4 SEG
Density
0.4
0.2
Density plot of individuals along the first discriminant function from the discriminant analysis of principal components (DAPC).
0.0 -4 -2 2 4 6
Axis of Variation
Waters et al. 2015

7. Aim: Determine traits that may reduce the fitness of captive-born individuals in the wild
Objectives:
Link key fitness traits to loci using two methods.
Compare trait-linked loci to regions of divergence to determine which traits respond to genetic adaptation to captivity.
Products:
Genetic tools for monitoring populations
Adjusted hatchery management practices(?)
Information for risk assessment

8. Aim: Determine traits that may reduce the fitness of captive-born individuals in the wild
Objectives:
Link key fitness traits to loci using two methods.
Compare trait-linked loci to regions of divergence to determine which traits respond to genetic adaptation to captivity.
Products:
Genetic tools for monitoring populations
Adjusted hatchery management practices(?)
Information for risk assessment

9. Multi-Trait Mapping Reveals Candidate Regions
Ot014373_Ots05p
0.0
Ot030861
3.9
Ot046573
4.0
Ot033859
5.1
Ot024786_Ots05p
8.5
Ot007708
9.8
Ot007867_Ots05q
88.8
Ot010589_Ots05q
124.1
Ots05
Ot006371_Ots10q
Ot019910_Ots10p
58.7
Ot001901
125.1
125.9
Ot011177_Ots10q
126.2
Ot022577_Ots10q
Ot034980
131.1
Ot003788_IOts10
Ot055415
Ot034443_IOts10
Ot030321_Ots10q
134.0
Ots10
- Return time
- Fork length
- Weight
- Age at maturity
- Run time, Brieuc et al. 2015
68.6
Ot019910_Ots10p
- Single test, outlier locus
- Multi-test, outlier locus
Chinook salmon

10. Aim: Determine traits that may reduce the fitness of captive-born individuals in the wild
Objectives:
Link key fitness traits to loci using two methods.
Compare trait-linked loci to regions of divergence to determine which traits respond to genetic adaptation to captivity.
Products:
Genetic tools for monitoring populations
Adjusted hatchery management practices(?)
Information for risk assessment

11. Possible Signs of Domestication
Moving average
of divergence
95% CI of null expectations
FST
Loci and regions of the genome consistently divergent in the SEG line when compared to the P1 founders
FST
Map Position

12. Temporal changes in “outlier” loci
FST
FST
Bayes
Temporal
Bayes and temporal
Sliding window

13. Temporal changes in “outlier” loci
FST
FST
Bayes
Temporal
Bayes and temporal
Sliding window

14. Temporal changes in “outlier” loci
FST
FST
Bayes
Temporal
Bayes and temporal
Sliding window

15. Temporal changes in “outlier” loci
FST
FST
Bayes
Temporal
Bayes and temporal
Sliding window

16. Linking Traits and Selection
Do trait-linked loci separate INT and SEG lines?
Look for overlap between loci associated with traits and outlier loci
Null results ≠ no domestication

17. Has Domestication Selection Affected Return Time?
PC 1 (9.9 %)
PC 2 (9.1 %)
F1H
F1W
F2I
F2S
F3I
F3S
F4I
F4S
F1W: F1 Wild
F1H: F1 Hatchery
F2I: F2 INT
F2S: F2 SEG
F3I: F3 INT
F3S: F3 SEG
F4I: F4 INT
F4S: F4 SEG
26 markers linked to return timing
Some challenges:
Distance of markers from causative loci
Discriminating drift from selection

18. Mixed effects model: Hatchery line is not significant
Has Domestication Selection Affected Return Time?
Wild Females
Wild Males
INT Females
INT Males
SEG Females
SEG Males
200
190
180
Return Date
170
160
150
140
2000
2005
2010
2015
Return Year
Mixed effects model: Hatchery line is not significant

19. Temporal changes in “outlier” loci
FST
FST
Bayes
Temporal
Bayes and temporal
Sliding window

20. Moving forward: Bridging the gap between science and policy
Share data early and often, even if components of research are not mature
Iterative process with managers and policy makers
Translation of science to policy assisted by solutions-driven research

21. Acknowledgments Experimental lines:
Levi George, Melvin Sampson, Steve Schroder, Craig Busack,
past and present members of the Independent Scientific
Review Panel, and the Yakama Tribal Nation
Lab work:
Yakama Nation and Washington
Department of Fish and Wildlife personnel at Roza Dam Adult and CESRF
Isadora Jimenez-Hidalgo, Katrina van Raay, and Daniel Drinan
Interesting scientific discussions:
Michael Ford, Lorenz Hauser, Steve Schroder, two anonymous reviewers and Louis Bernatchez
Questions:
Funding: Federal Biop funds “Hatchery reform,” Washington Sea Grant, and the UW Hall Conservation Genetics Award

22. Questions? cwaters8@uw.edu

23. The Genetic Basis of Fitness-Related Traits in Chinook Salmon
Return time
Maturation time
Age at maturity
Weight
Forklength
Key Message: We used Random Forest analyses to identify markers associated with six fitness-related traits in adult Chinook salmon. This circos plot indicates that the genomic basis of these traits is complex and involves many loci. However, our mapping of multiple traits has revealed (potentially) functionally important regions of the genome, including regions on Ots05, Ots08, Ots10, Ots23 (two examples of such regions are on next slide). Additionally, by comparing trait-associated loci with loci potentially under selection (i.e. outlier loci), we find evidence that suggests these traits may be subjected to domestication selection.
Circos plot summarizing the results of Random Forest analyses for six fitness-related traits in adult Chinook salmon, conducted using 9108 loci and phenotypes from approximately 400 adult Chinook that were sampled across five generations. The outer track represents the linkage map for Chinook salmon with the centromeres in yellow; the chromosome numbers (Ots01 to Ots34) are indicated on the inner-most track of the plot. Bars in the remaining six tracks represent mapped loci associated with each of the phenotypic traits. Purple bars show mapped loci associated with return time to Roza Dam (n=19 loci), blue bars show mapped loci associated with maturation time (n=48 loci), red bars show mapped loci associated with age at maturity (n=26), dark green bars show mapped loci associated with body weight at Roza Dam (n=26), light blue bars show mapped loci associated with forklength at Roza dam (n=31 loci), and orange bars show mapped loci associated with daily growth coefficient (essentially a measure of the rate at which the fish lost weight between their collection at Roza Dam and their maturation in Cle Elum, n=18 loci).
Note: These bars only represent loci of known positions (including inferences made through alignments with Rainbow Trout and Atlantic salmon genomes).
Total number of loci identified for each trait (with % phenotypic variation explained in parentheses):
Return Time = 26 loci (29.2% of variation in trait explained)
Maturation Time = 68 loci (26.7% variation explained)
Age at Maturity = 30 loci (this is categorical so we determine optimal number of loci using the out-of-bag error rate, which was lowest (24.9%) with 30 loci)
Weight at Roza = 37 loci (31.5% variation explained)
Forklength at Roza = 44 loci (32.0% variation explained)
Daily Growth Coefficient = 26 loci (30.9% variation explained)
Daily growth rate

24. Exploring adaptive evolution in the hatchery environment: Return time
Key Message: Now that we’ve identified the genomic basis of fitness-related traits, we want to compare with results from previous outlier tests to determine if any traits are adaptively diverging due to hatchery rearing. Here, we compare loci associated with return time to outlier tests. Return time to the river has diverged between the integrated and segregated hatchery lines, with fish from the segregated line returning, on average, 1-6 days later than fish from the integrated line. By comparing to outlier loci, we find that one locus associated with return time on Ots12 – Ot005185_Ots12p – was identified as an outlier by FTEMP SEG and Bayescan, and is located within a genomic region that exhibited overlap among the three tests of adaptive divergence. Another locus - Ot035973_Ots12p – is located 0.01 cM away from another locus that was identified as an outlier by Ftemp in the segregated line. These loci are marked by an oval on the plot.
Circos plot summarizing the results of Random Forest analyses for adult return time to Roza dam, conducted using 9108 loci and phenotypes from 383 adult Chinook that were sampled across five generations. The outer track represents the linkage map for Chinook salmon with the centromeres in yellow; the chromosome numbers (Ots01 to Ots34) are indicated on the inner-most track of the plot. The positions of the 19 mapped loci associated with adult return time are indicated with lines on the outside of the plot. Outlier loci are represented as points on the third track; blue points represent outlier loci identified by FTEMP in the segregated line, purple points represent outlier loci identified by FTEMP in the integrated line, and orange points represent outlier loci identified by Bayescan. Genomic regions that exhibited overlap among three tests of adaptive divergence in the segregated line – FTEMP, Bayescan, and the sliding window analysis – are represented as red bars on the second track of the plot.
Note: Total number of loci identified for return time (with % phenotypic variation explained in parentheses):
Return Time = 26 loci (29.2% of variation in trait explained)
Note: The r package used to produce this plot must have been updated, and there is no way we can get the locus names to align right next to the lines. Marine and I have both tried for hours, and the author of the R package is useless. I can put the locus names next to the lines using individual text boxes, but this will take a long time. I’ll work on this but wanted to get you the main figures first.

25. Has Domestication Selection Affected Return Time?
Ot002848
Ot055858
0.0
Ot002570_Ots02p
2.1
Ot014760_Ots02p
15.3
Ot013334_Ots02p
23.9
Ot027342_Ots02p
36.3
Ot051761_Ots02p
100.3
Ots02
Ot035973_Ots12p
Ot019148_Ots12p
0.2
Ot043712
20.7
Ot005185_Ots12p
28.7
Ot016783_Ots12p
30.6
Ots12
- Predictor locus, this study
- Predictor locus, Brieuc et al. 2015
- Single test outlier locus
- Multi-test outlier locus
- Outlier region