1. Supplementation with local, natural-origin broodstock may minimize negative fitness impacts in the wild
Initial results of this study were published in 2012 for following 2 broodyears over two generations of adult to adult returns and evaluating reproductive success for hatchery and natural spring/summer Chinook in Johnson Creek. In this presentation, we have added an additional 3 broodyears of data.
Maureen Hess1
Craig Rabe2
Jason Vogel2
Doug Nelson2
Shawn Narum1

2. Types of hatchery programs
Supplementation – Prevent extirpation, rebuild natural production (integrated)
Reintroduction – Restore extirpated populations (outside stocks, integrated)
Harvest augmentation – Fish for harvest (often segregated)
Integrated program
Hatchery
Nature
Lower degree of domestication
Lower genetic risk to natural population
Segregated program
Because hatchery programs are intended to fulfill multiple objectives, the way in which broodstock is managed can vary quite a bit among different programs. Segregated programs function as two environments and two populations, and because hatchery fish are shuttled through the broodstock program each year (no input from natural fish), these programs have a higher degree of domestication and subsequent genetic risk to the natural population. Integrated programs which use some portion of natural fish in broodstock function as two environments, but one population.
Hatchery
Nature
Higher degree of domestication (“hatchery-adapted”)
Higher genetic risk to natural population

3. Types of hatchery programs
Supplementation – Prevent extirpation, rebuild natural production (integrated)
Proportion of natural-origin fish in broodstock and hatchery-origin fish on spawning grounds varies by program and year
Integrated program
Domestication and subsequent risk to natural population
% Natural-origin broodstock
Expectation:
??%
The proportion of NAT in broodstock and HAT on spawning grounds varies by program and year. The degree of domestication of the hatchery stock and subsequent risk to natural populations is expected to decrease with increasing proportion of NAT in broodstock. The Johnson Creek program is unique in that only natural-origin fish are used in the broodstock program each year.
Hatchery
Nature
100%
??%
Johnson Creek supplementation program = 100% natural-origin broodstock every year
Lower degree of domestication
Lower genetic risk to natural population

4. Spring/Summer Chinook Salmon in Johnson Creek Study system
Johnson Creek, adult weir
Nez Perce Tribe initiated supplementation program in 1998 WA ID OR
Only natural-origin returns used for broodstock
Hat
Hat
Nat
Johnson Creek is a tributary to the EFSF Salmon River in Idaho. This figure shows the number of redds for spring/summer Chinook beginning in 1958 in JC, as most populations declined throughout the Columbia River basin in the 1990s, there were only 5 redds counted in 1995 in Johnson Creek. The NPT initiated a supplementation program in 1998 to prevent the extirpation of the population. Every year since 1998, NP tribal biologists collect biological data and a fin tissue sample from all fish that return to weir (located below majority of spawning habitat). HAT and NAT fish are passed above the weir for natural spawning, and a portion of NAT fish are taken for broodstock each year.
Nat
Evaluate lifetime reproductive success of Chinook salmon in the wild at the initiation of supportive breeding (Hess et al Molecular Ecology)

5. Summary of dataset
Number of individuals by return year and origin
N = 9,111
# individuals sampled
This figure shows the number of adult returns to JC over a 15 year period from by origin. Over 9,000 tissue samples were collected by tribal biologists at the weir and on spawning ground surveys. This first hatchery-origin fish from the supplementation program began to return in 2001.
Natural
Hatchery
Unknown
Return year
15 years of data = 5 complete generations of adult to adult returns
Sampled high proportion of natural spawners (~90% of fish produced above weir genetically assign to parents)

6. Methods i.) Use DNA to reconstruct genetic pedigrees F1 F0 F23 4 5 F1
F1: produced in hatchery vs. in nature
F2: produced in nature by HAT and NAT parents 98 99 00 01 02 03 04 05 06 07 08 F2 09 10 11 12 13 F0
The DNA from the collection of tissue samples was used to reconstruct genetic pedigrees. This bubble diagram represents each return year, beginning with 1998 at the initiation of supplementation. This is defined as the F0 generation, a portion of natural fish used for broodstock and remaining spawn naturally above weir in that year. HAT and NAT offspring (F1) return in 2001, 02, and 03 at ages 3, 4, and 5. Both HAT and NAT spawn naturally in these years, and their NAT offspring return in With the current set of samples, we can evaluate 5 F0 broodyears of adult to adult returns over 2 generations. As you can see, given the generation time here, these types of studies can take a while to accumulate data.
5 F0 broodyears of adult to adult returns over 2 generations

7. Methods ii.) Use genetic pedigrees to quantify reproductive success
Reproductive success = How many offspring did each individual produce?
Potential Parents
# Offspring??
NAT
HAT
Genetic pedigrees allow for quantification of reproductive success, which simply quantifies the number of offspring produced by each potential spawner. Then a comparison of RS can be made by standardizing to NAT fish.
Avg # offspring produced by a natural fish
Avg # offspring produced by a hatchery fish
RRS =
Comparison of reproductive success (RS) between hatchery and natural

8. Objectives
1.) Demographic boost provided by the hatchery over two generations?
Nat
Hatchery
environment
Wild
Offspring &
Grand-offspring
1. Does taking a fish into the hatchery result in more wild born adults two generations later than if that fish had been allowed to spawn in the wild?

9. Objectives
1.) Demographic boost provided by the hatchery over two generations?
Wild
Hatchery
environment
Offspring
Grand-offspring
2.) Differences in reproductive success between hatchery-reared and natural-origin fish spawning naturally?
RRS VS

10. Objectives
1.) Demographic boost provided by the hatchery over two generations?
Wild
Hatchery
environment
Offspring
Grand-offspring
2.) Differences in reproductive success between hatchery-reared and natural-origin fish spawning naturally?
RRS VS
3.) Do hatchery-reared fish reduce the fitness of natural-origin fish?
RRS VS

11. Objective 1 i.) Demographic boost provided by the hatchery? F1 F23 4 5 F1
# F1 offspring produced in hatchery vs. in nature
# F2 grand-offspring produced in nature by HAT and NAT parents 98 99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 F2
To evaluate if a demographic boost was provided by the hatchery, we compared numbers of adult offspring produced by broodstock fish in the hatchery with the numbers of offspring produced by natural spawners
NAT
Hatchery
environment VS
NAT
HAT

12. Objective 1 i.) Demographic boost provided by the hatchery?
On average, fish taken into the hatchery produced nearly 5 times more adult offspring than naturally reproducing fish
Even though the survival advantages of the hatchery are no longer present in the second generation (because grand-offspring were produced in the wild), the demographic boost appears to be continued; where fish removed for broodstock produced on average 2.6 times as many adult grand-offspring than fish allowed to spawn naturally in BY 1998 through 2002.
The primary goal of the supplementation program was to prevent the extirpation of the population in Johnson Creek, and so far the hatchery program appears to have provided a boost to the natural population. Now it’s important to evaluate fitness differences and effects.
Survival advantage in the hatchery environment
* BY2003 grand-offspring doesn’t yet include BY2008 F2 assignments from 2013
+ Mean for BYs
Demographic boost continues into second generation

13. Objective 2
Reproductive success differences between hatchery and natural spawning in nature?
RRS VS 3 4 5 F1 98 99 00 01 02 03 04 05 06 07 08 09 10 11 12 13
NAT
HAT

14. Objective 2
Reproductive success differences between hatchery and natural spawning in nature?
Those that produce zero offspring, have no direct genetic effect on fitness
High variance in reproductive success - most produce zero returning adult offspring
Evaluate reproductive success in two ways
2,883
NAT
HAT
a.) Include all potential spawners regardless of whether they produced returning adult offspring or not
# potential parents,
b.) Include only successful spawners (produced at least 1 returning adult offspring)
This is a distribution of the numbers of potential parents producing specific numbers of offspring. As seen is all RS studies, there is high variance in RS where most individuals produce zero returning adult offspring, fewer individuals produce at least 1 offspring, and only a handful of fish are very successful in the tail of this distribution. Most fish don’t return adult offspring to the system for a variety of reasons, such as prespawn mortality (perhaps they arrived too late, or were too small and couldn’t compete to find a mate for example, maybe they were removed for broodstock). In any case, individuals that do not produce returning adult offspring have no direct genetic effect on fitness because they have not passed their DNA to the next generation. Because of this, we evaluated RS in two ways…
# offspring produced

15. Reproductive success differences between hatchery and natural spawning in nature?
All potential *
Hatchery rearing yielded fewer males that reproduced (possible sexual selection in action)
% successful parents ( )
NAT origin
HAT origin
Relative reproductive success (HAT / NAT)
RRS estimates similar between hatchery and natural fish, no statistical differences (recognize some years with low power due to sample size; average annual 95% CIs ranged ~0.65 and 1.50)
Only successful
Many hatchery jacks present, likely poor spawn success
This figures shows annual point estimates of RRS separately for females and age 4+ males. There is large variation in annual estimates with some years where hatchery males and females have lower RS than natural, and some years where RS for hatchery fish is higher than 1. The four estimates highlighted in gray are the combined annual estimates using two different methods (maximum likelihood and weighted geometric mean). Each estimate with an asterisk identifies a statistically significant difference, largely for reduced RS of hatchery origin males. Hatchery rearing yielded…
This figures shows RRS estimates when only fish passing on their genes to the next generation are included. RRS estimates similar…. *
Females
Males, age 4+

16. 3 types of matings in nature:
Objective 3
Do hatchery-reared fish reduce the fitness of natural-origin fish?
Parents
Offspring 98 99 00 01 02 03 04 05 06 07 08 09 10 11 12
3 types of matings in nature:
N x N
H x N
H x H
RRS VS
This evaluation is the cornerstone of getting at the question of whether hatchery fish reduce fitness of natural origin fish when they mate with them. Here we compared the numbers of offspring produced by each of the 3 types of matings that occurred above the weir in 6 return years. If hatchery fish reduce the fitness of wild fish, then we would expect this middle bar to be reduced, and possibly see an interaction effect when two hatchery fish mate.
HAT X
HAT
NAT X
NAT
HAT X
NAT

17. Objective 3
Do hatchery-reared fish reduce the fitness of natural-origin fish?
Combined RRS estimates, 6 years
No significant difference in RS of H x N and N x N (though possible interaction effect of HxH males)
Relative reproductive success (HAT / NAT)
Limited evidence of reduction in fitness of natural fish when they mate with hatchery fish
These figures show combined RRS over the 6 years using the 2 methods of max likelihood in black and weighted geomean in gray. Females on top half and age 4+ Males on bottom half. We found no sig…and therefore limited evidence of reduction in fitness of natural fish when they mate with hatchery fish.
Maximum likelihood
Weighted geomean

18. Estimating RRS from cross type data (e.g. NxN vs. HxN)
Fig. S4 in Christie et al. 2014
RRS analyses of mating types cannot identify pairs that produce zero offspring
Johnson Creek RRS estimates were ≥ 0.79 ; so little difference or directional bias in estimates of RRS
At lower RRS estimates, there is a larger difference between estimates with or without zeros
In reality, true RRS of salmon pops is likely in the middle – zeros represent both fish that didn’t spawn and fish that spawned but offspring didn’t return
Only successful (exclude pairs with zero offspring)
Christie et al point out that it’s not possible to identify pairs that produced zero offspring when examining mating types as was done in objective 3. They simulated RRS estimates to evaluate the effect of excluding pairs with zero detected offspring, and found that there is a larger difference in between RRS estimates with and without zeros at lower values of RRS. If all returning fish actually spawn then RRS with zeros may be closer to true value, however if pre-spawning mortality occurs, then RRS without zeros may be more appropriate. The RRS estimates in JC were ≥ 0.79 for all cross types, so there would be very little difference or directional bias in the cross estimates.
While estimating RRS from cross types has some drawbacks (ie., reduced sample size/low power, and possibility for directional bias), these analyses are necessary in order to gain understanding of whether hatchery fish have a direct impact to fitness of wild fish.
All potential (including pairs with zero offspring)

19. Conclusions
Objective 1 - Demographic Boost: Supplementation program provides a boost to the natural population
Objective 2 - Fitness Differences:
a.) Lower RS of hatchery fish; primarily in jacks and males that do not appear to have mated successfully
b.) Generally, equal reproductive success of H and N fish contributing offspring to the next generation
Objective 3 - Fitness Effects: No significant difference in reproductive success of HxH, HxN, and NxN mating types
Suggests Chinook salmon reared for a single generation in the hatchery had a limited and undetectable effect on the fitness of natural-origin fish in Johnson Creek
Photo credit: Bill Young

20. Why limited evidence of reduced RRS in Johnson Creek in the short-term?
Low statistical power in some annual estimates
Inability to detect significant differences does not equate to no fitness effects on natural population
Differences in hatchery rearing practices and management of broodstock
HOW can programs be managed to minimize potential for negative effects on wild fish?
One small piece of this puzzle, but likely important way to reduce negative impacts:
Hatchery
Nature
All RRS studies to date suffer from low statistical power particularly in annual estimates due to low sample size, and Johnson Creek is no exception. As combined estimates have shown however, there appears to be limited evidence of direct negative impacts to the natural population from hatchery fish. It’s important to recognize that the inability to detect significant differences does not equate to no fitness effects on the natural population. There are also differences among hatchery programs. In Johnson Creek, the broodstock management program is unique in that only natural-origin fish are used as broodstock each year. There is a risk to natural fish when hatchery fish mate with them, but that risk may be smaller or minimized for broodstock programs which minimize the numbers of hatchery fish in broodstock
~100% natural-origin in broodstock