# Presentation: 687528

## Grande Ronde Basin Spring Chinook: Relative Reproductive Success in Captive Chinook Salmon

**Melissa Baird****1****, Ewann Berntson****1****, Timothy Hoffnagle****2****, Steve Boe****3****, **
**Jim Harbeck****4****, Richard Carmichael****2****, Paul Moran****1**
**1**** National Marine Fisheries Service, Northwest Fisheries Science Center**
**2**** Oregon Department of Fish and Wildlife**
**3**** Confederated Tribes of the Umatilla Indian Reservation**
**4**** Nez Perce Tribe Department of Fisheries Resources Management**

**Notes:**
Presenting data from our lab, out of our genetic monitoring and evaluation project in the Snake River basin. 

A number of collaborators:  Nez Perce Tribe, CTUIR, and ODFW

The work was done by Melissa Baird, who is here, so I may refer any of the difficult questions to her! 

## Catherine Creek

**Catherine Creek**

**Notes:**
What we want to know:  How are supplementation programs doing?
	--goal is to increase the numbers of fish spawning naturally in the system
	--don’t want to spend money if we aren’t getting the results we are hoping for.  
	--Can count # of fish returning, but returning is only part of the goal
	--want to increase # of fish spawning naturally, and we don’t know for sure who is reproducing.   
	--Observing redd behavior is suggestive of parentage, but looking at resulting juveniles tells us more reliably about RS.  

Can use microsatellite information to reconstruct pedigrees, tells us who is reproducing
	--with that same technique, can also look at survival, both in river and ocean portions of the life history.  
	--Can also look at variance in RS in the hatchery, compare to the crosses that were made.  
	--Do some families do very well and others not at all, or is it fairly even across families?

## Project Design

- Goal is to sample 100% of returning adults
- Representative sampling of parr, smolts
- Genotyped for 10 microsatellites
- Pedigrees reconstructed by exclusion
- Relative Reproductive Success (RRS) calculated, normalized to wild

**Notes:**
Goal is to sample 100% of returning adults. 
	--Adults sampled when they return to the weir
	--representative wild parr sampled by electrofishing, ~200 per river per year
	--Smolts taken from smolt traps as they head downstream.

Note: weir efficiency low at times:  
	--Catherine Creek 60% in 2002 adults, then 95% for remaining years.
	--Lostine 50-75% for 2001-2004, then 94% for 2005.  (Low efficiencies surely account for large number of missing parents (~50% over all years)
	--No evidence that having the weir blown out would bias the results, just results in missing parents.  In order for there to be bias, you’d have to suggest that all of the fish coming through when the weir was down were hatchery (or wild).  Not likely.

Genotyped for 10 msat loci (much like DNA fingerprinting, description to follow)

Pedigrees reconstructed by exclusion—i.e. no mismatches allowed between putative parents and offspring

RRS calculations:
	--(number observed matings)/(number expected matings) (based on number of fish put over the weir).  
	--Normalized to wild, so wild RS = 1, and can compare hatchery to that.  
	--Hatchery RS > 1 means the hatchery fish did better than wild, and RS < 1 means they did more poorly.

## Pedigree analysis match-up

**Pedigree analysis match-up**

**Notes:**
Type of DNA fingerprinting:  basically a genetic profile for each fish.  

Example above for a single genetic region (locus)
	--parents on the top and 3 potential offspring on the bottom
	--two copies of each locus in each parent, and each offspring gets one copy from mom and one from dad.  
	--the the middle juvenile is the offspring of the two adults pictured.  
	--Juvenile on right is a half-sib (got the 224 from the mother, but had to have a different dad).  
	--Juvenile on the left is not a sibling of either adult pictured.

Add more loci, (10 total loci in this study), you end up with 10 unique values for each fish.  Very high statistical power for discerning parentage (i.e., very unlikely that two fish will share the same genotypes at all 10 loci just by chance).

## Catherine Creek and Lostine River

- Returning adults are progeny of captive brood fish, plus conventional supplementation programs
- Early in the program—1.5 generations

**Notes:**
Lostine and Catherine Creek captive brood started BY 1995, collected wild parr in 1996
Lostine conventional program started BY 1997, collection of wild returning adults.
Catherine Creek conventional program started BY 2001, collection of wild returning adults.

(Movement of cap brood fish)
WC parr (500 from each river) sent to Lookingglass originally, now to Wallowa hatchery to be raised until smolts.
Smolts are sent 1⁄2 to Bonneville, and 1⁄2 to Manchester.  Spawned at Bonneville(?), eggs sent to Oxbow hatchery until eyed, then to Irrigon until fry, then Lookingglass until pre-smolt.  Smolts taken to acclimation sites.

Conventional supplementation programs:  take returning adults into Lookingglass, spawn, and raise until smolts.  Smolts released from acclimation ponds.

## Number of Samples Run by Location

| Lostine River |  |  |
| --- | --- | --- |
| Year | Life Stage | # |
| 2001 | Adults | 533 |
| 2002 | WC Parr | 192 |
| 2002 | Adults | 586 |
| 2003 | WC Parr | 192 |
| 2003 | Adults | 435 |
| 2004 | WC Parr | 192 |
| 2005 | Smolts | 192 |
| 2004  | Adults | 879 |
| 2005 | WC Parr | 192 |
| 2005 | Adults | 481 |
| 2006  | WC Parr | 191 |

| Catherine Creek |  |  |
| --- | --- | --- |
| Year | Life Stage | # |
| 2002 | Adults | 244 |
| 2003 | WC Parr | 192 |
| 2003 | Adults | 431 |
| 2004 | WC Parr | 192 |
| 2005 | Smolts | 159 |
| 2004 | Adults | 190 |
| 2005 | WC Parr | 192 |
| 2005 | Adults | 141 |
| 2006 | WC Parr | 192 |

**Notes:**
Samples run by location

4 years of returning adults for each location, includes both parr for each year and smolts for one year (BY2003).  Decent sample sizes.

Color bands indicate pairs of samples run (i.e., 2002 returning adults, and resulting 2003 parr). 

## Hatchery/Wild returns

**Notes:**
Not same scales—lower fish return in CC, higher in Lostine

Roughly equal hatchery/wild some years, disproportionate other years.

BY 2004 and BY 2005, hatchery outnumber wild 2:1 or more

Ratios of hatchery/wild could very well be affecting RS

## Slide 8

**Notes:**
Show results for each river, Catherine Creek first: overall summary of hatchery vs. wild RS

Numbers calculated are observed matings/expected matings (based on numbers of fish put over the weir), normalized to 1 for wild on Y axis.

X axis is by BY, noting parr vs. smolt

Average over all collections RRS = 1.04

Hatchery success trades off year by year, some years higher and some years lower than wild.  No clear pattern.  No significant differences, measured by contingency tests.

## Slide 9

**Notes:**
More specific breakdown, by sex and origin.  

WF = wild females
HF = hatchery females
WM = wild males
HM = hatchery males

Again, no clear pattern. 

Hatchery females tend to do better than hatchery males, with the exception of BY 2005 (HM do better).  

## Slide 10

**Notes:**
Success by mating class, females listed first:
	--WW = wild x wild
	--WH = wild female x hatchery male
	--HW = hatchery female x wild male
	--HH = hatchery x hatchery

Looking for indications that a particular type of mating class did better or worse than others (if hatchery fish do less well, would expect to see HH matings doing the worst.  Or if there is an advantage to having a wild female (or male), might expect those mating classes to do better.

Again, no clear pattern here.  

## Slide 11

**Notes:**
Lostine River now, average over all collections = 0.94.

Lumped by origin, mostly hatchery lower than wild, but two years of higher (one much higher, doubled to be exact).

## p < 0.05

*p* < 0.05

**Notes:**
Looking at sex and origin

Only BY 2005 by sex/origin that is significantly different from expected.  HM driving the higher success of hatchery fish in BY 2005.

Without that year, RRS H = 0.73.

## Slide 13

**Notes:**
By mating class:

Pretty much all over the place.

## Jacks

- Jacks found in relatively low numbers
- They do contribute
- Lower RS than expected, but some individuals have higher RS
- Suggests a large variance in RS for jacks compared to adults

**Notes:**
Jacks found, low numbers (~10-20 each year for CC, 20-200 in Lostine).  

(see slide) 

Most virile example:  one jack produced 7 offspring with 4 different females

## Precocial parr

- Approximately 150 caught in traps in 2006
- Most were BY 2005, 5-10% were BY 2004
- Found their parents, but unable to detect any of their offspring
- Low likelihood of sampling offspring of PP  though
- Would like to make note of families producing PP

**Notes:**
Precocial parr found in screw traps throughout collection years, first collected in 2006 and included in analyses.  

59 from Lostine and 91 from CC 

Most were ones, 5-10% were twos

Found their parents but no offspring.

Not surprising statistically, unless they were highly fecund 

Will continue to include in the analyses.

Like to note if particular families tend to produce PP, or if randomly produced

## Results of Chinook pedigree studies

- Approximately equal RRS seen across years between hatchery and wild fish in both rivers
- Jacks do contribute, but less than expected by number over the weir
- Precocial parr gave no sampled offspring, but not surprising

**Notes:**
RRS approximately equal between wild and hatchery Chinook in both CC and Lostine River.

Jacks do contribute, but less than expected

PP yielded no sampled offspring

## Comparison to O. mykissLittle Sheep Creek, Imnaha

- Little Sheep is older supplementation program (est. 1982, ~5 generations)
- Large resident population
*O. mykiss* hatchery rearing is accelerated
- Chinook are (in part) progeny of captive brood

**Notes:**
Perhaps most interesting when viewed in the context of comparisons to other studies.  

In O. mykiss from the Imnaha system, Little Sheep Creek, and see very different results.

a neighboring region, different species.  Also differences in the hatchery programs (see slide).

## Slide 18

**Notes:**
Lumping sex, comparing only hatchery vs. wild origin.  

X axis is same, also by BY

Average over all years = 0.44

Significantly lower RRS for hatchery fish, all 4 years.

## p = 0.0009

*p* = 0.0009

*p* = 0.0001

*p* = 0.0206

*p* = 0.0000

**Notes:**
By sex and origin, again, all are significantly different from expected.

No pattern for hatchery females relative to hatchery males 

2003, hatchery males appear to have nearly equal RS to wild males—due to a single, unmarked hatchery male (had 11 offspring with a single wild female).  
	-unmarked hatchery fish are usually designated at the weir based on fin erosion patterns, as they have no other markings/tags
	-*possible* that it was really a wild fish (if assume wild, then numbers fall right in line with pattern of previous 3 years)
	-if truly a hatchery male, speaks to the large variance in reproductive success on an individual level

## p = 0.0014

*p* = 0.0014

*p* = 0.0001

*p* = 0.0000

*p* = 0.0152

**Notes:**
All matings other than WW are less successful (except that one HM noted from 2003)

HH matings do the most poorly of the 4 categories, consistently.

## Conclusions from Little Sheep

- Hatchery steelhead have significantly lower RRS than wild counterparts in Little Sheep Creek.
- Little difference between hatchery males and hatchery females in performance.

## Supplementation programs in the Columbia River basin

**0**

**0.2**

**0.4**

**0.6**

**0.8**

**1**

**1.2**

**0**

**1**

**2**

**3**

**4**

**5**

**6**

**Hatchery Generations**

**Relative Fitness **

- Hood R. Sthd

- (Cww x Cww)

- Hood R. Sthd

- (Cww x Ccw)

- Wenatchee

- Chinook

- Deschutes

- Sthd

| Triangles = egg-to-parr/smolt, Diamonds = adult-to-parr/smolt, Squares = lifetime 

Species: Dark blue = steelhead, yellow = Chinook |
| --- |
|  |

- Catherine Cr.

- Chinook

**Notes:**
From Barry Berejikian, comparison of additional RS studies of supplementation programs in the Columbia River Basin.  All use local broodstock, none from out-of-basin.

Colors indicate species:  steelhead are dark blue, Chinook are yellow
Shapes indicate type of analysis:  triangle is egg-to-parr/smolt, diamonds are adult-to-parr/smolt, and squares are adult-to-adult.

Y axis is same as in previous graphs, showing relative fitness of 1 for wild fish.  X axis shows number of generations of captivity for hatchery program.

Comparing these results to recently published Araki studies:  An up-to-date picture of local broodstock supplementation programs from the Columbia River Basin.

Cww = captive fish from 2 wild parents
Ccw = captive fish from 1 wild parent, 1 captive parent

Majority of studies show hatchery significantly lower RS than wild, even with as few as 2 generations in captivity
	--Not all though—differences in species? Differences in rearing techniques?
	--Araki et al. isolated genetic causes, but the other studies have a combination of genetic/environmental effects.

Need more years of data, more systems.  Many variables in play!

Peer-reviewed (Hood River, Araki et al. 2007, Deschutes Reisenbichler & McIntyre, 1977) and unpublished (Little Sheep & Grande Ronde in prep, Wenatchee from Murdoch et al. 2007 BPA report)

## Conclusions

- Chinook show equal fitness for hatchery vs. wild in Grande Ronde
- Different results for other species in the Columbia basin
- Difficult to generalize—species, location may have effect

**Notes:**
Grande Ronde Chinook appear to have equal fitness, hatchery vs. wild

Some would like to generalize across species and systems, but see varying results in currently published and in-progress studies.

## WHY do we see such big differences between species and systems?  

- WHY do we see such big differences between species and systems?
- What factors are involved?

- Why?

**Notes:**
What we all want to know about this work, what is REALLY going on to create these differences??

CC and Lostine programs are young, ~1.5 generations, so may see the same drop in subsequent generations.  But may not!  Might be something different about GR.

More years, more systems are needed.  Interesting to look at full generation too (like the Araki study), not just adult-parr/smolt.

## Acknowledgements

- This project was funded through BPA contract # 198909600
- Samples provided by ODFW, Nez Perce, and CTUIR