1. S. L. Schroder3, A. Fritts3, M. V. Johnston2,
Trends in Demographic and Phenotypic Traits of Hatchery- and Natural-Origin Upper Yakima River Spring Chinook Salmon
C. M. Knudsen1, W. J. Bosch2,
S. L. Schroder3, A. Fritts3, M. V. Johnston2,
and D. E. Fast2
1 Oncorh Consulting
2 Yakama Nation
3 Washington Department of Fish and Wildlife

2. Objectives
How has the mean size-at-maturity of UY natural and hatchery populations changed over time relative to Naches wild control?
Has the proportion of natural or hatchery origin jacks changed over time?
Does the proportion of jacks naturally spawning or used as broodstock influence future jack production?
Does the sex composition of natural and hatchery populations differ?
Has mean natural and hatchery origin egg size changed over time?
Do PIT and non-PIT SARs still differ?

3. Definitions
Natural Origin (NO)– progeny of naturally spawning parents. Parents could be natural or hatchery origin.
Hatchery Origin
Supplementation Hatchery (SH) Origin – Parental broodstock of natural origin only, one generation of domestication. Supplement naturally spawning population, integrated population.
Hatchery Control (HC) Origin – Parental broodstock of hatchery origin only. Multiple generations of domestication. Are not allowed to naturally spawn, segregated hatchery population.
Wild Control – Naches population

4. The YKFP spring chinook hatchery program was designed to minimize domestication effects
use only natural-origin broodstock
take no more than 50% of the NO returns into the hatchery
utilize factorial crosses during artificial matings
limit the proportion of NO jacks in the broodstock
Mean = 12.7% (range 6.0 – 29.2)
randomly mate individuals
use “best culture practices” such as low rearing densities
volitionally release juveniles at sizes larger than, but comparable to, wild-origin smolts

5. Yearling Smolt Fork Length at Chandler 2006 (BY2004)
(LOWESS trend lines shown) 83 93
103
113
123
133
143
Julian date 80
100
120
140
160
180
Fork length (mm)
Hatchery origin (○)
Natural origin (x)
LOWESS trend lines were used to indicate trends over time.

6. Yearling Smolt Fork Length at Chandler 2007 (BY2005)
160
150
Hatchery origin (○)
140
130
Fork length (mm)
120
110
Natural origin (x)
100 90 88 98
108
118
128
138
148
Julian date

7. Yakima River Basin

8. Roza Dam Adult Monitoring Facility
All adults passing upstream are examined, hatchery fish identified by marks, and natural origin broodstock collected and transported to the Cle Elum Hatchery Facility..

9. Trends In Traits Over Broodyears
900
Naches
850 NO
800 SH
Phenotypic trait
750 HC
700
LOWESS trend lines - For each X value where a Y value is to be calculated, the LOWESS technique performs a regression on points in a moving range around the X value, where the values in the moving range are weighted according to their distance from this central X value.
650
600
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
Broodyears

10. Size-at-Age
Mean POHP Differences : age 3: 2.7 cm; age 4: 1.7 cm; age 5: 2.7 cm
Mean ByWt Differences : age 3: 0.3 kg; age 4: 0.3 kg; age 5: 0.8 kg
Representing a divergence in body size of between 0.5 and 1.0 SD

11. Age 3 Jacks POHP length (cm) Brood Year UpYak NO Δ Hat Control
Supp. Hatch □ 46 45 44 43
POHP length (cm) 42 41 40 39
1995
2000
2005
2010
Brood Year

12. Linear Trends in Length - Age 346 NO 45
Regression (SH and NO)
r2>0.48, p<0.02
ANCOVA
Equal slopes p=0.565 44 SH HC 43
POHP (cm) 42 41
What’s missing? No Naches wild control samples. Of the past 12 years 10 had sample sizes of just 0 or 1. 40 SH
NOR HC 39 38
1995
2000
2005
Brood Year

13. Jack Size-at-Age
Age 3 jacks have significantly increased in size over time in both hatchery and natural origin UY populations at the same rate (cm/yr)
NO jacks are significantly larger than SH jacks and have been since the first generation of hatchery jack production
Yet, SH smolts are equal to or larger than NO smolts, typically leading to larger size-at-age but younger age-at-maturation

14. Trends in Length – NO, Naches Age 4
2000
2002
2004
2006
1998
Brood Year 58 60 62 64 66
POHP length (cm) SH
Nach NO HC

15. Linear Trends in Length - Age 4
1998
2000
2002
2004
2006
Brood Year 57 58 59 60 61 62 63 64 65 66
POHP (cm)
Regression
r2=0.06, p>0.84
ANCOVA
Equal slopes p=0.947
Naches NO

16. No significant linear trend inSH
Nach NO HC 66
No significant linear trend in
Naches, UY NO, or SH (p=0.32) 64 62
POHP length (cm) 60 58
1998
2000
2002
2004
2006
Return Year

17. Age 4 Size-at-Age
While differing in mean size, Naches (a true wild control population) and U Yakima NO age 4 fish exhibited the same lack of trend in size over time
SH origin population also showed no significant trend over time, but is converging on the NO population
No apparent negative effect (decrease in mean size) on NO fish despite 56% of naturally spawning fish are hatchery origin on average

18. Gender Identification
From 1997 to 2009 we estimated gender ratios from fish collected at RAMF and then taken to CESRF and held to maturity
All adipose fin clipped fish were inspected and gender identified visually, but errors were approximately 20-30% for males and 10% for females
Beginning in 2010, an ultrasound device (Honda HS-101V) was used on all fish passing RAMF increasing gender-specific data by more than an order of magnitude

19. Sampling At Roza Adult Trap Video provided by P. Huffman, YN
Joe Hoptowit
Checked for ad clip, elastomer and CWT tags
Weighed and measured length
Identified gender
PIT tagged
DNA sampled
Put a caudal fin clip to ID as HC or SH
Video provided by P. Huffman, YN

20. Sampling At Roza Adult Trap
28 seconds total time, ~1 second gender ID
Checked for ad clip, elastomer and CWT tags
Weighed and measured POHP and FL
Identified gender
PIT tagged
DNA sampled
Joe Hoptowit
Checked for ad clip, elastomer and CWT tags
Weighed and measured length
Identified gender
PIT tagged
DNA sampled
Put a caudal fin clip to ID as HC or SH

21. Gender Identification 2010
There were a total of 624 fish classified to gender using ultrasound and then held to maturity at CESRF
621 (99.5%) were corrected classified
All 9,749 fish passing RAMF were classified to gender in 2010

22. Gender Comparison BY2006 (Ages 3 and 4)30 40 50 60 70
Female
Male
Percent
HC (n=1137)
SH (n=7325)
NO (n=3470)
Pearson X2 = , df = 2, p<0.001

23. Gender Comparison BY2006 (Age 4 only)
Pearson X2 = 5.21, df = 2, p = 0.074 20 30 40 50 60 70
Female
Male
Gender
Percent
HC (n=743)
SH (n=5774)
NO (n=2734)

24. Why aren’t the F:M ratios of age 4 hatchery fish skewed toward females more than Natural Origin fish?
BY 2006 had 40-54% minijack production in SH and HC males
BY2006 SH and HC jack production was ~50% greater than NO fish (36% vs 22%)
Yet, there was <3% difference in the proportion of adult age 4 females and males and no significant difference even with very large sample sizes
More work is needed to understand this issue
What are wild precocious male production rates?
Compare Female recruits/Female spawner rates

25. Trends In Jack BY Proportions

26. 0.4 0.3 Prop Jacks 0.2 0.1 0.0 Brood year UpYak NO Δ Hat Control ○
Supp. Hatch □
0.4
0.3
Prop Jacks
0.2
0.1
0.0
1997
1999
2001
2003
2005
2007
Brood year

27. UpYak NO Δ
Hat Control
Supp. Hatch □
0.4
RY2009
0.3
Broodyear 2006 (RY 2009) was significantly higher for both NO and SH populations.
Prop Jacks
0.2
0.1
Broodyear 2006 was significantly higher for both NO and SH populations.
0.0
1997
1999
2001
2003
2005
2007
Brood year

28. UpYak NO Δ
Hat Control
Supp. Hatch □
0.4
0.3
Broodyear 2006 (RY 2009) was significantly higher for both NO and SH populations.
Prop Jacks
0.2
0.1
0.0
1997
1999
2001
2003
2005
2007
Brood year

29. Proportion Age 3 Jacks Over TimeSH NO HC
0.4
Natural Origin
0.3
R2 = 0.486, p=0.01
Proportion Jacks
0.2
0.1
Significant trend drivcen by the 2006 point. Remove that and the regerssion is no longer significant and line is flat.
0.0
1998
2000
2002
2004
2006
Brood Year

30. Proportion Age 3 Jacks Over TimeSH NO HC
0.4
SH Origin
0.3
Proportion Jacks
0.2
R2 = 0.581, p=0.01
0.1
0.0
1998
2000
2002
2004
2006
Brood Year

31. Proportion Age 3 Jacks Over TimeSH NO HC
0.4
HC Origin
0.3
Proportion Jacks
0.2
R2 = 0.002, p=0.91
0.1
0.0
1998
2000
2002
2004
2006
Brood Year

32. Proportion Jacks Spawned vs Proportion Jacks Produced
0.1
0.2
0.3
0.4
0.5
Proportion Naturally Spawning Jacks (Return Year)
Prop. jacks produced (Brood year)
Natural Origin Jacks ( )
BY = (0.0195(RY)) R 2
= 0.010, p=0.783, n=10
Natural Spawning
2009

33. Prop. jacks produced (Brood year)
Proportion Jacks Spawned vs Proportion Jacks Produced
Artificial Spawning
Hatchery Origin Jacks (Δ)
BY = (0.415(RY)) R 2
= 0.302, p=0.100, n=10
0.4
2009
0.3
0.2
Prop. jacks produced (Brood year)
0.1
0.1
0.2
0.3
0.4
0.5
Proportion Jacks Broodstock (Return Year)

34. Linear Trends in Spawn Timing

35. Linear Trends in Spawn Timing
Regression
R2<0.16, p>0.17
ANCOVA
Equal slopes p=0.872
Nach<NO Hat=NO R
NO hatchery 2.3 days earlier than NO river
Based on redd counts
NO river
270
NO hatchery
Median Julian Spawn Date
Naches
260
NO Hatchery median is 2.3 days earlier than NO river (redds)
Naches is 12.3 days earlier than NO river
250
1995
2000
2005
2010
Return Year

36. Linear Trends in Spawn Timing
Naches SH HC NO hatch NO river
270
NO hatchery
Median Spawn Date HC
260 SH
NO Hatchery median is 2.3 days earlier than NO river (redds)
250
1995
2000
2005
2010
Return Year

37. Trends In Egg Size (Mass)

38. Trends In Egg Size (Mass)
0.22 SH NO
0.21 HC
0.20
Mean Egg wt (g)
0.19
0.18
0.17
1998
2000
2002
2004
2006
2008
2010
Return year

39. r2 > 0.8, regression p<0.001 Slopes equal p=0.177
Nach
2010
6.1
6.0 NO
5.9
ln(Fry body mass)
5.8 NO SH
Nach HC
5.7
ANCOVA
r2 > 0.8, regression p<0.001
Slopes equal p=0.177
Origin effects P<0.001
5.6
Why should we care about egg sizes anyway? What makes them important and are they biologically important here?
Fry body size is tightly correlated with egg size and early growth rate, dominance, and survival are positively correlated with fry body size.
Shows significant differences between our wild control, Naches, and our NO up. Yakima population. A locally adapted phenotypic trait.
5.5
5.1
5.2
5.3
5.4
5.5
5.6
5.7
ln(Egg mass)

40. HC SH NO ln(Fry body mass) ANCOVA Slopes equal p=0.032
6.1 HC
6.0 SH NO
5.9
ln(Fry body mass)
5.8 NO SH
Nach HC
5.7
5.6
ANCOVA
Slopes equal p=0.032
P<0.001, all r2 >0.8
The rate at which fry body mass increases relative to the increase in egg weight is greatest for HC fry and lowest for NO fry. Again, why should we care?
When we combined these relationships with the mean egg mass values for 2010 I pointed out in an earlier slide we can calculate what the expected mean fry body weight will be.
5.5
5.1
5.2
5.3
5.4
5.5
5.6
5.7
ln(Egg mass)

41. Estimated Fry Mass 2010 Due to combination of larger HC eggs and
Greater “Fry body mass/mg egg mass”
400
HC 12.3%
larger
HC 15.2%
larger
SH 2.6%
larger
Fry Body Mass (mg)
300
HC fry are estimated to be 15% heavier that NO fry in Due to a combination of larger HC egg mass and the greater rate of fry body mass increase per unit egg mass increase.
I would guess that in a paired test of dominance the fish with 15% greater body weight would dominate the majority of the time. If that is true, then this is a biologically significant difference between NO, SH and HC fry.
200 HC SH NO
Origin

42. Comparison of PIT vs Non-PIT SARs
broods mean PIT tag loss = 18.4% (17.2% -19.5%)
Mean PIT tag induced mortality = 10%
What’s happened since then ( broods)?

43. Comparison of PIT vs Non-PIT SARs
Brood
Year
PIT SAR
PIT SAR corrected
Non-PIT
SAR
Ratio corrected
PIT/Non-PIT SAR
1997
1.50%
1.84%
1.81%
1.015
1998
1.06%
1.30%
1.31%
0.994
1999
0.06%
0.07%
0.11%
0.694
2000
0.40%
0.49%
0.48%
1.027
2001
0.22%
0.27%
0.32%
0.839
2002
0.25%
0.31%
0.28%
1.103
2003
0.08%
0.10%
0.21%
0.456
2004
0.34%
0.42%
0.61%
0.687
2005
0.35%
0.43%
0.79%
0.544
2006
1.16%
1.42%
1.001

44. Conclusions – Size-at-age Jacks
Age 3 SH and HC jacks were significantly smaller than NO fish, but all populations were increasing in size over time at the same rate.
SH and HC jacks NS difference in size most years.
Unable to use age 3 Naches to compare to UY fish to show and compare trends over time due to low sample sizes.

45. Conclusions – Size-at-age Age 4
Age 4 Naches and UY NO fish show the same trends over time indicating that naturally spawning SH fish have not impacted NO size-at-age.
Age 4 populations did not increase significantly in size over time, but SH and HC fish are now closer in size to NO fish, though still significantly smaller.

46. Conclusions – Jack Production Trends
Hatchery jack production is significantly greater than NO jack production (11% vs 23% before BY2006)
Jack production increased significantly in BY2006 in both SH and NO fish
Perhaps due to the increasing size-at-age of jacks which is likely driven by marine environmental conditions

47. Conclusions – Gender Differences
When all ages are analyzed, hatchery origin fish have a significantly higher proportion of males than NO fish
If just age 4 fish are examined (which make up 70-95% of a cohort on average) there is no significant difference between NO, SH and HC gender proportions
More work needed here

48. Conclusions – Effects of Spawning Jacks
The proportion of SH males maturing as jacks was not significantly effected by the proportion of jacks naturally spawning (range 3% to 50%)
The proportion of NO males maturing as jacks was not significantly effected by the proportion of NO jacks used as broodstock (range 3% to 29%)
Managing the proportion of jacks naturally spawning or in broodstock is not likely to have significant effects on subsequent jack production in UY spring Chinook salmon
These results do not necessarily hold for other spring or fall Chinook populations

49. Conclusions – Other
In recent years HC and SH egg mass has been larger than NO egg mass
In 2010 HC fry were 15% larger than NO fry due to larger eggs and higher Egg Mass-to-Fry Mass conversion rate
Spawn timing of hatchery fish at CESRF was significantly earlier than NO fish, but no population showed significant temporal trends
PIT tagged SARs were significantly lower than Non-PIT tagged SARs in 5 of 10 brood years

50. Acknowledgements Yakama Nation Roza Adult Monitoring Facility Crew
Cle Elum Supplementation Research Facility Crew
WDFW Ecological Interactions Crew
Bonneville Power Administration for providing funding through the Yakima/Klickitat Fishery Project Monitoring and Evaluation Program
I’d like to acknowledge the hard work and efforts by the Yakama Nation’s RAMF crew and the CESRF crew. Their cooperation and help was critical in making this work possible. And Patricia Smith (COTR) and BPA for funding support.