Nez Perce TribeDepartment of Fisheries Resources Management

William Young, Paul Kucera and Jay Hesse

The Nez Perce Tribe Listed Stock Salmonid Gamete Preservation

• Snake River spring/summer chinook

• Snake River steelhead– Both listed as

threatened under the ESA

Number of redds counted in 6 rivers in the Snake River basin from 1958-2002

0

1000

2000

3000

4000

5000

6000

1958 1963 1968 1973 1978 1983 1988 1993 1998

year

Nu

mb

er o

f R

edd

s

Annual redd counts

10 year moving ave.

Project Chronology

• 1992 – First collections, LSRCP funded, UI and WSU collaborations

• 1996 – BPA proposal• 1997 – First collections as a BPA funded project• 2001 – Second BPA funding cycle

Regional Support and Collaborations

• Cost Share– LSRCP

– WSU

– UI

• Regional Support and Benefit– IDFG

– WDFW

– ODFW

– Kootenai Tribe

Snake River Salmonid Gamete Preservation Plan Goal

• Preserve the genetic diversity of Pacific northwest salmonids for conservation and recovery efforts

• Long term– Increase effective number of breeders - Nb

– Insurance against catastrophic population collapse

– Maintain future options

• Short term– Conventional hatchery broodstock management

• Inadequate number of males

• Avoid sib matings

– Captive broodstock programs

Applications of Cryopreservation to Preserve Genetic Diversity

Collection Objectives

• 100 individuals / year for one generation from each spawning aggregation– Chinook Salmon– Steelhead

Effective Population Size - Ne

• Ne is the size of an ideal population that maintains genetic variation at the same rate as a real population (N) of interest

• Factors that cause a real population to diverge from an ideal population– unequal sex ratios– nondiscrete generations– nonrandom mating– unequal family sizes– variable population size

The relationship between Nb and N

• Nb/N ratios for anadromous fish are typically 0.1 to 0.4

• Nb of approximately 50

– 95% probability of rare allele retention

• Requires N = 125-500 / generation

Total genetic diversity

Among populationgenetic diversity

Marsh Creek

Upper Salmon

Imnaha River

Lostine River

Pahsimeroi River

South Fork SalmonRiver

Rapid River

Big Creek

Lake Creek

UPGMA –Nei’s Genetic Distance

Among Population Genetic Diversity of Cryopreserved Samples

1999 Little Sheep mt Haplotype Distribution

(N = 15)

LSC ST1 LSC ST2 LSC ST9 LSC ST19

2000 Little Sheep mt Haplotype Distribution

(N =13)

LSC ST1 LSC ST2 LSC ST19

2001 Little Sheep mt Haplotype Distribution

(N = 20)

LSC ST1 LSC ST2 LSC ST19

Within Population GeneticDiversity

Among brood yeargenetic variation

Effective Brood Year Analysis

• A way to measure the composition of gamete samples collected from adults spanning multiple generations.

• Strive for an even representation of fish from different brood years across multiple generations.

EBY 1 EBY 2 EBY 3 EBY 4 EBY 5

Year 1

Year 2

Year 3

Year 4

Year 5

5 34

5 34

5 34

5 43

534

Total

100

100

100

100

100

0

20

40

60

80

100

120

1 2 3 4 5

Brood Year

Num

ber

of G

amet

e Sa

mpl

es

2000

1999

1998

1997

1996

Gamete Collections Under Ideal Circumstances

EBY 1 EBY 2 EBY 3 EBY 4 EBY 5

Year 1

Year 2

Year 3

Year 4

Year 5

Year 6

Year 7

5 34

5 34

5 34

5 34

5 34

5 43

534

.

.

.Year n

Total

23

16

38

26

33

14

41

SFSR Chinook Salmon – Effective Brood Year analysis

0

20

40

60

80

100

1 2 3 4 5

Effective Brood Year

Gam

ete

Sam

ples

2003

2002

2001

2000

1999

1998

1997

1996

Project Successes

• Largest salmonid genebank in North America• 2240 chinook salmon gamete samples preserved

from 13 spawning aggregations• 1210 steelhead gamete samples preserved from 12

spawning aggregations• Annual fertilization trials• Annual genetic analyses • Numerous experiments aimed at improving the

viability of cryopreserved sperm• Experiments aimed at assessing the viability of

fish produced using cryopreserved sperm

2004 2003 2002 2001 2000 1999 1998 1997 1996 1995 1994 1993 1992 Totals

Lostine River 15 16 19 33 18 2 3 2 3 1 4 116Upper Grande Ronde

5 10 8 9 32

Catherine Creek 5 8 5 11 29

Rapid River 51 68 98 217

South Fork Salmon 15 26 23 44 54 93 45 45 19 364

Lake Creek 26 32 18 28 15 6 3 4 3 135

Johnson Creek 60 54 58 62 35 5 17 7 298

Big Creek 23 31 21 50 7 0 1 6 0 0 0 10 7 156

Capehorn Creek 0 15 1 2 1 0 6 2 27

Marsh Creek 5 16 34 24 7 0 2 4 92

Pahsimeroi River 15 39 50 50 31 185

Upper Salmon River 25 20 53 48 40 40 41 51 318

Imnaha River 15 23 7 37 71 95 79 41 33 42 22 465

Totals 194 266 286 398 349 340 295 162 58 43 26 10 7 2434

Chinook Salmon Gamete Collections, 1992 - 2004

Totals

Lostine River 101

Upper Grande Ronde 27

Catherine Creek 24

Rapid River 217

South Fork Salmon 349

Lake Creek 109

Johnson Creek 238

Big Creek 133

Capehorn Creek 27

Marsh Creek 87

Pahsimeroi River 185

Upper Salmon River 293

Imnaha River 450

Totals 2240

Chinook Salmon Gamete Collections, 1992 - 2003

TRT Chinook Salmon Populations• Grande Ronde Basin

– Catherine Creek– Wallowa/Lostine Rivers– Minam River– Upper Grande Ronde– Wenaha River

• Imnaha Basin– Big Sheep Creek– Imnaha mainstream

• Lower Snake Basin– Tucannon River– Asotin Creek

• South Fork Salmon Basin– Secesh River– SFSR– EFSFSR/Johnson Creek

• Salmon River Tribs– Chamberlain Creek– Little Salmon River

• Middle Fork Salmon Basin– Bear Valley/Elk Creeks– Big Creek– Camas Creek– MFSR below Indian Creek– Pistol Creek– Marsh Creek– Sulphur Creek– Loon Creek– MFSR above Indian Creek

• Upper Salmon Basin– Valley Creek– Lemhi River– NF Salmon River– Pahsimeroi River– EF Salmon River– Upper Salmon River– Yankee Fork

2004 2003 2002 2001 2000 1999 1998 1997 1994 1993 Totals

North Fork Clearwater 64 81 89 62 296

Selway River 5 5

Fish Creek 1 1 1 10 13

Grande Ronde River 1 1 2

South Fork Salmon 27 17 44

Johnson Creek 1 1 2 4

Pahsimeroi River 63 60 40 47 210

Imnaha River 2 2

Little Sheep Creek 100 70 95 78 52 25 25 5 450

Cow Creek 2 2

Lightning Creek 1 1

Snake River 60 73 98 76 307

Totals 128 90 283 295 283 212 25 5 5 10 1336

Steelhead Gamete Collections, 1993 - 2004

Totals

North Fork Clearwater296

Selway River 5

Fish Creek 13

Grande Ronde River 2

South Fork Salmon River 44

Johnson Creek 4

Pahsimeroi River 210

Imnaha River 2

Little Sheep Creek 450

Cow Creek 2

Lightning Creek 1

Snake River 307

Totals 1336

Steelhead Gamete Collections, 1993 - 2004

TRT Steelhead Populations

• Lower Snake Basin– Tucannon River

– Asotin Creek

• Clearwater Basin– Lower Clearwater

– South Fork

– Lolo Creek

– Lochsa River

– Selway River

• Grande Ronde Basin– Lower Grande Ronde

– Joseph Creek

– Wallowa River

– Upper Grande Ronde

• Salmon Basin– Little Salmon

– South Fork

– Secesh River

– Chamberlain Creek

– Big, Camas, Loon

– Upper Middle Fork

– North Fork

– Lemhi River

– Pahsimeroi River

– East Fork

– Upper Salmon

• Imnaha Basin– Imnaha River

• Hells Canyon– Hells Canyon

Genetic Analyses – Chinook Salmon

• Average Heterozygosity – 2 microsatellite loci

– Imnaha River .59 206 450

– Lostine River .54 24 101

– Rapid River .53 147 217

– Lake Creek .47 48 109

– SFSR .57 192 349

– Big Creek .61 60 133

– Marsh Creek .58 30 87

– Pahsimeroi River .53 88 185

– Upper Salmon River .58 79 293

H NTotalSamples

Genetic Analyses - Steelhead

• Mitochondrial Haplotype Analysis – D-loop sequencing

– Dworshak 296 41 4

– Little Sheep Creek 350 48 4

– Pahsimeroi River 210 42 4

– Oxbow Hatchery 307 44 5

Total Analyzed # haplotypes

Future Directions

• Continue to collect at current level• Work to increase regional support for the project• Maintain a collaboration with the USDA National

Animal Germplasm Program• Establish a regional repository

Acknowledgments

• Lower Snake River Compensation Project

• Bonneville Power Administration

• University Collaborators

• Joe Cloud, Gary Thorgaard, Paul Wheeler

• Nez Perce Tribe

• Jay Hesse, Mike Blenden, Mary Edwards, Nym Johnnie, Robyn Armstrong, Neal Espinosa, Cameron Albee, Joe McCormack, the McCall field office