Nez Perce Tribe Department of Fisheries Resources illiam Young, Paul Kucera and Jay Hess The Nez Perce Tribe Listed Stock Salmonid Gamete Preservation
Mar 27, 2015
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