Using Full Parental Genotyping to Using Full Parental Genotyping to Determine the Efficacy of Streamside Determine the Efficacy of Streamside

Incubators for Rearing Hatchery-Origin Incubators for Rearing Hatchery-Origin Steelhead Eggs and Increasing Steelhead Eggs and Increasing

Population Abundance in the Yankee Population Abundance in the Yankee Fork Salmon River, Idaho.Fork Salmon River, Idaho.

ByBy

Lytle P. DennyLytle P. DennyK.A. Tardy, and C. LopezK.A. Tardy, and C. Lopez

Shoshone-Bannock TribesShoshone-Bannock TribesFish & Wildlife DepartmentFish & Wildlife Department

March 4, 2008March 4, 2008

SSI Program SSI Program

BackgroundBackground SSI GoalSSI Goal SSI ObjectivesSSI Objectives SSI Methods SSI Methods M & E GoalM & E Goal M & E ObjectivesM & E Objectives M & E MethodsM & E Methods Results Results DiscussionDiscussion

BackgroundBackground Stream-Side Incubator (SSI) Program initiated in Stream-Side Incubator (SSI) Program initiated in

1995 in Upper Salmon River (Figure 1)1995 in Upper Salmon River (Figure 1) Initial Cooperators included Initial Cooperators included

– Trout UnlimitedTrout Unlimited– BLMBLM– USFSUSFS– Upper Salmon Basin Watershed ProjectUpper Salmon Basin Watershed Project– IDFGIDFG– Private landownersPrivate landowners

Site are located in five tributaries of the Upper Site are located in five tributaries of the Upper Salmon River (Figure 2)Salmon River (Figure 2)

Incubation methods included using refrigerators, Incubation methods included using refrigerators, whitlock-vibrant boxes, Jordan-Scotty whitlock-vibrant boxes, Jordan-Scotty condominiums,“haddix boxes,” wood incubators, condominiums,“haddix boxes,” wood incubators, and lastly upwellers.and lastly upwellers.

BackgroundBackground Snake River Steelhead ESU listed October 17, Snake River Steelhead ESU listed October 17,

1997; no distinctions were made between A-run 1997; no distinctions were made between A-run or B-run summer steelheador B-run summer steelhead

SBT envisioned using natural steelhead for SBT envisioned using natural steelhead for broodstock, unfortunately none were availablebroodstock, unfortunately none were available

Early M & E efforts guided by Technical Early M & E efforts guided by Technical Committee includingCommittee including– IDFGIDFG– USFSUSFS– USBWPUSBWP– BLMBLM– SBTSBT

M & E efforts beyond estimating fry production M & E efforts beyond estimating fry production were unsuccessfulwere unsuccessful

SBT completed M & E Plan in 2005SBT completed M & E Plan in 2005– Focus efforts in Yankee Fork Salmon RiverFocus efforts in Yankee Fork Salmon River– Use DNA Parentage Analysis;Use DNA Parentage Analysis;

SSI GoalSSI Goal

Reintroduce and recover native Reintroduce and recover native salmonids to vacant and critically salmonids to vacant and critically under-seeded habitats until under-seeded habitats until remaining populations can become remaining populations can become self-sustaining through natural self-sustaining through natural productionproduction

SSI ObjectivesSSI Objectives

Incubate approximately 1.0 million Incubate approximately 1.0 million eyed-eggs in five Upper Salmon River eyed-eggs in five Upper Salmon River tributariestributaries– Yankee ForkYankee Fork 375,000375,000– Panther CreekPanther Creek 250,000250,000– Basin CreekBasin Creek 125,000125,000– Morgan CreekMorgan Creek 125,000125,000– Indian CreekIndian Creek 125,000125,000

Achieve >90% hatch successAchieve >90% hatch success

SSI MethodsSSI Methods

Trapping and spawning conducted at Trapping and spawning conducted at Sawtooth Fish HatcherySawtooth Fish Hatchery– Approximately 99 adult pairs needed to Approximately 99 adult pairs needed to

achieve 375,000 eyed eggsachieve 375,000 eyed eggs4,200 eggs/female * 90% green egg to eyed 4,200 eggs/female * 90% green egg to eyed

egg survivalegg survival

– Adults spawned one-to-oneAdults spawned one-to-one– Estimate fecundityEstimate fecundity– Eggs checked for BKD; IDFG Fish HealthEggs checked for BKD; IDFG Fish Health

SSI MethodsSSI Methods

Egg Incubation (green to eyed)Egg Incubation (green to eyed)– Following SFH standard protocolFollowing SFH standard protocol

Egg Incubation (eyed to fry)Egg Incubation (eyed to fry)– Stream-side IncubatorsStream-side Incubators

Incubated on natural river waterIncubated on natural river waterTemperature, DO, and sedimentation are site Temperature, DO, and sedimentation are site

specificspecificFlow is adjustedFlow is adjusted

Hatch success/fry seededHatch success/fry seeded– Count dead eggs and/or fryCount dead eggs and/or fry

M & E GoalM & E Goal

Monitor and Evaluate the Tribes’ Monitor and Evaluate the Tribes’ hatchery steelhead supplementation hatchery steelhead supplementation activities in Yankee Fork so that activities in Yankee Fork so that operations can be adaptively operations can be adaptively managed to optimize hatchery and managed to optimize hatchery and natural production, provide dispersal, natural production, provide dispersal, sustain harvest, and minimize sustain harvest, and minimize ecological impacts.ecological impacts.

M & E ObjectivesM & E Objectives

1.1. Determine if program objectives for Determine if program objectives for contribution rate of hatchery fish are contribution rate of hatchery fish are being achieved and can be improved.being achieved and can be improved.

2.2. Determine the increases in natural Determine the increases in natural production that results from production that results from supplementation of steelhead in Yankee supplementation of steelhead in Yankee Fork and relate this information to Fork and relate this information to possible limiting factors.possible limiting factors.

3.3. Communicate monitoring and evaluation Communicate monitoring and evaluation findings to resource managers.findings to resource managers.

M & E MethodsM & E Methods Spawn adult steelhead – one-to-one matingsSpawn adult steelhead – one-to-one matings Collect genetic samples from all brood fishCollect genetic samples from all brood fish Genotype parents at 14 u-sat lociGenotype parents at 14 u-sat loci Outplant known families (eyed eggs) in Outplant known families (eyed eggs) in

incubatorsincubators Collect genetic sample from age-0Collect genetic sample from age-0++ and age-1 and age-1++

juvenile steelhead in Yankee Fork in subsequent juvenile steelhead in Yankee Fork in subsequent yearsyears

Genotype unknown juveniles at 14 u-sat lociGenotype unknown juveniles at 14 u-sat loci Perform parentage analysis on parent broodfish Perform parentage analysis on parent broodfish

and unknown juvenilesand unknown juveniles

1. Spawn Hatchery Adults

M & E ApproachM & E Approach2. Collect and Incubate Eggs

F1 generation

3. Incubate Eyed- eggs in incubators

4. Release fry volitionally

5. Collect 0+ parr during first fall

6. Collect 1+ parr during second fall

M & E MethodsM & E Methods

Population size point estimates made for Population size point estimates made for all Yankee Fork age-0all Yankee Fork age-0++ and age-1 and age-1++ O. O. mykissmykiss– Randomly select sampling sitesRandomly select sampling sites– Perform 3-pass removal electrofishing with Perform 3-pass removal electrofishing with

block netsblock nets– Measure fork length, mass, and collect tissue Measure fork length, mass, and collect tissue

and scale samplesand scale samples– Analyze condition factorAnalyze condition factor

M & E MethodsM & E Methods

Perform parental exclusion/pedigree Perform parental exclusion/pedigree analysis of adult broodstock to Yankee analysis of adult broodstock to Yankee Fork juvenile O. mykissFork juvenile O. mykiss– Use genetic markers to identify SSI progeny Use genetic markers to identify SSI progeny

from naturally produced progenyfrom naturally produced progeny Determine relative abundance of SSI progeny and Determine relative abundance of SSI progeny and

natural origin progenynatural origin progeny Estimate SSI survival from egg to fryEstimate SSI survival from egg to fry

Study Study YearYear

20062006 20072007 20082008 20092009 20102010 20112011 20122012 20132013 20142014 20152015 20162016 20172017 20182018

BY1 (P BY1 (P Gen.)Gen.)

Egg-Egg-plantplant

F1 Gen.F1 Gen. 0+0+ 1+1+ 2+2+ A1A1 A1A1 A1A1

F2 Gen.F2 Gen. 0+0+ 0+0+ 0+0+ A1A1 A1A1 A1A1 A1A1

BY2 (P BY2 (P Gen.)Gen.)

-- Egg- Egg- plantplant

F1 Gen.F1 Gen. 0+0+ 1+1+ 2+2+ A2A2 A2A2 A2A2

F2 Gen. F2 Gen. 0+0+ 0+0+ 0+0+ A2A2 A2A2 A2A2 A2A2

BY3 (P BY3 (P Gen.)Gen.)

-- Egg- Egg- plantplant

F1 Gen.F1 Gen. 0+0+ 1+1+ 2+2+ A3A3 A3A3 A3A3

F2 Gen.F2 Gen. 0+0+ 0+0+ 0+0+ A3A3 A3A3 A3A3 A3A3

Field IdentificationField Identification

Step 1. Field ID Step 2. Genetic ID

Physical tag/mark?

Y

N

Hatchery smoltRainbow Trout Outplant

Parented byhatchery broodstock orNatural-origin?

SAMPLE COLLECTED

Do not sample

Hatchery-origin

Natural-origin

Juvenile (unknown origin)

Sawtooth Parent (M)

Sawtooth Parent (F)

Sawtooth Parent (M)

SSI Outplant

ResultsResults

In 2006, 52 parent pairs were In 2006, 52 parent pairs were spawnedspawned

Outplanted approximately 214,750 Outplanted approximately 214,750 eyed-eggs in four incubatorseyed-eggs in four incubators

Lost one incubator because of an elkLost one incubator because of an elk Average hatch success was 98.6% Average hatch success was 98.6%

without Jordan Creek incubatorwithout Jordan Creek incubator 155,908 fry successfully emigrated155,908 fry successfully emigrated

ResultsResults

In 2006, we sampled 18 randomly In 2006, we sampled 18 randomly stratified reaches and collected stratified reaches and collected approximately 349 age-0approximately 349 age-0++ O. mykiss. O. mykiss.

In 2007, we sampled 21 randomly In 2007, we sampled 21 randomly statified reaches and collected statified reaches and collected approximately 123 age-1approximately 123 age-1++ O. mykiss. O. mykiss.

All adult and juvenile tissue samples All adult and juvenile tissue samples sent to Abernathy Fish Technology sent to Abernathy Fish Technology Center for DNA parentage analysis Center for DNA parentage analysis

2006 O.mykiss Length Frequency Distribution

Length (mm)

30 50 70 90 110 130 150 170 190 210 230 250 270 290

Co

un

t

0

20

40

60

80

100

120

140

160

2007 O. mykiss Length Frequency Distribution

Length (mm)

30 50 70 90 110 130 150 170 190 210 230 250 270

Fre

qu

en

cy

0

100

200

300

400

500

600

Total estimated age-0Total estimated age-0++ O. mykiss abundance and estimated streamside O. mykiss abundance and estimated streamside progeny abundance.progeny abundance. Stratum four shows the highest abundance of incubator Stratum four shows the highest abundance of incubator progeny at 50% of the population. Overall estimated age-0progeny at 50% of the population. Overall estimated age-0++ O. mykissO. mykiss equaled equaled 17,850 (± 2207) juveniles in 2006 with 4,268 (± 1244) individuals being from 17,850 (± 2207) juveniles in 2006 with 4,268 (± 1244) individuals being from stream-side incubator origin. We estimate that 23.9% (95% C.I. = 19.3 – stream-side incubator origin. We estimate that 23.9% (95% C.I. = 19.3 – 27.5%) of the Yankee Fork steelhead population in 2006 originated from 27.5%) of the Yankee Fork steelhead population in 2006 originated from supplementation program.supplementation program.

Ab

un

da

nce

Fre

qu

en

cy

0

2000

4000

6000

12000

14000

16000

18000

20000

Estimated Total AbundanceEstimated Streamside Progeny Abundace

Average condition and length of natural (unidentified) versus streamside Average condition and length of natural (unidentified) versus streamside incubator progeny (identified).incubator progeny (identified). There is no difference in mean condition factor There is no difference in mean condition factor or mean length between identified streamside incubator progeny and natural or mean length between identified streamside incubator progeny and natural spawning steelhead in YF.spawning steelhead in YF.

0+ Unidentified 0+ Identified 1+ Unidentified 1+ Identified

Ave

rag

e C

on

ditio

n F

acto

r (m

ass x

10

5 /le

ng

th3)

0.7

0.8

0.9

1.0

1.1

1.2

1.3

1.4

Ave

rag

e L

en

gth

(m

m)

20

40

60

80

100

120

140

160

180

200

220

240BY06 Average ConditionBY06 0+ Average LengthBY06 1+ Average Length

Relative abundance of salmonid species in Yankee Fork during 2006. Relative abundance of salmonid species in Yankee Fork during 2006. Steelhead is the Steelhead is the most ubiquitous species throughout Yankee Fork equaling >50% richness in five of the most ubiquitous species throughout Yankee Fork equaling >50% richness in five of the six strata sampled. Bull trout were the most dominant species in stratum five while six strata sampled. Bull trout were the most dominant species in stratum five while chinook and cutthroat abundances were highest in stratum four and seven, respectively.chinook and cutthroat abundances were highest in stratum four and seven, respectively.

Percent

0 20 40 60 80 100

Str

atu

m

0

1

2

3

4

5

6

7

SteelheadChinookBull TroutCutthroatWhitefish

Relative abundance of salmonid species in Yankee Fork during 2007. Relative abundance of salmonid species in Yankee Fork during 2007. Steelhead is the Steelhead is the most ubiquitous species throughout Yankee Fork equaling >60% richness in six of the most ubiquitous species throughout Yankee Fork equaling >60% richness in six of the seven strata sampled. Bull trout were again the most dominant species in stratum five seven strata sampled. Bull trout were again the most dominant species in stratum five while chinook and cutthroat abundances were highest in stratum four and seven, while chinook and cutthroat abundances were highest in stratum four and seven, respectively.respectively.

Percent

0 20 40 60 80 100

Str

atu

m

1

2

3

4

5

6

7

SteelheadChinookBull TroutCutthroatWhitefish

Neighbor-Joining phylogram topology and genetic distance relationship Neighbor-Joining phylogram topology and genetic distance relationship between 8 analysis groups. Values at nodes indicate bootstrap support among between 8 analysis groups. Values at nodes indicate bootstrap support among 1000 replicate data sets. 1000 replicate data sets.

Stratum #7

Stratum #3

Stratum #4 & 5

Stratum #6

Stratum #1

Stratum #2

2006 Broodstock

Assigned HAT progeny

0.002

99.9

60.5

A.

The neighbor-Joining phylogram topology and genetic distance The neighbor-Joining phylogram topology and genetic distance relationship between 8 analysis groups, and age class differences relationship between 8 analysis groups, and age class differences within groups.within groups.

Stratum #7(Age-1+)

Stratum #7(Age-0+)

Stratum #3(Age-0+)

Stratum #1(Age-0+)

Stratum #3(Age-1+)

Stratum #4 & 5

Stratum #6(Age-1+)

Stratum #1(Age-1+)

Stratum #2(Age-1+)

Stratum #2(Age-0+)

0.01

B.

DiscussionDiscussion Parentage analysis indicates that SSI juveniles successfully Parentage analysis indicates that SSI juveniles successfully

emerge and survive in-stream through their first year of emerge and survive in-stream through their first year of life.life.

It is very difficult to speculate the fate of juvenile steelhead It is very difficult to speculate the fate of juvenile steelhead after their first year of life under current program after their first year of life under current program operations.operations.

Parentage analysis provides a foundation for Parentage analysis provides a foundation for understanding movement of juvenile steelhead.understanding movement of juvenile steelhead.

Movement of age-0+ fish is relatively small and Movement of age-0+ fish is relatively small and downstream from incubators.downstream from incubators.

Interestingly, 100% of all juveniles sampled in Upper Interestingly, 100% of all juveniles sampled in Upper Yankee Fork were SSI origin and this area is likely an Yankee Fork were SSI origin and this area is likely an excellent area to bolster supplementationexcellent area to bolster supplementation

DiscussionDiscussion

SSI produce parr (23.9% age-0SSI produce parr (23.9% age-0++)) No statistical difference in condition or length of No statistical difference in condition or length of

SSI progeny and natural-origin progenySSI progeny and natural-origin progeny Achieve outplanting objective of 375,000 eyed Achieve outplanting objective of 375,000 eyed

eggseggs Increase sampling for better resolution between Increase sampling for better resolution between

sitessites Habitat is relatively vacant and can support Habitat is relatively vacant and can support

increases in supplementationincreases in supplementation– 2006 density 0.027 fish/m2006 density 0.027 fish/m22

DiscussionDiscussion

Predominate age class is 50-80mmPredominate age class is 50-80mm Migration time and age at migration is unknown, Migration time and age at migration is unknown,

however, we sample few fish above 80mm however, we sample few fish above 80mm indicating 1indicating 1++ juveniles may be migrating from the juveniles may be migrating from the Yankee Fork before their second fallYankee Fork before their second fall

RecommendationsRecommendations

Increase supplementationIncrease supplementation Increase sampling effortsIncrease sampling efforts Operate rotary screw trap and Operate rotary screw trap and

enumerate migrating juvenilesenumerate migrating juveniles Need adult enumeration (i.e. weir)Need adult enumeration (i.e. weir)

ACKNOWLEDGEMENTSACKNOWLEDGEMENTS• Sawtooth Fish Hatchery

•Brent Snider•Roger Elmore•Jocelyn Hatch•Phil Stone•Danielle Corfch•Caleb Price•Lars Alsager•Mel Hughes

•Abernathy Fish Technology Center- Conservation Genetics Laboratory

•William Ardren•Andrew Matala

•LSRCP•Scott Marshall•Chris Starr•Joe Krakker

US Forest Service

Volunteers•Jared Moss•Garret “Dr. Death” Galloway•Ty Broncho

SBT•Andy Kohler•Rodney Burns