Genetic Population Structure of Chinook Salmon in the California Central Valley

Scott M. Blankenship, Christophe Lemaire, John Carlos Garza

Southwest Fisheries Science Center

Santa Cruz Laboratory

• Objectives

• Background

• Population analysis

• Phylogenetic analysis

• Individual assignment

• Conclusions

Outline

Primary: Describe population structure and the distribution of genetic variation for Central Valley chinook salmon populations to help guide recovery and restoration efforts.

Secondary: Create comprehensive database

• Boundaries among populations• Geneflow• Effective population sizes• Demographic trajectory• Hatchery interactions

Objectives

Ecosystem Restoration Program - CALFEDGoal 1: At-Risk Species

• Chinook salmon an important species

• ecological – abundant component of ichthyofauna• scientific – most diverse life-history of Pacific Salmon• economic – major recreational and commercial fisheries• cultural – tribal fishery in coastal California.

• Evolutionary Significant Units (ESU)

• Fall/Late Fall• Spring• Winter

Background

BackgroundPopulation Comparisons

1) Allele frequency differences

Pop 1

Allele size

obse

rved

Allele size

obse

rved

Pop 3

Allele size

obse

rved

Pop 2

Allele size

obse

rved

Pop 4

2) Trees1

2

3

4

UpperKlamath

Columbia fall

CA Central Valley

Lower Columbia

North CA

coast

OR coastWA coast

Waples et al. Evolution 58(2), 2004

Background – Allozymes (protein markers)C

olumbia spring

coastal Klam

ath

Puget Sound

Strait of G

eorgia

Vancouver Is.

Central British Columbia Interior

Fraser

Background – Microsatellites (nuclear DNA)

Banks et al. 2000 CJFAS 57:915

0.01

Winter

SpringButte Creek

SpringDeer & Mill Creeks

Fall

Late-fall

100

71

99

Sampling – California Dept. Fish and Game

Battle Creek – fall Mill Creek – springMill Creek – fallDeer Creek – springDeer Creek – fall Butte Creek – spring Butte Creek – fall Feather River – fall Feather Hatchery – springFeather Hatchery – fall American River – fall Nimbus Hatchery – fall

Mokelumne Hatchery – fall Stanislaus River – fall Toulumne River – fall Merced River – fallMerced Hatchery – fall

Sacramento River San Joaquin RiverBY BY

Coastal California BY

Klamath River – fall

200220022002200220022002200220022003200220022002

20022002200220022002

2002

Sampling – California Dept. Fish and Game

Battle Creek – fall Mill Creek – springMill Creek – fallDeer Creek – springDeer Creek – fall Butte Creek – spring Butte Creek – fall Feather River – fall Feather Hatchery – springFeather Hatchery – fall American River – fall Nimbus Hatchery – fall

Mokelumne Hatchery – fall Stanislaus River – fall Toulumne River – fall Merced River – fallMerced Hatchery – fall

Sacramento River San Joaquin RiverN N

Coastal California N

Klamath River – fall

10057798334969678656953

100

8491755789

31

Population Analysis – Within population

SampleMean allele Richness HWC FIS

Battle Creek (f) Mill Creek (sp)Mill Creek (f)Deer Creek (sp)Deer Creek (f) Butte Creek (sp)Butte Creek (f) Feather River (f) Feather Hatchery (sp)Feather Hatchery (f) American River (f) Nimbus Hatchery (f) Mokelumne Hatchery (f) Stanislaus River (f) Toulumne River (f) Merced River (f) Merced Hatchery (f)Klamath River (f)

Proportion LD

9.889.28

10.069.63

10.228.72

10.5010.55

10.329.85

10.4510.3610.4810.1610.2510.428.62

Population Analysis – Within population (23 Loci)

Hn.b

0.5

0.55

0.6

0.65

0.7

0.75

0.8

0.85

0.9

0.95

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

Population

Ex

pe

cte

d U

nb

ias

ed

He

tero

zyg

os

ity

6.00

6.50

7.00

7.50

8.00

8.50

9.00

9.50

10.00

10.50

11.00

All

ele

ric

hn

es

s

Expected Unbiased Heterozygosity vs. Allele Richness (23 loci)

Battle (f)

Mill (sp)

Mill (f)

Deer (sp)

Deer (f)

Butte (sp)

Butte (f)

Feath (f)

FeathH

(sp)

Feath H

(f)

Am

eric (f)

Nim

bus (f)

Mokel (f)

Stanis (f)

Toulu (f)

Merced (f)

Mer H

(f)

Klam

ath(f)

Population Analysis – Within population (23 Loci)

SampleMean allele Richness

HWCequilibrium FIS

Battle Creek (f) Mill Creek (sp)Mill Creek (f)Deer Creek (sp)Deer Creek (f) Butte Creek (sp)Butte Creek (f) Feather River (f) Feather Hatchery (sp)Feather Hatchery (f) American River (f) Nimbus Hatchery (f) Mokelumne Hatchery (f) Stanislaus River (f) Toulumne River (f) Merced River (f) Merced Hatchery (f)Klamath River (f)

0.040.110.050.090.050.070.040.040.040.060.040.060.040.090.050.070.040.11

Proportion LD

NoNoNoNoNoNoNoNoNoNoNoNoNoNoNoNoNoNo

0.11***0.07***0.10***0.11***0.13***0.12***0.14***0.12***0.08**0.10***0.14***0.08***0.08***0.13***0.05*0.16***0.17***0.06

9.889.2810.069.6310.228.7210.5010.55

10.329.8510.4510.3610.4810.1610.2510.428.62

Population Analysis – Among population (23 loci)

OverallWild (no Hatchery)Central Valley WildCentral ValleyWithin SpringWithin FallWithin Hatcheries

0.022***0.024***0.017***0.017***0.020***0.015***0.015***

FST1Population Group

1 Weir and Cockerham (1984)

All Populations 0.056Coastal 0.036Central Valley 0.017

FST1 Group

Coastal CA Dataset

Hatchery Fall vs. FallHatchery vs. wild counterpartSpring vs. FallKlamath vs. CV

0.0180.0180.0300.082

FST1Population Group

Mean Pairwise

Phylogenetic AnalysisReynolds-distanceReynolds, Weir, and Cockerham's (1983)

MillF

DeerF

BattleF

MercedF

Am

ericanF

FeatherF Fe

athe

rHS

MillS

DeerSFeatherHFMokelumHF

Nim

busHF

Toulum

neF

Me

rcedH

FS

tanislsFButteC

kF

KlamathF

0.01

ButteS

Phylogenetic AnalysisReynolds-distanceReynolds, Weir, and Cockerham's (1983)

100

Butte (f)

American (f)

Merced (f)

Mokelumne Hatchery (f)

Nimbus Hatchery (f) Deer (f) Battle (f)

Mill (f)

Feather (f)

Feather Hatchery (sp)

Butte (sp)

Deer (sp)

Mill (sp)

Klamath (f)

Merced Hatchery (f)

Toulumne (f)

Stanislaus (f)

Feather Hatchery (f)

Consensus Tree1000 Bootstraps

Phylogenetic Analysis

100

Consensus Tree1000 Bootstraps

Butte (f)

American (f)Merced (f)

Mokelumne Hatchery (f)Nimbus Hatchery (f)

Deer (f) Battle (f)

Mill (f)Feather (f)

Feather Hatchery (sp)Butte (sp)

Deer (sp)

Mill (sp)

Klamath (f)Merced Hatchery (f)

Toulumne (f) Stanislaus (f)

Feather Hatchery (f)

840671

567

spring

SanJoaquin

Phylogenetic Analysis

100

Consensus Tree1000 Bootstraps

Butte (f)

American (f)Merced (f)

Mokelumne Hatchery (f)Nimbus Hatchery (f)

Deer (f) Battle (f)

Mill (f)Feather (f)

Feather Hatchery (sp)Butte (sp)

Deer (sp)

Mill (sp)

Klamath (f)Merced Hatchery (f)

Toulumne (f) Stanislaus (f)

Feather Hatchery (f)

840671

567

Individual Assignment – ESU level

Fall/Late Fall 98Spring 69Klamath 100

ESU % Correct

ESU % Correct

Klamath 99Coastal CA 97

79 (excluding Feather Hatchery sp.)

Individual Assignment – ESU level

ESU % Correct

ESU % Correct

Klamath 99Coastal CA 97

Lineage % Correct

Mill/Deer (sp) 72Butte (sp) 84

Fall/Late Fall 98Spring 79Klamath 100

Individual Assignment – Watershed level

Battle Creek Mill CreekDeer CreekButte CreekFeather RiverAmerican River

Mokelumne River Stanislaus RiverToulumne RiverMerced River

System % Correct

Sacramento River 78

San Joaquin River 65

253737554736

Watershed % Correct

27622853

Individual Assignment – Watershed level

Battle Creek Mill CreekDeer CreekButte CreekFeather RiverAmerican River

Mokelumne River Stanislaus RiverToulumne RiverMerced River

253737554736

Watershed % Correct

27622853

Watershed % CorrectCoastal CA

Klamath RiverMad RiverEel RiverNoyo RiverWages CreekRussian River

97 86 94 88100 83

Battle Creek – fall Mill Creek – springMill Creek – fallDeer Creek – springDeer Creek – fall Butte Creek – spring Butte Creek – fall Feather River – fall Feather Hatchery – springFeather Hatchery – fall American River – fall Nimbus Hatchery – fall

Mokelumne Hatchery – fall Stanislaus River – fall Toulumne River – fall Merced River – fallMerced Hatchery – fall

Sacramento River San Joaquin River% Correct

Coastal California

Klamath River – fall

255221510484361735341533

2762280574

100

Individual Assignment – Population level

% Correct

% Correct

• Genetic data show low differentiation among Central Valley populations, and genetic distances are smaller than those of other salmonid populations in California.

Conclusions

•Hatchery populations do not necessarily reflect their wild counterparts, but are not extremely divergent.

•Population genetic data are consistent with ESU designations.

•Genetic data indicate that run timing is more important than geography for describing genetic structure.

•Phylogenetic analysis suggests recent population radiation or substantial recent geneflow.

Laboratory

Celeste GallardoAmy BouckCheryl Dean

Funding

US Fish & WildlifeService

Southwest FisheriesScience Center

Samples

California Dept. Fish & Game

Acknowledgements

Alice Low Randal BenthinRich Dixon

Jennifer Navicky