genetic population structure of chinook salmon in the california central valley scott m....
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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.
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