1. 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

2. Objectives Background Population analysis Phylogenetic analysis Individual assignment Conclusions Outline

3. 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 - CALFED Goal 1: At-Risk Species

4. 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

5. Population Comparisons 1) Allele frequency differences Pop 1 Allele size observed Allele size observed Pop 3 Allele size observed Pop 2 Allele size observed Pop 4 2) Trees 1 2 3 4

6. Upper Klamath Columbia fall CA Central Valley Lower Columbia North CA coast OR coast WA coast Waples et al. Evolution 58(2), 2004 Background – Allozymes (protein markers) Columbia spring coastal Klamath Puget Sound Strait of Georgia Vancouver Is. Central British Columbia Interior Fraser

7. Background – Microsatellites (nuclear DNA) Banks et al. 2000 CJFAS 57:915 0.01 Winter Spring Butte Creek Spring Deer & Mill Creeks Fall Late-fall 100 71 99

8. Sampling – California Dept. Fish and Game Battle Creek – fall Mill Creek – spring Mill Creek – fall Deer Creek – spring Deer Creek – fall Butte Creek – spring Butte Creek – fall Feather River – fall Feather Hatchery – spring Feather Hatchery – fall American River – fall Nimbus Hatchery – fall Mokelumne Hatchery – fall Stanislaus River – fall Toulumne River – fall Merced River – fall Merced Hatchery – fall Sacramento RiverSan Joaquin RiverBY Coastal CaliforniaBY Klamath River – fall 2002 2003 2002

9. Sampling – California Dept. Fish and Game Battle Creek – fall Mill Creek – spring Mill Creek – fall Deer Creek – spring Deer Creek – fall Butte Creek – spring Butte Creek – fall Feather River – fall Feather Hatchery – spring Feather Hatchery – fall American River – fall Nimbus Hatchery – fall Mokelumne Hatchery – fall Stanislaus River – fall Toulumne River – fall Merced River – fall Merced Hatchery – fall Sacramento RiverSan Joaquin RiverNN Coastal CaliforniaN Klamath River – fall 100 57 79 83 34 96 78 65 69 53 100 84 91 75 57 89 31

10. Population Analysis – Within population Sample Mean allele Richness HWC F IS 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 9.88 9.28 10.06 9.63 10.22 8.72 10.50 10.55 10.32 9.85 10.45 10.36 10.48 10.16 10.25 10.42 8.62

11. Population Analysis – Within population (23 Loci) 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) Americ (f) Nimbus (f) Mokel (f)Stanis (f) Toulu (f) Merced (f)Mer H(f)Klamath(f)

12. Population Analysis – Within population (23 Loci) Sample Mean allele Richness HWC equilibrium F IS 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) 0.04 0.11 0.05 0.09 0.05 0.07 0.04 0.06 0.04 0.06 0.04 0.09 0.05 0.07 0.04 0.11 Proportion LD No 0.11*** 0.07*** 0.10*** 0.11*** 0.13*** 0.12*** 0.14*** 0.12*** 0.08** 0.10*** 0.14*** 0.08*** 0.13*** 0.05* 0.16*** 0.17*** 0.06 9.88 9.28 10.06 9.63 10.22 8.72 10.50 10.55 10.32 9.85 10.45 10.36 10.48 10.16 10.25 10.42 8.62

13. Population Analysis – Among population (23 loci) Overall Wild (no Hatchery) Central Valley Wild Central Valley Within Spring Within Fall Within Hatcheries 0.022*** 0.024*** 0.017*** 0.020*** 0.015*** F ST 1 Population Group 1 Weir and Cockerham (1984) All Populations 0.056 Coastal 0.036 Central Valley 0.017 F ST 1 Group Coastal CA Dataset Hatchery Fall vs. Fall Hatchery vs. wild counterpart Spring vs. Fall Klamath vs. CV 0.018 0.030 0.082 F ST 1 Population Group Mean Pairwise

14. Phylogenetic Analysis Reynolds-distance Reynolds, Weir, and Cockerham's (1983) MillF DeerF BattleF MercedF AmericanF FeatherF FeatherHS MillS DeerS FeatherHF MokelumHF NimbusHF ToulumneF MercedHF StanislsF ButteCkF KlamathF 0.01 ButteS

15. Phylogenetic Analysis Reynolds-distance Reynolds, 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 Tree 1000 Bootstraps

16. Phylogenetic Analysis 100 Consensus Tree 1000 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) 840 671 567 spring San Joaquin

17. Phylogenetic Analysis 100 Consensus Tree 1000 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) 840 671 567

18. Individual Assignment – ESU level Fall/Late Fall 98 Spring 69 Klamath 100 ESU % Correct Klamath 99 Coastal CA 97 79 (excluding Feather Hatchery sp.)

19. Individual Assignment – ESU level ESU % Correct Klamath 99 Coastal CA 97 Lineage % Correct Mill/Deer (sp) 72 Butte (sp) 84 Fall/Late Fall 98 Spring 79 Klamath 100

20. Individual Assignment – Watershed level Battle Creek Mill Creek Deer Creek Butte Creek Feather River American River Mokelumne River Stanislaus River Toulumne River Merced River System % Correct Sacramento River 78 San Joaquin River 65 25 37 55 47 36 Watershed % Correct 27 62 28 53

21. Individual Assignment – Watershed level Battle Creek Mill Creek Deer Creek Butte Creek Feather River American River Mokelumne River Stanislaus River Toulumne River Merced River 25 37 55 47 36 Watershed % Correct 27 62 28 53 Watershed % Correct Coastal CA Klamath River Mad River Eel River Noyo River Wages Creek Russian River 97 86 94 88 100 83

22. Battle Creek – fall Mill Creek – spring Mill Creek – fall Deer Creek – spring Deer Creek – fall Butte Creek – spring Butte Creek – fall Feather River – fall Feather Hatchery – spring Feather Hatchery – fall American River – fall Nimbus Hatchery – fall Mokelumne Hatchery – fall Stanislaus River – fall Toulumne River – fall Merced River – fall Merced Hatchery – fall Sacramento RiverSan Joaquin River % Correct Coastal California Klamath River – fall 25 52 21 51 04 84 36 17 35 34 15 33 27 62 28 05 74 100 Individual Assignment – Population level % Correct

23. 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.

24. Laboratory Celeste Gallardo Amy Bouck Cheryl Dean Funding US Fish & Wildlife Service Southwest Fisheries Science Center Samples California Dept. Fish & Game Acknowledgements Alice Low Randal Benthin Rich Dixon Jennifer Navicky