Genetic Population Structure of Chinook Salmon in the California Central Valley Scott M. Blankenship, Christophe Lemaire, John Carlos Garza Southwest Fisheries.

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Presentation transcript:

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 - CALFED Goal 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

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

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

Background – Microsatellites (nuclear DNA) Banks et al CJFAS 57: Winter Spring Butte Creek Spring Deer & Mill Creeks Fall Late-fall

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

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

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

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)

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) 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***

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 Coastal Central Valley F ST 1 Group Coastal CA Dataset Hatchery Fall vs. Fall Hatchery vs. wild counterpart Spring vs. Fall Klamath vs. CV F ST 1 Population Group Mean Pairwise

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

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

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) spring San Joaquin

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)

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

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

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 Watershed % Correct

Individual Assignment – Watershed level Battle Creek Mill Creek Deer Creek Butte Creek Feather River American River Mokelumne River Stanislaus River Toulumne River Merced River Watershed % Correct Watershed % Correct Coastal CA Klamath River Mad River Eel River Noyo River Wages Creek Russian River

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 Individual Assignment – Population level % 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 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