William P. Young1, Andrew P. Matala2, Shawn R. Narum2 and Jason Vogel1

1Nez Perce TribeDepartment of Fisheries Resources Management

2Columbia River Intertribal Fish CommissionHagerman Genetics Lab

A demographic evaluation of hatchery- and natural-origin Chinook salmon and its impacton the population genetic structure in the South Fork Salmon River

Objective:•Evaluate the impacts of management activities and demography on the genetic diversity of Chinook salmon

• Within the upper SFSR population

• within the South Fork Salmon River (SFSR) Major Population Group (MPG)

• among MPGs within the Snake River Sp/su Chinook salmon ESU

• Measures of genetic diversity

• Spawner abundance

• Spawner distribution

• Hatchery fraction

•Among MPGs within the Snake River basin ESU• Philopatry

• Landscape/geography

•Among populations within the SFSR MPG

• upper SFSR

• Johnson Creek

• Secesh River

•Within the upper SFSR, HOR and NOR spawners

• 4 sections downstream of a weir

• 1 section upstream of a weir

Effects of management and demography across multiple spatial scales

small

large

Management and demographic structure

-upper SFSR

• Large segregated (H x H) mitigation hatchery program

• Started in 1978, mixed origin• 100% marking in 1995

• Significant hatchery- and natural-origin spawning upstream and downstream of the weir

• Pass all unclipped fish above the weir• Hatchery outplants downstream of the

weir and to the EFSFSR• Significant sport and tribal harvest

Management and demographic structure Johnson Creek - East Fork South Fork Salmon River (EFSFSR)

population

• Supplementation hatchery program • N x N broodstock• Initiated in 1997• No AD clip, 100% cwt & VIE marks

• Significant natural- and hatchery-origin spawning upstream of a weir

• Minimal tribal harvest

Management and demographic structure

-Secesh River

• Managed for natural spawning• Minimal hatchery influence (strays)• Significant natural-origin spawning• Minimal tribal harvest

Johnson Creek weirMcCall Hatchery weir

•Spawning ground surveys•Weir captures

Methods

0

200

400

600

800

Weir to Dime CreekDime Creek to Unnamed TributaryPoverty FlatLodgepole CG to Phoebe CreekAbove weir (Stolle Meadows)

Ann

ual r

edd

coun

ts

1996

2008

2000

2004

Index of Spawner Abundance - upper SFSR, 1996-2008

Stolle Meadows, Sec AW

41.4%

Weir to unnamed tributary, Sec 01 & 02

76.4%

Natural

Hatchery

Lodgepole CG to Phoebe Creek,Sec 04

10.2%

Hatchery Fraction- upper SFSR, 1996-2008

Poverty Flat,Sec 03

21.2%

McCall Hatchery weir

Spawner Distribution- Upper SFSR

above weir below weir0

100

200

300

400

500

Stolle Meadows(Above weir)

Below weir

Ave

rage

red

d co

unts

  Secesh JCtotal SFSR

Secesh 1JC 0.91* 1SFSR 0.82* 0.73* 1

Ave

rage

an

nu

al r

edd

cou

nts

0

200

400

600

800

1000

1200

Index of Spawner Abundance – SFSR MPG, 1996 - 2008

Secesh JC Upper SFSR

26%

13%

61%

*P < 0.005

Pearson Correlation

Secesh RiverStray HOR = 4.7%

Johnson CreekStray HOR = 3.4%Endemic HOR = 47%

Hatchery Fraction- SFSR MPG, 1996-2008

SFSRApproximate HOR = 40%

MPG level Spawner

Distribution

•Major spawning areas in headwaters•Populations are separated by areas of unsuitable spawning habitat

• High gradient• Large substrate

•Likely influenced historic metapopulation structure and diversity

Summary – upper SFSR

•Spawner abundance - Similar annual redd count variation upstream and downstream of the weir

•Hatchery Fraction - highest in the two sections just below the weir, significant in all sections, including above the weir.

•Spawner Distribution - spawning distributed almost continuous. Little to no spawning Chinook salmon in the lower 15 kilometers

Conclusions – SFSR MPG

•Spawner Abundance – high spawner variation across years.

•Hatchery fraction – minor influence of strays in JC and Secesh

•Spawner distribution - major spawning areas separated by areas of unsuitable spawning habitat (high gradient, large substrate)

•Historic genetic relationships between the SFSR MPG other MPGs within the Snake River basin ESU appear to have been conserved.

• Philopatry

• Landscape/geography

•Three distinct populations persist in the SFSR MPG

• widely varying abundance, composition and distribution.

• widely varying management intensity

•De facto hatchery integration in the upper SFSR

• Leaky weir, ISS supplementation

• Significant HOR spawners downstream of the weir

Spatial Scale

small

largelarge

JC

JCsupp

SCT01

SCT04

SCT02

SCT03

HAT2001

HAT2002

HAT2000

SCT-AW

Secesh

Nei: 0.01

98.9

63.8

98.9

GENETIC DISTANCE:Radial tree topology – greater proximity equals greater similarity

2.

3.

4.

5.

1.

1.) Imnaha River

2.) Grande Ronde & Clearwater

3.) SFSR : three upper SFSR groups two Johnson Creek & Secesh River

4.) Middle Fork Salmon River

5.) Upper Salmon River

Narum et al. 2007. Transactions of the American Fisheries Society 136:1252-1262.

In the context of larger scope Snake River studies.

Acknowledgements

•Nez Perce Tribe• Neal Espinosa• Mike Blenden• Cameron Albee• Rick Orme• Jay Hesse• Ryan Kinzer• Craig Rabe• Field Crews

•Idaho Department of Fish and Game

• John Cassinelli• Brian Leth• Kim Apperson• Field Crews