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A demographic evaluation of hatchery- and natural-origin Chinook salmon and its impact on the population genetic structure in the South Fork Salmon River. William P. Young 1 , Andrew P. Matala 2 , Shawn R. Narum 2 and Jason Vogel 1 1 Nez Perce Tribe

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slide1

A demographic evaluation of hatchery- and

natural-origin Chinook salmon and its impact

on the population genetic structure in the

South Fork Salmon River

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

1Nez Perce Tribe

Department of Fisheries Resources Management

2Columbia River Intertribal Fish Commission

Hagerman Genetics Lab

slide2

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
slide3

Effects of management and demography across multiple spatial scales

large

  • 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

small

slide4

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
slide5

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
slide6

Management and demographic structure

-Secesh River

  • Managed for natural spawning
  • Minimal hatchery influence (strays)
  • Significant natural-origin spawning
  • Minimal tribal harvest
slide7

Methods

  • Spawning ground surveys
  • Weir captures

McCall Hatchery weir

Johnson Creek weir

slide8

Annual redd counts

2008

2004

2000

1996

Index of Spawner Abundance - upper SFSR, 1996-2008

slide9

10.2%

Natural

Hatchery

Lodgepole CG to

Phoebe Creek,

Sec 04

21.2%

Poverty Flat,

Sec 03

76.4%

41.4%

Weir to unnamed tributary,

Sec 01 & 02

StolleMeadows,

Sec AW

Hatchery Fraction

- upper SFSR, 1996-2008

slide10

Stolle Meadows

(Above weir)

Below weir

Spawner Distribution

- Upper SFSR

Average redd counts

McCall Hatchery weir

slide11

Index of Spawner Abundance

– SFSR MPG, 1996 - 2008

Pearson Correlation

61%

26%

13%

*P < 0.005

Secesh

JC

Upper SFSR

slide12

Hatchery Fraction

- SFSR MPG, 1996-2008

Secesh River

Stray HOR = 4.7%

SFSR

Approximate HOR = 40%

Johnson Creek

Stray HOR = 3.4%

Endemic HOR = 47%

slide13

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
slide14

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
slide15

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)
slide16

Spatial Scale

  • 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

large

large

small

slide17

GENETIC DISTANCE:

Radial tree topology – greater proximity equals greater similarity

In the context of larger scope Snake River studies.

JCsupp

4.

Secesh

5.

HAT2002

3.

JC

98.9

98.9

HAT2000

63.8

1.

2.

SCT01

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

SCT03

SCT-AW

Nei: 0.01

SCT04

HAT2001

SCT02

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

slide18

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