Genetic Stock Structure of Skagit River Basin winter steelhead

Todd W. Kassler and Kenneth I. Warheit

Washington Department of Fish and Wildlife

March 13 - 15, 2012

Acknowledgements Seattle City Light

Ed Connor, Dave Pflug

Skagit River System Cooperative Eric Beamer, Bob Hayman, Pete Kairis, Jade Luckhurst, Jeff Meyer,

Larry Wasserman

Upper Skagit Tribe Rebecca Bernard, Jon-Paul Shannahan

WA Department of Fish and Wildlife (WDFW) Brett Barkdull, Cheryl Dean, Curt Kraemer, Anne Marshall, Steve Stout

Wild Fish Conservancy

Bill McMillan

Background

Joint project between Seattle City Light, Skagit River System Cooperative, Upper Skagit Tribe, WA Department of Fish and Wildlife (WDFW), Wild Fish Conservancy

Project objective is to assess the genetic diversity of steelhead and resident O.mykiss in the Skagit River basin

78 Collections were made – 2,634 individuals were analyzed adults – 30 collections – 625 individuals

juveniles – 22 collections – 714 individualsresident O.mykiss – 21 collections – 950 individualsfishery samples – 5 collections – 345 individuals

Genetic analysis using 15 microsatellite DNA loci

Background

Individuals with cutthroat alleles were identified

Cutthroat alleles have been identified in previous analysis using known cutthroat samples

If individual had only one cutthroat allele the genotype at the locus was zeroed. If an individual had more than one cutthroat allele the entire individual was dropped

Collections – AdultsCode Location Life Stage Total N

08DQ, 09BN, 10AO, 11BI upper Skagit River adults 81

09BM*, 10AS mid Skagit River adults 42

10LG mid Skagit R. ¼ pounders adults 10

10AQ Suiattle River adults 51

81AAA, 83AAA, 08DR, 08MS,09DU, 10AR, 11BN Sauk River adults 148

10CQ, 11BK Finney Creek adults 53

08LF, 09CF, 10AN Marblemount Hatchery adults 151

10KA Marblemount early timed adults 18

10MZ Chilliwack Hatchery adults 71

* - collection included telemetry samples

Collections – JuvenilesCode Location Life Stage Total N

07MT, 10AZ upper Skagit River juveniles 68

09EI, 10AY lower Skagit River juveniles 48

07MU, 08MK, 09IY, 10BB County Line Ponds juveniles 74

07MS, 10BA Bacon Creek juveniles 57

09IZ, 10BC Goodell Creek juveniles 88

09EE, 10AV lower Cascade River juveniles 98

10AW Suiattle River juveniles 60

10AX Sauk River juveniles 50

10BK Diobsud Creek juveniles 47

09EH, 10AT Finney Creek juveniles 105

Collections – resident O. mykiss

Code Location Life Stage Total N

09ES, 10BF N.F. Cascade River residents 98

09EU, 10BG Big Creek (trib to Suiattle River) residents 96

09ET, 10BE Clear Creek (trib to Sauk River) residents 98

09EV, 10BD upper Finney Creek residents 85

09EL, 10AU Baker River above Baker Lake residents 74

06AF, 09MA, 10BH Ross Lake residents 135

02FB Roland Creek residents 97

05NG Dry Creek residents 62

09JA, 10BI Stetattle Creek residents 76

09JB, 10BJ Blackwater Creek residents 67

Collections – adults, juveniles, and residents

Location Adults Juveniles Residents

N.F. Cascade River 09DS, 10AP (4) 09EE (49) 09ES, 10BF (98)10AV (49)

Suiattle River (Big Creek) 10AQ, 11BM (51) 10AW (60) 09EU (46)10BG (50)

Sauk River (Clear Creek) 81AAA, 83AAA, 10AX (50) 09ET, 10BE (98)09DU, 10AR, 11BN (130)

upper Finney Creek 10CQ, 11BK (53) 09EH (54) 09EU (46)10AT (51) 10BD (48)

Laboratory Methods

DNA was extracted from an assortment of different tissue types

PCR amplification was performed using microsatellite loci Amplified products were run through an ABI-3730 Genetic

Analyzer Microsatellite electropherograms were scored using

GENEMAPPER software v.3.7 Microsatellite data was binned using SPAN allele naming

Comparisons for Data Analyses -

HW and Genotypic Differentiation • Temporal collections were grouped

Adult collections - 9 groups Juvenile collections - 14 groups Resident collections - 16 groups

Adults and Juveniles Adults, Juveniles, and Residents same watershed

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GEN

ETIX Chilliwack

Skagit natural-origin

Marblemount

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upper Skagit middle Skagit Suiatle Sauk Finney Nat vs Nat

upper Skagit **** 0.0002 0.0008 0.0005 0.0007 0.0006

middle Skagit **** -0.0012 0.0004 0.0006

Suiatle **** -0.0006 0.0039

Sauk **** 0.0011

Finney ****

Hoh R. Natural

S.F. Hoh R. Natural

up Hoh R.

Bogachiel R.

Calawah R.

Solduc R. Natural Nat vs Nat

Hoh R. Natural **** -0.0013 -0.0010 0.0025 -0.0004 0.0007 0.0004

S.F. Hoh R. Natural **** -0.0029 0.0001 -0.0014 0.0032

upper Hoh R. Natural **** 0.0064 0.0015 0.0019

Bogachiel R. Natural **** -0.0028 0.0008

Calawah R. Natural **** -0.0007

Solduc R. Natural ****

Adult Collections – Natural vs Natural

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TAdult Collections – Natural vs Hatchery

upper Skagitmiddle Skagit Suiatle Sauk Finney

winter Hat vs Nat

Marblemount 0.0196 0.0230 0.0254 0.0263 0.0199 0.0208

Chiliwack 0.0193 0.0161 0.0189 0.0176 0.0222

Hoh R. NaturalS.F. Hoh R.

Naturalup Hoh R.

NaturalBogachiel R. Natural

Calawah R. Natural

Solduc R. Natural

winter Hat vs Nat

Cook Cr. Hatchery 0.0179 0.0189 0.0223 0.0334 0.0317 0.0256 0.0238

Salmon R. Hatchery 0.0292 0.0278 0.0297 0.0416 0.0421 0.0375

Bogachiel R. Hatchery 0.0192 0.0180 0.0224 0.0265 0.0257 0.0233Clipped

STHD in Hoh R. 0.0159 0.0121 0.0189 0.0276 0.0258 0.0235

Elochoman R. Hatchery 0.0155 0.0133 0.0156 0.0199 0.0156 0.0183

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EFigure 2. Structure plot showing percent membership of each individual steelhead and the population average into the groups that STRUCTURE found in the dataset. Individuals with more than one color in the bar likely have mixed ancestry. The group number identifies the collections with similar ancestry.

Adult / Juvenile Collections - STRUCTURE

Res

iden

t Col

lect

ions

- G

ENET

IX

Cascade

Big Cr. Clear Cr.

Baker/Finney

upper Skagit

Blackwater

Resident Collections – STRUCTURE (K = 7)

Adults, Juveniles, and Residents - GENETIX

Cascade Sauk

Suiattle Finney

Conclusions

Natural-origin Adult steelhead in the Skagit Basin are not differentiated

Natural and Hatchery-origin steelhead are differentiated

Juvenile steelhead in Skagit Basin are not differentiated from the Adult collections

Percentage of hatchery ancestry in natural-origin collections of Adult and Juvenile steelhead is about the same

Resident collections are differentiated to steelhead collections (Adults and Juveniles)