Paul Moran Conservation Biology Division Northwest Fisheries Science Center

1. Paul Moran Conservation Biology Division Northwest Fisheries Science Center Interlaboratory Standardization of Coast-wide Chinook Salmon Genetic Data for International Harvest ManagementYear 2 Progress Report Portland, Oregon30 November 2005

2. GAPS Collaborators 2005 Anton Antonovich, Alaska Department of Fish and Game Bill Ardren, US Fish and Wildlife Service, Abernathy Melissa Baird, Northwest Fisheries Science Center Michael Banks, Oregon State University Terry Beacham, Canadian Department of Fisheries and Oceans Reneé Bellinger, Oregon State University Scott Blankenship, Southwest Fisheries Science Center Craig Busak, Washington Department of Fish and Wildlife Matt Campbell, Idaho Department of Fish and Game Cheryl Dean, Southwest Fisheries Science Center Nick Decovich, Alaska Department of Fish and Game Carlos Garza, Southwest Fisheries Science Center Chuck Guthrie, Alaska Fisheries Science Center, Auk Bay Eric Kretschmer, US Fish and Wildlife Service, Anchorage David Kuligowski, Northwest Fisheries Science Center Tricia Lundrigan, University of Washington Paul Moran, Northwest Fisheries Science Center Shawn Narum, Columbia River Intertribal Fish Commission Devon Perce, Southwest Fisheries Science Center Madison Powell, University of Idaho Lisa Seeb, Alaska Department of Fish and Game Jim Shaklee, Washington Department of Fish and Wildlife Christian Smith, Alaska Department of Fish and Game Ora Stefanowski, US Fish and Wildlife Service Jeff Stephenson, Columbia River Intertribal Fish Commission Janine Supernault, Canadian Department of Fisheries and Oceans David Teel, Northwest Fisheries Science Center Bill Templin, Alaska Department of Fish and Game Don VanDoornik, Northwest Fisheries Science Center Ken Warheit, Washington Department of Fish and Wildlife John Wenburg, US Fish and Wildlife Service Richard Wilmot, Alaska Fisheries Science Center Ruth Withler, Canadian Department of Fisheries and Oceans Sewall Young, Washington Department of Fish and Wildlife

3. Chinook microsatellite standardization objectives • Develop a standardized coast-wide DNA baseline that will resolve lineages and stocks within the region for which the CTC is responsible • Facilitate future expansion of the DNA baseline and addition of novel genetic markers through exchange of DNA samples • Develop a data base application to support the dissemination and growth of the baseline

4. 7 0 7 5 8 0 8 5 9 0 9 5 1 0 0 4 . 1 4 b p 6 s t i 2 0 0 0 n 5 u 1 5 0 0 t 1 0 0 0 n e 4 5 0 0 c s e r Number of laboratories 3 7 5 . 0 0 L 1 0 0 . 0 0 K o u l 8 9 . 0 7 9 3 . 2 1 f 2 e v 4 . 2 5 b p i t a 1 l e 1 5 0 0 R 0 1 0 0 0 5 0 0 Microsatellite marker (N = 62) 7 5 . 0 0 1 0 0 . 0 0 L K 8 5 . 3 2 8 9 . 5 7 F r a g m e n t s i z e ( b p ) Challenges to microsatellite standardization Few loci in common Precise but inaccurate sizing

5. 2-Year GAPS study design • Year 1: Standardization • Select a common set of markers • Standardize allele designations • Select baseline populations for year 2 • Year 2: Baseline development • Verification via blind samples • Sample exchange • Data collection and storage • Power analysis

6. Samples 500-sample survey set (10 individuals from each of 47 populations, range-wide) 96-sample reference set (8 individuals from each of 12 regions) 96-sample blind tests (diverse mixture samples) 15,000-sample baseline set (144 individuals from each of 105 populations ) *Current focus on microsatellites, future interest in SNPs “Marker (=locus) sets” and “Sample sets” Markers* • 62 sponsored loci • 25 candidate loci • 13 finalists for baseline construction

7. Blind test of standardization

8. Partially corrected concordance

9. Example blind test errors from one of the laboratories No. Source of Error 6 Faint or large allele dropout - DNA quality 4 Conversion typo 4 Sample order? 1 Artifact?

10. Current Chinook Coast-wide baseline • ~16,000 individuals • 110 populations (>230 samples) • 37 regions, Gulf of AK to Central Valley CA • Preliminary analyses complete • Descriptive pop gen • Power analysis

12. Standardized GAPS loci • Alleles per locus: 37.6 (7 – 71) • Heterozygosity: 0.85 (0.52 – 0.95) • FST: 0.071 (0.03 – 0.22)

13. L Fraser Washington Coast E Vancouver Is S Puget Sound Willamette W Vancouver Is N Puget Sound L Columbia fa U Fraser Columbia tule Mid Fraser L Columbia sp N Thompson Deschutes fall U Columbia su/fa L Thompson Snake R fa U Columbia sp California CV Snake sp/su Central BC Coast S Mainland California Coast L Skeena Alaska/BC Transboundary N California, S Oregon Coast NSE Alaska; Chilkat NSE Alaska; King Salmon Klamath Basin SSE Alaska Rogue SSE Alaska; Stikine Mid Oregon Coast Nass N Gulf Coast; Alsek Washington Coast U Skeena N Gulf Coast; Situk CTC Coast-wide microsatellite baseline 2005

14. Simulated 100% “mixture” analysis

15. Simulated mixed fishery sample

16. CTC Coast-wide microsatellite baseline 2005 Washington Coast E Vancouver Is S Puget Sound Willamette W Vancouver Is N Puget Sound L Columbia fa U Fraser Columbia tule Mid Fraser L Columbia sp N Thompson Deschutes fa U Columbia su/fa L Thompson Snake R fa Columbia sp California CV Snake sp/su Central BC Coast S Mainland California Coast L Skeena Alaska/BC Transboundary N California, S Oregon Coast NSE Alaska; Chilkat NSE Alaska; King Salmon Klamath Basin SSE Alaska Rogue SSE Alaska; Stikine Mid Oregon Coast Nass N Gulf Coast; Alsek Washington Coast U Skeena N Gulf Coast; Situk

17. Results summary • Concordant genotyping among laboratories • High heterozygosity (~500 alleles) • No obvious HW departures or linkage disequilibrium • High concordance with previous genetic studies • Powerful mixture analyses, both proportional estimates and individual assignment

18. Ahead… • Expand baseline • Comprehensive power analysis • Safe and secure repository for data • QC and certification of new labs