1. Interlaboratory Standardization of Coast-wide Chinook Salmon Genetic Data for International Harvest Management Year 2 Progress Report Paul Moran Conservation Biology Division Northwest Fisheries Science Center Portland, Oregon 30 November 2005

2. 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 GAPS Collaborators 2005

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. Few loci in common Precise but inaccurate sizing Challenges to microsatellite standardization

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. “Marker (=locus) sets” and “Sample sets” Markers* 62 sponsored loci 25 candidate loci 13 finalists for baseline construction 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

7. Blind test of standardization A) Initial submission LocusLab 1Lab 2Lab 3Lab 4Lab 5Lab 6Lab 7Lab 8Lab 9 Averag e Ogo20.9871.000 0.9930.0001.0000.9931.0000.886 Ogo40.4391.000 0.9951.0000.0000.9950.9940.9900.824 Oki1000.9781.000 0.9701.0000.994 OMM10801.000 0.9951.000 0.0001.0000.9941.0000.995 Ots201b0.9841.000 0.9930.9950.9851.0000.990 Ots208b0.9941.000 0.9950.9700.9950.996 Ots2111.000 0.9941.0000.9930.9550.9940.9850.9940.884 Ots2120.9891.000 0.9890.9950.9941.0000.886 Ots2130.9871.0000.9821.0000.9850.0001.000 0.999 Ots3M1.000 0.9880.9941.0000.0001.000 0.9950.980 Ots91.000 0.8231.000 0.991 OtsG4740.9951.000 0.999 Ssa4080.9870.9291.000 0.991 Average0.9490.9950.9970.9990.9980.5970.9980.9910.9980.955

8. Partially corrected concordance B) Partially corrected LocusLab 1Lab 2Lab 3Lab 4Lab 5Lab 6Lab 7Lab 8Lab 9Average Ogo20.9871.000 0.9930.9881.0000.9931.0000.996 Ogo40.9941.000 0.9951.0000.9680.9950.9940.9900.993 Oki1000.9781.000 0.9701.0000.994 OMM10801.000 0.9951.000 0.9381.0000.9941.0000.995 Ots201b0.9841.000 0.9930.9950.9851.0000.990 Ots208b0.9941.000 0.9950.9700.9950.996 Ots2111.000 0.9941.0000.9930.9550.9940.9850.994 Ots2120.9891.000 0.9890.9950.9941.0000.992 Ots2130.9871.0000.9821.0000.9850.9941.000 0.999 Ots3M1.000 0.9880.9941.0000.9491.000 0.9950.980 Ots91.000 0.9791.000 0.991 OtsG4740.9951.000 0.999 Ssa4080.9870.9291.000 0.991 Average0.9920.9950.9970.9990.9980.9810.9980.9910.9980.994

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

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) F ST : 0.071 (0.03 – 0.22)

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

14. Simulated 100% “mixture” analysis

15. Simulated mixed fishery sample

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

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