1. Detecting Introgressive Hybridization between Segregated Hatchery and Wild Populations Part II Kenneth I. Warheit 2014 Pacific Coast Steelhead Management Meeting Skamania Lodge, WA March 18, 2014

2. Prolog 1 Segregated hatchery programs – Early winter: Chambers (native PS) – Early summer: Skamania (native Col. River) Monitor wild populations for hatchery strays – Ecological and genetic effects The Problem: – For closely related populations, identifying hatchery, wild, and hybrid categories is problematic Early winter in Puget Sound Early summer in Columbia River

3. Prolog 2: Why Part II? At AFS – Western in Boise ID April 2013 I showed high error rate using Structure and NewHybrids when assigning individuals to hatchery, pure, and hybrid categories. Error due to recency of common ancestor But I did not provide an answer as to how to overcome this problem

4. Objectives 1.Introduce a method that incorporates assignment error into estimating hatchery, wild, and hybrid proportions of populations 2.Provide summary estimates of hatchery-wild introgression for north Puget Sound populations 3.Offer a preliminary estimate as to causes of inter-basin differences in introgression Introgression = hybridization between hatchery and wild

5. Added Complication Native Puget Sound (e.g., PS winter) Non-native PS (e.g., Chambers in PS) Non-native L. Col River (e.g., Skamania in PS) F ST = 0.06 F ST = 0.03

6. B W S B W W W B S Sample location Early winter hatchery (Chambers) Early summer hatchery (Skamania) Both EWH & ESH Seattle Thanks to Anne Marshall for the base map X

7. Basin Wild Hatchery OUDIPN EWHESH Green411483042 Snohomish10533335 Stillaguamish5222400 Skagit8332197na Samish1173na Nooksack52219 40na 1318202771597 Samples OU = operational unit (group of collections) DIP = Demographically independent population

8. Assign Wild Samples to Groups Genotype samples using 192 SNPs (WDFW Panels E and F) Program Structure Groups – Wild (winter- or summer-run) – Early Winter Hatchery lineage – Early Summer Hatchery lineage – Hybrids Summarized as proportions for each – OU – DIP Provide estimates of introgression UNCORRECTED for assignment error

9. Modeled Populations Simulate – Wild, Early Winter Hatchery, Early Summer Hatchery – Hybrids – Designed to model Puget Sound populations Program Structure – Known source Modeled populations used to estimate assignment error – Wild (winter- or summer-run) – Early Winter Hatchery lineage – Early Summer Hatchery lineage – Hybrids

10. Past Present MS* Model Parameters Locus mutation rate 4N o  = 20 Population growth Stable Populations Three # samples from each pop 500 Phylogenetic relationship Hierarchical Divergent Dates A = 0.24N o generations (Whidbey) B = 0.12N o generations (Whidbey) A = 0.16N o generations (Nooksack) B = 0.13N o generations (Nooksack) Pop 1 (“PS Wild”) Pop 2 (“Early Winter Hatchery”) Pop 3 (“Early Summer Hatchery”) A B a1 a2Pop 3 Pop 2Pop 1 * Program MS Richard Hudson. 2002

11. Modeled Populations Simulate – Wild, Early Winter Hatchery, Early Summer Hatchery – Hybrids – Designed to model Puget Sound populations Program Structure – Known source Modeled populations used to estimate assignment error – Wild (winter- or summer-run) – Early Winter Hatchery lineage – Early Summer Hatchery lineage – Hybrids

12. Error for k = 2 (Part I)

13. Wild Early Winter Hatchery (EWH) Early Summer Hatchery (ESH) Hybrid: EWH-WildHybrid: ESH-WildHybrid: EWH-ESH Wild EWH ESH Structure Assignments (Part II)

14. Assigned Category Source Category Early Winter Hatchery (EWH) Hybrid: EWH - Wild Hybrid: ESH - Wild Early Summer Hatchery (ESH) Wild Hybrid: EWH - ESH Total Assigned Total that should be assigned - No Call Assignment Error Rate Whidbey Basin Model Early Winter Hatchery (EWH)65511341566844937 0.22 Hybrid: EWH - Wild216625581229331162920 0.46 Hybrid: ESH - Wild011514242637612782 0.16 Early Summer Hatchery (ESH)008783901591085963 0.23 Wild51537906931931956 0.26 Hybrid: EWH - ESH611840983507727803 0.30 NoCall63802183744197639 na Total Source1000 6000 0.29 NoCall Rate0.060.080.220.04 0.200.11 Soure Error Rate Total0.350.380.490.160.310.490.36 Soure Error Rate Assigned Only0.300.320.340.130.280.370.29 Error | Assignment

15. Correcting Structure assignments using estimated error rates from modeled populations

16.  0,  1,  2 = parameters from resampling error matrix Y = empirical UNCORRECTED estimate X i = estimated Source or CORRECTED proportions i= 0 to 1.0 at 0.001 intervals Estimated Source Proportion L (  0,  1,  2 |Y=0.21, X) Maximum = 8.85 Source Target proportion where likelihood is maximized = 0.16 Likelihood equation for Normal Regression Y = 0.21

17. Results

18. Basin Introgression EWHESH Green Average OU0.120.00 Green River Winter-Run0.110.00 Snohomish Average OU0.080.22 North Fork Skykomish Summer-Run0.000.55 Tolt River Summer-Run0.000.48 Snoqualmie River Winter-Run0.280.00 Snohomish / Skykomish R Winter-Run0.00 Pilchuck R Winter-Run0.00 Stilly Average OU0.000.09 Canyon Creek Summer-Run0.00 Deer Creek Summer-Run0.000.02 Skagit Average OU0.02 Mainstem Skagit R Summer- and Winter-Run0.00 Sauk R Summer- and Winter-Run0.00 Nookachamps Creek Winter-Run0.00 Samish0.170.00 Nooksack Average OU0.020.03 Nooksack R Winter-Run0.000.02 South Fork Nooksack R Summer-Run0.00

19. Off-station Releases Off-station Releases (2-year offset) / Wild Escapement Off-station Releases (2-year offset) / Wild Escapement Introgression Averaged across all Operational UnitsAveraged across all DIPs – all samples r 2 = 0.81 r 2 = 0.94 Thanks to Brian Missildine and Christina Iverson for releases and escapement data

20. Acknowledgments Shannon Knapp (formerly WDFW, NMSU) WDFW Molecular Genetics Lab – Sarah Bell, Todd Kassler, Mo Small, Sewall Young SCL, tribal, and WDFW Region 4 field staff Todd Seamons (WDFW) HGMP group: – Jim Scott, Annette Hoffmann, Kelly Cunningham, Brian Missildine, Beata Dymowska Funding: Seattle City Light, Washington State General and Wildlife Funds