Detecting Introgressive Hybridization between Segregated Hatchery and Wild Populations Part II Kenneth I. Warheit 2014 Pacific Coast Steelhead Management.

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Presentation transcript:

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

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

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

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

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

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

Basin Wild Hatchery OUDIPN EWHESH Green Snohomish Stillaguamish Skagit na Samish1173na Nooksack na Samples OU = operational unit (group of collections) DIP = Demographically independent population

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

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

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

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

Error for k = 2 (Part I)

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

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) Hybrid: EWH - Wild Hybrid: ESH - Wild Early Summer Hatchery (ESH) Wild Hybrid: EWH - ESH NoCall na Total Source NoCall Rate Soure Error Rate Total Soure Error Rate Assigned Only Error | Assignment

Correcting Structure assignments using estimated error rates from modeled populations

 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 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

Results

Basin Introgression EWHESH Green Average OU Green River Winter-Run Snohomish Average OU North Fork Skykomish Summer-Run Tolt River Summer-Run Snoqualmie River Winter-Run Snohomish / Skykomish R Winter-Run0.00 Pilchuck R Winter-Run0.00 Stilly Average OU Canyon Creek Summer-Run0.00 Deer Creek Summer-Run Skagit Average OU0.02 Mainstem Skagit R Summer- and Winter-Run0.00 Sauk R Summer- and Winter-Run0.00 Nookachamps Creek Winter-Run0.00 Samish Nooksack Average OU Nooksack R Winter-Run South Fork Nooksack R Summer-Run0.00

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

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