Detecting Introgressive Hybridization between Segregated Hatchery and Wild Populations
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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 Median Q-value (+- 1 SE across 10 iterations) 1 Pop 1 "Hatchery" Pop 2 "Wild" F1 Hybrid Simulation Individuals (for each group, sorted by "hatchery" Q-value) 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 F ST = 0.03 F ST = 0.06
6 Sample location W W S B Early winter hatchery (Chambers) Early summer hatchery (Skamania) Both EWH & ESH W Seattle B S X W B Thanks to Anne Marshall for the base map
7 Samples Basin Wild Hatchery OU DIP N EWH ESH Green Snohomish Stillaguamish Skagit na Samish na na Nooksack na 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 a1 MS* Model Parameters Locus mutation rate 4N o m = 20 Population growth A a2 Pop 3 Stable Populations Three # samples from each pop 500 B Phylogenetic relationship Hierarchical Divergent Dates Pop 1 Pop 2 A = 4N o generations (Whidbey) B = 2N o generations (Whidbey) A = 6N o generations (Nooksack) B = 3N o generations (Nooksack) Present Pop 1 ( PS Wild ) Pop 2 ( Early Winter Hatchery ) Pop 3 ( Early Summer Hatchery ) * 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) Median Q-value (+- 1 SE across 10 iterations) 1 Pop 1 "Hatchery" Pop 2 "Wild" F1 Hybrid Simulation Individuals (for each group, sorted by "hatchery" Q-value)
13 Structure Assignments (Part II) ESH Wild Early Winter Hatchery (EWH) Early Summer Hatchery (ESH) Hybrid: EWH-Wild Hybrid: ESH-Wild Hybrid: EWH-ESH
14 Whidbey Basin Model 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 Source Category Assigned Category 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
15 Correcting Structure assignments using estimated error rates from modeled populations
16 Likelihood equation for Normal Regression L ( 0, 1, 2 Y=1, X) L 2 0, 1,, Y X 1 2 (2 i ) 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 e ( ) 2 Y 0 1X i 9 8 Maximum = 8.85 Y = Source Target proportion where likelihood is maximized = Estimated Source Proportion
17 Results
18 Nooksack Skagit Stilly Snohomish Green Basin Introgression EWH ESH Average OU Green River Winter-Run Average OU North Fork Skykomish Summer-Run Tolt River Summer-Run Snoqualmie River Winter-Run Snohomish / Skykomish R Winter-Run Pilchuck R Winter-Run Average OU Canyon Creek Summer-Run Deer Creek Summer-Run Average OU Mainstem Skagit R Summer- and Winter-Run Sauk R Summer- and Winter-Run Nookachamps Creek Winter-Run Samish Average OU Nooksack R Winter-Run South Fork Nooksack R Summer-Run
19 Introgression Averaged across all Operational Units Averaged across all DIPs all samples x 10 5 Off-station Releases x 10 5 Off-station Releases Off-station Releases (2-year offset) / Wild Escapement Off-station Releases (2-year offset) / Wild Escapement 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
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