1 / 20

Kenneth I. Warheit

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)

geoffrey-hogan
Download Presentation

Kenneth I. Warheit

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Detecting Introgressive Hybridization between Segregated Hatchery and Wild PopulationsPart 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 • Introduce a method that incorporates assignment error into estimating hatchery, wild, and hybrid proportions of populations • Provide summary estimates of hatchery-wild introgression for north Puget Sound populations • Offer a preliminary estimate as to causes of inter-basin differences in introgression Introgression = hybridization between hatchery and wild

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

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

  7. 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 MS* Model Parameters Locus mutation rate 4Nom = 20 Population growth Stable Populations Three # samples from each pop 500 Phylogenetic relationship Hierarchical Divergent Dates A = 0.24No generations (Whidbey) B = 0.12No generations (Whidbey) A = 0.16No generations (Nooksack) B = 0.13No generations (Nooksack) a1 A a2 Pop 3 B Pop 1 Pop 2 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)

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

  14. Error | Assignment

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

  16. Likelihood equation for Normal Regression b0,b1 , s2 = parameters from resampling error matrix Y= empirical UNCORRECTED estimate Xi= estimated Source or CORRECTED proportions i= 0 to 1.0 at 0.001 intervals Y = 0.21 Maximum = 8.85 L (b0,b1,s2|Y=0.21, X) Source Target proportion where likelihood is maximized = 0.16 Estimated Source Proportion

  17. Results

  18. Averaged across all Operational Units Averaged across all DIPs – all samples Off-station Releases Off-station Releases Introgression r2 = 0.94 r2 = 0.81 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

  19. 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

More Related