Detecting Introgressive Hybridization between Segregated Hatchery and

Wild PopulationsPart II

Kenneth I. Warheit

2014 Pacific Coast Steelhead Management MeetingSkamania 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

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Med

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Simulation

Pop 1 "Hatchery"Pop 2 "Wild"F1 Hybrid

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)

FST = 0.06

FST = 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

BasinWild Hatchery

OU DIP N EWH ESH

Green 4 1 148 30 42

Snohomish 10 5 333 35 35

Stillaguamish 5 2 224 0 0

Skagit 8 3 321 97 na

Samish 1 1 73 na na

Nooksack 5 2 219 40 na

1318 202 77 1597

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 ParametersLocus mutation rate

4Nom = 20

Population growthStable

PopulationsThree

# samples from each pop500

Phylogenetic relationshipHierarchical

Divergent DatesA = 0.24No generations (Whidbey)B = 0.12No generations (Whidbey)

A = 0.16No generations (Nooksack)B = 0.13No generations (Nooksack)

Pop 1(“PS Wild”)

Pop 2(“Early Winter

Hatchery”)

Pop 3(“Early Summer

Hatchery”)

A

B

a1

a2 Pop 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

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alue

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acr

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)

Simulation

Pop 1 "Hatchery"Pop 2 "Wild"F1 Hybrid

Error for k = 2 (Part I)

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Wild Early Winter Hatchery (EWH)

Early Summer Hatchery (ESH)

Hybrid: EWH-Wild Hybrid: ESH-Wild Hybrid: 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 Mod

el

Early Winter Hatchery (EWH) 655 113 4 1 5 66 844 937 0.22Hybrid: EWH - Wild 216 625 58 1 229 33 1162 920 0.46Hybrid: ESH - Wild 0 11 514 24 26 37 612 782 0.16Early Summer Hatchery (ESH) 0 0 87 839 0 159 1085 963 0.23Wild 5 153 79 0 693 1 931 956 0.26Hybrid: EWH - ESH 61 18 40 98 3 507 727 803 0.30NoCall 63 80 218 37 44 197 639 naTotal Source 1000 1000 1000 1000 1000 1000 6000 0.29

NoCall Rate 0.06 0.08 0.22 0.04 0.04 0.20 0.11 Soure Error Rate Total 0.35 0.38 0.49 0.16 0.31 0.49 0.36Soure Error Rate Assigned Only 0.30 0.32 0.34 0.13 0.28 0.37 0.29

Error | Assignment

Correcting Structure assignments using estimated error rates from

modeled populations

20 12

1( )2

20 1 2

1, , | ,

(2 )

iY X

i

Y X e

L

b0 ,b1 , s2 = parameters from resampling error matrix Y = empirical UNCORRECTED estimateXi = estimated Source or CORRECTED proportions

i= 0 to 1.0 at 0.001 intervals

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Estimated Source Proportion

L (b

0,b1,s

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

BasinIntrogression

EWH ESH

Green Average OU 0.12 0.00Green River Winter-Run 0.11 0.00

Snohomish

Average OU 0.08 0.22North Fork Skykomish Summer-Run 0.00 0.55Tolt River Summer-Run 0.00 0.48Snoqualmie River Winter-Run 0.28 0.00Snohomish / Skykomish R Winter-Run 0.00 0.00Pilchuck R Winter-Run 0.00 0.00

StillyAverage OU 0.00 0.09Canyon Creek Summer-Run 0.00 0.00Deer Creek Summer-Run 0.00 0.02

Skagit

Average OU 0.02 0.02Mainstem Skagit R Summer- and Winter-Run 0.00 0.00Sauk R Summer- and Winter-Run 0.00 0.00Nookachamps Creek Winter-Run 0.00 0.00

Samish 0.17 0.00

Nooksack

Average OU 0.02 0.03Nooksack R Winter-Run 0.00 0.02South Fork Nooksack R Summer-Run 0.00 0.00

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Off-station Releases Off-station Releases

Off-station Releases (2-year offset) /Wild Escapement

Off-station Releases (2-year offset) /Wild Escapement

Intr

ogre

ssio

nAveraged across all Operational Units Averaged across all DIPs – all samples

r2 = 0.81r2 = 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