Quantifying Genetic Diversity Steelhead Stocks

Eric Parkinson, Art Tautz, Bob Hooton

BC Min. Water, Land & Air Protection

Photo: E. Keeley

~70 spp.

B.C.950,000 km2

Tennessee110,000 km2

Geographic area and the number of native species

of Freshwater Fish

~250spp.

Why care about genetic diversity:BC has very few species but lots of

Intraspecific diversity

Post-Glacial Dispersal RoutesBering Refuge

Queen Charlotte Refuge

Columbia RefugeCoastal Refuge

Missouri Refuge

Edge of Ice Sheet

Why so few species?

Geoclimatic diversity results in local adaption

Ecozones of BC

Why so much intraspecific diversity?

Fish Species at Risk in B.C.Three Directions

1. Systematic assessment of all species

2. Focal studies on specific species that are judged to be most at risk

3. Identify populations representing rare or endangered ecotypes within each species

1:50,000 Lakes and Streams (i.e. Lakes >1 ha)

Digital BC Watershed Atlas

Linked to info on: Stream length, size, gradient, flow, lake influence, species records, land use, stocking

records, terrain maps, geology etc. for 20,000 3rd order & greater watersheds

Steelhead Distribution in BC

Out of RangeRainbow TroutSteelhead

Steelhead Stock Structure

The smallest independent unit– stock = VSP?– Genetically isolated– Large enough to be viable

Genetic Groups of Stocks share:– Major Phylogenetic Associations = ESU? – Adaptation to a common environment = Strata?

Management Groups have similar: – Exploitation rates, hatchery influence, management goals – Can cut across genetic groups

Steelhead Stock Structure

The smallest independent unit– stock = VSP?– Genetically isolated– Large enough to be viable

Genetic Groups of Stocks share:– Major Phylogenetic Associations = ESU? – Adaptation to a common environment = Strata?

Management Groups have similar: – Exploitation rates, hatchery influence, management goals – Can cut across genetic groups

Steelhead Stock Structure

The smallest independent unit– stock = VSP?– Genetically isolated– Large enough to be viable

Genetic Groups of Stocks share:– Major Phylogenetic Associations = ESU? – Adaptation to a common environment = Strata?

Management Groups have similar: – Exploitation rates, hatchery influence, management goals – Can cut across genetic groups

Chehalis R.Weaver Cr.

Examples of adaptive and molecular differences among Steelhead in adjacent streamsRule: Every watershed that empties into either

the ocean or a large river contains a stock

650

700

750

800

Oyster River Quinsam River

Len

gth

at M

atu

rity

(mm

)

LDH and MDH Allozyme Frequencies

Stock Structure is quantified using data on genetic and phenotypic differences

Exclude Very Small Watersheds“Viable Salmonid Population”

Use various measures of size– Stream order and magnitude– Watershed area– Length of anadromous stream

Goal is a Viable Population– Run size > 20– 5 yr generation gives > 100

– Ne > 30?

Defining Steelhead Population Structure• Size, location, and drainage links come from

the Watershed Atlas• Find all independent stocks• Eliminate very small streams• Review by Regional Biologists

~ 630 viable steelhead stocks

in~ 580 BC streams

Most steelhead stocks are in small watersheds

Steelhead Stock Structure

The smallest independent unit– stock = VSP?– Genetically isolated– Large enough to be viable

Genetic Groups of Stocks share:– Major Phylogenetic Associations = ESU? – Adaptation to a common environment = Strata?

Management Groups have similar: – Exploitation rates, hatchery influence, management goals – Can cut across genetic groups

Major Phylogenetic Lineages

Species

Breeding isolation

Recent, incomplete Ancient, complete

Sel

ecti

ve F

orc

es

Weak

StrongDisruptive

StrongConvergent

Populations

Diverge into different ecotypes

Maintains similar ecotypes

Cryptic species

Steelhead Phylogenetic Groups:

Defined using patterns of molecular genetic

variation

Queen Charlotte Glacial Refuge

South Coast Refuge

South Interior Refuge

Major Phylogenetic Lineages

Species

Breeding isolation

Recent, incomplete Ancient, complete

Sel

ecti

ve F

orc

es

Weak

StrongDisruptive

StrongConvergent

Populations

Diverge into different ecotypes

Maintainssimilar ecotypes

Cryptic species

Database of Steelhead Stocks

Watershed Code

DFO Escapement

Database

Hatchery Records

FISS Records

Land Form Databases

Land Use Databases

The Watershed Code links the Stock Database to a variety of useful info

Low Lake Influence Land (%Area)Freshwater (%Area)

Large Watersheds Stream Magnitude (max)Watershed AreaStream Order (max)

Cold, High Relief, Temperature (min)High Elevation Elevation (std.dev)

Ice (%area)Elevation (max)Elevation (mean)Elev >800m (%Area) Alpine (%area)Temperature (mean)Elev <300m (%Area)

Watershed Type Variable

High elevation Minimum ElevationInterior Migration DistanceDry Water Yield

Moderate Gradient 16-30%Gradient Gradient 9-15%

>70% gradient51-60% gradient

Low Gradient, Gradient 31-50Low Relief Gradient 3-8%

Elev 300-800mWetlands (%Area)

Cold, Temperature (max)High Latitude Latitude

Land Form Data can Characterize Watersheds Using Principle Components Analysis

e.g. of a Principle Component

Interior, Dry Coastal, Wet

Habitat differences can be used as a

proxy for adaptive differentiation

Interior, Dry Coastal, Wet

Low relief, Warm Cold High Relief

rare

common

Which stocks have the most unusual habitat?-Interior Watersheds-Low relief coastal-Lake Influence coastal

6

15

10

12

16

17

8

13

3

2

5

1

9

11

14

7

4

15

16 17

13

14

1012

9

11

6

8

7

54

21

3

Genetic Distance from Molecular Markers

2 ESUs

17 Stocks

4 Ecotypes(strata?)

Geographic Layout

Large Lake Piscivores

Coastal Summer-Run Steelhead

Interior Fall-Run Steelhead

Phylogenetic Groups

Interior

South Coast

North Coast

Ecotypes cut across Phlylogenetic Groups

Ecotypes

Phylogenetic vs. Adaptive Structure

Contrast with US Pacific NW

Only 3 ESUs– In a Province the size of

Wash, Ore, Calif, Idaho combined

Lots of very small coastal stocks– Rocky, heavily-indented

coastline

Reason: BC was almost entirely glaciated

Steelhead Stock Structure

The smallest independent unit– stock = VSP?– Genetically isolated– Large enough to be viable

Genetic Groups of Stocks share:– Major Phylogenetic Associations = ESU? – Adaptation to a common environment = Strata?

Management Groups have similar: – Exploitation rates, hatchery influence, management goals – Can cut across genetic groups

Ecotypic Grouping in Steelhead - Run Timing

June-JulySept-OctDec-April

Peak Time of River Entry

Hatchery History of Steelhead Stocks

Currently StockedStocked Prior to 1993Never Stocked

HatcheryHistory

Which stocks and ecotypes have not had any hatchery influence?

June-JulySept-OctDec-April

Peak Time of River Entry

Currently StockedPrior to 1993

HatcheryHistory

Land use data can be used to identify habitat concerns

0.00

0.20

0.40

0.60

0.80

1.00

< 5% 5-10% 10-20% >20%

Percent of Area Logged

Pro

po

rtio

n o

f W

ater

shed

s

BC

VanIs

BC

VanIs

} < 300m Elevation

} >50% Gradient

Management Units can also be groups of stocks that share common management goals, issues and policies

Steelhead Stock Structure

Define the Distribution Define Stock Structure (VSP?)

– Use associations between geographical isolation and molecular genetic variation

Define Genetic Groups– Major Phylogenetic groups share a

common ancestry (ESU?)– Ecotypes share common environments

(Strata?) Define Management groups

Conservation StatusHealthyConservation ConcernExtreme Conservation Concern

NeutralConvergent Disruptive

Selection gradient

Ge

net

ic is

ola

tion

Re

cen

t, in

com

ple

teA

nci

ent

, co

mpl

ete

Adaptive differentiation

Diff

ere

ntia

tion

at n

eut

ral l

oci

Size of Unit

NAME COQUITLAM PITT STOCK_NO_(WShedCode) 100024500 100026700ORDER 4 6MAGNITUDE 81 525CONNECTS_T 100 100CONNECTS_AT (km) 34 37Number of 3rd Order streams 4 14Watershed Area (km2) 270 1355MGMTAGG Nfraser NfraserSTATUS ExtremeCC ExtremeCCX Albers 1233606 1243044Y Albers 488653 507775Run Timing Winter WinterHatchery Classification Wild WildLast Date Stocked Jun-96Max Size (g) 192Max Number 500000Max Size since 1993 (g) 192Max No since 1993 9211Monitored? No NoAnadromous Length (km) 17.78 84.4Distance from Ocean (km) 34 37ObStructions Yes YesHarvest Analysis Observation Yes YesSteelhead Observation Yes YesSalmon Spp Observation Yes YesCoho Observation Yes YesRainbow Observation Yes Yes

Other useful info

Fish Presence/AbsenceInformation is used t

11111

Steelhead Sportfish RecordSteelhead Inventory Record

Salmon Inventory RecordCoho Inventory Record

Rainbow Trout Record

110

1110110

110

111

1110

11111

11110

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11111

110

101

11111

111

110

110110

10111

111

110

10111

110

11111

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1111111111

1111111111

100

01100

0

0

1111110

10110

11111

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110

1100

110110

1110 0

10110

11111

P<0.01

P<0.01

SamplesWithin

Streams

AdjacentStreams

<20 km <200 km Regions

Geographic Range

Inde

x of

Var

ianc

e in

Allo

zym

e Fr

eque

ncy

LDH

SOD

Allozyme Frequencies in Steelhead

vary among adjacent streams

Rainbow Trout Distribution in BC

Out of RangeRainbow Trout

Rules for defining stocks

Find all streams that enter the Ocean Directly

Find “Large” river tributaries Apply size constraints based on

measures of watershed size