Quantifying Genetic Diversity Steelhead Stocks
Eric Parkinson, Art Tautz, Bob Hooton
BC Min. Water, Land & Air Protection
Photo: E. Keeley
Why care about genetic diversity:
BC has very few species but lots of
Intraspecific diversity
Geographic area and the
number of native species
of Freshwater Fish
~70 spp.
B.C.
950,000 km2
~250
spp.
Tennessee
110,000 km2
Why so few species?
Bering Refuge
Queen Charlotte
Refuge
Post-Glacial Dispersal Routes
Edge of
Ice Sheet
Missouri
Refuge
Coastal Refuge
Columbia Refuge
Why so much intraspecific diversity?
Geoclimatic diversity
results in local adaption
Ecozones of BC
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
Digital BC Watershed Atlas
1:50,000 Lakes and Streams
(i.e. Lakes >1 ha)
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 Range
Rainbow Trout
Steelhead
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
Stock Structure is quantified using data on
genetic and phenotypic differences
Length at Maturity (mm)
800
Weaver Cr.
Chehalis R.
750
700
650
Oyster River
Quinsam River
LDH and MDH Allozyme Frequencies
Examples of adaptive and molecular differences among
Steelhead in adjacent streams
Rule: Every watershed that empties into either
the ocean or a large river contains a stock
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
Selective Forces
Strong
Disruptive
Weak
Strong
Convergent
Diverge into
different ecotypes
Populations
Maintains
similar ecotypes
Recent, incomplete
Species
Cryptic species
Major Phylogenetic
Lineages
Ancient, complete
Breeding isolation
Steelhead Phylogenetic
Groups:
Defined using patterns
of molecular genetic
variation
Queen
Charlotte
Glacial
Refuge
South Coast
Refuge
South Interior
Refuge
Selective Forces
Strong
Disruptive
Weak
Strong
Convergent
Diverge into
different ecotypes
Populations
Maintains
similar ecotypes
Recent, incomplete
Species
Cryptic species
Major Phylogenetic
Lineages
Ancient, complete
Breeding isolation
Database of
Steelhead Stocks
The Watershed Code links
the Stock Database to a
variety of useful info
Land Use
Databases
Watershed Code
DFO
Escapement
Database
Hatchery
Records
Land Form
Databases
FISS
Records
Land Form Data can Characterize Watersheds
Using Principle Components Analysis
Watershed Type
High elevation
Interior
Dry
Moderate
Gradient
Variable
Minimum Elevation
Migration Distance
Water Yield
Gradient 16-30%
Gradient 9-15%
>70% gradient
51-60% gradient
Low Gradient,
Low Relief
Gradient 31-50
Gradient 3-8%
Elev 300-800m
Wetlands (%Area)
Cold,
High Latitude
Temperature (max)
Latitude
Low Lake Influence
Land (%Area)
Freshwater (%Area)
Large Watersheds Stream Magnitude (max)
Watershed Area
Stream 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)
e.g. of a Principle Component
Interior, Dry
Coastal, Wet
Habitat differences can be used as a
proxy for adaptive differentiation
Low relief, Warm
Cold High Relief
Interior, Dry
Coastal, Wet
Which stocks have the
most unusual habitat?
-Interior Watersheds
-Low relief coastal
-Lake Influence coastal
rare
common
17 Stocks
4 Ecotypes
(strata?)
1
2
1
2
3
3
4
4
5
5
6
7
6
7
8
8
9
9
10
10
2 ESUs
11
12
11
13
14
15
16
12
13
14
15
16
17
17
Genetic Distance from Molecular Markers
Geographic Layout
Phylogenetic vs. Adaptive Structure
Ecotypes cut across Phlylogenetic Groups
Phylogenetic Groups
Interior
North Coast
South Coast
Ecotypes
Large Lake Piscivores
Interior Fall-Run Steelhead
Coastal Summer-Run Steelhead
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
Peak Time of
River Entry
June-July
Sept-Oct
Dec-April
Ecotypic Grouping in Steelhead - Run Timing
Hatchery
History
Currently Stocked
Stocked Prior to 1993
Never Stocked
Hatchery History of Steelhead Stocks
Peak Time of
River Entry
June-July
Sept-Oct
Dec-April
Hatchery
History
Currently Stocked
Prior to 1993
Which stocks and ecotypes have not had any
hatchery influence?
BC
VanIs
BC
VanIs
1.00
Proportion of Watersheds
Land use data can
be used to identify
habitat concerns
0.80
} < 300m Elevation
} >50% Gradient
0.60
0.40
0.20
0.00
< 5%
5-10%
10-20%
Percent of Area Logged
>20%
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 Status
Healthy
Conservation Concern
Extreme Conservation Concern
Genetic isolation
Ancient,
complete
Differentiation at neutral loci
Recent,
incomplete
Adaptive differentiation
Convergent
Neutral
Selection gradient
Disruptive
Other useful info
NAME
COQUITLAM
PITT
STOCK_NO_(WShedCode)
100024500
100026700
ORDER
MAGNITUDE
CONNECTS_T
CONNECTS_AT (km)
Number of 3rd Order streams
Watershed Area (km2)
MGMTAGG
STATUS
X Albers
Y Albers
Run Timing
Hatchery Classification
Last Date Stocked
Max Size (g)
Max Number
Max Size since 1993 (g)
Max No since 1993
Monitored?
Anadromous Length (km)
Distance from Ocean (km)
ObStructions
Harvest Analysis Observation
Steelhead Observation
Salmon Spp Observation
Coho Observation
Rainbow Observation
4
81
100
34
4
270
Nfraser
ExtremeCC
1233606
488653
Winter
Wild
Jun-96
192
500000
192
9211
No
17.78
34
Yes
Yes
Yes
Yes
Yes
Yes
6
525
100
37
14
1355
Nfraser
ExtremeCC
1243044
507775
Winter
Wild
No
84.4
37
Yes
Yes
Yes
Yes
Yes
Yes
110
110
110
110
11111
0
11111
110
110
11110
1110
1110
110
0
11111
111 11111
11111
110
1110
110 110
111 101
110
10111 10110
111
10111
11111
11111
110
1111
0
10110
11111
0
11111
1
100
11111
0
11111
100
11111
11111
11111
11111
110
110
11111
Rainbow Trout Record
Coho Inventory Record
Salmon Inventory Record
Steelhead Inventory Record
Steelhead Sportfish Record
Fish Presence/Absence
Information is used t
Allozyme Frequencies in Steelhead
Index of Variance in Allozyme
Frequency
vary among adjacent streams
P<0.01
LDH
SOD
P<0.01
Samples
Within
Streams
Adjacent
Streams
<20 km
<200 km
Geographic Range
Regions
Rainbow Trout Distribution in BC
Out of Range
Rainbow 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
