Appendix B
Upper Columbia Salmon Recovery Plan
Description of spatial structure and diversity of spring Chinook and steelhead populations within the
Upper Columbia Basin
Summary and scoring system for spatial structure and diversity metrics, ICTRT draft table, April 27, 2005. Scores as follows: Very low = 2, Low = 1,
Moderate = 0, High = -1
Assessed Risk
Goal
A. Allowing
natural rates
and levels of
spatiallymediated
processes.
Mechanism
1. Maintain natural
distribution of
spawning
aggregates.
B. Maintaining 1. Maintain natural
natural levels of patterns of
variation.
phenotypic and
genotypic
expression.
Factor
Metrics
Metric Factor
Mechanism
Goal
Population
R-level R-level
R-level
R-level
R-level
a. Number and
spatial
arrangement of
spawning areas.
A.1.a
Number of MSAs, distribution
of MSAs, and quantity of
habitat outside MSAs.
A.1.a
A.1.a
b. Spatial extent
or range of
population
A.1.b
Proportion of historical range
A.1.b
occupied and
presence/absence of spawners
in MSAs
A.1.b
c. Increase or
A.1.c.
decrease gaps or
continuities
between
spawning
aggregates.
Change in gap distances and
spawner distribution.
A.1.c
A.1.c
a. Major life
B.1.a
history strategies.
Distribution of major life history B.1.a
expression within a population
B.1.a
b. Phenotypic
variation.
Reduction in variability of traits, B.1.b
shift in mean value of trait, loss
of traits.
B.1.b
Upper Columbia Salmon Recovery Plan
B.1.b
Mean of A.1.a., Mean of A.1.a., Lowest score
A.1.b, A.1.c.
A.1.b, A.1.c.
(highest risk) of
the two goals
Lowest score
(highest risk)
B1 Mech.
Score or Mean
of B.1, B.2, B.3,
and B.4,
whichever is
lower (higher
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Assessed Risk
Goal
Mechanism
Factor
c. Genetic
variation.
2. Maintain natural a. Spawner
patterns of gene
composition.
flow.
Metrics
B.1.c
Genetic analysis
encompassing within and
between population variation
Metric Factor
Mechanism
Goal
Population
R-level R-level
R-level
R-level
R-level
B.1.c
risk)
B.1.c
B.2.a(1) Proportion of natural spawners B.2.a(1) Lowest
that are hatchery fish, life
score
history similarity, proportion of
(highest
broodstock that is of natural
risk)
origin, degree of selectivity in
broodstock collection (w/in
pop)
Lowest score
(highest risk)
B.2.a(2) Proportion of natural spawners B.2.a(2)
that are hatchery strays (out of
pop., but within ESU)
B.2.a(3) Proportion of natural spawners B.2.a(3)
that are hatchery strays (out of
ESU)
3. Maintain
occupancy in a
natural variety of
available habitat
types.
a. Distribution of B.3.a
population across
habitat types.
4. Maintain
a. Change in
B.4.a
integrity of natural natural processes
systems.
or impacts.
Upper Columbia Salmon Recovery Plan
Habitat diversity index and
occupancy.
B.3.a
B.3.a
B.3.a
Cumulative selectivity score
across all relevant impacts
B.4.a
B.4.a
B.4.a
2
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Population: Wenatchee Spring Chinook
VSP Parameters: Spatial Structure and Diversity
Metric A.1.a (Number of MSAs, distribution of MSAs, and quantity of habitat outside MSAs.)
The Wenatchee spring Chinook population has four MSA’s (Chiwawa, Nason, White, and Little
Wenatchee) separated by 4 separate confluences so it is at very low risk. The intrinsic potential
analysis also identified four mSA’s (Icicle, Chumstick, Peshastin, and Mission) that are all below
Tumwater canyon.
Metric A.1.b (Proportion of historical range occupied and presence/absence of spawners in
MSAs)
The range of spawning distribution has been reduced in the mSA’s below Tumwater Canyon, but
this represents less than 25% of the habitat within the historical distribution based on the intrinsic
potential analysis, which confirmed that most of the available habitat was in the four MSA’s
above Tumwater Canyon. Therefore, the population is at low risk for this metric.
Metric A.1.c (Change in gap distances and spawner distribution.)
There has been no increase or decrease in gaps between MSA’s for the Wenatchee spring
Chinook population, placing it at very low risk. However, if this criteria was intended to cover
increases in gaps between mSA’s, then the population would be at high risk, because of gaps
greater than 5 km between the four mSA’s. Therefore, taking into account both mSA’s and
MSA’s we conclude that the population is at moderate risk.
Metric B.1.a (Distribution of major life history expression within a population)
The Wenatchee spring Chinook population is very low risk, because no major life history
strategies have been lost.
Metric B.1.b (Reduction in variability of traits, shift in mean value of trait, loss of traits.)
We do not have data available for this metric. Even if we determined that there was a change to
one or more traits we do not know what the exact baseline is because changes likely occurred
before there was biological monitoring. Therefore, we will assume that there has been some
change and increase in variance for 2 or more traits placing the population at moderate risk.
Metric B.1.c (Genetic analysis encompassing within and between population variation)
The Wenatchee spring Chinook population was determined to be at moderate risk for genetic
variation based on evidence of divergence in one of the MSA’s (White River) (Ford et al. 2001).
Metric B.2.a.1 (Proportion of natural spawners that are hatchery fish, life history similarity,
proportion of broodstock that is of natural origin, degree of selectivity in broodstock collection
(w/in pop).
The Chiwawa River integrated program strays to other non-target MSA’s and commonly makes
up greater than 10 % of the spawner composition in Nason Creek and the White and Little
Wenatchee Rivers, based on comprehensive data collected in 2001 and 2002 (Tonseth 2003;
Tonseth 2004) and because the program has been in existence for three generations (adult returns
Upper Columbia Salmon Recovery Plan
3
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
since 1993) the population at high risk. Spawner composition data was not reliable before 2000
based on small sample sizes and low sampling probability (A. Murdoch, personal
communication, WDFW) so it is not possible to evaluate this metric over a longer time interval.
Metric B.2.a.2 (Proportion of natural spawners that are hatchery strays (out of Pop, but within
the ESU)
Out of population (but within ESU) origin strays comprised 0% and 1.8% of the naturally
spawning population in 2001 and 2002, respectively. Therefore, the population is at very low
risk with respect to this metric.
Metric B.2.a.3 (Proportion of natural spawners that are hatchery strays (out of ESU))
Although Pastor (2004) determined that stray rates were < 1% for the LNFH, he included fish
that were “in route” to the hatchery and he did not evaluate spawner composition on the
spawning grounds. The Wenatchee spring Chinook population is at high risk with respect to this
metric due to the presence of non-local (outside the ESU origin) stocks on the spawning grounds,
which include both LNFH and other stocks from hatcheries outside the Upper Columbia ESU. In
2001, non-local stocks were 11% of the overall spawner composition (in areas other than Icicle
Creek) and 23 % of the wild spawner population (Tonseth 2003). In 2002 non-local stocks were
8 % of the overall spawner composition (in areas other than Icicle Creek and Peshastin Creek)
and 15 % of the wild spawner population. Icicle Creek and Peshastin Creek were not included in
these estimates because they are directly planted with juvenile and adult non-local origin fish
(Carson stock). If we were to include these two mSA’s in the spawner composition analysis the
overall spawner composition in the Wenatchee River Basin was comprised on 26 % and 21 %
non-local stocks. We evaluated this metric 3 different ways because we were unsure of exactly
which proportion to use in the risk assessment. Its possible that 2 years of data is not sufficient to
evaluate this metric and our risk assessment could change with the inclusion of survey results
from 2003 and 2004. It has been determined that the mark rate for hatchery fish was insufficient
to determine spawner composition prior to 2000 (Andrew Murdoch, personal communication).
Metric B.3.a (Habitat diversity index and occupancy.)
We do not have the complete habitat diversity index analysis at this time, so we cannot evaluate
the percent change from historic to current. However, the loss of spawning spring Chinook from
the lower mSA’s represents a truncation in the range of elevation and the loss of one ecoregion.
This resulted in less than a 20% change in the diversity metric, resulting in a rating of moderate
risk.
Metric B.4.a (Cumulative selectivity score across all relevant impacts)
No empirical data exists for this metric. We determined that alterations to the hydrograph,
predation, size selective harvest, and size selective migration barriers all have a selectivity score
of 1, resulting in a cumulative score for the population of 4, which would be a score of moderate
risk for a large complex (type B) population using the scoring system provided by the ICTRT as
of March 22, 2005.
Conclusions (Wenatchee spring Chinook)
Upper Columbia Salmon Recovery Plan
4
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
The Wenatchee spring Chinook population was determined to be at low risk for goal A (allowing
natural rates and levels of spatially mediated processes) but high risk for goal B (Maintaining
natural levels of variation) resulting in an overall high risk rating. There were three metrics that
were contributing to the population being at high risk. First, Chiwawa River hatchery fish (local
origin stock) represent more than 10 % of the spawner composition in the non-target MSA’s and
the program has been in place for over 3 generations. Second, the high proportion (8-26%) of
LNFH fish (out-of-ESU stock) on the spawning grounds. Third, the loss of all minor spawning
areas below Tumwater Canyon (Icicle, Chumstick, Peshastin, Mission) lead to a high risk rating
due to a reduction in the range of spawning elevations and the loss of an ecoregion. With the
current scoring system provided by the ICTRT, it would be possible to achieve an overall rating
of moderate risk if both of the hatchery related problems were fixed or if one of the low elevation
mSA’s (i.e. Peshastin Creek) were occupied with natural origin spring Chinook.
There were several metrics where data was inadequate or not readily accessible to complete this
assessment with enough certainty to be confident that we came to the right conclusion. However,
only one of them had the potential to change the overall score of the population. The genetic
analysis needs to be presented in a manor that is consistent with rating this metric. We concluded
that there was some divergence in the population based on the genetic analysis from the White
River and that was enough to use a risk rating of moderate. However, there is no guidance as to
how to measure the level of divergence within each MSA and what the benchmark is to move a
population from one risk level to another.
Additionally, we assumed that minor spawning areas (mSA) were not part of the distribution gap
metric (A.1.c). If they had been then the score for that metric would have changed from
moderate to high because there is currently no natural origin spring Chinook using any of the
tributaries below Tumwater Canyon. However, the mean score for that mechanism (maintain
natural distribution of spawning aggregates) would only have dropped from 1 to 2/3, which
would not have changed the low risk rating regarding this metric.
Upper Columbia Salmon Recovery Plan
5
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Table X1 Spatial Structure and diversity scoring system summary for the Wenatchee River spring Chinook population
Assessed Risk
Metric Factor Mechanism
Goal
A. Allowing
natural rates and
levels of spatiallymediated
processes.
B. Maintaining
natural levels of
variation.
Mechanism
1. Maintain natural
distribution of
spawning
aggregates.
1. Maintain natural
patterns of
phenotypic and
genotypic
expression.
Factor
Metrics
a. Number and
A.1.a
spatial arangement
of spawning areas.
Number of MSAs, distribution of
VL (2)
MSAs, and quantity of habitat outside
MSAs.
VL (2)
b. Spatial extent or A.1.b
range of population
Proportion of historical range
occupied and presence/absence of
spawners in MSAs
L (1)
L (1)
c. Increase or
decrease gaps or
continuities
between spawning
aggregates.
A.1.c.
Change in gap distances and
spawner distribution.
M (0)
M (0)
a. Major life history
strategies.
B.1.a
Distribution of major life history
expression within a population
VL (2)
VL (2)
b. Phenotypic
variation.
B.1.b
Reduction in variability of traits, shift
in mean value of trait, loss of traits.
M (0)
M (0)
Genetic analysis encompassing
within and between population
variation
M (0)
M (0)
B.2.a(1) Proportion of natural spawners that
are hatchery fish, life history
similarity, proportion of broodstock
that is of natural origin, degree of
selectivity in broodstock collection
(w/in pop)
H (-1)
H (-1)
B.2.a(2) Proportion of natural spawners that
are hatchery strays (out of pop., but
within ESU)
VL (2)
c. Genetic variation. B.1.c
2. Maintain natural
patterns of gene
flow.
R-level R-level
a. Spawner
composition.
Upper Columbia Salmon Recovery Plan
6
R-level
Goal Population
R-level
Low RIsk
(mean = 1)
Low
Risk
M (0)
High
Risk
R-level
High Risk
H (-1)
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Assessed Risk
Metric Factor Mechanism
Goal
Mechanism
Factor
Metrics
R-level R-level
B.2.a(3) Proportion of natural spawners that
are hatchery strays (out of ESU)
H (-1)
R-level
3. Maintain
occupancy in a
natural variety of
available habitat
types.
a. Distribution of
population across
habitat types.
B.3.a
Habitat diversity index and
occupancy.
H (-1)
H (-1)
H (-1)
4.Maintain integrity
of natural systems.
a. Change in
natural processes
or impacts.
B.4.a
Cumulative selectivity score across
all relevant impacts
M (0)
M (0)
M (0)
Goal Population
R-level
R-level
Scores as follows: Very low = 2, Low = 1, Moderate = 0, High = -1
Upper Columbia Salmon Recovery Plan
7
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Population: Wenatchee Steelhead
VSP Parameters: Spatial Structure and Diversity
Metric A.1.a (Number of MSAs, distribution of MSAs, and quantity of habitat outside MSAs.)
The Wenatchee steelhead population has five intrinsic potential MSA’s (Chiwawa River, Nason
Creek , Icicle Creek, Chumstick Creek, and Peshastin Creek) and 13 mSA’s, these include the
White and Little Wenatchee Rivers, Mission Creek, as well as small tributaries to the Columbia
downstream from the Wenatchee confluence such as Squilchuck, Tarpiscan, Trinidad,
Quilomene, and other Creeks (see ICTRT MSA map). For the MSA’s, only Chumstick Creek is
blocked by artificial barriers because the LNFH recently began providing passage for returning
adult steelhead to access upper Icicle Creek. Although the level of occupancy is unknown in
many of the mSA’s and there are some artificial barriers that hider distribution, we are relatively
certain that the mSA’s combine for more than 75 % of the capacity of an MSA so the population
is at very low risk for this metric.
Metric A.1.b (Proportion of historical range occupied and presence/absence of spawners in
MSAs)
Efforts to monitor the distribution and abundance of spawning steelhead have been expanded in
recent years (2001-2004), but we still do not have comprehensive, long-term data sets to rate this
metric for the entire Wenatchee watershed. Since levels of occupancy have not been defined, we
assume that the presence of redds and “suitable but unoccupied” habitat are adequate for rating
this metric. Steelhead have been observed spawning in Chiwawa, Beaver, Nason, Wenatchee
mainstem, lower Icicle, Peshastin, and Mission Creek drainages (Tonseth and Viola 2003;
Murdoch et al. 2004; Tonseth 2004; USFS unpublished data). Additional surveys have been
conducted in the Little Wenatchee and White Rivers and very few to zero redds have been
observed, despite suitable habitat. Also, suitable habitat exists in Chiwaukum Creek, Colockum
Creek, Tarpiscan Creek, Quilomene/Brushy Creeks, Willow Springs (Trinidad Creek), and
Skookumchuck Creek. Significant habitat degradation and migration barriers exist in Skinney,
Chumstick, Mission, Squilchuck, Stemilt, and Johnson Creeks. Although we do not have a
quantitative analysis of the percent of historical distribution that is currently occupied, we
conclude from the above information that the Wenatchee steelhead population is at moderate
risk for this metric based on the loss of 1 of 4 MSA’s and degraded habitat or barriers in
approximately half of the mSA’s.
Metric A.1.c (Change in gap distances and spawner distribution.)
Based on the loss of Chumstick Creek and the very low level of occupancy in the White and
Little Wenatchee Rivers we conclude that the population is at moderate risk.
Metric B.1.a (Distribution of major life history expression within a population)
The Wenatchee steelhead population is very low risk, because no major life history strategies
have been lost.
Metric B.1.b (Reduction in variability of traits, shift in mean value of trait, loss of traits.)
We do not have data available for this metric. Even if we determined that there was a change to
one or more traits we do not know what the exact baseline is because changes likely occurred
Upper Columbia Salmon Recovery Plan
8
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
before there was biological monitoring. Therefore, we will assume that there has been some
change and increase in variance for 2 or more traits placing the population at moderate risk.
Metric B.1.c (Genetic analysis encompassing within and between population variation)
We did not have an adequate data set to evaluate the genetic variation within the Wenatchee
steelhead population. Two previous genetic analyses have shown a degree of genetic variation
among the Upper Columbia steelhead samples, with inconclusive results regarding evidence of
geographic population structure (Chapman et al. 1994; Ford et al. 2001). Therefore, we will
assume that the Wenatchee population is at moderate risk for this metric until a more refined
analysis can be conducted to prove that a higher or lower risk rating is justified.
Metric B.2.a.1 (Proportion of natural spawners that are hatchery fish, life history similarity,
proportion of broodstock that is of natural origin, degree of selectivity in broodstock collection
(w/in pop).
We do not have estimates of spawner composition for the various MSA’s and mSA’s of the
Wenatchee steelhead population because carcasses cannot be obtained in sufficient numbers
from the spawning ground surveys. However, between 2001 and 2004 an average of 47% (range
30-69%) of the females passing Tumwater Dam were of wild origin (Tonseth 2004). The long
term integrated program in the Wenatchee Basin collects fish at Dryden Dam (lower mainstem)
and releases them at various locations throughout the upper basin, thereby mixing the progeny
from various MSA’s and not encouraging local adaptation within the population. Therefore, the
population is at high risk for this metric.
Metric B.2.a.2 (Proportion of natural spawners that are hatchery strays (out of population, but
within the ESU)
We have no data to evaluate the proportion of out of population hatchery strays on the spawning
grounds of the Wenatchee population. Therefore, we will use the default rating of moderate risk
for this metric.
Metric B.2.a.3 (Proportion of natural spawners that are hatchery strays (out of ESU)
We have no data to evaluate the proportion of out of ESU hatchery strays on the spawning
grounds of the Wenatchee population.
Therefore, we will use the default rating of moderate risk for this metric.
Metric B.3.a (Habitat diversity index and occupancy.)
We do not have the complete habitat diversity index analysis at this time, so we cannot evaluate
the percent change from historic to current. However, steelhead are known to inhabit the range of
elevations and ecoregions present in the Wenatchee basin, so we conclude the population is at
low risk for this metric.
Metric B.4.a (Cumulative selectivity score across all relevant impacts)
No empirical data exists for this metric. We determined that alterations to the hydrograph,
predation, size selective harvest, and size selective migration barriers all have a selectivity score
of 1, resulting in a cumulative score for the population of 4, which would be a score of moderate
Upper Columbia Salmon Recovery Plan
9
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
risk for a large complex (type B) population using the scoring system provided by the ICTRT as
of March 22, 2005.
Conclusions (Wenatchee steelhead)
The Wenatchee steelhead population was determined to be at low risk for goal A (allowing
natural rates and levels of spatially mediated processes) and moderate risk for goal B
(Maintaining natural levels of variation) resulting in an overall moderate risk rating. The only
metric that was rated at high risk was the proportion of natural spawners that were hatchery fish
(B.2.a.1), because the progeny of broodstock collected at Dryden Dam are not collected from and
released back into specific MSA’s. This high risk factor for integrated within population
hatchery fish was moderated at the mechanism level because we had no reason to suspect that
spawner composition would be above moderate risk levels for out-of-population or out-of-ESU
hatchery fish on the spawning grounds. We also did not have a genetics study that had
conclusive results that would help us determine the risk level associated with the observed
genotypic variation. If a comprehensive genetic analysis were applied to specific MSA’s and
compared to the genetic diversity criteria then the results of this risk assessment could change the
conclusion to high risk. We also recognize that this detailed genetic analysis will probably be
necessary in order to move the population into the low risk category.
Upper Columbia Salmon Recovery Plan
10
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Table X2 Spatial Structure and diversity scoring system summary for the Wenatchee River steelhead population
Assessed Risk
Metric Factor Mechanism
Goal
A. Allowing
natural rates and
levels of spatiallymediated
processes.
B. Maintaining
natural levels of
variation.
Mechanism
1. Maintain natural
distribution of
spawning
aggregates.
1. Maintain natural
patterns of
phenotypic and
genotypic
expression.
2. Maintain natural
patterns of gene
flow.
Factor
Metrics
R-level R-level
a. Number and
A.1.a
spatial arangement
of spawning areas.
Number of MSAs, distribution of
MSAs, and quantity of habitat
outside MSAs.
VL (2)
VL (2)
b. Spatial extent or A.1.b
range of population
Proportion of historical range
M (0)
occupied and presence/absence of
spawners in MSAs
M (0)
c. Increase or
A.1.c.
decrease gaps or
continuities
between spawning
aggregates.
Change in gap distances and
spawner distribution.
M (0)
M (0)
a. Major life history B.1.a
strategies.
Distribution of major life history
expression within a population
VL (2)
VL (2)
b. Phenotypic
variation.
B.1.b
Reduction in variability of traits, shift M(0)
in mean value of trait, loss of traits.
M(0)
c. Genetic
variation.
B.1.c
Genetic analysis encompassing
within and between population
variation
M (0)
M (0)
a. Spawner
composition.
B.2.a(1) Proportion of natural spawners that H (-1)
are hatchery fish, life history
similarity, proportion of broodstock
that is of natural origin, degree of
selectivity in broodstock collection
(w/in pop)
H (-1)
R-level
Goal
Population
R-level
R-level
Low Risk
(mean=2/3)
Low Risk
M (0)
Moderate
Risk
(mean = 0)
Moderate
Risk
H (-1)
B.2.a(2) Proportion of natural spawners that M (0)
are hatchery strays (out of pop., but
within ESU)
Upper Columbia Salmon Recovery Plan
11
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Assessed Risk
Metric Factor Mechanism
Goal
Mechanism
Factor
Metrics
R-level R-level
R-level
Goal
Population
R-level
R-level
B.2.a(3) Proportion of natural spawners that M (0)
are hatchery strays (out of ESU)
3. Maintain
occupancy in a
natural variety of
available habitat
types.
a. Distribution of
population across
habitat types.
B.3.a
Habitat diversity index and
occupancy.
L (1)
L (1)
L (1)
4.Maintain integrity
of natural systems.
a. Change in
natural processes
or impacts.
B.4.a
Cumulative selectivity score across M (0)
all relevant impacts
M (0)
M (0)
Scores as follows: Very low = 2, Low = 1, Moderate = 0, High = -1
Upper Columbia Salmon Recovery Plan
12
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Population: Entiat Spring Chinook
VSP Parameters: Spatial Structure and Diversity
Metric A.1.a (Number of MSAs, distribution of MSAs, and quantity of habitat outside MSAs.)
The Entiat only has one MSA for spring Chinook. The Mad River branch is part of the single
MSA, and its capacity is too low to offer any substantial risk moderation. There are no other
areas outside the single MSA so the population is at high risk for this metric, but that risk is
inherent of this small population. It was always high risk due to historically simple spatial
structure.
Metric A.1.b (Proportion of historical range occupied and presence/absence of spawners in
MSAs)
The range of spawning distribution has been reduced due to the loss of the lower Entiat
mainstem as spring Chinook spawning habitat. In recent years, no spring Chinook spawning has
been detected below river mile 13, presumably because of the degraded condition of the habitat
due to channelization and the high abundance of Summer/Fall Chinook in the lower Entiat
(Hamstreet and Carie 2004). This represents a reduction in range in the 25-50% range placing the
population at moderate risk for this metric.
Metric A.1.c (Change in gap distances and spawner distribution.)
There is only one MSA in the Entiat, and there is no artificial 5 km gaps within the MSA so the
risk level for this metric is moderate.
Metric B.1.a (Distribution of major life history expression within a population)
The Entiat spring Chinook population is low risk, because no major life history strategies have
been lost.
Metric B.1.b (Reduction in variability of traits, shift in mean value of trait, loss of traits.)
We do not have data available for this metric. Even if we determined that there was a change to
one or more traits we would not know what the exact baseline was because changes likely
occurred before there was biological monitoring. Therefore, we will assume that there has been
some change and increase in variance for 2 or more traits placing the population at moderate
risk.
Metric B.1.c (Genetic analysis encompassing within and between population variation)
The Entiat spring Chinook population is at high risk for genetic variation, based on recent
genetic analysis conducted by Ford et al. (2003) where it was stated:
The similarity of the Entiat River wild samples and the Entiat NFH samples
suggests that Entiat NFH salmon have successfully spawned and introgressed
into or replaced the natural Entiat River population.
However; In that study the sample size was small and it only covered a limited number of years
when spawning escapement of non-local origin hatchery fish was very high; therefore its
Upper Columbia Salmon Recovery Plan
13
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
possible that the Entiat spring Chinook population could have less risk if genetic samples were
evaluated over a longer time period with larger sample sizes.
Metric B.2.a.1 (Proportion of natural spawners that are hatchery fish, life history similarity,
proportion of broodstock that is of natural origin, degree of selectivity in broodstock collection
(w/in pop))
There is no supplementation program for spring Chinook in the Entiat basin. Therefore, this
metric is not applicable to the Entiat spring Chinook population.
Metric B.2.a.2 (Proportion of natural spawners that are hatchery strays (out of Pop, but within
the ESU)
In 2003, 4% of the spawning population was estimated to be from other hatchery populations
within the Upper Columbia ESU. The ICTRT has not yet developed a risk rating table for this
metric, however, we assumed that proportions between 2-5% were low risk, placing the Entiat at
low risk with respect to this metric.
Metric B.2.a.3 (Proportion of natural spawners that are hatchery strays (out of ESU))
The Entiat spring Chinook population is high risk due to the Entiat NFH propagating non-local
stock where the broodstock must volunteer to the hatchery and all others are allowed to migrate
past the hatchery and spawn with the natural population. In 2003, 22% of the carcass recoveries
were adipose absent and 60% of the adipose absent carcass recoveries were from stock origins
outside the ESU (Hamstreet and Carie 2003). When comparing the expanded spawner abundance
to the expanded carcass recoveries the proportion of out-of-ESU origin spawners was 15%.
Metric B.3.a (Habitat diversity index and occupancy.)
We do not have the complete habitat diversity index analysis at this time, so we cannot evaluate
the percent change from historic to current. However, the loss of spawning spring Chinook from
the lower 13 miles of the Entiat Basin represents a truncation in the range of elevation and the
loss of one ecoregion. This will probably result in a 20% or greater reduction in the diversity
metric, resulting in a rating of high risk.
Metric B.4.a (Cumulative selectivity score across all relevant impacts)
No empirical data exists for this metric. We determined that alterations to the hydrograph,
predation, size selective harvest, and size selective migration barriers all have a selectivity score
of 1, resulting in a cumulative score for the population of 4, which would be a score of high risk
for a small-simple (type A) population using the scoring system provided by the ICTRT as of
March 22, 2005. However, there needs to be some further explanation of why a series of
potential low selectivity mechanisms adds up to high risk. It seems that moderate risk is a more
appropriate score since we really do not know the level of selectivity or if the selective
mechanisms are synergistic or antagonistic.
Conclusions (Entiat Spring Chinook)
The Entiat spring Chinook population was determined to be at moderate risk for goal A
(allowing natural rates and levels of spatially mediated processes) but high risk for goal B
(Maintaining natural levels of variation) resulting in an overall high risk rating. The population
Upper Columbia Salmon Recovery Plan
14
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
could never achieve low risk for goal A due to its inherently simple spatial structure, based on
the criteria provided in the ICTRT guidance. However, it could achieve an overall moderate risk
rating by addressing several issues related to goal B. There were two metrics that were
contributing to the population being at high risk and both were related to the same cause, the
Entiat National Fish Hatchery propagating non-local origin spring Chinook and allowing them to
access the spawning grounds. This contributed directly to a high risk rating for metric B.2.a.2.
and indirectly to a high risk score for mechanism B.1.c. However, these conclusions were based
on limited data from one year of spawner composition surveys and a genetic analysis that only
included two years (Ford et al. 2003; Hamstreet and Carie 2004).
Upper Columbia Salmon Recovery Plan
15
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Table X3 Spatial Structure and diversity scoring system summary for the Entiat spring Chinook population
Assessed Risk
Metric Factor Mechanism
Goal
A. Allowing
natural rates and
levels of spatiallymediated
processes.
B. Maintaining
natural levels of
variation.
Mechanism
1. Maintain natural
distribution of
spawning
aggregates.
1. Maintain natural
patterns of
phenotypic and
genotypic
expression.
Factor
Metrics
a. Number and
A.1.a
spatial arrangement
of spawning areas.
Number of MSAs, distribution of
MSAs, and quantity of habitat
outside MSAs.
H (-1)
H (-1)
b. Spatial extent or A.1.b
range of population
Proportion of historical range
occupied and presence/absence of
spawners in MSAs
M (0)
M (0)
c. Increase or
decrease gaps or
continuities
between spawning
aggregates.
A.1.c.
Change in gap distances and
spawner distribution.
M (0)
M (0)
a. Major life history
strategies.
B.1.a
Distribution of major life history
expression within a population
L (1)
L (1)
b. Phenotypic
variation.
B.1.b
Reduction in variability of traits, shift
in mean value of trait, loss of traits.
M (0)
M (0)
Genetic analysis encompassing
within and between population
variation
H (-1)
H (-1)
B.2.a(1) Proportion of natural spawners that
are hatchery fish, life history
similarity, proportion of broodstock
that is of natural origin, degree of
selectivity in broodstock collection
(w/in pop)
NA
H (-1)
B.2.a(2) Proportion of natural spawners that
are hatchery strays (out of pop., but
within ESU)
L (1)
c. Genetic variation. B.1.c
2. Maintain natural
patterns of gene
flow.
R-level R-level
a. Spawner
composition.
Upper Columbia Salmon Recovery Plan
16
R-level
Goal
Population
R-level
R-level
M (mean = 0.33)
Moderate High Risk
Risk
H (-1)
High Risk
H (-1)
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Assessed Risk
Metric Factor Mechanism
Goal
Mechanism
Factor
Metrics
R-level R-level
B.2.a(3) Proportion of natural spawners that
are hatchery strays (out of ESU)
H (-1)
R-level
3. Maintain
occupancy in a
natural variety of
available habitat
types.
a. Distribution of
population across
habitat types.
B.3.a
Habitat diversity index and
occupancy.
H(-1)
H(-1)
H (-1)
4.Maintain integrity
of natural systems.
a. Change in
natural processes
or impacts.
B.4.a
Cumulative selectivity score across
all relevant impacts
M (0)
M (0)
M (0)
Goal
Population
R-level
R-level
Scores as follows: Very low = 2, Low = 1, Moderate = 0, High = -1
Upper Columbia Salmon Recovery Plan
17
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Population: Entiat Steelhead
VSP Parameters: Spatial Structure and Diversity
Metric A.1.a (Number of MSAs, distribution of MSAs, and quantity of habitat outside MSAs.)
The Entiat only has one MSA for steelhead. The Mad River branch is part of the single MSA,
and its capacity is too low to offer any substantial risk moderation. There are no other areas
outside the single MSA so the population is at high risk for this metric, but that risk is inherent
of this small population. It was always high risk due to historically simple spatial structure.
Metric A.1.b (Proportion of historical range occupied and presence/absence of spawners in
MSAs)
Steelhead have been observed throughout the most of the suspected historic range, based on
expanded redd surveys in 2003 (CCCD 2004). Although we have not quantified the current
distribution versus the intrinsic potential maps, we are relatively certain that current spawners
have access to functional habitat to over 75% of their historical range; therefore, the population
is at low risk for this metric.
Metric A.1.c (Change in gap distances and spawner distribution.)
There is only one MSA in the Entiat, and there is no artificial 5 km gaps within the MSA so the
risk level for this metric is moderate.
Metric B.1.a (Distribution of major life history expression within a population)
The Entiat steelhead population is low risk, because no major life history strategies have been
lost.
Metric B.1.b (Reduction in variability of traits, shift in mean value of trait, loss of traits.)
We do not have data available for this metric. Even if we determined that there was a change to
one or more traits we would not know what the exact baseline was because changes likely
occurred before there was biological monitoring. Therefore, we will assume that there has been
some change and increase in variance for 2 or more traits placing the population at moderate
risk.
Metric B.1.c (Genetic analysis encompassing within and between population variation)
We did not have an adequate data set to evaluate the genetic variation within the Entiat steelhead
population. Two previous genetic analyses have shown a degree of genetic variation among the
Upper Columbia steelhead samples, with inconclusive results regarding evidence of geographic
population structure (Chapman et al. 1994; Ford et al. 2001). Therefore, we will assume that the
Entiat population is at moderate risk for this metric, until a more refined analysis can be
conducted to prove that a higher or lower risk rating is justified.
Metric B.2.a.1 (Proportion of natural spawners that are hatchery fish, life history similarity,
proportion of broodstock that is of natural origin, degree of selectivity in broodstock collection
(w/in pop))
Upper Columbia Salmon Recovery Plan
18
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
There is no supplementation program for steelhead in the Entiat basin. Therefore, this metric is
not applicable to the Entiat steelhead population.
Metric B.2.a.2 (Proportion of natural spawners that are hatchery strays (out of Pop, but within
the ESU)
No data exists for the spawner composition of steelhead in the Entiat basin, but it is believed that
a high proportion of fish spawning in the Entiat are of hatchery origin. Additionally, there is
substantial risk of strays from the Wells hatchery program because of the inter-dam difference in
adult counts between Rocky Reach and Wells Dam. Also, the Wenatchee steelhead program
raises steelhead at Turtle Rock (Columbia River) and large numbers of the Wenatchee steelhead
have been observed at the Wells trap. Therefore, because of these obvious threats we conclude
that the Entiat is at high risk for within ESU hatchery strays. However, data needs to be
collected to verify if these threats are being realized on the spawning grounds of the Entiat
population.
Metric B.2.a.3 (Proportion of natural spawners that are hatchery strays (out of ESU))
We have no data to evaluate the proportion of out of ESU hatchery strays on the spawning
grounds of the Entiat population.
Therefore, we will use the default rating of moderate risk for this metric.
Metric B.3.a (Habitat diversity index and occupancy.)
We do not have the complete habitat diversity index analysis at this time, so we cannot evaluate
the percent change from historic to current. However, the broad range of distribution of steelhead
observed in the 2003 spawning ground surveys indicates that the population is utilizing a
historic-like range in elevations, stream widths, ecoregions and other factors that might provide
diversity to the population. Therefore, the Entiat steelhead population is at low risk for this
metric.
Metric B.4.a (Cumulative selectivity score across all relevant impacts)
No empirical data exists for this metric. We determined that alterations to the hydrograph,
predation, and size selective harvest, are potential risks of selective pressures on the Entiat
steelhead population. These potential impacts have not been quantified, but we believe that in the
absence of empirical data and more guidance on how to conduct a risk assessment, a reasonable
conclusion is that the population is at moderate risk for this metric.
Conclusions (Entiat Steelhead)
The Entiat steelhead population was determined to be at low risk for goal A (allowing natural
rates and levels of spatially mediated processes) and moderate risk for goal B (Maintaining
natural levels of variation) resulting in an overall moderate risk rating. The only metric that was
rated at high risk was the proportion of out-of-population (but within ESU) spawners that were
hatchery fish (B.2.a.2), because of the threat of strays from the Wells and Wenatchee hatchery
programs. This high risk factor for inter population hatchery strays was moderated at the
mechanism level because we had no reason to suspect that spawner composition would be above
moderate risk levels for out-of-population or out-of-ESU hatchery fish on the spawning grounds.
We also did not have a genetics study that had conclusive results that would help us determine
Upper Columbia Salmon Recovery Plan
19
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
the risk level associated with the observed genotypic variation. If a comprehensive genetic
analysis were applied to adequate sample sizes of natural origin Entiat steelhead across multiple
brood years then the results of this risk assessment could change the conclusion to high risk. We
also recognize that this detailed genetic analysis will probably be necessary in order to move the
population into the low risk category.
Upper Columbia Salmon Recovery Plan
20
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Table X4 Spatial Structure and diversity scoring system summary for the Entiat River steelhead population
Assessed Risk
Metric Factor Mechanism
Goal
A. Allowing
natural rates and
levels of spatiallymediated
processes.
B. Maintaining
natural levels of
variation.
Mechanism
1. Maintain natural
distribution of
spawning
aggregates.
1. Maintain natural
patterns of
phenotypic and
genotypic
expression.
2. Maintain natural
patterns of gene
flow.
Factor
Metrics
R-level R-level
a. Number and
A.1.a
spatial arangement
of spawning areas.
Number of MSAs, distribution of
MSAs, and quantity of habitat
outside MSAs.
H (-1)
H (-1)
b. Spatial extent or A.1.b
range of population
Proportion of historical range
L (1)
occupied and presence/absence of
spawners in MSAs
L (1)
c. Increase or
A.1.c.
decrease gaps or
continuities
between spawning
aggregates.
Change in gap distances and
spawner distribution.
M (0)
M (0)
a. Major life history B.1.a
strategies.
Distribution of major life history
expression within a population
VL (2)
VL (2)
b. Phenotypic
variation.
B.1.b
Reduction in variability of traits, shift M(0)
in mean value of trait, loss of traits.
M(0)
c. Genetic
variation.
B.1.c
Genetic analysis encompassing
within and between population
variation
M (0)
M (0)
a. Spawner
composition.
B.2.a(1) Proportion of natural spawners that M (0)
are hatchery fish, life history
similarity, proportion of broodstock
that is of natural origin, degree of
selectivity in broodstock collection
(w/in pop)
H (-1)
R-level
Goal
Population
R-level
R-level
Moderate Risk Moderate
(mean =0)
Risk
M (0)
Moderate
Risk
Moderate
Risk
(mean = 0)
H (-1)
B.2.a(2) Proportion of natural spawners that H (-1)
are hatchery strays (out of pop., but
within ESU)
Upper Columbia Salmon Recovery Plan
21
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Assessed Risk
Metric Factor Mechanism
Goal
Mechanism
Factor
Metrics
R-level R-level
R-level
Goal
Population
R-level
R-level
B.2.a(3) Proportion of natural spawners that M (0)
are hatchery strays (out of ESU)
3. Maintain
occupancy in a
natural variety of
available habitat
types.
a. Distribution of
population across
habitat types.
B.3.a
Habitat diversity index and
occupancy.
L (1)
L (1)
L (1)
4.Maintain integrity
of natural systems.
a. Change in
natural processes
or impacts.
B.4.a
Cumulative selectivity score across M (0)
all relevant impacts
M (0)
M (0)
Scores as follows: Very low = 2, Low = 1, Moderate = 0, High = -1
Upper Columbia Salmon Recovery Plan
22
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Population: Methow Spring Chinook
VSP Parameters: Spatial Structure and Diversity
Metric A.1.a (Number of MSAs, distribution of MSAs, and quantity of habitat outside MSAs.)
The ICTRT MSA analysis identified three MSAs for Methow spring Chinook population (Upper
Methow, Chewuch, and Twisp), and one mSA (Methow mainstem between the Chewuch and
Twisp Rivers). These MSA’s have been consistently occupied by spring Chinook in all years
when spawning ground surveys were conducted (Humling and Snow 2004). Therefore, the
population is at low risk for this metric. There were two years (1996 and 1998) when no
spawning ground surveys were conducted because all spring Chinook were collected at Wells
Dam during the trapping period. The assumption was that there was no wild spawning in those
years; however, that assumption was not tested by conducting the surveys to see if the trap really
was 100% effective and that no fish passed the facility before or after the trapping period.
Regardless, it is likely that the MSA’s were unoccupied or occupied at extremely low levels in 2
of the last 10 years. We are uncertain how this might effect the risk rating, but assume that
because of the high level of occupancy following the zero passage years that the risk level was
not affected.
Metric A.1.b (Proportion of historical range occupied and presence/absence of spawners in
MSAs)
Spring Chinook consistently occupy all of the MSA’s identified in the ICTRT MSA analysis,
however, the abundance of spring Chinook was very low (5 redds) in the middle mainstem mSA
in 2003 (Humling and Snow 2004). Also, in recent years (2001-present), the range of spawning
distribution has not been reduced in the MSAs in the Methow basin so the population would be
at very low risk for this metric. However, we did not use a 10 year data set and the very low
abundances in the mid-late 1990’s would probably increase the risk level to moderate or even
high, considering that no wild fish were allowed to pass Wells Dam during the trapping period in
1996 and 1998. Additionally, during low water years, the flow and temperature in the lower
Twisp and Chewuch rivers can delay or impede fish passage to the suitable habitat in the middle
and upper reaches of these rivers, creating an interaction between habitat conditions and
abundance that leads to poor spatial structure in some years. Therefore, considering all the
factors and conditions we suggest using a risk level of moderate for this metric.
Metric A.1.c (Change in gap distances and spawner distribution.)
Low flows and high temperatures due to anthropogenic effects in the lower Twisp and Chewuch
Rivers have created gaps of 5 km or more in the distribution of spawning spring Chinook,
placing the population at high risk for this metric.
Metric B.1.a (Distribution of major life history expression within a population)
The Methow spring Chinook population is very low risk, because no major life history strategies
have been lost.
Metric B.1.b (Reduction in variability of traits, shift in mean value of trait, loss of traits.)
We do not have data available for this metric. Even if we determined that there was a change to
one or more traits we do not know what the exact baseline is because changes likely occurred
Upper Columbia Salmon Recovery Plan
23
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
before there was biological monitoring. Therefore, we will assume that there has been some
change and increase in variance for 2 or more traits placing the population at moderate risk.
Metric B.1.c (Genetic analysis encompassing within and between population variation)
The Methow spring Chinook population is at high risk for genetic variation. Although the
GCMP mixed the stocks, there is evidence of some divergence in the Twisp River (Ford et al.
2001). However, the hatchery stocks currently used in the upper Methow and Chewuch programs
still contain a large percentage of Carson lineage, and hatchery fish comprise high proportions
(40-98%) of fish on the spawning grounds (Humling and Snow 2004).
Metric B.2.a.1 (Proportion of natural spawners that are hatchery fish, life history similarity,
proportion of broodstock that is of natural origin, degree of selectivity in broodstock collection
(w/in pop).
The Methow population is at high risk for this metric due to Carson stock being propagated in
the basin in the recent past and the high proportion of Carson lineage in the MetComp stock
currently used at the Methow State Fish Hatchery and Winthrop National Fish Hatchery.
Metric B.2.a.2 Proportion of natural spawners that are hatchery strays (out of pop., but within
ESU)
In 2003, 0% if the coded wire tag recoveries (n = 422) were from other Upper Columbia
populations of spring Chinook (Humling and Snow 2003). Therefore, we conclude that the
population is at low risk with respect to this metric, however, we recognize that more years of
spawner composition data is needed to have a high level of certainty in this conclusion.
Metric B.2.a.3 Proportion of natural spawners that are hatchery strays (out of ESU)
In 2003, there was a 1% spawner composition (Humling and Snow 2004) of hatchery fish from
outside the population, but the hatcheries are propagating a composite stock that has outside the
ESU lineage so the population is at moderate risk for this metric. (we should report the current
% and the hatchery protocol that is designed to reduce the proportion of Carson-lineage through
time).
Metric B.3.a (Habitat diversity index and occupancy.)
We do not have the complete habitat diversity index analysis at this time, so we cannot evaluate
the percent change from historic to current. However, there has been no loss of spawning spring
Chinook from the lower range of elevations and no loss of ecoregions from the distribution so
the population is at low risk for this metric.
Metric B.4.a (Cumulative selectivity score across all relevant impacts)
No empirical data exists for this metric. We determined that alterations to the hydrograph,
predation, size selective harvest, and size selective migration barriers all have a selectivity score
of 1, resulting in a cumulative score for the population of 4, which would be a score of moderate
risk for a large complex (type B) population using the scoring system provided by the ICTRT as
of March 22, 2005.
Conclusions (Methow spring Chinook)
Upper Columbia Salmon Recovery Plan
24
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
The Methow spring Chinook population was determined to be at moderate risk for goal A
(allowing natural rates and levels of spatially mediated processes) but high risk for goal B
(maintaining natural levels of variation) resulting in an overall high risk rating. There were two
metrics that were contributing to the population being at high risk. First, genetic variation was at
high risk due to very little divergence occurring within the population (Ford et al. 2001; ICTRT
2003 draft population identification report). Second, the threat to genetic variation has not been
removed since Carson stock were propagated in the basin in the recent past and there is still a
high proportion of Carson lineage in the MetComp stock currently used at the Methow State Fish
Hatchery and Winthrop National Fish Hatchery. Habitat actions are likely to improve the
spawner gap distances between the MSA’s and improve the goal A status from moderate to low
risk; however, actions within the hatchery programs will be necessary to move the population to
a status that can meet the diversity requirements of a VSP.
Upper Columbia Salmon Recovery Plan
25
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Table X5 Spatial Structure and diversity scoring system summary for the Methow River spring Chinook population
Assessed Risk
Metric Factor Mechanism
Goal
A. Allowing
natural rates and
levels of spatiallymediated
processes.
B. Maintaining
natural levels of
variation.
Mechanism
1. Maintain natural
distribution of
spawning
aggregates.
1. Maintain natural
patterns of
phenotypic and
genotypic
expression.
Factor
Metrics
a. Number and
A.1.a
spatial arangement
of spawning areas.
Number of MSAs, distribution of
MSAs, and quantity of habitat
outside MSAs.
L (1)
L (1)
b. Spatial extent or A.1.b
range of population
Proportion of historical range
occupied and presence/absence of
spawners in MSAs
M (0)
M (0)
c. Increase or
A.1.c.
decrease gaps or
continuities
between spawning
aggregates.
Change in gap distances and
spawner distribution.
H (-1)
H (-1)
a. Major life history B.1.a
strategies.
Distribution of major life history
expression within a population
VL (2)
VL (2)
b. Phenotypic
variation.
Reduction in variability of traits, shift M (0)
in mean value of trait, loss of traits.
M (0)
Genetic analysis encompassing
within and between population
variation
H (-1)
H (-1)
H (-1)
H (-1)
B.1.b
c. Genetic variation. B.1.c
2. Maintain natural
patterns of gene
flow.
R-level R-level
a. Spawner
composition.
B.2.a(1) Proportion of natural spawners that
are hatchery fish, life history
similarity, proportion of broodstock
that is of natural origin, degree of
selectivity in broodstock collection
(w/in pop)
R-level
Goal
Population
R-level
R-level
Moderate Risk Moderate High Risk
(mean = 0)
Risk
H (-1)
High Risk
H (-1)
B.2.a(2) Proportion of natural spawners that L (1)
are hatchery strays (out of pop., but
within ESU)
Upper Columbia Salmon Recovery Plan
26
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Assessed Risk
Metric Factor Mechanism
Goal
Mechanism
Factor
Metrics
R-level R-level
B.2.a(3) Proportion of natural spawners that
are hatchery strays (out of ESU)
M (0)
R-level
3. Maintain
occupancy in a
natural variety of
available habitat
types.
a. Distribution of
population across
habitat types.
B.3.a
Habitat diversity index and
occupancy.
L (1)
L (1)
L (1)
4.Maintain integrity
of natural systems.
a. Change in
natural processes
or impacts.
B.4.a
Cumulative selectivity score across
all relevant impacts
M (0)
M (0)
M (0)
Goal
Population
R-level
R-level
Scores as follows: Very low = 2, Low = 1, Moderate = 0, High = -1
Upper Columbia Salmon Recovery Plan
27
December 2005 Draft
Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Population: Methow Steelhead
VSP Parameters: Spatial Structure and Diversity
Metric A.1.a (Number of MSAs, distribution of MSAs, and quantity of habitat outside MSAs.)
The Methow steelhead population has four intrinsic potential MSA’s (Upper Methow River,
Chewuch River, Twisp River, and Beaver Creek) and four mSA’s (Gold, Libby, French, and
Black Canyon Creeks) (ICTRT MSA map). We do not have a long time series analysis to
evaluate occupancy of the MSA’s; however, based on recent spawning ground surveys, all four
MSA’s were occupied from 2001-2004, with the lowest average of 41 redds (2002-2004)
occurring in Beaver Creek (Snow 2003; Humling and Snow 2004). These estimates do not
separate out the hatchery fish and since natural origin fish were only approximately 10% of the
population (based on fish trapped at Wells Dam), its possible that there were few to no natural
origin steelhead present in Beaver Creek in 2003.
Based on ICTRT criteria, it appears that occupied mSA’s do not need to be factored into the risk
assessment if there are at least 4 occupied MSA’s. However, the mSA’s appear to not be
occupied, or have not been formally surveyed, based on recent redd surveys conducted by
WDFW (Snow 2003; Humling and Snow 2004). Although two redds were located in Gold Creek
in 2003, no redds were found there in 2002 or 2004 and no redds were found in Black Canyon
Creek in 2004 (Snow 2003; Humling and Snow 2004).
Therefore, based solely on MSA’s, we conclude that the Methow steelhead population is at very
low risk for this metric.
Taking into account the relatively short time series of the available data, the high proportion of
hatchery fish in the spawner composition, and the absence of spawners from most or all mSA’s,
we do not have a high degree of certainty that the population is at very low risk and a slightly
more risky status may be warranted.
Metric A.1.b (Proportion of historical range occupied and presence/absence of spawners in
MSAs)
Efforts to monitor the distribution and abundance of spawning steelhead have been expanded in
recent years (2001-2004), but we still do not have comprehensive, long-term data sets to rate this
metric for the entire Methow watershed (Snow and Jateff 2001; Jateff and Snow 2002; Snow
2003; Humling and Snow 2004). Although the vast majority of adult steelhead passing Wells
Dam were of hatchery origin (90.5%), there was still 748 wild steelhead spawners for the
Methow Basin (Humling and Snow 2004). Since levels of occupancy have not been defined, we
assume that the presence of redds and “suitable but unoccupied” habitat are adequate for rating
this metric. Steelhead have been observed spawning in each of the MSA’s and several of the
tributaries within each MSA, ranging from a low of 8% in the Chewuch to a high of 49% in the
Upper Methow (Humling and Snow 2004).
Although we do not have a quantitative analysis of the percent of historical distribution that is
currently occupied, we conclude from the above information that the Methow steelhead
population is at low risk for this metric because spawners are present in all MSA’s.
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Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Metric A.1.c (Change in gap distances and spawner distribution.)
There are still some migration obstructions in the Methow Basin; however, due to the
widespread spatial distribution of spawners in 2004, we conclude that there were no increases in
gaps between spawning aggregates for the Methow steelhead population and it is at low risk for
this metric.
Metric B.1.a (Distribution of major life history expression within a population)
There is both anadromous and resident life histories represented in the Methow steelhead
population; therefore it is at very low risk for this metric.
Metric B.1.b (Reduction in variability of traits, shift in mean value of trait, loss of traits.)
We do not have data available for this metric. Even if we determined that there was a change to
one or more traits we do not know what the exact baseline is because changes likely occurred
before there was biological monitoring. Therefore, we will assume that there has been some
change and increase in variance for 2 or more traits placing the population at moderate risk.
Metric B.1.c (Genetic analysis encompassing within and between population variation)
We did not have an adequate data set to evaluate the genetic variation within the Methow
steelhead population. Two previous genetic analyses have shown a degree of genetic variation
among the Upper Columbia steelhead samples, with inconclusive results regarding evidence of
geographic population structure (Chapman et al. 1994; Ford et al. 2001). Therefore, we will
assume that the Methow steelhead population is at moderate risk for this metric until a more
refined analysis can be conducted to prove that a higher or lower risk rating is justified.
Metric B.2.a.1 (Proportion of natural spawners that are hatchery fish, life history similarity,
proportion of broodstock that is of natural origin, degree of selectivity in broodstock collection
(w/in pop).
We do not have estimates of spawner composition for the various MSA’s and mSA’s of the
Methow steelhead population because carcasses cannot be obtained in sufficient numbers from
the spawning ground surveys. However, in 2004 only 9.5 % of the steelhead passing Wells Dam
were natural origin (Humling and Snow 2004). This is similar to the proportion of wild fish from
previous years (Kirk Truscott, personal communication). Adult steelhead are trapped at Wells
Dam (mainstem Columbia River) that could be from any of the MSA’s within the Methow or
from the Okanogan steelhead population and releases them at various locations throughout the
Methow, thereby mixing the progeny from various MSA’s and not encouraging local adaptation
within the population or between the Methow and Okanogan population. Therefore, we conclude
that the population is at high risk for this metric.
Additionally, although the Wells hatchery program does use wild fish, the NMFS BiOp restricts
the broodstock to no more than 33% natural origin fish, regardless of the run size (NMFS 2002).
This constraint limits the opportunity to meet production requirements with all wild fish during
years of high abundance, a practice that would reduce the genetic risk of the hatchery program.
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Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Metric B.2.a.2 (Proportion of natural spawners that are hatchery strays (out of pop., but within
the ESU))
The Wells hatchery program mixes Methow and Okanogan origin fish and there has been high
numbers of Wenatchee steelhead observed at Wells Dam, presumably because they are reared on
Columbia River water at the Turtle Rock facility before release in the Wenatchee (ask Kirk
Truscott for data and reference). There is currently no way to determine if Wenatchee steelhead
do show up on the spawning grounds of the Methow basin and efforts to monitor this risk need to
be conducted. Therefore, given the lack of data on spawner composition and the apparent threat
that the Wenatchee strays pose, we believe that the population is at high risk for this metric.
Metric B.2.a.3 (Proportion of natural spawners that are hatchery strays (out of ESU))
The Methow steelhead population is at low risk since there is no evidence of non-local (outside
the ESU) hatchery fish passing Wells Dam (ask Kirk Truscott for data and reference).
Metric B.3.a (Habitat diversity index and occupancy)
We do not have the complete habitat diversity index analysis at this time, so we cannot evaluate
the percent change from historic to current. However, steelhead are known to inhabit the range of
elevations and ecoregions present in the Methow basin, so we conclude the population is at low
risk for this metric.
Metric B.4.a (Cumulative selectivity score across all relevant impacts)
No empirical data exists for this metric. We determined that alterations to the hydrograph,
predation, size selective harvest, and size selective migration barriers all have a selectivity score
of 1, resulting in a cumulative score for the population of 4, which would be a score of moderate
risk for a large complex (type B) population using the scoring system provided by the ICTRT as
of March 22, 2005.
Conclusions (Methow steelhead)
The Methow steelhead population was determined to be at low risk for goal A (allowing natural
rates and levels of spatially mediated processes) and moderate risk for goal B (Maintaining
natural levels of variation) resulting in an overall moderate risk rating. The two metrics that were
rated at high risk were the proportion of natural spawners that were hatchery fish (B.2.a.1), but
those risk levels were moderated at the mechanism level by the fact that the other metrics for
goal B were low to moderate risk. However, we were very uncertain about the phenotypic and
genotypic variation risk levels and determined that because the analysis was inconclusive,
moderate risk was the most appropriate rating. However, the hatchery practices, though
necessary to maintain abundance, pose a threat to genetic diversity and the combination of
uncertain genetic variation and an existing threat should result in a high risk rating. We believe
that if the threat can be removed that the population should be able to achieve moderate to low
risk for spatial structure and diversity. The solutions for addressing the threat include localized
broodstock collection and juvenile acclimation (population and MSA specific programs),
reducing stray rates, and allowing higher proportions of natural origin spawners in the
broodstock when run size is sufficient.
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Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Table X6 Spatial Structure and diversity scoring system summary for the Methow River steelhead population
Assessed Risk
Metric Factor Mechanism
Goal
A. Allowing
natural rates and
levels of spatiallymediated
processes.
B. Maintaining
natural levels of
variation.
Mechanism
1. Maintain natural
distribution of
spawning
aggregates.
1. Maintain natural
patterns of
phenotypic and
genotypic
expression.
2. Maintain natural
patterns of gene
flow.
Factor
Metrics
R-level R-level
a. Number and
A.1.a
spatial arangement
of spawning areas.
Number of MSAs, distribution of
MSAs, and quantity of habitat
outside MSAs.
VL (2)
VL (2)
b. Spatial extent or A.1.b
range of population
Proportion of historical range
L (1)
occupied and presence/absence of
spawners in MSAs
L (1)
c. Increase or
A.1.c.
decrease gaps or
continuities
between spawning
aggregates.
Change in gap distances and
spawner distribution.
L (1)
L (1)
a. Major life history B.1.a
strategies.
Distribution of major life history
expression within a population
VL (2)
VL (2)
b. Phenotypic
variation.
B.1.b
Reduction in variability of traits, shift M(0)
in mean value of trait, loss of traits.
M(0)
c. Genetic
variation.
B.1.c
Genetic analysis encompassing
within and between population
variation
M (0)
M (0)
a. Spawner
composition.
B.2.a(1) Proportion of natural spawners that H (-1)
are hatchery fish, life history
similarity, proportion of broodstock
that is of natural origin, degree of
selectivity in broodstock collection
(w/in pop)
H (-1)
R-level
Goal
Population
R-level
R-level
Low Risk
Low Risk
(mean = 1.25)
M (0)
Moderate
Risk
Moderate
Risk
(mean = 0)
H (-1)
B.2.a(2) Proportion of natural spawners that H (-1)
are hatchery strays (out of pop., but
within ESU)
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Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Assessed Risk
Metric Factor Mechanism
Goal
Mechanism
Factor
Metrics
R-level R-level
R-level
Goal
Population
R-level
R-level
B.2.a(3) Proportion of natural spawners that L (1)
are hatchery strays (out of ESU)
3. Maintain
occupancy in a
natural variety of
available habitat
types.
a. Distribution of
population across
habitat types.
B.3.a
Habitat diversity index and
occupancy.
L (1)
L (1)
L (1)
4.Maintain integrity
of natural systems.
a. Change in
natural processes
or impacts.
B.4.a
Cumulative selectivity score across M (0)
all relevant impacts
M (0)
M (0)
Scores as follows: Very low = 2, Low = 1, Moderate = 0, High = -1
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Appendix B: Description of spatial structure and diversity of spring Chinook and steelhead
populations within the Upper Columbia Basin
Okanogan Steelhead
Not enough information is available to evaluate the status of spatial structure and diversity of the
natural origin steelhead in the Okanogan Basin. A recent project to monitor anadromous fish in
the Okanogan Basin was initiated in 2004, and data collected under this effort should allow for a
species status assessment in the future (OBMEP 2004). Until this data is adequate to make an
informed risk assessment, we assume that the Okanogan steelhead population is at high risk with
respect to spatial structure and diversity.
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