Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
page 1
Appendix S2. Calculation of Habitat-Based Indices of Population Size
Intrinsic Potential Capacity (IPkm)
The intrinsic potential habitat index reflects suitability of stream reaches for salmon spawning and
rearing (Agrawal et al. 2005; Burnett et al. 2007). The index is comprised of multiple persistent
landscape features that are not easily modified by anthropogenic influences. Variants of this index are
being used to estimate historical fish abundance by many organizations around the Pacific Northwest
USA in salmon recovery planning efforts (Steel and Sheer 2003; Cooney and Holzer 2006; Sheer et al.
2009). Although versions differ with respect to the exact features included, they all attempt to represent
inherent geomorphic and hydrologic properties of stream reaches (Sheer et al. 2009), irrespective of
more transient features defining habitat quality. These relationships are defined by species-specific
preferences synthesized from field observations and published literature (see Burnett et al. 2007).
We used results for Chinook salmon and steelhead in the Lower Columbia and Willamette basins that
were calculated by S. Busch et al. (NOAA NWFSC, pers. comm.; manuscript in review). The three
landscape features included in calculations were: (1) stream gradient, (2) bankfull stream width, and (3)
valley confinement. Each of these features was modeled in a geographic information system (GIS) from
a 1:100,000 stream hydrology network and an associated 10-m digital elevation model, and related to
salmon suitability using the specific functions shown in Figures 1 (Chinook salmon) and 2 (steelhead).
Individual scores for each of the three landscape features were combined into a geometric mean score
for each stream reach. Reach-level scores, which had no units, were multiplied by reach length (km), for
the final metric IPkm (intrinsic potential kilometers). The total IPkm score for each population was the
sum of reach-level IPkm scores for all reaches accessible to fish.
Users of IPkm, including Busch et al., are actively seeking ways to validate the metric with respect to its
ability to predict population-level fish abundances (Sheer et al. 2009). Previous studies have found
significant positive relationships between other habitat-based measures of spawning habitat and
observed spawner abundance (Schick and Lindley 2007), effective population size Ne (Shrimpton and
Heath 2003) or equilibrium spawner abundance in the absence of fish harvest (Liermann et al. 2010).
IPkm was correlated with accessible watershed area (km2; r > 0.5 for all ESUs), the metric used by
Liermann et al. (2010) to predict equilibrium population size for Chinook salmon along the Pacific coast.
Population Viability and Habitat Quality Scores
The Willamette-Lower Columbia Technical Recovery Team (TRT; www.nwfsc.noaa.gov/trt/wlc.cfm) is a
multi-stakeholder group, convened by NOAA Fisheries to develop recovery plans required for
threatened and endangered salmon in the Willamette-Lower Recovery planning region, as required by
the Endangered Species Act (ESA). Their mission was to evaluate the status of the ESA-listed
anadromous salmonids within their region and to conduct a risk assessment to evaluate the vulnerability
Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
page 2
of salmon to extinction. The TRT assessed status and vulnerability for both the evolutionarily significant
units (ESUs; Waples 1991; 1998) and the populations (Myers et al. 2006) within each ESU.
In their analysis, the TRT developed scores to represent levels of population persistence over the
subsequent 100 years (McElhany et al. 2003; Table 1). This analysis included evaluation of four key
attributes: (1) abundance and productivity, (2) diversity, (3) spatial structure, and (4) habitat quality.
Each of these scores incorporated various forms of uncertainty. These four attributes were scored
independently, and the population viability score was the simple weighted mean of these four scores,
where the weight of the abundance and productivity score was double that of the other three.
Population-level viability scores for Chinook salmon (Oncorhyncus tshawytscha) ranged from 0.1 to 2.2,
and steelhead (O. mykiss) ranged from 0.2 to 1.9 for ESA-listed populations (Table 2).
Abundance and productivity were modeled using a population viability approach, parameterized with
empirical time series of spawner counts or redd counts on index reaches for populations where data
were available. The stocking history of hatchery fish was incorporated into this score. The remaining
three categories relied on a combination of data, maps and expert opinion. Spatial structure was scored
on the basis of the amount and distribution of habitat currently accessible to anadromous salmonids
compared to that presumed to be accessible historically (pre-European settlement, ca. 1800). Diversity
was scored on the basis of the variety of life history phenotypes present, within-population genetic
diversity or effective population size measures, use of diverse habitats, and resilience and adaptation to
environmental fluctuations. Habitat was scored on the basis of a measure of the current status of
habitat within areas occupied by the population, and a measure of the likely trend in habitat conditions,
given anticipated future changes to the environment. Habitat scores were estimated by experts from a
suite of habitat variables (physical, food source, water quality etc.) at a variety of index locations.
Complete details are available in McElhany et al. (2003).
We used these scores to represent population size for two scenarios in our graph theoretical analysis.
Reduced habitat quality scenario
We represented population size in this scenario by multiplying the IPkm (from part I) by the habitat
score assigned by the TRT (see above). We called this new metric IP.HQI (intrinsic potential, weighted by
the habitat quality index). Before multiplying, we standardized the TRT habitat scores, which originally
ranged from 0 to 4 (Table 1), by their maximum species-specific value. New scores ranged between 0
and 1, and acted as a proportional weight to downgrade the amount of suitable habitat available to fish
according to its habitat quality. For example, the Lewis River fall Chinook population had an IPkm of 257
km, a habitat score of 1.23, and the maximum habitat score for all fall Chinook populations was 1.73
(Table 2). Therefore, the value of IP.HQI for fall Chinook in the Lewis River equaled (1.23/1.73)*257, or
183 km. We used this metric to represent population size in the graph theoretical analysis.
Myriad scenario
We represented population size in this scenario as above, except instead of using the habitat score, we
used the entire population viability score as a weighting factor for IPkm; we called the resulting new
metric IP.PPI (intrinsic potential, weighted by the population performance index). Recall from above that
Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
page 3
the population viability score incorporated 4 component scores: abundance and productivity, spatial
structure, diversity, and habitat.
We evaluated how closely IP.PPI scores matched empirical spawner abundances for populations which
had data (Figure 3). This assessment is somewhat circular because the same empirical data were used in
construction of the viability scores. However this is our only means of assessing how well IP.PPI
corresponds with observed population densities in recent decades, which is what we aimed to represent
in this scenario. Unexplained variation may be caused, in part, by conditions experienced by salmon in
the ocean, biological interactions, and our inability to parse hatchery and wild spawners.
Table 1. Extinction risk associated with each population persistence category.
Population
persistence category
Probability of population
persistence in 100 years
0
0–40%
Either extinct or very high risk of extinction.
1
40–75%
Relatively high risk of extinction in 100 years.
2
75–95%
Moderate risk of extinction in 100 years.
3
95–99%
Low (negligible) risk of extinction in 100 years (viable
salmonid population).
4
>99%
Source: McElhany et al. (2003)
Description
Very low risk of extinction in 100 years.
Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
page 4
Table 2. Geographic coordinates of population location, and metrics used to represent population size.
Population
Length
IPkm*
Latitude Longitude accessible
(km)
(km)
IP-HQI
(km)
IP-PPI
(km)
TRT
TRT
Empirical
Habitat Viability Spawner
Score
Score Abundance†
Fall Chinook
Big Creek
Big White Salmon R
Chinook River
Clackamas River
Clatskanie River
Coweeman River
Elochoman River
Grays River
Hood River
Kalama River
Lewis River
Lewis River Bright
Lower Cowlitz River
Lower Gorge Tribs
Mill Creek
Salmon Creek
Sandy River
Sandy River Bright
Scappoose River
Toutle River
Upper Cowlitz River
Upper Gorge Tribs
Washougal River
Youngs Bay
46.183
45.746
46.285
45.376
46.094
46.154
46.25
46.364
45.605
46.045
45.931
45.931
46.41
45.566
46.224
45.706
45.468
45.468
45.769
46.325
--45.695
45.625
46.115
-123.668
-121.523
-123.984
-122.393
-123.171
-122.779
-123.317
-123.561
-121.634
-122.805
-122.710
-122.710
-122.928
-122.186
-123.225
-122.656
-122.284
-122.284
-122.874
-122.714
---121.731
-122.270
-123.811
205
3
46
1245
466
212
325
375
116
62
508
508
1057
109
302
147
296
296
492
444
0
55
82
466
98
3
32
370
156
78
116
148
36
22
257
257
443
35
116
156
108
108
187
179
1
13
77
213
69
1
23
224
98
67
74
107
21
18
183
257
226
26
70
111
79
85
107
117
0
9
59
165
54
1
17
174
90
71
61
76
16
17
189
257
255
13
55
81
55
67
87
57
0
5
58
111
1.2
0.8
1.2
1.1
1.1
1.5
1.1
1.3
1.0
1.4
1.2
1.7
0.9
1.3
1.1
1.2
1.3
1.4
1.0
1.1
1.0
1.3
1.3
1.3
1.2
0.9
1.1
1.0
1.2
2.0
1.1
1.1
0.9
1.7
1.6
2.2
1.2
0.8
1.0
1.1
1.1
1.3
1.0
0.7
0.3
0.9
1.6
1.1
--44.312
--45.12
45.556
46.071
44.14
43.997
44.998
45.894
44.787
45.379
44.414
--46.252
---
---122.714
---122.075
-121.689
-122.513
-122.609
-122.906
-122.486
-122.429
-122.610
-122.092
-122.625
---122.570
---
3
495
0
508
51
238
520
277
903
201
212
296
866
0
444
0
3
235
0
298
113
90
376
138
661
105
226
194
444
0
239
1
0
143
0
287
93
68
376
61
383
94
118
181
273
0
107
0
0
81
0
263
37
42
370
47
218
25
85
194
199
0
50
0
0.0
1.1
0.0
1.7
1.4
1.3
1.8
0.8
1.0
1.6
0.9
1.6
1.1
0.0
0.8
0.0
0.1
0.7
0.3
1.7
0.6
0.9
1.9
0.6
0.6
0.4
0.7
1.9
0.8
0.1
0.4
0.3
397
330
566
568
267
3713
646
9715
2800
1174
3513
1580
2921
0.96
0.07
0.99
0.94
1.0
0.91
0.86
1.0
1.0
0.94
0.63
0.63
0.84
0.91
0.99
0.96
0.74
0.74
0.92
0.8
0.0
1.0
0.55
1.0
Spring Chinook
Big White Salmon R
Calapooia
Cispus River
Clackamas River
Hood River
Kalama River
McKenzie
MF Willamette
Molalla
NF Lewis River
North Santiam
Sandy River
South Santiam
Tilton River
Toutle River
Upper Cowlitz River
2596
358
2592
669
1676
285
0.02
0.56
0.0
1.0
0.97
0.97
0.80
0.34
0.65
0.27
0.58
0.74
0.74
0.0
0.76
0.0
Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
Population
Length
IPkm*
Latitude Longitude accessible
(km)
(km)
IP-HQI
(km)
IP-PPI
(km)
144
162
170
38
104
143
155
163
210
50
119
143
page 5
TRT
TRT
Empirical
Habitat Viability Spawner
Score
Score Abundance†
Summer steelhead
Hood River
Kalama River
EF Lewis River
NF Lewis River
Washougal River
Wind River
45.637
46.051
45.84
45.931
45.612
45.838
-121.599
-122.625
-122.434
-122.710
-122.219
-121.944
64
308
349
242
103
96
219
198
267
150
153
143
1.3
1.7
1.3
0.5
1.4
2.0
1.3
1.5
1.5
0.6
1.4
1.9
450
623
364
228
648
0.98
0.85
0.83
0.2
0.64
0.95
Winter steelhead
0.42
Calapooia
44.391 -122.985
559
187
164
165
1.4
1.5
281
0.0
Cispus River
----0
0
0
0
0.5
0.4
0.95
Clackamas River
45.192 -122.177
1463
750
670
688
1.4
1.5
2048
0.79
Coweeman River
46.174 -122.758
277
159
129
116
1.3
1.2
388
0.84
Lower Cowlitz River 46.368 -122.935
1196
601
364
404
1.0
1.1
0.0
Upper Cowlitz River
----0
1
0
0
0.4
0.4
0.83
Lower Gorge Tribs 45.566 -122.186
131
70
61
41
1.4
1.0
1.0
Upper Gorge Tribs 45.727 -121.795
73
35
30
21
1.4
1.0
0.97
Hood River
45.529 -121.578
134
149
123
145
1.3
1.6
580
0.64
Kalama River
46.043 -122.821
71
15
14
15
1.5
1.7
601
0.83
EF Lewis River
45.832 -122.532
8
267
233
205
1.4
1.3
445
0.20
NF Lewis River
45.931 -122.710
242
150
99
77
1.0
0.9
0.67
Molalla
45.119 -122.535
982
799
631
561
1.2
1.2
1879
0.92
Salmon Creek
45.709 -122.643
154
161
60
87
0.6
0.9
0.71
Sandy River
45.395 -122.199
421
335
329
303
1.5
1.5
2000
0.45
North Santiam
44.788 -122.742
225
292
229
252
1.2
1.5
3227
0.68
South Santiam
44.412 -122.759
972
628
491
553
1.2
1.5
2033
0.0
Tilton River
----0
0
0
0
0.2
0.2
0.68
NF Toutle River
46.377 -122.596
350
271
165
205
1.0
1.3
0.85
SF Toutle River
46.282 -122.644
188
112
112
107
1.6
1.6
636
0.64
Washougal River
45.625 -122.308
444
153
108
85
1.1
0.9
251
0.70
West Side Tribs
45.134 -123.258
1053
1337
1056
971
1.2
1.2
*These values represent areas currently accessible to populations (populations above dams have no location; latitude and
longitude are null (---)). Values were increased for the historical scenario to include all reaches above hydropower dams where
fish had been observed, and for the reintroduction scenario for the population to be reintroduced.
† Data come from the Salmon Population Summary database, Northwest Fisheries Science Center
(https://www.webapps.nwfsc.noaa.gov/apex/f?p=238:home:0), and are medians of annual estimates (range = 9 to 46 years;
mean and median = 33 years per population).
Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
page 6
Figure 1. Curves used by Busch et al. (NOAA Northwest Fisheries Science Center, pers. comm.) in
creating the intrinsic potential habitat index for Chinook salmon in the Willamette and Lower Columbia
basins. Reprinted from Sheer et al. (2009), page 14. The original caption read: “Gradient when reach
width is > 25 m; b) gradient when reach width is between 2 and 25 m; c) ratio of valley width to bankfull
width; d) bankfull width.”
Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
page 7
Figure 2. Curves originally described by Burnett et al. (2007), and used by Busch et al. (NOAA Northwest
Fisheries Science Center, pers. comm.) in creating the intrinsic potential habitat index for steelhead in
the Willamette and Lower Columbia basins. Reprinted from Sheer et al. (2009), page 20.
page 8
3500
Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
2500
2000
1500
500
1000
Spawner Abundance
3000
r = 0.34
0
100
200
300
400
500
600
700
IP.PPI (km)
Figure 3. Relationship between IP.PPI (IPkm, weighted by the TRT’s population viability score) and
empirical spawner abundance for populations where data were available (n = 36 of 68 total
populations). Note: The Fall Chinook Lewis River Bright population was an outlier at 9,715 spawners and
an IP.PPI score of 257, and was removed from this plot. When this population was included, the
correlation was weaker (r=0.28).
Fullerton et al., Human influence on the spatial structure of threatened Pacific salmon metapopulations
Conservation Biology Supporting Information Appendix S2
page 9
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