Ecological Applications, 9(1), 1999, pp. 301±319 ᭧ 1999 by the Ecological Society of America

MULTISCALE THERMAL REFUGIA AND STREAM HABITAT ASSOCIATIONS OF CHINOOK SALMON IN NORTHEASTERN OREGON

CHRISTIAN E. TORGERSEN,1 DAVID M. PRICE,1 HIRAM W. L I,2 AND BRUCE A. MCINTOSH3 1Oregon Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331 USA 2Biological Resources Division, U. S. Geological Survey, Oregon Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331 USA 3Department of Forest Science, Oregon State University, Corvallis, Oregon 97331 USA

Abstract. We quanti®ed distribution and behavior of adult spring chinook salmon (Oncorhynchus tshawytscha) related to patterns of stream temperature and physical habitat at channel-unit, reach-, and section-level spatial scales in a wilderness stream and a disturbed stream in the John Day River basin in northeastern Oregon. We investigated the effectiveness of thermal remote sensing for analyzing spatial patterns of stream temperature and assessed habitat selection by spring chinook salmon, evaluating whether thermal refugia might be responsible for the persistence of these stocks in rivers where water temperatures frequently exceed their upper tolerance levels (25ЊC) during spawning migration. By presenting stream temperature and the ecology of chinook salmon in a historical context, we could evaluate how changes in riverine habitat and thermal spatial structure, which can be caused by land- use practices, may in¯uence distributional patterns of chinook salmon. Thermal remote sensing provided spatially continuous maps of stream temperature for reaches used by chinook salmon in the upper subbasins of the Middle Fork and North Fork John Day River. Electivity analysis and logistic regression were used to test for associations between the longitudinal distribution of salmon and cool-water areas and stream habitat characteristics. Chinook salmon were distributed nonuniformly in reaches throughout each stream. Salmon distribution and cool water temperature patterns were most strongly related at reach-level spatial scales in the warm stream, the Middle Fork (maximum likelihood ratio: P Ͻ 0.01), and most weakly related in the cold stream, the North Fork (P Ͼ 0.30). Pools were preferred by adult chinook salmon in both subbasins (Bonferroni con®dence interval: P Յ 0.05); however, rif¯es were used proportionately more frequently in the North Fork than in the Middle Fork. Our observations of thermal refugia and their use by chinook salmon at multiple spatial scales reveal that, although heterogeneity in the longitudinal stream tem- perature pro®le may be viewed as an ecological warning sign, thermal patchiness in streams also should be recognized for its biological potential to provide habitat for species existing at the margin of their environmental tolerances. Key words: behavioral thermoregulation; habitat association; logistic regression; Oregon; patch- iness; salmon, adult chinook; salmonid ecology; spawning habitat; stream temperature; thermal remote sensing; thermal mapping; thermal refugia.

INTRODUCTION peratures exceed their upper tolerances (Gibson 1966, Thermal refugia protect biotic communities from ex- Kaya et al. 1977, Berman and Quinn 1991). Laboratory treme thermal disturbances and are most numerous in experiments with rainbow trout (Oncorhynchus mykiss) intact riverine systems with extensive coupling of the and brown trout (Salmo trutta) also have demonstrated main channel with streamside forests, ¯oodplain for- behavioral thermoregulation for periods of up to six ests, and groundwater (Bilby 1984, Sedell et al. 1990). weeks and with distinct diel patterns (Reynolds and Coldwater and warmwater ®shes, and the organisms on Casterlin 1979, Gregory and Anderson 1983). In which they feed (Vannote and Sweeney 1980, Tait et streams of the John Day River basin, higher densities al. 1994), respond to thermal heterogeneity and require of rainbow trout were supported in those watersheds speci®c ranges of temperature to survive and reproduce with lower daily maximum water temperatures and (Nielsen et al. 1994, Peterson and Rabeni 1996). Sev- greater riparian canopy (Li et al. 1994). Salmonids in eral species of salmon and trout thermoregulate be- warm streams respond to gradients in the longitudinal haviorally by moving to cooler areas, such as seeps and temperature pro®le by occupying cooler upstream con¯uences with cold streams, when surrounding tem- reaches (Theurer et al. 1985, Roper et al. 1994). In the Yakima River in Washington, adult spring chinook Manuscript received 13 October 1997; revised 26 March salmon (Oncorhynchus tshawytscha) tagged with tem- 1998; accepted 31 March 1998. perature-sensitive radio transmitters behaviorally ther- 301 302 CHRISTIAN E. TORGERSEN ET AL. Ecological Applications Vol. 9, No. 1 moregulated to maintain internal temperatures 2.5ЊC compare the behavioral response of chinook salmon to lower than ambient stream temperatures in surrounding thermal patterns in two river environments with con- habitats (Berman and Quinn 1991). trasting geomorphology and land use. Temperature relationships between aquatic organ- isms and their environment, as well as the potential for ECOLOGICAL AND HISTORICAL SETTING alterations of such systems by humans, must be un- The John Day River is the longest river system in derstood to insure protection of threatened ®sh species the state of Oregon without permanent impoundments. and other aquatic organisms (Amour 1991). Elevated In total linear distance, the John Day River and its stream temperatures are an important physical effect North, Middle, and South forks comprise Ͼ800 km of resulting from land-use practices, with consequences free-¯owing river. Draining the fourth largest hydro- for aquatic ecosystems. Stream temperatures typically logic basin in Oregon, the John Day is one of only 42 increase when riparian vegetation is removed though rivers in the contiguous United States that exceed 200 forestry and agriculture, effectively reducing shade km in length and are free-¯owing (Benke 1990). Of cover, causing channel widening, and ultimately ex- these 42 rivers, the John Day is one of only eight rivers posing the stream channel to direct insolation (Brown that possess federal protection status under the Wild 1983, Ward 1985, Beschta et al. 1987). Several studies and Scenic River Act (United States Congress, 1978). have demonstrated that removal of riparian vegetation Though it has remained free of permanent impound- along tributaries can lead to increased water temper- ments, this river has been altered over the last two atures (Hewlett and Fortson 1982, Barton et al. 1985, centuries of settlement and agricultural development. Beschta and Taylor 1988, Holtby 1988). The river and its wild salmon stocks have partially The physical, chemical, and biological components recovered from habitat degradation that occurred in the of stream systems interact collectively to form and con- 1930s and 1940s (Oregon Water Resources Department trol habitats of ®shes. These abiotic and biotic factors 1986). Compared to spring chinook salmon stocks list- are built on a physical habitat template determined by ed or proposed threatened under the Endangered Spe- basin-wide parameters of climate, geology, vegetation, cies Act (United States Congress, 1973) in neighboring and adjacent land-use practices (Poff and Ward 1990). subbasins of the Columbia and Snake rivers, the John Human alterations to the landscape can harm the aquat- Day River stock has not required protection by the ic environment of salmonid ®shes directly through hab- National Marine Fisheries Service. Currently one of itat degradation and indirectly through alteration of the healthiest runs of naturally spawning spring chi- stream thermal regimes (Chamberlin et al. 1991, Fur- nook salmon in the Columbia Basin (Oregon Depart- niss et al. 1991, Nelson et al. 1991, Platts 1991). These ment of Fish and Wildlife 1995), the John Day stock effects are far-reaching temporally and spatially and is still considered depressed by the National Marine must not be underestimated when considering any as- Fisheries Service (1998). Indeed, this stock was listed pect of biological interactions in lotic systems (Hicks as ``of special concern,'' i.e., relatively minor distur- et al. 1991, Bisson et al. 1992, Minshall 1993). The bances could threaten its existence (Nehlsen et al. hierarchical spatial structure of hydrologic drainage ba- 1991). sins and their nested network of streams lend them- selves to a multiscale investigative approach when as- Study area sessing ecological pattern and process with respect to Our study area included the upper sections of the land-use in¯uences (Frissell et al. 1986, Gregory et al. Middle Fork and North Fork of the John Day River in 1991, Johnson and Gage 1997). northeastern Oregon (Fig. 1). The John Day River is a Our objective was to quantify how spatial patterns large tributary entering the Columbia River 320 km of stream temperature in¯uence habitat selection by from the Paci®c Ocean. From the mouth of the Colum- adult spring chinook salmon. We assessed the distri- bia River, adult chinook salmon ascend three hydro- bution of adult chinook salmon and thermal refugia at electric dams and migrate upstream ϳ600 km to reach multiple spatial scalesÐfrom individual pool/rif¯e the headwater reaches of the John Day basin. Spring habitats to entire river sectionsÐand we propose that chinook spawning areas are currently limited to three thermal remote sensing is an effective tool for longi- John Day subbasins: the upper main stem of the John tudinal analysis of water temperature in river systems. Day River, the upper Middle Fork, and the upper North We hypothesized that stream temperature is patchy at Fork (Lindsay et al. 1986). varied spatial scales, and the distribution of chinook The upper Middle Fork and North Fork lie in the salmon is patchy and positively associated with cool- Greenhorn and Elkhorn ranges, respectively, in the water areas at channel unit and reach-level spatial Blue Mountains. Columbia River basalt underlies most scales. Our speci®c research objectives were to (1) as- of the lower North Fork and Middle Fork subbasins, sess the effectiveness of thermal remote sensing for and the headwater reaches consist of folded metamor- detecting spatial pattern in stream temperature at mul- phosed rocks partially overlain by volcanic tuff (Orr tiple scales, (2) identify thermal and habitat character- et al. 1992). Elevations in the Middle Fork and North istics in key reaches used by chinook salmon, and (3) Fork subbasins range from 2200 m above sea level in February 1999 SALMON ECOLOGY AND THERMAL REFUGIA 303

FIG. 1. Upper John Day River basin in northeastern Oregon. Study sections on the North Fork and Middle Fork are demarcated by black bar symbols annotated with route interval locations. Route intervals were 1-km segments in distance along the river's path. the headwaters to 600 m near the mouth of the North mer highs can reach 27ЊC. Summer base ¯ow in both Fork. The upper Middle Fork meanders northwesterly rivers consists primarily of springs in headwater reach- through rangelands in alluvial valleys and alluviated es. Snowmelt sources for springs persist longer into the canyons (sensu Bisson and Montgomery 1996). In con- summer in the North Fork subbasin. trast, the North Fork ¯ows westward through steep col- The upper Middle Fork subbasin is vegetated pri- luvial and alluviated canyons. Average river gradient marily with Pinus ponderosa on south-facing slopes in the North Fork study section is 1.2%, 0.9% greater and mixed conifer forest (Pinus ponderosa and Abies than in the Middle Fork study section. Stream widths grandis) on north-facing slopes. Sparse riparian veg- at base ¯ow in the study sections vary between 2±23 etation consists of black cottonwood (Populus tricho- m in the Middle Fork and 2±34 m in the North Fork. carpa) snags, Douglas hawthorn (Crataegus dougla- Maximum pool depths range from2mintheMiddle sii), and graminoid communities dominated by sedges Fork to3mintheNorth Fork. and grasses. In the North Fork, steep topography and The Middle Fork and North Fork form the largest well-forested upslopes characteristic of the Abies gran- tributary to the main stem John Day River and drain dis zone (Franklin and Dyrness 1973) provide shade 6800 km2 (30% of the John Day basin) and contribute for the river lined with willow (Salix spp.) and red alder 60% of the average annual discharge. The respective (Alnus rubra). average annual discharges of the Middle Fork and Land use and resource extraction, such as road build- North Fork are 8 and 38 m3/s. Precipitation in the John ing, logging, and grazing, continue to affect the riverine Day basin is directly related to elevation; the lower environments of both the Middle Fork and North Fork basin receives as little as 23 cm/yr, whereas the upper (Mosgrove 1980, Oregon Water Resources Department portions of the basin receive Ͼ100 cm/yr. Seventy per- 1986). Large-scale dredge mining is no longer con- cent of annual precipitation in the John Day basin falls ducted in the John Day study area, but mining in the as snow and rain during November through May, with 1930s and 1940s has left a legacy of mine tailings in peak stream ¯ows of meltwater occurring in April and both streams. The Malheur National Forest contains May. Less than 10% of the annual precipitation falls most of the upper Middle Fork subbasin except for during the hot, dry summer. Daily air temperatures in privately owned, low gradient alluvial valleys; these the study area vary from winter lows of Ϫ18ЊC to sum- provide most of the spawning and rearing habitat for mer highs of Ͼ30ЊC. Summer water temperatures in spring chinook salmon. The Umatilla National Forest the Middle Fork study area often reach 30ЊC during and the North Fork John Day Wilderness encompass low ¯ow years. Water temperatures in the North Fork the entire upper North Fork basin. In contrast to the study section are cooler on average, but maximum sum- relatively pristine upper North Fork, the upper Middle 304 CHRISTIAN E. TORGERSEN ET AL. Ecological Applications Vol. 9, No. 1

Fork is subject to intensive land use. The alluvial val- METHODS leys of the Middle Fork have been drained and chan- We used an empirical approach to assess the distri- nelized and are currently used for cattle grazing. bution and behavior of spring chinook salmon with Spring chinook salmon respect to aquatic habitat. Our conceptual model was that salmon occurrence (the response variable) is re- Compared to neighboring basins, the John Day River lated to spatial patterns of stream temperature and and its tributaries are a refuge for spring chinook salm- stream habitat characteristics (explanatory variables), on, yet the spawning reaches today represent only a i.e., channel gradient, width-to-depth ratio, pool vol- small fraction of the probable presettlement (ϳ1800) ume, and pool occurrence. We expected the longitu- distribution (Li et al. 1995). Estimates place historical dinal distribution of salmon to take one of two theo- numbers of spring chinook in the John Day basin at 2± retical forms: (1) a uniform distribution, with the salm- 6ϫ the current number (Oregon Water Resources De- on evenly distributed throughout the study section, or partment 1986). Historical accounts indicate that the (2) a patchy pattern, e.g., with the salmon clustered spatial extent of spring chinook salmon spawning hab- either in one short reach or in several disjunct patches. itat extended farther downstream than the current dis- The null hypothesis was that the longitudinal distri- tribution (Ogden 1826, 1829). Though dams on the bution and density of salmon is uniform or independent lower Columbia River likely reduced spring chinook of stream temperature and habitat variables. The work- salmon in the John Day River (Oregon Department of ing hypothesis was that salmon cluster in reaches with Fish and Wildlife 1995), habitat alteration throughout preferred habitat, i.e., relatively cool water, avoiding the basin continues to affect their habitat in the upper reaches with unsuitable habitat. We expected that salm- reaches of the John Day basin (Lindsay et al. 1986, on may be responding to multiple habitat characteris- Wissmar et al. 1994, Lichatowich and Mobrand 1995, tics simultaneously and that the relative importance of National Marine Fisheries Service 1998). habitat characteristics would differ between subbasins. Adult spring chinook salmon enter natal streams in Given the close relationships among habitat variables, spring, several months before spawning, when water we also expected some correlations among explanatory temperatures are still within preferred tolerance zones variables. for migration. Peak migration rates of adult spring chi- nook correspond with peak ¯ows during May and June Salmon and habitat distribution (B. A. McIntosh, unpublished data). The salmon must remain, or hold, in headwater streams before they Continuous sections of known spring chinook hold- spawn in fall. They often are exposed to high ambient ing habitat (Oregon Water Resources Department 1986, stream temperatures and low ¯ow conditions, especial- Fig. 1) were systematically surveyed to map and obtain ly in agricultural and range lands where stream ¯ow is exhaustive counts of adult chinook salmon during late diverted for irrigation and shade from riparian vege- July and early August in the Middle Fork (route in- tation is greatly reduced. In accordance with the Q10 tervals 72±113) and the North Fork (route intervals 95± principle, energy expenditure in ®shes increases at el- 168). To minimize disturbance to salmon, surveys took evated temperatures (Wootton 1990) and the reproduc- place prior to peak daily temperatures. Adult salmon tive performance of migrating and holding salmon with were located and counted visually using two-person ®nite energy reserves is compromised when stream teams consisting of a diver, equipped with mask and temperatures rise above thermal tolerance zones (Van snorkel, and an observer/data recorder on shore. Geo- der Kraak and Pankhurst 1997). In addition to the direct graphic locations of salmon were recorded using a effects of high temperature on metabolic rate, the sus- global positioning system (GPS) with differential cor- ceptibility of coldwater ®shes to infection and disease rection (accurate to 10 m) and 1:24 000 scale topo- increases when they are thermally stressed (Schreck graphic maps (accurate to 200 m). Habitat use data for and Li 1991). chinook salmon were collected on channel unit type High stream temperatures throughout the lower (e.g., pool/rif¯e), number of ®sh, behavior, instream reaches of the John Day River restrict spring chinook cover (i.e., boulder, turbulence, large woody debris, and salmon to the upper portions of the basin. Ambient undercut banks), water temperature, depth, and domi- water temperatures in spawning reaches for spring chi- nant substrate composition for each channel unit con- nook in the Middle Fork and the main stem John Day taining salmon. Detailed hand-drawn maps of channel River frequently exceed both the thermal optima cited unit morphology, riparian cover, and ®sh locations at for spring chinook migration (16ЊC) and spawning the subunit scale served as ®eld references for thermal (14ЊC) and the upper zone of thermal tolerance (22ЊC) imagery. (Bell 1986, Armour 1991, Bjornn and Reiser 1991). Information on the seasonal movement patterns of Spring chinook no longer oversummer in the lower salmon was necessary for determining the degree to reaches of the John Day basin because water temper- which salmon were moving while distributional sur- atures there consistently exceed the upper incipient le- veys were being conducted. In a related study (con- thal level of 25ЊC. ducted concurrently and during the previous year), ra- February 1999 SALMON ECOLOGY AND THERMAL REFUGIA 305 diotelemetry of tagged spring chinook salmon in the imum air temperatures for 5 August and 8 August were Middle Fork and North Fork con®rmed that the distri- 33.9ЊC and 32.2ЊC, respectively. Thermal imagery in bution of salmon varied little during the holding phase; the 8±12 ␮m wave band was collected with a calibrated tagged salmon typically occupied the same channel unit Thermovision 800 thermal imager (AGEMA Infrared during this phase (D. M. Price and B. A. McIntosh, Systems) from a helicopter ¯ying 40 km/h in an up- unpublished data). stream direction at 250±300 m above the river surface Stream habitat survey data were collected separately at an oblique angle of 35±40Њ from the nadir. Main- from distributional ®sh surveys. Habitat survey data taining a constant height above the ground was dif®cult were necessary for comparing overall habitat use by due to complications such as air currents and steep chinook salmon to spatial patterns of habitat avail- canyon walls. With a 20Њ ®eld of view and an image ability in each study basin. Continuous sections of size of 140 ϫ 140 pixels, the thermal imagery had a known salmon habitat on the Middle Fork and North ground resolution of 20±60 cm. Analog image data Fork were surveyed systematically to map and quantify were calibrated for an emissivity of 0.96, converted to in-stream habitat characteristics, i.e., pool/rif¯e fre- Celsius temperature, digitized, and stored in-¯ight at a quency and stream channel dimensions. Stream surveys rate of 3 frames/s on the hard drive of an onboard were conducted after Hankin and Reeves (1988) during computer. Time of day, frame number, and pixel sta- base ¯ow conditions in the month of October in Middle tistics were stored in header ®les associated with each Fork (1993) and North Fork (1994) study sections (see digital image. Fig. 1). Pool volumes were calculated from corrected estimates of pool surface area and mean depth (Bisson Image processing and GIS et al. 1982, Bisson and Montgomery 1996). We used IMAGINE image processing software (ER- Thermal patterns DAS 1995) to display and analyze thermal imagery. Temporal and spatial water temperature patterns Image processing involved four steps: (1) extraction were assessed using digital temperature recorders at and decompression of raw data from 8-mm data tapes, point locations and thermal remote sensing of stream (2) composition of image mosaics, and (3) thermal clas- reaches. Six temperature recorders (Onset, accuracy si®cation of mosaics. Raw image data (32-bit ¯oating Ϯ0.2ЊC) were placed individually at the upper and low- point) were extracted, individually or collectively, from er boundaries of each study section (two each in the compressed ®le archives according to frame reference Middle and North forks, and two in a tributary of the numbers, which corresponded to the exact date and North Fork) and programmed to record temperature time of image acquisition. To compose image mosaics, every 30 min to provide information on daily and sea- the gray-scale images were rotated and aligned indi- sonal water temperature ¯uctuations and serve as tem- vidually with 20±30% overlap and digitally stitched in perature ground-truth points for thermal imagery. Dur- a downstream direction using a ``last overlay'' tech- ing remote sensing over¯ights, simultaneous ground- nique (ERDAS 1995). Constructing mosaics in a down- truth measurements also were collected manually to stream direction masked temperature distortions on the compare radiant temperatures recorded in the imagery trailing edge of each image. Supervised classi®cation to actual kinetic water temperatures. Water temperature was applied to colorize thermal image mosaics in 1ЊC measurements were made with hand-held, calibrated increments. No attempt was made to correct for spatial digital thermometers (accurate to Ϯ0.1ЊC) in rif¯e and distortion in the image mosaics caused by the varying pool habitats at the surface and in the water column. oblique angle at which the imagery was collected. Remote sensing and airborne videographic methods Ground measurements of known channel unit dimen- have been used effectively in a variety of inland hy- sions, roads, and bridges were used to determine the drologic applications (Ellis and Woitowich 1989, Ran- approximate map scale of each image mosaic. go 1994, Crowther et al. 1995, Hardy and Shoemaker Digital hydrography data (1:100 000 scale) provided 1995). Thermal remote sensing methods have dem- the map template in a geographical information system onstrated potential as tools for spatial analysis of ter- (GIS) for spatial analyses of salmon distribution, restrial and aquatic systems (Atwell et al. 1971, Hick stream temperature, and aquatic habitat. Locational ®sh and Carlton 1991, Luvall and Holbo 1991, Jessup et distribution and temperature data from GPS and to- al. 1997). We used low altitude forward-looking infra- pographic maps were entered and organized in the GIS. red (FLIR), collected in the ®rst week of August 1994, Stream survey data were georeferenced (within Ϯ200 to map spatially continuous patterns of stream tem- m) to hydrography layers using Arc/Info (ESRI 1996) perature. Thermography contractors surveyed ϳ120 dynamic segmentation techniques (Radko 1997). To fa- km of the Middle Fork and North Fork on two cloudless cilitate statistical analysis of point data, such as salmon days at 1430±1600 in the afternoon to capture peak locations and temperature sample points from remote daily water temperatures. Mean daily stream temper- sensing, the route-measure, or ``route interval,'' co- atures in both basins were 1.6ЊC higher during the 5 ordinate system was employed (ESRI 1996). In the August over¯ight than on the 8 August over¯ight. Max- GIS, route-measure coordinates were assigned to salm- 306 CHRISTIAN E. TORGERSEN ET AL. Ecological Applications Vol. 9, No. 1 on locations and stream temperature and habitat data gitudinal pro®le analysis because it examines the func- layers. tional relationship between a binary response variable and categorical explanatory variables, and it requires Statistical analysis no assumptions regarding normality or covariance The objective of statistical analysis was to compare structure (Hosmer and Lemeshow 1989, Trexler and peaks and troughs, or patchiness, in numbers of salmon Travis 1993). Rieman and McIntyre (1995) and Wiley with stream temperature and habitat patterns along the et al. (1997) used logistic regression in a similar man- longitudinal stream pro®le and determine the presence ner to analyze ®sh species presence or absence with of signi®cant (P Յ 0.05) associations. Habitat use/ respect to stream habitat and hydrologic basin char- availability analysis and logistic regression were used acteristics. We used logistic regression to analyze peaks to assess associations of chinook salmon occurrence and troughs (binary response) in the longitudinal pro- with stream temperature and habitat variables. The hab- ®le of salmon density (see Table 1) and quanti®ed how itat variables entered for analysis were stream gradient, variation in salmon density was explained by peaks channel width-to-depth ratio, and volume and number and troughs in longitudinal pro®les of stream temper- of large pools (Table 1). Pools were considered large ature and habitat (explanatory variables). Explanatory if they were Ն0.7 m deep, the approximate mean depth variables and interactions were tested for associations of pools used by salmon in both North and Middle Fork with salmon density using the maximum likelihood study sections. For longitudinal analysis, peaks and method (SAS Institute 1990). Regression models were troughs in salmon numbers, temperature, and stream selected using multiple logistic regression with step- habitat were de®ned relative to the expected mean or wise variable selection (␣ϭ0.05) in SAS and the like- median values for each study section (Table 1). Ex- lihood-ratio test outlined by Trexler and Travis (1993). pected values represent a uniform distribution to which the actual clustered distribution of salmon and stream RESULTS habitat variables may be compared. Remote sensing of stream temperature Longitudinal spatial pro®les.ÐAs explained in the preceding section on GIS methods, the records of each Thermal remote sensing integrated with a GIS en- variable were geographically referenced with route- abled us to use a multiscale approach to examine ther- measure coordinates. The variables were summarized mal patterns in streams. Point pattern maps of stream longitudinally in 1-km bins either as sums or means temperature were constructed to display and quantify and plotted vs. route-measure coordinate, i.e., distance section-level longitudinal temperature patterns in each downstream by the river's path. As each bin represents 60-km study section (Fig. 2). Temperature maps were a sampling unit, the spatial resolution of longitudinal generated in a GIS using stream temperatures sampled analysis was 1 km, and the extent of analysis was equal from individual thermal images. Ten sample points to the length of each study section: 52 km in the Middle were selected in the thalweg and averaged for each Fork and 75 km in the North Fork. The three advantages image frame. Because the imagery was not collected of the 1-km-bin approach are that (1) data are sum- with simultaneous geographic coordinates, the images marized according to the speci®ed spatial scale of anal- were georeferenced after the ¯ight based on known ysis, i.e., reach level, (2) geographic positioning of the landmarks such as channel curvature, roads, and bridg- data along the longitudinal pro®le is preserved, and (3) es that could be detected in the imagery. Image loca- the analysis is suited to the sampling interval in the tions between known ground locations were positioned longitudinal temperature pro®les. using linear interpolation. Spacing of sampled image Temperature and habitat associations.ÐHabitat use frames was 675 Ϯ 297 m ([mean Ϯ 1 SD], n ϭ 85 patterns of salmon were analyzed by comparing elec- frames) in the Middle Fork and 783 Ϯ 200 m (n ϭ 90 tivity indices for reach-level and channel unit charac- frames) in the North Fork. Continuously recording data teristics. Ivlev's electivity index is a dimensionless loggers were used in each study section to progres- number that compares the proportion of resource used sively correct for elapsed ¯ight time and associated by an animal to the proportion available in a speci®ed stream temperature change. The duration of over¯ights area of study (Manly et al. 1993). Electivity indices in each subbasin did not exceed 1 h, during which time range from Ϫ1 and approach ϩ1, where negative values stream temperature increased by 0.6±1.2ЊC. Temporal suggest avoidance and positive values suggest selec- temperature corrections were made within, not across, tion. Simultaneous Bonferroni con®dence intervals (␣ subbasins. ϭ 0.05) were calculated to determine whether prefer- Ground-truth data from automatic temperature re- ence or avoidance responses were statistically signi®- corders and manual measurements collected during re- cant (White and Garrott 1990). mote sensing over¯ights veri®ed that image tempera- Multiple logistic regression was used to analyze the tures were accurate. Surface water temperature mea- spatial association of salmon occurrence with longi- sured by FLIR was a good indicator of water temper- tudinal patterns of stream temperature and stream hab- ature; however, careful image interpretation was itat variables. Logistic regression is well suited to lon- necessary to avoid sampling temperatures from non- February 1999 SALMON ECOLOGY AND THERMAL REFUGIA 307

TABLE 1. Expected values de®ning peaks and troughs in the longitudinal distribution of chinook salmon and reach-level habitat characteristics in the John Day River, Oregon. Numbers in parentheses are coef®cients of variation.

Expected value Category Middle Fork North Fork Categorical variable² Mean Salmon (no.) 3 (1.49) 5 (1.50) Salmon density (P) Pool volume (m3)³ 316 (1.27) 1042 (1.12) Pool volume (P) Pools (no.)³ 2 (0.85) 3 (0.68) Pool density (P) Median Water temperature (ЊC) 24 (0.04) 21 (0.08) Temperature (T) Gradient (%) 0.6 (0.46) 1.2 (0.53) Channel gradient (T) Width : depth 31 (0.37) 48 (0.18) Width : depth (T) Notes: Peaks and troughs de®ne categorical variables used in logistic regression. Values were calculated from 1-km reach totals and means for salmon and habitat variables depicted in Fig. 5. For all analyses n ϭ 92 salmon in the Middle Fork; n ϭ 302 salmon in the North Fork. ² Letters in parentheses indicate whether the category of interest for each variable was a peak (P) or a trough (T) relative to expected values. ³ Reach-level analysis includes deep pools (depth Ն0.7 m) only.

Fig. 2. Thermal remote sensing of stream temperature patterns in the (a) Middle Fork and (b) North Fork John Day River, Oregon, at the section-level spatial scale. The speci®c reaches outlined by black squares contained the highest concentration of chinook salmon in each study section. These black squares also show the location and spatial extent of subsequent thermal image mosaics in Fig. 3. 308 CHRISTIAN E. TORGERSEN ET AL. Ecological Applications Vol. 9, No. 1 water stream features such as rocks, wood, and vege- North Fork. Total number and average density of salm- tation in thermal images. It was also critical to deter- on was greater in the North Fork study section (see mine the degree of vertical mixing in the water column, Table 1). Of the salmon holding in the Middle Fork, so that surface water temperature measurements could 86% occurred in alluvial valley as opposed to canyon be con®rmed as valid representations of stream tem- reaches. Focal points for salmon holding in the Middle perature. Manual temperature measurements in several Fork were low gradient meadows with pronounced deep pools revealed that vertical mixing, ostensibly due channel meandering. Salmon were distributed through- to stream¯ow within the water column, was thorough out the North Fork study section, but focal holding even in pools Ͼ2 m deep. Field observations of kinetic reaches were located in colluvial canyons with deep water temperature compared to radiant temperatures (n bedrock-formed pools in the North Fork John Day Wil- ϭ 13 comparisons) revealed a 1:1 relationship (P Ͻ derness. Salmon were distributed nonuniformly 0.0001, r2 ϭ 0.97) without accounting for confounding throughout each of the study sections, indicating ap- factors such as shade, depth, and overhanging vege- parent preferences for certain reaches (Fig. 5). Peaks tation. The difference between kinetic and radiant tem- in salmon density in the Middle Fork corresponded perature averaged 0.4ЊC (data spread Ϯ 0.1 SE). with peaks in pool density and volume and troughs in Analysis of thermal image mosaics facilitated de- the stream temperature pro®le (Fig. 5A), whereas peak tection of stream temperature patterns at reach, channel densities of salmon in the North Fork coincided with unit, and subunit spatial scales in selected reaches with localized, relatively low troughs in width-to-depth ratio high densities of salmon in Middle and North Fork and peaks in pool volume (Fig. 5B). Salmon in the study reaches. Reach-level thermal mosaics were use- North Fork were dispersed throughout the study section ful for examining the thermal context of stream features in approximately normal distribution, with low num- (Fig. 3). The high spatial resolution (20±60 cm) of the bers in both the highest and lowest temperature zones. imagery effectively resolved thermal anomalies asso- Stream habitat.ÐRif¯es were the dominant stream ciated with irrigation channels, tributary and ground- habitat type by surface area in the Middle Fork and water inputs, and riparian vegetation related to solar North Fork study sections (Table 2). The longitudinal aspect and soil moisture gradients. The ¯ow of sub- distribution of pool density and volume in the Middle surface water through cut-off meanders and other sub- Fork and North Fork exhibited clustered patterns (Fig. surface pathways was recognizable in thermal imagery 5). In the Middle Fork, stream reaches with the highest as an area of increased soil moisture characterized by concentrations of pool volume were located in the relatively low temperature and increased emissivity due downstream portion of the study section, whereas to soil water content. reaches with the highest pool density were located in Locations of holding spring chinook salmon in se- the upper portion of the study section (Fig. 5A). Sev- lected reaches were examined qualitatively with respect enty-eight percent of total pool volume in the Middle to ®ne-scale (i.e., channel unit and subunit) surface Fork study section was concentrated in low gradient water temperature patterns in the imagery (Fig. 4). With alluvial valleys. Pool volume in the North Fork was the aid of hand-drawn maps sketched during ®sh sur- highest in the downstream portion of the study section veys, the positions of salmon were superimposed on where stream gradient was relatively low; however, thermal imagery via overlays. Qualitative analysis at several localized reaches with high pool volume were channel and subunit spatial scales was based on visual present upstream in high gradient, bedrock-dominated interpretation only; no areal measurements of temper- stream sections (Fig. 5B). Relatively low troughs in ature regions were calculated from the imagery. Due width-to-depth ratio were spatially associated with to varying sensor angles during data collection, image reaches containing large numbers of pool habitats. mosaics were not photogrammetrically correct and Comparisons of pool habitats in the North Fork and therefore were not georeferenced in the GIS. However, Middle Fork clearly indicated that even at base ¯ow visual interpretation in conjunction with sketched ®eld conditions the North Fork study section had far more maps was instructive in several instances where salmon large, deep pools available as holding habitat for salm- were holding in cool-water patches associated with lat- on (Fig. 6). eral subsurface water ¯ow. Fine-scale analysis of ther- Stream temperature.ÐStream temperature patterns mal pattern was conducted only in selected reaches in in the North Fork and Middle Fork showed general the Middle and North Fork study sections because the warming trends in the downstream direction punctuated spatial resolution of imagery differed somewhat be- by cool and warm anomalies (Fig. 7). Overall maxi- tween basins, and construction and management of mum reach temperatures were higher in the Middle larger image mosaics was cost prohibitive and exceed- Fork, even after accounting for daily temperature dif- ed our existing computer hardware capabilities. ferences between aerial survey dates. In the Middle Fork, thermal gradients between reaches were steeper Distribution of salmon and aquatic habitat and stream temperature patterns were generally more Salmon distribution.ÐWe observed 92 adult spring complex and patchy compared to the North Fork. Lon- chinook salmon in the Middle Fork and 302 in the gitudinal temperature variations of 3±4ЊC occurred fre- February 1999 SALMON ECOLOGY AND THERMAL REFUGIA 309

Fig. 3. Reach-level patterns of stream temperature in the (a) Middle Fork and (b) North Fork John Day River, Oregon. Annotations explain features in thermal imagery, and black squares indicate the location and spatial extent of subsequent thermal image mosaics in Fig. 4. For thermal color classi®cation, see Fig. 2. Temperatures Ͼ27ЊC are scaled in gray tones from dark (cool) to light (warm).

Fig. 4. Thermal patterns in rif¯e/pool sequences in the (a) Middle Fork and (b) North Fork John Day River, Oregon. Annotations explain features and indicate locations of salmon in thermal image mosaics. For thermal color classi®cation, see Fig. 2. Temperatures Ͼ27ЊC are scaled in gray tones from dark (cool) to light (warm). 310 CHRISTIAN E. TORGERSEN ET AL. Ecological Applications Vol. 9, No. 1

FIG. 5. Longitudinal stream pro®les of salmon numbers, stream temperature, and stream habitat in the (a) Middle Fork and (b) North Fork study sections. Data are summarized by means (solid black lines) or densities (black bars) in 1-km intervals. Mean width : depth was calculated from a LOWESS curve after Chambers (1983). Dashed vertical lines trace peaks in salmon density for alignment with stream habitat pro®les. Dashed horizontal lines represent reach medians or densities described in Table 1. quently over relatively short distances in the Middle Middle Fork displayed distinct troughs and peaks cor- Fork, whereas in the North Fork variations over similar responding respectively with alluvial valley reaches distances rarely exceeded 2ЊC. and localized shallow, exposed reaches. Lateral Broad spatial patterns of stream temperature in the groundwater inputs were most likely a source of cool- Middle Fork and North Fork appeared to be associated ing in some alluvial valleys of the Middle Fork. In the with major landscape features such as tributaries and North Fork, anomalies in the downstream warming valley morphology. Downstream from the spring-fed trend were apparent at 12 km and 24 km downstream source of the Middle Fork, stream temperatures in the from the source (Fig. 7). The trough at 12 km was longitudinal pro®le increased dramatically by 4ЊC, de- caused by a cold tributary, and the trough at 24 km creased by 2ЊC, and then peaked at 25ЊC (Fig. 7). Rapid corresponded with a deeply incised, topographically cooling occurred when a large volume tributary entered shaded canyon. A steep warming gradient in the North the Middle Fork 8 km downstream from the source. In Fork thermal pro®le occurred between 15 and 21 km a downstream direction, stream temperatures in the from the source. Over the length of this section, the February 1999 SALMON ECOLOGY AND THERMAL REFUGIA 311

TABLE 2. Analysis of habitat use and availability by spring chinook salmon in the John Day River, Oregon. Channel-unit and reach-level habitat selection by chinook salmon is described using electivity index and 95% con®dence intervals indicating statistically signi®cant preference or avoidance.

Middle Fork North Fork Proportion of Bonferroni Proportion of Bonferroni habitat in river con®dence habitat in river con®dence section intervals² section intervals² Occu- Avail- Lower Upper Electiv- Occu- Avail- Lower Upper Variables pied able 95% 95% ity³ pied able 95% 95% Electivity³ Channel unit variable Pool 0.98 0.13 0.94 1.02 0.77 0.82 0.20 0.77 0.88 0.61 Rif¯e 0.02 0.87 Ϫ0.02 0.06 Ϫ0.95 0.18 0.80 0.12 0.23 Ϫ0.64 Reach variable Temperature (T) 0.78 0.57 0.69 0.88 0.16 0.56 0.48 0.49 0.62 0.07 Pool volume (P) 0.58 0.34 0.49 0.73 0.28 0.55 0.34 0.48 0.61 0.23 Pool density (P) 0.73 0.40 0.62 0.83 0.29 0.44 0.44 0.36 0.50 0.00NS Gradient (T) 0.47 0.34 0.35 0.58 0.15 0.57 0.50 0.50 0.63 0.06NS Width : depth (T) 0.64 0.43 0.53 0.75 0.20 0.44 0.53 0.38 0.50 Ϫ0.09 Notes: Reach-level selection was determined by the location of salmon in peaks (P) or troughs (T) in the longitudinal distribution of stream habitat. See Table 1 for explanations of reach variables. ² If the Bonferroni con®dence interval includes the availability proportion, then the hypothesis of no preference or avoidance of this habitat type cannot be rejected. ³ Ivlev's electivity index is equivalent to (Pu Ϫ Pa)/(Pu ϩ Pa), where Pu is the proportion of resource used, and Pa is the proportion of the resource available. The index ranges from Ϫ1 and approaches ϩ1; negative values suggest avoidance, and positive values suggest preference. NS Indicates that avoidance or preference was not statistically signi®cant (Bonferroni con®dence interval: P Ͼ 0.05). stream received direct solar inputs as it ¯owed south- Fork, 98 and 82% of the salmon were in pools. Elec- westerly through a forest burn site in a comparatively tivities for pool habitats were signi®cant in both study wide valley with limited topographic and riparian shad- sections (Bonferroni con®dence interval: P Յ 0.05). ing. Electivity for pool habitats was highest in the Middle Fork, where depth was often the only form of cover. Habitat use vs. availability Rif¯e use by holding salmon was highest in the North Channel unit analysis.ÐPools were the channel unit Fork (18%) compared to the Middle Fork (2%). habitat most frequently used by spring chinook salmon Reach level analysis.ÐElectivity analysis of reach and they were used proportionately more than their habitat characteristics revealed that salmon in the Mid- availability in both Middle (13%) and North Fork dle Fork selected reaches that were relatively cool, low (20%) study sections (Table 2). In the Middle and North in gradient and width-to-depth ratio, and high in pool volume and pool density (Table 2). In the Middle Fork, 78% of the salmon holding in the Middle Fork were located in cool-water reaches (Table 2). In the North Fork, 56% of the salmon were located in reaches where stream temperature was lower than expected. Electivity for cool-water reaches in the Middle Fork was twice as high as in the North Fork. Analysis of salmon in the North Fork showed signi®cant positive election of cool-water reaches and reaches containing above av- erage pool volume (Bonferroni con®dence interval: P Յ 0.05). Salmon in the North Fork showed signi®cant avoidance of reaches with below average width-to- depth ratio (Table 2). Electivity indices in the North Fork for cool-water reaches and low width-to-depth ratio were relatively low compared to the strong pref- erence for pool volume. Logistic regression In the Middle Fork, the longitudinal distribution of salmon was strongly associated with patterns of stream FIG. 6. Histogram comparisons of pool volume and max- imum depth in the Middle Fork (MF) and North Fork (NF) temperature. Bivariate logistic regression of salmon study sections of the John Day River, Oregon. density, stream temperature, and habitat variables re- 312 CHRISTIAN E. TORGERSEN ET AL. Ecological Applications Vol. 9, No. 1

FIG. 7. Longitudinal pro®les of stream temperatures sampled from thermal imagery in the Middle Fork (MF) and North Fork (NF) study sections of the John Day River, Oregon. Point temperatures are annotated with generalized reach descriptions. Dashed horizontal lines at 23ЊC allow for direct comparisons between respective study sections. vealed signi®cant positive associations of salmon den- sity of salmon in the Middle Fork (Table 4). There was sity with cool-water reaches, pool density, pool vol- a statistically signi®cant interaction between cool-wa- ume, and low width-to-depth ratio (Table 3). The high- ter reach and pool density, indicating that both vari- est odds ratio for the variables predicting salmon den- ables are important with respect to salmon holding be- sity was reported for cool-water reaches. Stepwise havior. Odds ratios and chi-squared scores were highest logistic regression selected only cool-water reach and for cool-water reaches as predictors of salmon density. pool density as signi®cant variables explaining the den- Pool density was no more important than cool-water

TABLE 3. Estimated coef®cients from bivariate logistic regression of reach-level stream habitat variables explaining the distribution of spring chinook salmon in the John Day River, Oregon.

Ninety-®ve percent CL Estimated for odds ratios§ regression Wald Odds Reach variable df coef®cient² ␹2 P ratio³ Lower Upper Middle Fork Temperature (T) 1 2.43 Ϯ 0.59 16.88 Ͻ0.001 11.40 3.57 36.40 Pool volume (P) 1 1.07 Ϯ 0.46 5.47 0.019 2.93 1.19 7.20 Pool density (P) 1 1.91 Ϯ 0.51 13.77 Ͻ0.001 6.73 2.46 18.42 Gradient (T) 1 Ϫ0.19 Ϯ 0.45 0.19 0.663 0.82 0.34 1.97 Width : depth (T) 1 1.16 Ϯ 0.46 6.31 0.012 3.20 1.29 7.92 North Fork Temperature (T) 1 Ϫ0.25 Ϯ 0.28 0.79 0.376 0.78 0.45 1.36 Pool volume (P) 1 1.42 Ϯ 0.30 22.82 Ͻ0.001 4.15 2.32 7.45 Pool density (P) 1 Ϫ1.04 Ϯ 0.29 12.87 Ͻ0.001 0.36 0.20 0.63 Gradient (T) 1 0.75 Ϯ 0.28 6.97 0.008 2.11 1.21 3.67 Width : depth (T) 1 Ϫ0.94 Ϯ 0.29 10.65 0.001 0.39 0.22 0.69 Notes: In the logistic model, peaks (P) and troughs (T) in the longitudinal distribution of stream habitat were categorical explanatory variables used to predict the reach density of chinook salmon. See Table 1 for descriptions of reach variables. ² Regression coef®cients are depicted as estimate Ϯ 1 SE. ³ To make odds ratios interpretable for salmon occurrence, response data were ordered in the logistic model such that high salmon density (response variable) was assigned a categorical value of 1. § Wald con®dence limits (CL) are reported for odds ratios. February 1999 SALMON ECOLOGY AND THERMAL REFUGIA 313

TABLE 4. Stepwise model selection results from multiple logistic regression of reach-level stream habitat variables explaining the distribution of spring chinook salmon in the John Day River, Oregon.

Ninety-®ve percent CL Estimated for odds ratios࿣ regression Wald Odds Reach variable coef®cient² ␹2 P³ ratio§ Lower Upper Middle Fork Temperature (T) 1.96 Ϯ 0.63 9.62 0.002 7.10 2.05 24.47 Pool density (P) 1.31 Ϯ 0.57 5.23 0.022 3.72 1.21 11.48 North Fork Pool volume (P) 2.63 Ϯ 0.44 35.51 Ͻ0.001 13.10 5.85 33.00 Pool density (P) Ϫ2.09 Ϯ 0.42 25.00 Ͻ0.001 0.12 0.05 0.28 Width : depth (T) Ϫ0.76 Ϯ 0.34 4.94 0.030 0.50 0.24 0.91 Temperature (T) 0.71 Ϯ 0.35 4.09 0.043 2.04 1.02 4.09 Notes: In the stepwise model, peaks (P) and troughs (T) in the longitudinal distribution of stream habitat were categorical explanatory variables used to predict the reach density of chinook salmon. See Table 1 for descriptions of reach variables. Regression statistics for the Middle Fork model (2 df) were: deviance (Ϫ2 log L) ϭ 116.17 (intercept only) and 91.10 (intercept and covariates). Regression statistics for the North Fork model (4 df) were: deviance (Ϫ2 log L) ϭ 316.64 (intercept only) and 251.06 (intercept and covariates). ² Regression coef®cients are depicted as estimate Ϯ 1 SE. ³ The signi®cance level for stepwise variable selection was 0.05. § To make odds ratios interpretable for salmon occurrence, response data were ordered in the logistic model such that high salmon density (response variable) was assigned a categorical value of 1. ࿣ Wald con®dence limits (CL) are reported for odds ratios. reaches in predicting the density of salmon in the Mid- es within each subbasin. In the Middle Fork, most salm- dle Fork (maximum likelihood ratio: P Ͻ 0.05). The on held and spawned in low gradient, unconstrained ®nal stepwise model including cool-water reach and reaches, whereas in the upper North Fork where alluvial pool density correctly predicted 78% of the observa- valleys were not available, salmon selected both high tions of salmon in the Middle Fork study section. and low gradient reaches primarily within the North In the North Fork study section, peaks in salmon Fork John Day Wilderness. In both subbasins, pools numbers did not correspond consistently with low were selected by adult spring chinook, but between the stream temperatures. Bivariate logistic regression re- two streams, rif¯es were used more extensively in the vealed positive associations of salmon density with North Fork. stream gradient and pool volume (P Ͻ 0.01) and neg- Landscape level stream temperature patterns showed ative associations with low width-to-depth ratio and overall downstream warming trends. Inter-reach vari- pool density (Table 3). Stepwise variable selection in- ation in thalweg temperature on the order of 3ЊC oc- dicated that after accounting for pool volume, pool den- curred in both subbasins, but spatial patterns of water sity, width-to-depth ratio, and cool-water reach, stream temperature in the Middle Fork were more complex gradient no longer signi®cantly explained salmon den- and irregular compared to the North Fork. The coldest sity patterns (Table 4). Stepwise results also revealed reaches available to salmon within the Middle Fork that after pool volume, pool density, and width-to- study area were situated in low gradient, unconstrained depth ratio were entered in the logistic model, the in- reaches where the cooling in¯uence of subsurface ¯ow clusion of cool-water reach added minimal but signif- was apparent. The degree of behavioral thermoregu- icant (P Յ 0.05) explanatory power to the model. An lation by salmon depended entirely on the spatial scale interaction term for pool volume and cool-water reach of temperature comparisons, particularly in the Middle was statistically signi®cant, indicating the importance Fork where stream temperature was the most variable. of both pool volume and water temperature in the ®nal The reach-level association between salmon distribu- model. Ninety-®ve percent con®dence intervals for tion and stream temperature patterns was strongest in odds ratios of these two variables indicated a signi®- the warmest study section, the Middle Fork, and weak- cantly greater in¯uence of pool volume over cool-water est in the coldest study section, the North Fork. reach on the density of salmon in the North Fork. The ®nal stepwise model, including pool volume, pool den- Thermal refugia at multiple spatial scales sity, width-to-depth ratio, and cool-water reach, cor- Spring chinook salmon continue to exist in the upper rectly predicted 80% of the observations of salmon in Middle Fork John Day River in spite of maximum daily the North Fork. temperatures that exceed 25ЊC, the upper lethal limit for adult chinook salmon. Based on the ®ndings of DISCUSSION Gibson (1966), Kaya et al. (1977), and Berman and Spring chinook salmon were distributed unevenly Quinn (1991), our expectations were that salmon in throughout each of the North and Middle Fork study warm water would seek and utilize cold tributary con- sections, indicating that salmon preferred certain reach- ¯uences, cold pools, and pockets of cool water adjacent 314 CHRISTIAN E. TORGERSEN ET AL. Ecological Applications Vol. 9, No. 1 to the main stream. Several recent studies have sought which ®sh temperatures are compared. For this reason to identify the use of cool-water refugia by trout and it is necessary to examine extensive temperature pat- salmon (Matthews et al. 1994, Nakamoto 1994, Nielsen terns within and among stream reaches before con- et al. 1994). Nielsen et al. (1994) observed juvenile cluding that ®sh are responding, or not responding, to and adult steelhead (Oncorhynchus mykiss) in cold temperature patterns. Thermal imagery is particularly pools where surface water temperatures were 3±9ЊC useful in this situation because it can guide temperature warmer than those at the bottom. Berman and Quinn measurements and the placement of temperature mon- (1991) reported that adult spring chinook salmon be- itors for subsequent comparison with ®sh focal tem- haviorally thermoregulated to maintain internal tem- peratures. It also facilitates analysis of spatially con- peratures 2.5ЊC cooler than ambient water tempera- tinuous thermal patterns in entire river sections. The tures. Interest in behavioral thermoregulation has fo- disadvantages of the remote sensing approach are that cused typically on cold pools and microhabitats used one acquires only a snapshot in time of stream tem- by salmonid ®shes when ambient water temperatures perature patterns, and measurements are limited to sur- exceed upper levels of tolerance. These thermal refugia face temperature alone. Therefore, ground-based work in streams subject to high summer temperatures and is necessary to integrate spatially continuous, but tem- seasonally low ¯ows may explain the persistence of porally constrained, thermal imagery with temporally coldwater ®shes in warmwater (Ͼ25ЊC) environments continuous, but spatially limited, temperature monitor because even relatively minor differences in temper- data. ature are ecologically relevant for ®sh (Somero and Hofmann 1997). Habitat selection by spring chinook salmon As a complement to investigations of thermal refugia Resource selection by animals is determined by com- at microhabitat and channel unit levels, we examined paring the use of a particular resource or habitat by an temperature patterns across spatial scales of subunit, animal with its availability in the natural environment. channel unit, reach, and section. We used thermal re- Data on resource use are relatively simple to obtain mote sensing to assess multiscale patterns of stream and can be quanti®ed using nonbiased procedures temperature and to identify cool-water areas needing (White and Garrot 1990). However, determination of more detailed ground-based examination. We found the habitat available to a particular individual is often that increasing the scale of observation was instructive highly subjective (Manly et al. 1993). Our research in elucidating patterns of behavioral thermoregulation addressed the use and availability of cool-water areas by spring chinook salmon. Preliminary radiotelemetry and stream habitat by spring chinook salmon. Deter- analysis of salmon behavior conducted at microhabitat mination of what was available to salmon was prob- spatial scales suggested that salmon in the Middle Fork lematic because summer low ¯ow conditions physi- were not behaviorally thermoregulating, even during a cally prevented the movement of salmon between particularly warm summer when water temperatures reaches containing thermal refugia. Inter-reach move- reached 29ЊC in exposed stream reaches (D. M. Price ment patterns of salmon may also have been limited and B. A. McIntosh, unpublished data). Therefore, the during the summer prespawning phase because high preliminary conclusion was that chinook salmon were stream temperatures inhibited exploratory behavior. not behaviorally thermoregulating in the Middle Fork The coldest water temperatures in the North Fork John Day River because either they were adapted to and the Middle Fork were located in the headwaters of high water temperature or cold-water habitats were each subbasin. Theoretically, if temperature were the simply not available. Indeed, pools in the Middle Fork primary determinant of habitat selection, salmon would were not thermally strati®ed (C. E. Torgersen, personal be clustered in these reaches, especially in the North observation) like the deep pools described by Nielsen Fork where headwater reaches were accessible through- et al. (1994). However, analysis of thermal imagery out the summer. The assumption regarding the North from the same summer revealed that the reaches con- Fork salmon is that stream temperatures below a certain taining the greatest number of salmon were relatively threshold would be selected equally in the absence of cold reaches. Even within small-scale pool±rif¯e se- other habitat factors. In the Middle Fork, the combi- quences, the extent to which we perceived thermoreg- nation of water removal for irrigation and low mid- ulatory behavior by salmon depended directly on where summer ¯ows effectively made passage to headwater main channel temperatures were sampled. reaches physically impossible for salmon. In the Mid- It is critical to specify the spatial scale of analysis dle Fork, the salmon that occupied headwater locations in studies of behavioral thermoregulation by ®shes in during the summer most likely arrived in the spring the natural environment. A thermal refuge is de®ned when ¯ows were suf®cient to allow passage. by the temperature difference between the coldest re- Summer holding habitats were selected by salmon gion within a refuge and the surrounding habitat. in the spring when stream ¯ow was high and stream Stream temperatures are spatially autocorrelated; there- temperatures were low, so habitats must have been se- fore, the degree, or signi®cance, of behavioral ther- lected based on criteria independent of temperature, moregulation depends entirely on the locations to such as channel morphology and chemical factors car- February 1999 SALMON ECOLOGY AND THERMAL REFUGIA 315 ried by groundwater and subsurface ¯ow. Use of pool ¯ow. Increased rif¯e use by chinook salmon in colder habitats is an effective adaptation by spring chinook, streams is related to other factors such as rif¯e depth especially in the Middle Fork, where pools are often as a form of cover, but depth, too, in¯uences water the only form of small-scale thermal refuge available. temperature (Brown 1983). Preliminary results Relatively deep pools are geomorphically recognizable throughout northeastern Oregon have demonstrated independent of stream ¯ow, and suitable spawning that spring chinook salmon occupied rif¯e habitats gravels typically accumulate in downstream pool mar- more frequently in cold streams than in warm streams, gins. Large, deep pools are generally considered the even when pool habitats were available (D. M. Price primary freshwater holding habitat used by chinook and B. A. McIntosh, unpublished data). throughout their range (Healey 1991). However, pools alone are not the primary determinant of habitat se- Reach selection lection by spring chinook salmon. Highest reach den- Resource selection by ®shes occurs across multiple sity of large pools (depth Ն0.7 m) in both the North spatial and temporal scales (Schlosser 1991). Bayley Fork and Middle Fork occurs downstream of the reach- and Li (1992) noted that resource selection can follow es occupied by salmon. Stream temperatures in the a hierarchy of habitat scales, with selection in each downstream reaches of both streams exceed the tol- order being conditional on higher (small-scale) or low- erance level for spring chinook, thus rendering nu- er (large-scale) orders. For example, during summer, merous downstream pool habitats inaccessible to salm- spring chinook in the Middle Fork used relatively cold on. This indicates that trade-offs between pool avail- reaches; however, salmon migrated in spring and actual ability and stream temperature play important roles in habitat selection at that time was more likely based on determining the longitudinal extent and carrying ca- physical reach characteristics and in-stream chemical pacity of spring chinook holding habitat. cues, because water temperatures were far below sum- Energy costs of midsummer exploration for cool- mer maxima. Once within a reach of choice, the salmon water reaches may be prohibitive for salmon in warm- sought cover such as pools, undercut banks, and ther- water environments. An adult spring chinook salmon mal refugia if they were available at channel unit and residing throughout the summer in freshwater is op- subunit levels. erating on a limited energy budget. Ceasing to feed in Anadromous salmonids return to natal streams and freshwater, it lives off its own protein and fat reserves, tributaries by following imprinted chemical cues to lo- so that reproductive success and survival depend on cate the same ``kind'' of water in which they emerged the ability of the salmon to conserve energy prior to and matured (Johnsen and Hasler 1980, Johannesson and in preparation for spawning (Gilhousen 1980). 1982, Thorpe 1988). In marginal habitats such as the Spring chinook salmon derive energy savings by uti- Middle Fork, the ability to locate limited habitats suit- lizing thermal refugia and low velocity habitats to low- able for holding and spawning within a 100-km length er their basal and active metabolic rates (Berman and of river is critical for survival. Quinn (1993) reviews Quinn 1991; T. P. Quinn, Fisheries Research Institute evidence that salmon released as smolts in a particular and Center for Streamside Studies, University of Wash- section of a river were more likely to return there than ington, Seattle, Washington, personal communication). other sections. Suitable spawning habitat is even more Total energy losses can be reduced substantially over limited in most rivers than super®cial observation may the prespawning period by salmon occupying cooler suggest because chinook require subgravel ¯ow to aer- habitats and thus avoiding warm water. For spring chi- ate eggs, which require high dissolved oxygen levels nook salmon (1.8±6.1 kg) in the Yakima River (a neigh- (Burger et al. 1985, Healey 1991). Thorpe (1994) noted boring river in the Columbia Basin), a 2.5ЊC reduction that the homing instinct of adult salmonids to their natal in temperature could produce a 12±20% decline in ba- streams can either function as insurance, such as in the sal metabolic rate (Berman and Quinn 1991). Middle Fork, or lead to extinction of stocks in the event Our observations in the Middle Fork John Day River of localized environmental disturbances. reveal that spring chinook salmon derive energy sav- Prior to human disturbances to the landscape, un- ings through habitat selection. Temperature differences constrained reaches in the upper Middle Fork probably of Ͼ3ЊC between reaches in the Middle Fork represent functioned even more effectively as reach level thermal substantial energy savings for spring chinook salmon refugia for spring chinook (Sedell et al. 1990). Wide occupying cool reaches. Energy constraints suggest alluvial valleys with multiple pool/rif¯e sequences and that movement of salmon between reaches should be complex side-channel/backwater habitats increase the limited during summer. Indeed, results from two years potential for groundwater connectivity and exchange of radio-telemetry in the Middle Fork revealed that with the stream channel (Brunke and Gonser 1997). spring chinook have a small summer home range lim- These complex ¯oodplain features are apparent in the ited most frequently to a single pool (D. M. Price and Middle Fork only as relics visible in aerial photographs B. A. McIntosh, unpublished data). Selection of pools and thermal imagery, but in some reaches the hydro- appears to be a behavioral adaptation for coping with geologic template still buffers the stream ecosystem warm temperatures in addition to providing refuge from against human perturbations such as grazing and chan- 316 CHRISTIAN E. TORGERSEN ET AL. Ecological Applications Vol. 9, No. 1 nelization. For example, in the major holding and districts in the Malheur and Umatilla National Forests for spawning reaches of the Middle Fork ϳ10 km from the providing logistical assistance in the ®eld and the Aquatic/ Lands Interaction Group at the Paci®c Northwest Research source, water temperatures were 3±4ЊC cooler than Station in Corvallis, Oregon for GIS and computing support. downstream habitats, and groundwater dynamics ap- Thermographic services were provided by R. Horvath and K. peared to be the principal factor moderating stream Gunderson at the Environmental Research Institute of Mich- temperature. The alluvial valley 13 km downstream igan (ERIM). We also thank T. Reeve, E. Brown, J. Overby, C. Karchesky, and numerous dedicated ®eld assistants who from the source of the Middle Fork is one such reach helped conduct ®sh and stream habitat surveys. Financial where groundwater dynamics apparently maintain sub- support for this project was provided by the Bonneville Power optimal, but tolerable, spawning and holding habitat Administration (project No. 88-108), the U.S. Environmental for chinook salmon in spite of grazing, channelization, Protection Agency (EPA) and the Intelligence Community's and railroad construction. Government Applications Task Force, the Confederated Tribes of the Warm Springs Reservation, and the EPA/Na- Restoration implications of patchiness in tional Science Foundation Joint Watershed Research Program (grant R82-4774-010). The authors are grateful for the thor- lotic systems ough review and statistical guidance provided by J. A. Jones. The varied spatial and temporal patterns of resource Critical reviews from R. A. Stein, T. P. Quinn, and an anon- patches comprising a landscape mosaic to which bio- ymous reviewer greatly improved the manuscript. Publication of this paper was supported, in part, by the Thomas G. Scott logical organisms respond have long been the focus of Achievement Grant. This paper is Technical Report No. terrestrial biogeography and landscape ecology (Brown 11,434 of the Oregon Agricultural Experiment Station. and Gibson 1983, Forman and Godron 1986, Kotliar LITERATURE CITED and Wiens 1990). Recent applications of landscape- Armour, C. L. 1991. Guidance for evaluating and recom- based models and patch dynamics theory in lotic sys- mending temperature regimes to protect ®sh. U.S. Fish tems have shown promise for addressing increasingly Wildlife Service Biological Report 90(20). critical issues of stream habitat fragmentation (Pringle Atwell, B. H., R. B. MacDonald, and L. A. Bartolucci. 1971. et al. 1988, Grossman et al. 1995). From a patch dy- Thermal mapping of streams from airborne radiometric scanning. 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