Table of Contents

Sierra Nevada Bio-region
Chapter 1: Ecological Integrity of Ecosystems - Aquatic Ecosystems

Current Condition

Introduction

Water is the overarching environment of aquatic ecosystems. The quantity and quality of water influences the habitat conditions for the fish, insects, and other living things that occupy aquatic habitats, figure below. “Connected” or continuous the water flow is integral to the functionality of flowing water aquatic ecosystems, such as streams or rivers . For example, are fish able to migrate up and down a river or creek as needed to fulfill their life history requirements? Are large woody debris and sediment delivered, sorted and routed through stream networks at appropriate rates? Are water temperatures throughout the stream networks conducive to habitat needs of aquatic organisms?

Conceptual diagram of aquatic ecosystem components and interactions.
[Comment:
The meaning of all the arrows is not clear. Need to add dams and diversions.
Grazing, roads, mining, recreation, vegetation management all contribute to invasive species establishment; this graphic suggests that there are no causes, when in fact, invasive species are symptoms, not first causes, of ecosystem transformation/change/conversion. Also, pesticides and other pollutants are missing from graphic].

aqconceptual.jpg



Key Ecological Integrity Indicators/Measures

Ecological indicators of aquatic ecosystems include both abiotic (non-living), and biotic (living) components of ecosystems associated with water. The abiotic factors include those related to water such as water quality, water quantity and seasonal flow patterns. There are many different living organisms that occur in aquatic ecosystems but there are several that are the focus here because of their widespread use as indicators of ecological integrity (benthic macrointertebrates—insects), noted value to humans, are carnivores and have broad connectivity needs for population stability (fish), or are vulnerable to numerous stressors (amphibians-frogs and salmanders). There are other indicators that are useful integrative indicators of overall aquatic ecosystem function, such as the proper functioning condition rating used by the USFS that incorporates water, riparian vegetation condition, and erosion history and potential in the terrestrial landscape.

Based upon the conceptual model and available existing information, the following list of indicators and measures were selected.

Element/Function
Indicator
Measure
Source
Biological Integrity
macroinvertebrate composition
indices in wadeable perennial streams
SWAMP - CA database

fish populations: native, desirable non-native, invasive/nuisance,
geographic distribution & status
PISCES database (USFS)

amphibian populations
geographic distribution & status
SNAMP –Cathy Brown, CDFG, NPS, Amphibian Population Task Force

fish/amphibian condition
health (parasites, genetic deformities diseases eg. Chytrid))
SNAMP –Cathy Brown, CDFG, NPS
Water Quality
(see also Chapt. 2)
stream characteristics
woody debris, fine substrate, pool depth
NRIS

nutrient levels



water temperature

NRIS

% of water bodies
rating
CA 305b list, state water board

Pathogens
E coli, giardia, etc.
?

Chemical pollutants
Pesticides/herbicides, diesel oil, mercury, etc.
?
Water Quantity
flow characteristics
hydrograph
USGS, DWD
Process- Connectivity
(see also Chapt. 2, and Drivers and Stressors Chapt.)
ability to migrate (gene flow), energy to flow and nutrient cycling to occur
presence/abundance of dams, % of network connected
DWR database
Process - Energy flow & nutrient cycling
litter inputs from riparian hardwoods
fire presence/absence
FACTS or NFPLAN database, fire severity monitoring

algae
index
literature
Integrated biotic and abiotic integrity
watershed condition
index
DUBCAP

Current Condition: Aquatic Ecosystems


Water quality

The National Forests in California have generally provided a high level of protection for the Sierra Nevada headwaters. For example, a recent statewide survey found that streams in forested watersheds were in better condition than streams in watersheds in any other land use (Ode 2007). Water quality of the Sacramento River and its tributaries, which drain primarily NFS lands, have generally good quality and support their beneficial uses (Domagalski and others 2000). Sediment and nutrient loads from forested watersheds in the Sierra Nevada, including large areas within national forests, were found to be substantially lower than loads from downstream agricultural areas and significantly lower than average pollutant loads nationwide (Kratzer and Shelton 1998). Ahearn and others (2005) compared water quality in the upper Consumnes River watershed, which is mostly national forest, to the more agricultural and heavily populated lower watershed, and found that “upland drainages tended to deliver dilute, clear waters to the lowlands, while lower elevation sub-watersheds produced more turbid waters with elevated levels of constituents” (p. 242). Nevertheless, resource-management and protection activities on NFS lands have the potential to result in nonpoint source pollution of the State’s waters, and continual efforts are needed to maintain and improve water quality.

In the Sierra, aquatic ecosystems are recognized as being one of the most degraded of all ecosystem types (Centers of Water and Wildland Resources 1996). Fifty percent of native amphibians were already at risk of extinction well over a decade ago (Jennings 1996). Current trends suggest there is an urgent need to proactively address the threats to aquatic ecosystems throughout the Sierra Nevada in order to preserve the critical ecosystems, species and resources they support (California Trout 2008, Derlet et al, 2010).

Water quality impairments

Over 20 water bodies on NFS lands in the Sierra Nevada are listed as impaired on the State’s 2010 303(d) list. However, only Eagle Lake, the Truckee River, and Lake Tahoe and its tributaries are listed for pollutants related to silviculture and livestock grazing, such as sediment, nutrients, and pathogens. Most of the other listings are for mercury and other metals resulting from historic mining, natural sources, or unknown sources.
Comment: Need to define the 303(d) list specifically, and list the 20 impaired water bodies in a table, and identify the pollutants and pathogens.

Other water quality issues related to road density and stream sedimentation in this overview:


Related to livestock grazing:

(document uploaded by author)

Related to ecological influence of introduced non-native species in streams:

Influence of Introduced Non-Native Species on Stream Ecosystems:


Trout introduced into historically fishless headwater streams (Yosemite) reduce the diversity and abundance of native endemic invertebrates, and alter food web function and form. Removal of trout above natural barriers may permit recovery of some invertebrates.

Herbst et al. 2009 (and unpublished monitoring in Kings Cyn NP)
(document uploaded by author)


The New Zealand Mud Snail (NZMS) alters the energy flow and food web of invaded streams, competes with native algae-grazers and although it takes over ecosystem processes for a time, may also go through boom-bust phases where recovery to a natural state can occur.

Moore et al. 2012
(document uploaded by author)

NZMS cannot survive in streams of low mineral content, where conductivity is below 50 uS, so most mid-to-high elevation streams of the Sierra are not likely to be vulnerable to invasion.

Herbst et al. 2008
(document uploaded by author)

Hydraulic mining and mercury contamination

Kattelmann (1996) considered hydraulic mining to be one of the two largest human-caused effects on streams in the Sierra Nevada (the other was water development infrastructure). Geologic sources of mercury in the Sierra Nevada are limited to relatively small areas of metamorphic rocks formed from ancient sea-floor volcanic rocks. However, historic gold mining introduced large quantities of mercury into streams of the Northern Sierra Nevada in the nineteenth century. Miners used mercury to amalgamate and recover gold during placer (alluvial), hard rock, and hydraulic mining. The greatest amounts of mercury were used at hydraulic mines.

Alpers and Hunerlach (2000) determined a relationship between intensity of historic hydraulic mining in the Northern Sierra Nevada and mercury contamination, expressed as the mass of mercury per mass of tissues in aquatic organisms. In order of increasing mercury concentration, the major rivers of the Northern Sierra Nevada were ranked:

  1. American
  2. Feather
  3. North and Middle Yuba
  4. South Yuba and Bear

These streams are all currently listed as impaired owing to excessive mercury concentrations.

The total amount of mercury lost to the environment from mining operations in the late nineteenth century in the Sierra Nevada may have been 3 to 8 million pounds or more (Alpers and Hunerlach, 2000). Most of this mercury probably remains in the river beds of the Sierra Nevada.

Sediment yields computed from reservoir sedimentation rates (Chapter 8) are relatively low, and are well within the range for forested lands in the western United States as reported by Patric and others (1984). The mean of 0.82 tons per acre per year is higher than the average of 0.165 reported by Patric and others (1984), but lower than the range of 2 to 5 tons per acre per year suggested as acceptable for agricultural lands (Wischmeier and Smith, 1978). Patric and others (1984) suggested that a sediment yield of 0.25 tons per acre per year would be a good estimate for undisturbed forest lands. Twelve of the 16 sedimentation rates reported in Chapter 8 for NFS lands in the Sierra Nevada are less than this estimate, although the reservoirs are located within areas of actively managed forests.

Estimates of potential road-related sediment yields in the absence of BMPs were computed by multiplying road miles by road erosion rates, summing erosion for all 3 processes (road surface, gully, and landslide), and dividing the totals by the number of NFS acres (government-owned acres only) on each National Forest (Table 11). “Low” estimated sediment yields range only from 0.01 to 0.02 tons per acre per year, with a mean of 0.01 tons per acre per year. “High” estimated deliveries range from 0.07 to 0.19 tons per acre per year, with a mean of 0.12 tons per acre per year. Total estimated road-related sediment delivery for the 10 Sierra Nevada National Forests ranged from 111,000 to 1.3 million tons per year.

Water Quantity


Water availability for human uses in California is dependent on the total volume of water falling as precipitation but also on the timing of hydrologic processes such as snowmelt and streamflow. Annual precipitation and streamflow are useful measures for evaluating water resources, but the temporal distribution of streamflow is also important given the highly seasonal nature of rainfall and snowfall. High peak flows do not add substantially to water storage, and present hazards to life and property, whereas summer baseflows, although the lowest flows of the year, are critically important for human welfare and aquatic habitats.

Factors Influencing Stream Temperature


According to PNW research, the primary contributor to daily fluctuations in water temperature is direct solar radiation (Johnson 2004; Thomas 2005). Daily fluctuations in stream temperature correspond with daily fluctuations in solar heating (Stoneman and Michael 1996, Webb and Zhang 1997), with the warmest summertime stream temperatures typically occurring in mid- to late afternoon and the coolest summertime stream temperatures occurring near daybreak (Poole et al 2001). For many years, air temperature was thought to be a major factor influencing the water temperature in streams. However, heat budget analysis, using data from streamside climate stations, showed that direct solar radiation, not air temperature, is the largest contributor to changes in daily temperature (Thomas 2005). Riparian shade has a marked influence on stream temperature, particularly in terms of moderating diel temperature variation (Broadmeadow et al. 2011). Hynes (1960) showed that water temperature was dependent on many parameters, including the altitude and aspect of the stream. Other contributing factors include flow regulation at dams and diversions, groundwater effluents, channel geometry (width to depth ratio), streambed composition and the length of time water spends flowing through interstitial spaces in the substrate (hyporheic zone). Bedrock reaches have wide daily summer stream temperature fluctuations, with high maxima and low minima. In contrast, stream reaches with gravel bottoms and belowground flows tend to have a much narrower range of daily fluctuations (Thomas 2005).

Stream Temperature Importance to Ecological Integrity


Water temperature influences virtually every biotic component of stream ecosystems, from the emergence of caddisflies to the bacteria that cycle nutrients (Hawkins et al. 1997; Thomas 2005), and is one of the parameters in stream ecology that determines the overall health of aquatic ecosystems (Coutant, 1999). Water temperature plays a key role in determining the distribution of many aquatic organisms (Magnuson et al. 1979; Vannote et al. 1980; Ebersole et al. 2001), and is one of the most important environmental factors affecting fish (Fry 1967, 1971; Hutchinson 1976). For example, temperature regimes influence migration, egg maturation, spawning, incubation success, growth, inter- and intraspecific competitive ability, and resistance to parasites, diseases, and pollutants (Armour 1991). Most aquatic organisms have a specific range of temperatures that they can tolerate (Coutant 1977). Temperature has been a particular focus for salmonid fishes, due to their requirement for relatively cold water (Elliott 1981). Research has linked salmonid distributions to several gauges of stream temperature, including elevation gradients associated with climate (Fausch et al. 1994; Flebbe 1994), groundwater temperature (Nakano et al. 1996), and surface water temperature (Eaton et al. 1995; Torgerson et al. 1999). The latter most directly affects fish (Dunham 2001). The distribution of fish within a small area may be related to small gradients in surface water temperatures (e.g., Nielsen et al. 1994; Peterson and Rabeni 1996; Ebersole et al. 2001), but distributions on a larger scale may be indicated by broad-scale climatic gradients (e.g., Fausch et al. 1994; Rieman et al. 1997; Dunham et al. 1999). Warm water temperatures can decrease dissolved oxygen in the water and can act as a barrier to migration (CDFG 2010). Several diseases that infect fish are kept in check by cold water (Thomas 2005).

Dams and Flow Regulation Affects to Water Temperature


Reservoir construction and associated flow regulation modify the thermal regime of rivers, often with significant ecological repercussions (Webb and Walling 1996). Temperature and erratic flow fluctuations in dam tailwaters have altered phenologies of macroinvertebrates and fish, drastically reducing aquatic biodiversity in comparison to unregulated stream segments (Stanford and Hauer 1992). Dams directly affect downstream temperature; the type of effect depends upon the specific mechanism of water release (e.g., top or bottom release) (Poole and Berman 2001). Releases from the hypolimnion of reservoirs may completely prevent species from living in a stretch of river where they are normally found or cause a reduction in their relative abundance (Victoria EPA 2004). However, dams can be operated to provide desirable stream temperature regimes directly downstream through selective withdrawal of water from varying reservoir depths (Stanford and Hauer 1992). Flow regulation dampens variation in both flow and temperature (Poole and Berman 2001). hyporheic flow to act as a temperature buffer, differential storage of heat and water over time must occur. Differential heat and water storage are driven by variation in stream temperature and flow. Therefore, potential for hyporheic exchange to act as a temperature buffer is reduced by flow regulation (Ward and Stanford 1995).

Water withdrawals and diversions (i.e., for irrigation, municipal water supply, or hydropower) cause a reduction in river discharge, which has been shown to affect water temperatures (Cassie 2006). Sinokrot & Gulliver (2000) showed that the reduction of river flow greatly influenced thermal regime, specifically resulting in the increased occurrence of high temperature events. They also demonstrated that increasing river discharge in a regulated system would reduce the number of days that the water temperature exceeded a threshold value.

Coldwater releases from reservoirs can have a profound impact on the downstream thermal regime (Troxler & Thackston 1977). The main thermal effects of impoundment and flow regulation include elevated mean annual water temperature, depressed summer maximum temperature, delay in the annual temperature cycle, and reduced diurnal temperature fluctuation (Webb & Walling 1996). Webb & Walling (1993) also showed that temperature below reservoirs is modified most strongly in winter compared with the normal thermal regime, and winter freezing can be eliminated entirely. Winter water temperature increase could potentially have a greater impact on aquatic ecosystems (e.g. incubation of salmonid eggs) than that caused by summer conditions (Cassie 2006). Water releases have been noted to influence the growth rate of fishes downstream of reservoirs (Robinson & Childs 2001). Steady reservoir discharge in summer, at relatively constant cooler temperature, results in attenuated diurnal variations in downstream temperatures compared to normal (unregulated) flow conditions (Lowney 2000).

Water temperature in Big Silver Creek, Eldorado NF, summer 2002.The elevation of the Big Silver Creek monitoring station is approximately 1,485 meters (4,872 feet) above sea level. Figure 1 illustrates a typical summer water temperature regime for an unregulated stream. The stream in this example exhibits diurnal water temperature fluctuations of 5-7°C, a gradual warming trend throughout June, and seasonal maximum temperatures in mid-to-late July.
Chap1_Aqua_WaterTemp.JPG



Water temperature in Big Silver Creek, July 8-14, 2002. This figure illustrates typical diurnal summer water temperature fluctuations of 5-7°C in Big Silver Creek, a stream with unregulated flow. Note that the daily maximum temperatures occur between 16:00 and 17:00, and the daily minimum temperatures occur between 08:00 and 09:00. RAWS data from a station immediately east of the temperature monitoring site indicate that there was cloud cover that passed over the Big Silver Creek drainage, corresponding with the lower maximum water temperature on June 11, 2002.
Chap1_Aquatics_WaterTemp2.jpg


Bald Mtn Loc California RAWS data from July 8-14, 2002.
Bald Mtn Loc California RAWS
http://www.raws.dri.edu/cgi-bin/rawMAIN.pl?caCBAL
Total Solar Radiation
(langleys)
Average Air Temperature
(°F)
Max. Air Temperature
(°F)
Min. Air Temperature
(°F)
Total
Precipitation
(°F)

736.3
75
90
57
0

737.4
85.3
98
73
0

732.9
89.8
101
80
0

468.5
84.6
97
77
0

681.6
84.6
97
74
0

716.7
83.9
96
72
0

708.2
79.8
93
69
0



Water temperature in Warner Creek and Grassy Swale, June - August, 20011. The elevations of the Warner Creek and Grassy Swale monitoring stations are approximately 1,521 meters (4,991 feet) and 1,888 meters (6,194 feet) above sea level, respectively. These two monitoring stations are separated by approximately 17.5 km (10.9 river miles). Figure 3-1 illustrates a typical relationship between water temperature regimes in connected streams with unregulated flows. The streams in this example exhibits diurnal water temperature fluctuations of 6-8°C, a gradual warming trend throughout June, and seasonal maximum temperatures in late July. These paired sites exhibit the typical inverse relationship between elevation and water temperature; in unregulated systems, water temperature generally increases at lower elevations. Exceptions may occur where there is substantial flow contribution from groundwater sources such as springs. Note that there was a “low amplitude” anomaly (low diurnal fluctuation) on June 28, 2011 that contrasts the preceding and following days in the series. RAWS data from stations immediately east and west of these temperature monitoring sites (Table 2) indicate that there was a precipitation event and associated cloud cover that passed over the Warner Creek drainage on June 28, 2011. The solar radiation data correspond very closely with the water temperature pattern from June 27-June 30. NOTE: These detailed temperature records, along with stage-level discharge are derived from the sentinel stream network (David Herbst, SNARL, herbst@lifesci.ucsb.edu; se powerpoint under the Macroinvertebrate monitoring section below).
Chap1_Aqua_WaterTemp4.jpg


RAWS data from Lassen Lodge and Chester, California for June 27-30, 2011.
Lassen Lodge California RAWS
http://www.raws.dri.edu/cgi-bin/rawMAIN.pl?caCLAS
Top of Form
DateBottom of Form
Total Solar Radiation
(langleys)
Average Air Temperature
(°F)
Max. Air Temperature
(°F)
Min. Air Temperature
(°F)
Total
Precipitation
(inches)
6/27/2011
667.4
69.7
85
58
0
6/28/2011
135.7
54.5
61
50
0.41
6/29/2011
235.7
51.4
60
47
0.15
6/30/2011
676.3
61.5
76
49
0
Bottom of Form
Chester California RAWS
http://www.raws.dri.edu/cgi-bin/rawMAIN.pl?caCCHS
Top of Form
DateBottom of Form
Total Solar Radiation
(langleys)
Average Air Temperature
(°F)
Max. Air Temperature
(°F)
Min. Air Temperature
(°F)
Total
Precipitation
(inches)
6/27/2011
742
63
81
44
0
6/28/2011
132.5
51.1
59
46
0.48
6/29/2011
596.2
54.2
65
43
0.01
6/30/2011
708.7
57.1
77
39
0


Water temperature in the Tuolumne River near Mather, CA, July 14-20, 2009. The elevation of the Tuolumne River near Mather, CA is approximately 741 meters (2,431 feet) above sea level. As illustrated in Figure 4, the flow in the Tuolumne River near Mather is regulated by discharge from Hetch Hetchy Dam, 19.2 km (11.9 river miles) upstream. The summer water temperature pattern in the Tuolumne River at Mather exhibits the attenuation in diurnal variability (approximately 4° C) that is typical of flow-regulated streams where water is steadily released from the hypolimnion of a reservoir. At the point of release below Hetch Hetchy Dam, the water temperature is presumed to be fairly constant as long as the water column in the reservoir remains stratified. In this example the diurnal temperature fluctuations primarily result from exposure to solar radiation between the point of release (Hetch Hetchy Dam) and the monitoring station near Mather, CA - 11.9 river miles downstream. Diurnal maximum temperatures were recorded at 16:00, and diurnal minimum temperatures at 07:00, similar to unregulated flow conditions.
Chap1_Aqua_WaterTemp6.jpg

Water temperature in the Tuolumne River in relationship to pulsed flows from Cherry Creek, July 14-20, 2009. The elevation of the Tuolumne River at Lumsden Campground is approximately 430 meters (1,411 feet) above sea level. As illustrated in Figure 4, Lumsden Campground is approximately 9.5 river miles (15.3 kilometers) downstream from the temperature monitoring site at Mather, CA. However, the water-temperature signature in the Tuolumne River at Lumsden Campground (Figure 5) exhibits the influence of daily pulsed releases from Cherry Reservoir. Stream discharge (flow) data from Cherry Creek below the Dion R. Holm Powerhouse (above the confluence with the Tuolumne River) exhibit the daily pulsed releases from Valley Dam (Cherry Reservoir). As a result of these releases of cold water from Cherry Reservoir, the water temperature in the Tuolumne River 9.5 river miles (15.3 kilometers) downstream exhibits an abrupt 5°C drop daily between 10:00 and 13:00, a period of time when temperatures in unregulated flow conditions are warming. The delayed temperature response in the Tuolumne River is an artifact of the 11.9 km (7.4 river miles) distance between the Cherry Creek gauging station and temperature probe at Lumsden Campground. Also note that the maximum daily water temperatures at Lumsden Campground are approximately 2-3°C colder than at the Mather monitoring site upstream (Figure 4-1), which is approximately 1,000 feet higher in elevation.
Chap1_Aqua_WaterTemp7.jpg


Water temperature in the S.F. American River below Slab Creek Reservoir, June-August, 2002. The elevation of the monitoring station in the S.F. American River below Slab Creek Reservoir is approximately 500 meters (1,640 feet) above sea level. Figure 6 illustrates a typical summer water temperature regime for a regulated stream near the point of release. The S.F. American River temperature monitoring site is approximately 375 meters downstream from Slab Creek Dam. The stream in this example exhibits attenuated diurnal water temperature fluctuations of approximately 1°C throughout the summer, a rapid warming trend in the last two weeks of June, and seasonal maximum temperatures in late June. Note the low seasonal maximum water temperature in this example (17.2°C), which appears to be incongruous with the relatively low elevation of the site on the S.F. American River.
Chap1_Aqua_WaterTemp8.jpg

Chap1_Aqua_WaterTemp9.jpg
Water temperature in the M.F. Cosumnes River and Cat Creek, June-August, 2011.
Chap1_Aqua_WaterTemp10.jpg



The elevations of the M.F. Cosumnes River at PiPi Campground and Cat Creek monitoring stations are approximately 1,175 meters (3,855 feet) and 1,667 meters (5,469 feet) above sea level, respectively. As illustrated in Figure 7, these two monitoring stations are separated by approximately 13.6 km (8.5 river miles). Figure 7-1 illustrates the combined influence of a melting snowpack and groundwater (springs/seeps) on water temperature regimes in connected streams with unregulated flows. The streams in this example exhibit diurnal water temperature fluctuations of 3-4°C in June, a gradual warming trend throughout June and July, and seasonal maximum temperatures in August. These paired sites also exhibit the typical inverse relationship between elevation and water temperature in late July and August. Water temperature generally increases at lower elevations in unregulated systems. However, there is substantial overlap in the temperature regimes of these two sites during late June and early July, followed by divergent temperature profiles from mid-July through August. This divergence is accompanied by greater attenuation of the diurnal temperature fluctuations in the M.F. Cosumnes River in comparison with Cat Creek. This attenuation is the result of flow contribution from groundwater sources such as springs. During the early summer (June), the groundwater influence is masked by flow contribution from the melting snowpack via Cat Creek and other tributaries. In early July, the predominant flow contributions to the M.F. Cosumnes River transition from surface to groundwater. As long as flow is snow-melt dominated, the stream temperature variation is more strongly correlated with solar radiation and air temperature. When the snowmelt recedes, groundwater dominates the stream discharge and the water temperatures become more decoupled from solar radiation and air temperature. NHD point data plotted in Figure 7-1 indicate seven mapped springs that contribute flow to the M.F. Cosumnes River upstream from PiPi Campground. Spring data are not comprehensive in NHD. Therefore, there may be additional (unmapped) springs contributing flow to the M.F. Cosumnes River.
NOTE: These detailed temperature records, along with stage-level discharge are derived from the sentinel stream network (David Herbst, SNARL, herbst@lifesci.ucsb.edu; se powerpoint under the Macroinvertebrate monitoring section below).


Aquatic Ecological Characteristics: Water Quantity


Water availability for human uses in California is dependent on the total volume of water falling as precipitation but also on the timing of hydrologic processes such as snowmelt and streamflow. Annual precipitation and streamflow are useful measures for evaluating water resources, but the temporal distribution of streamflow is also important given the highly seasonal nature of rainfall and snowfall. High peak flows do not add substantially to water storage, and present hazards to life and property, whereas summer baseflows, although the lowest flows of the year, are critically important for human welfare and aquatic habitats.

Annual precipitation and streamflow


Annual amounts of precipitation and streamflow are fundamental to assessing water resources on the Sierra Nevada National Forests. In this section, we present records of precipitation and streamflow provided by the National Weather Service, DWR, and USGS to help in evaluating conditions and trends. It is important to note that global climate change is expected to affect temperature, and hence the ratio of snow to rain, more than the total amount of precipitation (California Department of Water Resources, 2008).

As shown in Chapter 8, annual precipitation in the Sierra Nevada varies considerably. Maximum annual precipitation has been roughly 5 to 6 times higher than minimum annual precipitation over the past half century. No general trends in total precipitation are obvious, but warmer temperatures have increased the proportion of rain and decreased the proportion of snow in annual precipitation totals at mid-elevations (DWR, 2008).

The double-mass curves for stations on or near NFS lands (Chapter 8) all show subtle and alternating short-term trends in the past 50 years toward both slightly increased and decreased streamflow per inch of rainfall. The double-mass curve for the Merced River in Yosemite National Park is noticeably straighter than the curves for the stations on NFS lands. This may be an artifact of the different land management activities in the parks and forests, or other factors may be responsible.

Peak flows


Major floods during the historic period in the Sierra Nevada occurred in 1861-62, 1906, 1909, 1955, 1964, 1986, 1997, and 2005. Based on these dates, the frequency of large floods may be increasing. However, graphs of peak flows at USGS gaging stations in the Sierra Nevada do not suggest any systematic trends toward higher annual peak flows in the past 50 to 100 years (Chapter 8).

Ecological effects of rain-on-snow floods in headwater streams
: (document uploaded by author)

Rain-on-snow winter floods are one manifestation of climate change and studies of intact headwater stream habitats before and after the record winter flood of 1997 showed no changes in the invertebrate community. In contrast, most streams already disturbed by livestock grazing became dominated by opportunistic species and shifted to a more detritus-based food web structure. Intact headwater streams are habitat refuges.

Duration of baseflows


Baseflows are streamflows supplied by gradual discharge of groundwater and soil moisture to streams in periods between rainstorms or snowmelt periods. Baseflows are critical in California owing to the highly seasonal climate, in which almost all precipitation and snowmelt occurs between fall and late spring, and water demand for irrigation is highest during the summer. Summer baseflows are likely to be affected by changing climate owing to warmer temperatures that reduce snowpack and advance snowmelt.

Rough estimates of current baseflows were made by computing ratios of mean summer (July 1 to September 30) streamflows to mean annual streamflows for each year of record for 5 long-term USGS gaging stations on streams in the Sierra Nevada that are not regulated or diverted (Chapter 8). Although substantial regional variation is apparent, no clear trends in the proportion of streamflow occurring during the summer months are obvious.

Dams and reservoirs


Dams and reservoirs are one of the two most significant impacts to streams in the Sierra Nevada (Kattleman, 1996). All major rivers in the Sierra Nevada are impounded and regulated to some extent, with the exception of the Consumnes River. According to the Mountain Counties Regional Report in the 2009 update of the State Water Plan, a total of 76 reservoirs are located within the mountain counties (Plumas to Sequoia Counties). The reservoirs range in size from 0.0003 to 3.54 MAF, and total capacity of these reservoirs is 17.4 MAF.

Aquatic Ecological Characteristics: Fish


Approximately fifty kinds of fish are native to the Sierra Nevada; eleven of these taxa are found only in this range. The fish fauna and fisheries of the Sierra Nevada have changed dramatically since the massive influx of Euro-Americans began in 1850. Four broad patterns are evident:
  1. anadromous fishes, especially chinook salmon, have been excluded from most of the riverine habitat they once used on the west side of the range;
  2. most resident native fishes have declined in abundance, and the aquatic communities of which they are part have become fragmented, although a few species have had their ranges greatly expanded;
  3. thirty species of non-native fishes have been introduced into or have invaded most waters of the range, including extensive areas that were once fishless, mainly at high elevations; and
  4. Sierra Nevada fisheries have largely shifted from native fishes, especially salmon and other migratory fishes, to introduced fishes.

One reflection of these patterns is that of the fifty fishes native to the Sierra Nevada, ten (20%) are formally listed by the federal government as threatened or endangered species, 5 (10%) are in danger of extinction in the near future, ten (20%) are on a trajectory toward extinction if present trends continue, and fifteen (30%) are in long-term decline or have small isolated populations, but do not face extinction in the foreseeable future. The remaining 10 (20%) are of least concern (Moyle et al. 2011). Among the species that have largely disappeared from the range are Chinook salmon, steelhead, and five kinds of native trout. Fisheries for these species have been replaced, in part, by stream fisheries for nonnative trout, often of hatchery origin, and by reservoir fisheries. The introduction of trout into several thousand originally fishless lakes at high elevations has greatly expanded fishing opportunities but has also caused declines of native invertebrates and amphibians. Introduction of non-native fish species has also been the single biggest factor associated with fish declines in the Sierra Nevada. However, this factor is intimately tied to major habitat changes and other effects of dams and diversions, as well as habitat changes caused by a variety of streamside activities (Moyle et al. 1996). Fragmentation to fish and other aquatic habitat is addressed in Chapter 3, Drivers and Stressors.

Aquatic Ecological Characteristics: Amphibians


Despite over 300 million years of existence on Earth, more than 168 species are believed to have gone extinct in the last two decades and a further 43 percent of those remaining are in decline (AmphibiaWeb 2009). Habitat destruction, global climate change, introduced species, over-exploitation, UV-B radiation, chemical pollutants and emerging diseases appear to work synergistically creating a negative spiral for amphibians (AmphibiaWeb 2009).

This assessment focuses on high elevation Sierra Nevada stream, lake and meadow habitats, those most sensitive to effects of climate change and shifting seasonality of precipitation. Amphibian species included are primarily those with known restricted or recently contracted distributions and populations including: mountain yellow-legged frog (MYLF), Sierra Nevada mountain yellow-legged frog (SNMYLF), Cascades frog (RACA) and Yosemite toad (YOTO).

Amphibian characteristics by: types of characteristics and applicable species, landscape scale of the characteristics, how the characteristic is measured, and the source of the characteristic’s information.
Habitat Characteristics
Scale
Measures
Info Sources
Population Distribution - MYLF, SNMYLF, RACA, YOTO
Bioregional, Forest
Number of Populations, Acres Inhabited
R5 Monitoring, CDFW Basin-wide Surveys,
Population Abundance - MYLF, SNMYLF, RACA, YOTO
Bioregional, Forest
Estimated Numbers
R5 Monitoring, CDFW Basin-wide Surveys
Number & Ac Ft. Historically Fishless Lakes & Streams
Bioregional, Forest
Number pre-European Lakes/Streams (or drainage basins?), Acre Feet
CDFW Basin-wide Surveys
Number & Ac Ft. Currently Fishless Lakes & Streams
Bioregional, Forest
Number of Current Fishless Lakes/Streams (or drainage basins?), Acre Feet
CDFW Basin-wide Surveys
Distribution & Abundance of Bullfrogs
Bioregional, Forest
Number of HUC-6 Watersheds with known Bullfrog Presence
PSW & Academic Research, CDFW


How Amphibian Habitat Characteristics Were Selected & Why


The most basic criteria employed in selecting these characteristics is that they are 1) measureable, 2) data are available, and 3) tell us something important about amphibian populations and habitat. The premise underlying most of these measures is that small, isolated populations have less ability to survive and recover from random environmental events such as fire, disease, drought, etc.
  • Population Distribution of 4 Rare Species–Sodhi et al. (2008)evaluated a large body of world-wide amphibian decline literature (2,583 species) to reach the conclusion that species with limited (small) geographic range are most likely to experience severe decline as a result of greater habitat specificity in their life cycles. Therefore, broader distributions are preferred.
  • Population Abundance of 4 Rare Species– Chytrid research has demonstrated that large populations have better ability to persist following high level infections that kill many if not most individuals (Knapp et al. 2011). Large populations are better.
  • Number and Acre-Feet of Historically Fishless Lakes – Among the primary extinction drivers acting upon amphibians in the world today (chytrid, introduced fish, climate change, habitat loss), the broad-scale introduction of non-native and native trout into historically fishless lakes has significant negative effects on amphibians there (Pope and Long 2013). More was better.
  • Number and Acre-Feet of Currently Fishless Lakes – As above, and the more as a percentage of historic condition, the better.
  • Distribution and Abundance of Bullfrogs – A predator and competitor, this non-native invasive species has been moving into habitat and out-competing native amphibians as well as aquatic reptiles.

Current Condition of Amphibian Species and Habitat

  • Current Distribution relative to HistoricIn general, the distributions of these four high-elevation species are greatly contracted due to changing climate conditions, chytrid-induced die-offs, and habitat lost to introduced native and nonnative predators.
  • Population In general, the abundances of these four high-elevation species have significantly declined due to changing climate conditions, chytrid-induced die-offs, and habitat lost to introduced predators. Effects of UV-B radiation, and habitat loss due to human causes have also been implicated in the literature (Sodhi et al. 2008).
  • Habitat StatusMore potentially suitable habitat exists than is currently occupied by these species.

Amphibian Trends Under Current Management

  • Population–It is currently unclear whether current management in the form of roads, activities such as meadow trails, etc. are making a significant contribution to the over-arching major stressors described above. These major stressors are anticipated to continue to drive the populations toward an extinction vortex. It may be the best we can hope for as managers to is slow the process enough to allow science to find ways to conserve species and mitigate these stressors. Solid data back this declining trend and our level of certainty is high.
  • HabitatImproving as more introduced fish are no longer stocked into high mountain lakes or are actively removed. Improving management activities to restore hydrological function and restore water tables may also improve conditions, but it is too soon to tell whether these positive effects will be swamped by the global forces. The ability to discriminate trends from NFS management actions as opposed to global processes is low.

Amphibian trend monitoring within the Sierra Nevada Bio-region.
Trend Assessed
Key Management Question
Lead Proponent
Research
Model
Strategy
Changes in Population Distribution - MYLF, SNMYLF, RACA, YOTO
Have any of these distributions decreased?
R5 Monitoring coordinator, Research
X


Changes in Population Abundance - MYLF, SNMYLF, RACA, YOTO
Have populations of any of these 4 species decreased?
R5 Monitoring coordinator, Research
X


Change in Number & Ac Ft. of Fishless Lakes & Streams – Historic to Present
Have we decreased the number and ac-ft of fishless lakes & streams?
CDFW & Forests

Map

Changes in Distribution and Abundance of Bullfrogs
Has the distribution or abundance of bullfrogs increased?
R5 Monitoring coordinator, Research
X




Macroinvertebrates and Algae Monitoring Methods


To assess the biological water quality of streams, rivers and lakes in the Sierra Nevada national forests, and reach statistically valid conclusions about the overall quality of biological water resources on these forests requires considerable sampling effort because of the sheer size (more than 4 million hectares or 10 million acres) and highly variable topography. This broad-scale assessment is possible by application of a design based on probabilistic sampling (Stevens and Olsen 2003, 2004, Olsen 2008a, b), which is basis for monitoring in the Sierra Nevada national forests. Examples of such probabilistic monitoring plans are provided by State of California’s Perennial Stream Assessment (PSA) program (Ode et al. 2011) and Clean Water Act 305(b) Report (SWAMP 2006) assessing the state of the States waters. EPA EMAP’s stream and lake monitoring program has also been applied across the entire contiguous United States (EPA 2006, 2009).

Since the State’s PSA and the Forest Service’s Management Indicator Species (MIS) monitoring programs both utilize a probabilistic sampling with common design features, it was possible to combine the data from both programs to form a more robust evaluation. Stream and river sites were chosen from the National Hydrography Database (NHD) for 2nd through 4th- Stahler order perennial streams. Since the length of lower order streams far exceeds that of higher order streams, a random sample will select far more small streams compared to large ones. To compensate for this unequal representation resulting from a random sample and make sure that larger, 4th-order streams were adequately sampled, an equal number of sites from each of the three stream orders were targeted for sampling (Olsen 2008a).

Prior to deciding to sample a site, a map reconnaissance was conducted to assure access and appropriateness of the site for sampling. If a site was judged inaccessible due to extreme distance (> 7 miles from the trailhead), treacherous or unsafe terrain, or inappropriate for sampling because of significant activities not representative of national forest management like major water diversions, extensive private land in close proximity or flow manipulations not under the jurisdiction of the Forest Service, it was removed and another randomly selected site was substituted for it. The sample size was not large enough to evaluate trends in condition over the period of collection from 2000-10. In cases where multiple samples had been taken at a site using different collection methods (e.g. reach-wide vs. targeted riffle) or over two consecutive years, the average of the scores was used to represent the site.

Site condition scores were calculated using two models. The first utilized a multivariate RIVPACS (RiverInVertebratePredictionAndClassificationSystem) model developed under several contracts with the USFS Regional Office (Hawkins et al. 2000, Ode and Schiff 2009, Ode et al. 2011). The second model, a multimetric Index of Biotic Integrity (IBI) model developed for hydropower related impacts for the western Sierra Nevada region (Rehn 2009), was also utilized. The metrics developed to determine hydropower effects are robust and sensitive to a variety of impacts, so they are appropriate for evaluating impacts from a variety of stressors associated with land management activities.

To calculate a final site condition score, the average of the RIVPACS Observed-to-Expected (O/E) and IBI score for each site was calculated. IBI scores, which may range from 0-100% were standardized to unity by dividing each score by the mean score (i.e. 74) for reference sites in the entire State-wide PSA data set. It is believed that the average of these two models provides a more reliable assessment of stream conditions than either one individually.

According to the probabilistic sampling design, each site sampled represents a specific and variable perennial stream length (from 7 to 322 kms for this data set). Therefore, it was necessary to weigh the contribution of each sample site to the entire assessment by summing the weights for all sites falling into each condition category. Since two probabilistic designs (i.e. PSA and MIS) were united, it was necessary to recalculate and assign new weights based upon the new combination of 74 sites. Once the weights had been recalculated, the sum of weights for all sites in each condition category was determined. The result was an estimate of the total length of perennial stream in each of four condition categories: sites with scores greater than 0.85 were considered to be in excellent condition, sites scoring between 0.70-0.85 were in good condition, sites scoring between 0.55-0.70 were poor, and sites scoring less than 0.55 were very poor. Sites scoring in the excellent-good categories were considered comparable to reference or undegraded conditions; sites scoring as poor to very poor (less than 0.70) were considered degraded.

The ecological interpretation is that the threshold for degradation is 0.70. This means that less than 70% of the biological community expected to occur there in the absence of degrading impacts were actually observed; the habitat is not of sufficient quality to support the 30 percent of taxa that are missing.

Macroinvertebrates and Algae Assessment Programs

Assessments of Algae and Macroinvertebrate communities for aquatic ecosystem health are conducted by both state and federal programs. The sentinel stream network for detecting climate change effects on headwater ecosystems was established in 2010-2011-2012, collecting data from 24 streams in 7 National Forests and 3 National Parks in the Sierra. This adds to the assessment capacity for Sierra Nevada stream integrity and can be viewed here in more detail in a powerpoint presentation.
(uploaded by author)

Forest Service Management Indicator Species (MIS) Program

Approximately 290 invertebrate taxa were identified in collections from the 21 MIS stream and river sites, four of which were revisited. More than 15,000 specimens were identified; non-biting chironomid midges were the most abundant taxon with about 27% of the total. Mean taxa richness per site, a sensitive indicator metric, was 40, but varied widely from 9 for Greenhorn Creek, Tahoe National

Photographs from selected aquatic MIS sites: A) Willow Creek, Plumas National Forest- Score of 0.26; B) Greenhorn Creek, Tahoe National Forest- Score of 0.47; C) North Fork Tuolumne River, Stanislaus National Forest- Score of 0.90; and D) Jawbone Creek, Stanislaus National Forest- Score of 0.98. Sites A and B were in the very poor or degraded category. Note the poor development of riparian vegetation and uniform channel type without pool development. Sites C and D were in the excellent category. Note the variety of channel types, substrate sizes and well developed riparian vegetation. Coarse woody debris, which provides cover and channel stability, is also prominent at Jawbone Creek.

Chap1_Aqua_AquaticMIS.jpg





























State Perennial Stream Assessment (PSA)
The State’s Perennial Stream Assessment monitoring provided data from 53 sites. Thirty-nine of these sites had multiple scores because samples were collected by alternative protocols (e.g. targeted riffle vs. reach-wide; Rehn et al. 2007, Ode et al. 2011), so that the results from both collection methods could be compared for the State’s program development. For sites with multiple samples, the average site condition score was used.
Combined Results of Macroinvertebrates and Algae Assessment ProgramsThe data from the 21 MIS sites collected from 2009-2010 and 53 PSA sites collected from 2000-2010 were combined to cre a ize of 74 randomly selected sites scattered across the 10 national forests in the Sierra Nevada bioprovince (Figure 2). Overall, 35 sites or 46 percent were in excellent condition, 19 percent were good, 20 were poor and 15 percent were very poor. This means that 65 percent of streams were in reference (excellent-good) or undegraded condition and 35 percent were degraded (poor-very poor). When the sums of weights associated with the sites were calculated, 5,692 km or 78 percent of the 7,300 km of stream length assessed were in excellent-good condition, and 1,608 km or 22 percent were in poor-very poor condition (Figure 3). The total length of 2nd through 4th- Stahler order perennial streams on the Sierra Nevada national forests is 11,185 km or 6,950 mi. Therefore, the 74 sites sampled represent 63.3 percent of the entire perennial stream length (7,300/11,185 km) (Figure 4). A majority of the sites (54 percent) fell in the excellent condition category. The scores for sites collected by the Forest Service’s MIS program were better than those collected by the State PSA program.
Chap1_Aqua_AquaticMIS01.jpgDistribution and condition of 74 probabilistic bioassessment sites, 21 from the Forest Service Management Indicator Species (MIS) program and 53 from the State’s Perennial Stream Assessment (PSA) program. Site conditions were determined by averaging RIVPACS O/E and hydropower IBI scores
. Chap1_Aqua_AquaticMIS02.jpg
Percentages of perennial stream miles scoring in different condition categories. Overall, about 78 percent of all perennial stream miles were in reference (i.e. excellent to good) condition and 22 percent were degraded (poor to very poor) condition.
Chap1_Aqua_AquaticMIS03.jpg

Percentage of stream miles in each bioassessment condition class. The total distance of 2nd through 4th- Stahler order perennial streams on the Sierra Nevada national forests is 11,185 km or 6,950 mi. The 74 PSA and MIS sites represent a sample of about 65 percent of the total perennial stream distance in the Sierra Nevada Bioprovince. Overall, 47.8 percent of the all perennial stream miles in the Sierra Nevada Province and 78 percent of all stream miles surveyed were in reference (excellent-good) condition. About 17.5 percent of all perennial stream miles or 22 percent of surveyed stream miles were degraded (poor-very poor condition). Unevaluated sites were those not sampled because of extreme distance, treacherous and unsafe terrain, or presence of significant activities not representative of national forest management like major water diversions, extensive private land in close proximity or flow manipulations not under the jurisdiction of the Forest Service.
Lake Aquatic Management
A total of 114 aquatic invertebrate taxa were identified from collections at the 10 lake sites collected during 2009-2010; six of which were collected both years. Mean taxa richness was 17 and varied from a low of only 3 at Gilmore Lake on the Tahoe National Forest to 53 at Clear Lake on the Modoc National Forest, both in 2010. Estimated mean density of macroinvertebrates was 445 per m2 (range from 7 at Miller Lake in 2010 to 2,133 at Clear Lake in 2009). At present there are no accepted methods for evaluating lake condition based upon benthic macroinvertebrates alone so further conclusions are not yet possible.

It is noteworthy that Clear Lake on the Modoc National Forest had the highest species richness (53 invertebrate taxa) because it is the headwaters for the Lost River. Clear Lake and the Lost River are occupied by a genetically distinct population of Sacramento perch that was introduced by CDFG during the 1960s (Moyle 2002). The Sacramento perch Archoplites interruptus is the only native member of the family Centrarchidae west of the Rocky Mountains and has been almost entirely displaced from its native range in the Central Valley by centrarchids introduced from the eastern United States. Moyle et al. (2011) consider this species to be in danger of extinction in the near future if present trends continue.

Algae Monitoring Results

Diatoms and soft-bodied algae were collected at all stream sites during 2009-10 according to the standard SWAMP protocol (Fetscher et al. 2009). A total of 600 diatom valves were counted for each sample. Currently there is no formally established lab taxonomic standard protocol or data format to store the data collected.

The current SWAMP protocol for sampling stream algae includes methods for both diatoms and soft-bodied algae. Both algal types were collected during 2009. However, only diatom samples were collected during 2010 because of unreconciled issues over replicability of the soft-bodied algae protocol, and concerns about safety in the field regarding the handling of gluteraldehyde, which is a highly toxic preservative. Thus far about 220 algae taxa have been collected. Some diatom taxa appear to be ubiquitous and have occurred at every site (i.e. Encyonema silesiacum , Synedra ulna and pennate diatoms). Algae are proving to be sensitive habitat gauges of water quality, especially water chemistry attributes such as nitrate concentrations, which are associated with eutrophication (Blinn and Herbst 2003, 2007).
Conclusions from Macroinvertebrates and Algae Assessment Programs
In summary this is a preliminary compilation for biodiversity and bioassessment of aquatic resources of the Sierra Nevada Province. Overall, the percentage of stream sites meeting the objectives of the Clean Water act (i.e. reference condition, meaning they were judged to be in good to excellent condition) was estimated to be about 78% according to the combined multivariate RIVPACS and hydropower IBI models.

The estimate of about 78 percent of perennial stream miles in reference condition is fairly consistent with previous such estimates. The California State Clean Water Act 305(b) report (SWAMP 2006) concluded that about 67% of perennial stream miles in California were in reference or non-impaired condition. Ode et al. (2011) estimated that across the entire State, which included forested, urban and agricultural land use, only about 50% of perennial streams were considered to be in reference or unimpaired condition. For the Sierra Ecoregion, Ode et al (2011) calculated that about 65 percent of the perennial stream miles were in reference condition, which is lower than the combined MIS-PSA data set for the Sierran national forests.
Macroinvertebrates and Algae Science Synthesis
The following sections come directly from one of the draft Science Syntheses posted on the PSW website, Chapter 6.1 Watershed and Stream Aquatic Ecosystem (2013). At this time, it was not possible to summarize or paraphrase this critical piece of work, since we just received them. However, given the importance of the topic and varying inferences on effects to management, it is critical that the information be included for purposes of dialogue.

Excerpted from PSW Science Synthesis, 6.1 Watershed and Stream Ecosystems (2013) by Carolyn Hunsaker and Jonathan Long with contribution from David Herbst

“Natural patterns of variation in stream communities in space and time
Carter and Fend (2001) found that differences in the richness of invertebrates in riffle and pools appear to depend on annual discharge regime, and are more pronounced during low discharge years and disappear when flow is higher. This study, which took place on the Merced River in the Yosemite Valley, suggests that differences in erosional and depositional features between riffles and pools diminish when flows increase, so communities become more similar. An implication of this is that it is possible that flow regulation may influence the natural variations in habitat-based diversity and that channelization (eliminating riffle-pool geomorphology) may also produce less diverse assemblages of aquatic life and more limited ecosystem processes (such as nutrient recycling, productivity, organic matter transport, conversion, and decomposition). Beche and Resh (2007) found that traits related to adaptations to the environment vary in response to gradients of flow between years, from dry (drought) to wet (above average) conditions. Traits that provide adaptation to drying (e.g., desiccation resistance, aerial respiration) were more common in drought years, whereas traits permitting survival during high flows (e.g., flat body shape, drift dispersal) were more common in wet years. Prolonged drought or wet conditions result in shifts in trait composition. Despite this, there is redundancy in traits among taxa, so taxa can be replaced without loss in represented trait diversity. This suggests that it may be more difficult to conserve species diversity than trait diversity in the face of changing climate regime.
Erman (2002) studied the invertebrates of spring and springbrook (outflows) communities over 20 years to describe the biota and physical/chemical properties of Sierra Nevada cold springs. Results showed the individualistic nature of springs even within the same stream basin. Spring invertebrate assemblages differed greatly from one spring to another, as did timing of insect emergence and abundance of species. Invertebrate species richness was greater in deeper, more permanent springs, which were distinguished by high concentrations of dissolved ions, especially calcium. Spring permanence was also determined by direct observations over time, measurement of discharge variability, correlation of discharge with ionic concentration, and water dating. This study shows the high conservation value of spring habitats and the high levels of diversity that can serve as a biodiversity refugium in cold-water environments.”

During 2007 and 2008, 38 stream reaches in the Sierra Nevada and Southern Cascade Ranges, CA, were sampled for aquatic macro-invertebrates. These sites were simultantously sampled for meadow vegetation condition, greenline vegetation condition, and physical stream measurements using a modified Stream Condition Inventory (MSCI) to measure stream temperature, width-depth ratios, and mean bank angle (see attached document on Using aquatic macro-invertebrates as bioindicators and the relationship to livestock grazing in the Sierra Nevada and Southern Cascades Ranges, CA. Rosgen stream type was also determined for each site. A RIVPACS (River In Vertebrate Prediction and Classification System) bio-indicator score was calculated for each reach based on the presence of aquatic macro-invertebrates and each of the 38 reaches was determined to be either at reference of impaired condition based on the RIVPACS bio-indicator score. The areas sampled were on active grazing allotments administered by the US Forest Service and these sites are part of the USFS Region 5 Long Term Monitoring Project.
Results of the study indicate:
  1. meadow condition and greenline condition was not different between reference and impaired reaches as indicated by the RIVPACS bio-indicator score.
  2. Results indicate that a very weak positive relationship (P < 0.20) may exist between the greenline vegetation score and RIVPACS bio-indicator score and more studies are needed to confirm this.
  3. Mean bank angle, and overall indicator of stream channel functioning, was different between reference and impaired reaches as indicated by the RIVPACS bio-indicator score.
  4. Rosgen stream type was related to mean bank angle, meadow condition, and channel width to depth ratio therefore Rosgen stream type is an important factor in assessing bank angle and condition metrics.
  5. Rosgen stream type should be accounted for when making assessments of stream condition using macro-invertebrates as biometrics, and reference systems for scoring, such as RIVPACS, should be stratified by Rosgen type when making stream assessments.

This is a brief write-up about this study.


Fire effects
Beche et al. (2005) found minimal effects from prescribed fire on stream invertebrates in a Sierra Nevada study. Prescribed fire altered BMI community composition only within the first weeks post-fire, but there were no lasting (1 year) impacts on BMIs. Densities and percentage of sensitive taxa were significantly reduced after an intense wildfire on Angora Creek in the Lake Tahoe Basin, but there were no consistent changes in taxonomic richness or diversity (Oliver et al. 2012). Canopy cover and bank stability declined dramatically following the wildfire and substrate also changed substantially, with fine sediment more abundant and cobble less abundant post-fire. There were large reductions in relative abundances of shredder and scraper taxa, whereas collector-gatherer abundances increased. Community composition shifted away from pre-fire configurations, and continued to diverge in the second year following the fire. Scores from a regionally derived index of biotic integrity (IBI) were variable, but overall they were much lower in post-fire samples and did not show recovery after 2 years. This study demonstrated substantial post-fire effects to aquatic ecosystems even in the absence of large flooding or scouring events, and it showed that these effects can be transmitted downstream into unburned reaches. These findings, when compared to those from Beche et al. (2005), suggest that fire effects are strongly related to fire intensity.”
Forest management practices
“Although stream invertebrates have been an MIS for the Forest Service, little published information exists regarding effects of mechanical forest management practices (road building and maintenance, tree thinning and commercial harvesting, tractor piling of slash and burning) on stream invertebrates in the Sierra. A few publications exist on prescribed fire effects on stream invertebrates (see previous discussion). The usefulness of stream invertebrates for monitoring aquatic ecosystem condition and associated information gaps were recognized in the Adaptive Management Plan, Appendix E, of the Sierra Nevada Framework (USDA 2001, 2004), and one new research experiment exists (see sidebar on KREW above). McGurk and Fong (1995) found there was reduced diversity and increased dominance (most common taxa increase in fraction represented) in stream invertebrate communities in the Sierra Nevada when equivalent roaded area exceeded 5 percent (equivalent roaded area is an expression of landscape disturbance from roads and combined developed areas and logging).”

Aquatic Ecological Characteristics: Special Aquatic Habitats
Special aquatic habitats are areas of high biological diversity occupied by rare aquatic and terrestrial animal and plant species. These habitats attract a variety of terrestrial animals because they provide a concentrated food and water source. Special aquatic and riparian habitats may be sporadically distributed and uncommon compared to other habitat types like streams, rivers, and lakes. Typically, special habitats have specialized biotic communities with a high number of endemic species (Hynes 1970, Erman and Erman 1995, Erman 1996). Special habitats may represent environmental extremes with respect to water temperature, permanence, and chemistry, but they may also be stable environments, exhibiting little seasonal or annual variation. For example, cold water springs usually have a very constant year round discharge, temperature, and water chemistry. Other examples of specialized habitat types include hot springs, alkaline and caldera lakes (for example Mono Lake), fens, bogs, vernal pools, marshes, seeps, and snowmelt pools. Although special aquatic and riparian habitats contribute significantly to landscape and biological diversity, the biotic communities associated with special habitats are poorly known. Because special habitats are often small and isolated, they are sensitive to local impacts such as water diversions, mining, roads, and recreation. Even when special habitats connect to permanent water bodies, their local conditions and communities remain distinctive.
Cold spring habitats contribute significantly to biodiversity in areas where they occur. Erman and Erman (1990, 1995) surveyed 21 cold springs and their associated caddisfly fauna. They concluded that the biodiversity of cold spring fauna was highest in permanent springs with the highest discharge and calcium ion concentrations and the lowest solar radiation. Fauna of cold springs often represent rare, relict, and endemic species. Since cold springs are usually habitats that have been isolated for hundreds or thousands of years, they have quite distinctive fauna. Erman and Erman (1995) found that the average similarity between caddisfly species from separate springs was only 23 percent. A majority of caddisfly species (40 of 77) collected in the study area were present only in cold springs and spring-influenced streams.
Shepard (1993) noted that desert and eastern Sierra springs contain rich but poorly understood biodiversity. They are typically separated by distances of at least 12 miles, and dispersal between spring habitats is virtually impossible. Desert spring communities provide habitat for relictual species populations that became isolated as the climate become drier about 10,000 years ago. Although the fish species associated with springs are distinctive, invertebrates make up the great majority of the fauna. These invertebrates are microhabitat specialists. A particular species reaches its highest abundance where the combination of water depth, temperature, and velocity; substrate; and shade are most favorable. The most common aquatic invertebrates are insects, crustaceans, oligochaete worms, and mollusks. Spring snails in the family Hydrobiidae are often the most common macroinvertebrates present and they may reach densities of several thousand per square meter.
Fens are another poorly studied, sporadically occurring aquatic habitat in the Sierra Nevada. Erman and Erman (1975) studied several fens in the Sagehen Creek Basin and described general patterns there that may represent conditions elsewhere in the Region. Fens characteristically have flowing, mineral-rich water with high concentrations of calcium and magnesium ions, a pH ranging from near neutral to alkaline (pH 7.0 to 8.4), and shallow peat layers (less than 6.5 feet deep) . During the summer, fens undergo fluctuations in dissolved oxygen (from 35 to 95 percent saturation), temperature (from 9.5 to 30o centigrade), and water level. A few dozen moss and sedge species comprise the vegetation. Available oxygen is restricted closely to the water surface and fluctuates daily. The biotic community is limited to a few species. Most macroinvertebrates are oligochaete worms, nematodes, and aquatic flies. Water mites are often present at low abundances, and peaclams are rarely encountered.
Bogs are often confused with fens, but bogs receive nutrients from precipitation only. They also have a lower pH induced by sphagnum mosses as the mosses exchange hydrogen ions for mineral cations in the water. Moyle (1996) classified bogs as among the rarest of habitats in the Sierra Nevada/Modoc Plateau. Small, isolated bogs occur at high altitudes in the subalpine and headwaters zones of lakes and rivers in the southern Sierra (Barbour and Major 1990).
Spring Habitat Surveys
Broad-based surveys of special habitats have been conducted to a very limited degree over the Sierra Nevada region. One exception is the survey for springsnails of the family Hydrobiidae undertaken under terms of the 1998 Memorandum of Understanding Concerning the Conservation of Springsnails in the Great Basin, which was signed by five federal agencies, including the Forest Service, the Smithsonian Institution and The Nature Conservancy. Thousands of springs in the Great Basin were surveyed using the same protocol (Sada and Pohlmann 2002), many of which were located in the eastern foothills and mountains of the Sierra Nevada (Figure 1). Out of 127 sites surveyed under the Great Basin Springsnail MOU, Pyrgulopisis spp. occurred in 43, 11 of which were on National Forest lands. Tryonia occurred in 2 springs and Fluminicola at just one; none of these sites were on National Forest lands.

A second major survey effort was conducted under contract with Terry Frest and Ed Johannes of Deixis Consultants (2006, 2007). Surveys were directed at the northern Sierra Nevada national forests (i.e. Lassen Plumas, Tahoe, Eldorado and Lake Tahoe Basin Management Unit). A total of 222 sites, 201 of which were on national forest lands, were surveyed (Figure 1). Fluminicola spp. occurred at 41 sites, 35 of which are on national forest lands. Tryonia occurred at four sites, all of which are on national forest lands. Juga spp. (Family Pleuroceridae) occurred in 25 springs, 22 of which were on national forest lands. Snails in the family Pleuroceridae are often associated with springs.
In both the Great Basin and northern Sierra Nevada surveys, snails occurred in only about 25 percent of the springs surveyed. In the Great Basin surveys, Pyrgulopsis occurred at 34 percent (43/127) of sites surveyed and was the most commonly observed hydrobiid snail. Fluminicola was found at only one site. In contrast, Fluminicola was the most commonly observed hydrobiid in the northern Sierra Nevada surveys, where it occurred at 19 percent (41/222) of all sites surveyed. Pyrgulopsis was absent from the northern Sierra Nevada sites.
It is apparent from the figure below that extensive spring habitats of the Sierra Nevada Province remain unsurveyed. Several undescribed snail species were discovered during these spring habitat surveys and spring habitats contain both animal and plant species that may be confined to a single spring complex.
Locations of springs habitat surveys in the Sierra Nevada national forests for springsnails (Family Hydrobiidae) and Juga (Family Pleuroceridae). Vast areas of the Sierra Nevada Province spring habitats have not been systematically surveyed in spite of their importance to wildlife and the concentration of endemic and rare fauna that occur in such habitats.
Chap1_Aqua_AquaticMIS04.jpg
Aquatic Ecological Characteristics: Habitat Fragmentation

Habitat fragmentation is the loss of unity and cohesion and the splitting of habitat into isolated parts. Habitat fragmentation can result from physical, chemical or thermal barriers to species movements. The results of habitat fragmentation include isolation, loss of life history expression, reduced population genetic diversity, and increased vulnerability to disturbance and climate change.


Characteristics
Measure
Source
Dams
Length and distribution of habitat upstream of impassable dams
California Passage Assessment Database (PAD); SNDamFacilities_201024.gdb;
Cali_Dams.shp; National Hydrographic Dataset (NHD)
Diversions
Length and distribution of habitat upstream of impassable diversions
California Passage Assessment Database (PAD); SNDamFacilities_201024.gdb;
Cali_Dams.shp; National Hydrographic Dataset (NHD)
Diversions
Number and location of unscreened water diversions
State Water Resources Control Board database (EWRIM).
Dams & Diversions
Length and distribution of stream habitat with altered hydrograph and/or water temperature regimes downstream
NRIS AqS - Continuous H2O water temperature monitoring data; FERC relicensing data – H2O temperature and discharge data; USGS Gauge station data; California Data Exchange Center (CDEC), National Hydrographic Dataset (NHD)
Barriers at road-stream crossings
Length and distribution of habitat upstream of impassable road-stream crossing barriers
California Passage Assessment Database (PAD); NRIS AqS – Passage Characterization; WCATT -
A table of key characteristics for assessing aquatic habitat fragmentation. Various characteristics of habitat fragment types and measurements are displayed.


Fragmentation by Water Development
Water development has and is an important part of the economy and social development in California. The Sierra Nevada provides a large proportion of the water for agriculture in the central Valley, and food from California is an important supply for the country as well as internationally. California also has a very large population of people and they depend upon water sources on national forest lands, including the Sierra Nevada. These uses have resulted in a highly developed and modified water system in the Sierra Nevada. This has affected aquatic species, in particular fish and especially those that are anadromous and spend some of their life in the ocean, such as steelhead or salmon. Other fish that migrate or interbreed more locally, such as golden trout, may also be affected. Examples of fragmentation in wadeable streams are shown in the figures below for the southern portion of the bioregion.

Chap1_Aqua_AquaticMIS05.jpg
Fragmentation by Fire
Where populations have been constrained by habitat loss, fragmentation, and the expansion of exotic species, the probability for local extinctions linked to any disturbance has probably increased” (Rieman et al. 2003). If changes in fire patterns lead to larger, more severe disturbances than characteristic of at least the more recent evolutionary past for these species, the risks are compounded (i.e., fragmentation interacting with larger disturbances) (Dunham et al. 2003). Where these conditions coincide, the mitigation of extreme fires and their effects might benefit native fishes (Brown et al., 2001). However, higher severity fires can also benefit native fishes. In a study in Montana, native bull and cutthroat trout tended to increase with higher fire severity, particularly where debris flows occurred. (Sestrich et al. 2011). Similarly, in ponderosa pine and Douglas-fir forests of Idaho at 5-10 years post-fire, levels of aquatic insects emerging from streams were two and a half times greater in high-severity fire areas compared to unburned mature/old forest, and bats were nearly 5 times more abundant in riparian areas with high-severity fire than in unburned mature/old forest. (Malison and Baxter 2010).

“Limited evidence suggests vulnerability of fish to fire is contingent upon the quality of affected habitats, the amount and distribution of habitat (habitat fragmentation), and habitat specificity of the species in question. Species with narrow habitat requirements in highly degraded and fragmented systems are likely to be most vulnerable to fire and fire-related disturbance.” (Dunham et al. 2003)
“Effective pre-fire management activities will address factors that may render fish populations more vulnerable to the effects of fire (e.g., habitat degradation, fragmentation, and nonnative species)” (Dunham et al. 2003).“Proactive alternatives (pre-fire management) are most likely to have beneficial effects for fish, especially where habitat fragmentation and degradation have been identified as problems” (Dunham et al. 2003).

Fires can have substantial effects on streams and riparian systems and may threaten the persistence of some populations of fish, particularly those that are small and isolated (Rieman et al. 2003). Many fish populations are already depressed, small or isolated, and lack the resilience, diversity, or demographic support to rebound from disturbance (Rieman et al. 2003). According to Moyle and Williams (1990) and Moyle et al. (1996), many fish populations in the Sierra Nevada are restricted to small and often isolated remnants of a much larger and more continuous historical range. Moyle et al. (1996) determined that only 18 (45%) of the 40 fishes native to the Sierra Nevada have stable or expanding populations. Furthermore, Moyle and Randall (1996) evaluated the biological health of 100 Sierra-Nevada watersheds and found that less than half (43%) were in good to excellent condition. Regardless of the quality of local habitats, populations that are small and isolated are vulnerable” (Rieman et al. 2003).

“The potential impact of postfire changes on small, isolated populations can be devastating” (Spina & Tormey 2000).Remnant population networks and many of the remaining strongholds for native species are often found on public lands that now are key to the conservation of these species (Lee et al., 1997)” (Rieman et al. 2003).“Small and isolated populations do face greater risks of extinction (Dunham et al., 1999; Rieman and Dunham, 2000; Dunham et al. 2003).”“The influence of fire on persistence of native salmonid populations is highly variable. In some cases, local extinctions have been observed in response to fire, particularly in areas where populations of fishes have been isolated in small headwater streams” (Dunham et al. 2003).

Aquatic Ecological Characteristics: Watershed Condition

There have been two different watershed condition ratings for the Sierra Nevada. One is by the US Forest Service, using the Watershed Condition Framework. The second is in the CALFire Forest and Range Assessment Program (FRAP) report. Both are discussed here.


Forest Service Watershed Condition Framework
A total of 774 6th-field subwatersheds were assessed on the 10 Sierra Nevada National Forests in 2010 with the USFS Watershed Condition Framework, figure below. The subwatersheds ranged in size from 8,058 to 236,289 acres (including NFS and non-NFS lands), with a mean of 23,025 acres. The condition of different characteristics were rated by forest and district managers. There were multiple individual characteristics incorporated into the overall condition rating including: water quality, water quantity, habitat fragmentation, riparian habitat, in-stream logs, invasive species, native species, and other factors (need to make sure all are included).


Chap1_Aqua_AquaticMIS06.jpg
The first figure is the integrated index. Of these subwatersheds, 490 (63%) were classified as “functioning properly,” 280 (36%) were classified as “functioning at risk,” and 4 (0.5%) were classified as “impaired function.”



watconditionfrag.jpg
watconditionflow.jpg
watconditionwaterqual.jpg


California Forest And Range Assessment Program Report


The CALFire Forest and Range Assessment Program (FRAP) report evaluated watersheds for their value in providing water, based on surface water runoff, surface water storage, groundwater basins, and forest meadows. The Pit, North Fork Feather, East Branch North Fork Feather, Middle Fork Feather, North Fork and South Fork American, San Joaquin, and King River basins were rated as the watersheds with the highest water supply assets, all with composite scores of 100 of 100 possible points.

The FRAP report also evaluated threats to water supply within watersheds, based on impervious surfaces, future development, and climate change (snowpack change). The Truckee River was the only watershed in the Sierra Nevada that scored 100 of a possible 100 points for threats. The second highest composite threat score for a Sierra Nevada NFS watershed was 89.9 for the EB NF Feather River. Lake Tahoe was ranked third, with a composite score of 84.1. Threats to water quality were assessed, and of water bodies on NFS lands within Region 5 in the Sierra Nevada, only Lake Tahoe was listed as one of the “top” threatened watersheds.

Aquatic Ecosystem Literature Cited


Blinn, D.W. and D.B. Herbst. 2003. Use of diatoms and soft algae as indicators of stream abiotic determinants in the Lahontan Basin, USA. Final Report to the California Regional Water Quality Control Board, Lahontan Region and the California State Water Resources Control Board. Contract #01-119-160-0.
Blinn, D.W. and D.B. Herbst. 2007. Preliminary Index of Biological Integrity (IBI) for periphyton in the eastern Sierra Nevada, California – Unpublished, Draft Report.

EPA. 2006. Wadeable Streams Assessment: A Collaborative Survey of the Nation’s Streams, Office of Research and Development, Office of Water Washington, DC 20460; EPA 841-B-06-002. Available at http://www.epa.gov/owow/streamsurvey/
EPA. 2009. National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes. EPA 841-R-09-001. U.S. Environmental Protection Agency, Office of Water and Office of Research and Development, Washington, D.C.
EPA. 2011. 2012 National Lakes Assessment. Field Operations Manual. EPA 841-B-11-003. U.S. Environmental Protection Agency, Washington, DC. Available at http://www.cpcb.ku.edu/research/assets/2012_lakes/NLA%202012%20Field%20Operations%20Manual%202012.03.22.pdf
Fetscher, A.E., L. Busse, and P. R. Ode. 2009. Standard Operating Procedures for Collecting Stream Algae Samples and Associated Physical Habitat and Chemical Data for Ambient Bioassessments in California. California State Water Resources Control Board Surface Water Ambient Monitoring Program (SWAMP) Bioassessment SOP 002.
Hawkins, C.P., R.H. Norris, J.N. Hogue and J.W. Feminella. 2000. Development and evaluation of predictive models for measuring the biological integrity of streams. Ecological Applications 10:1456-1477.
Karr, J. R. 1991. Biological integrity: A long-neglected aspect of water resource management. Ecol. Appl. 1:66–84.
Karr, J. R., K. D. Fausch, P. L. Angermeier, P. R. Yant, and I. J. Schlosser. 1986. Assessing biological integrity in running waters: a method and its rationale. Ill. Nat. Hist. Surv. Spec. Publ. 5, Urbana, Ill. 28pp.
Moyle, P.B., 2002. Inland Fishes of California, Revised and Expanded. University of California Press, Berkeley. 502 pp.
Moyle, P.B., J.V.E. Katz, and R.M. Quiñones. 2011. Rapid decline of California’s native inland fishes: A status assessment. Biological Conservation 144:2414–2423.
Moyle, P. B., R. M. Yoshiyama, and R. A. Knapp. 1996. Status of fish and fisheries. Pages 953-973 In Sierra Nevada Ecosystem Project: Final report to Congress , Vol. II, assessments, commissioned reports, and background information. Davis: University of California, Centers for Water and Wildland Resources.
Ode. P.R., A.C. Rehn and J.T. May. 2005. A quantitative tool for assessing the integrity of southern coastal California streams. Environmental Management 35:493-504.

Ode, P.R., T.M. Kincaid, T. Fleming and A.C. Rehn. 2011. Ecological Condition Assessments of California’s Perennial Wadeable Streams: Highlights from the Surface Water Ambient Monitoring Program’s Perennial Streams Assessment (PSA) (2000-2007). A collaboration between the State Water Resources Control Board’s Non-Point Source Pollution Control Program (NPS Program), Surface Water Ambient Monitoring Program (SWAMP), California Department of Fish and Game Aquatic Bioassessment Laboratory, and the U.S. Environmental Protection Agency. Available at http://www.swrcb.ca.gov/water_issues/programs/swamp/docs/reports/psa_smmry_rpt.pdf .
Olsen, A.R. 2008a. USFS Region 5, Sierra Nevada National Forests, Stream Survey Design 2008. Environmental Protection Agency - National Health and Environmental Effects Research Laboratory, Western Ecology Division, Corvallis, OR
Olsen, A.R. 2008b. USFS Region 5, Sierra Nevada National Forests, Lake Survey Design 2008. Environmental Protection Agency - National Health and Environmental Effects Research Laboratory, Western Ecology Division, Corvallis, OR
Plafkin, J.L., M.T. Barbour, K.D. Porter, S.K. Gross, and R.M. Hughes. 1989. Rapid bioassessment protocols for use in streams and rivers: Benthic macroinvertebrates and fish. U.S. Environmental Protection Agency, Office of Water Regulations and Standards, Washington, D.C. EPA 440-4-89-001.
Poff, N.L., Allan J.D., Bain M.B., Karr J.R., Prestegaard K.L., Richter B.D., Sparks R.E. & Stromberg J.C. 1997. The natural flow regime: a paradigm for river conservation and restoration. Bioscience, 47, 769–784.
Poff, N.L., M.M. Brinson and J.W. Day, Jr. 2002. Aquatic Ecosystems & Global Climate Change. Potential Impacts on Inland Freshwater and Coastal Wetland Ecosystems in the United States. Special Publication prepared for the Pew Center on Global Climate Change, Available at
http://www.w.pewtrusts.com/uploadedFiles/wwwpewtrustsorg/Reports/Protecting_ocean_life/env_climate_aquaticecosystems.pdf
Rehn, A.C. 2009. Benthic macroinvertebrates as indicators of biological condition below hydropower dams on west slope Sierra Nevada streams, California, USA. River Research and Applications 25:208-228.
Resh, V.H. 1979. Sampling variability and life history features: Basic consideration in the design of aquatic insect studies. Journal of the Fisheries Research Board of Canada 36:290-311.
Resh, V.H. and J.K. Jackson. 1993. Rapid assessment approaches to biomonitoring using benthic macroinvertebrates. Pages 195-233 in D.M. Rosenberg and V.H. Resh (editors). Freshwater biomonitoring and benthic macroinvertebrates. Chapman and Hall, New York.
Stevens, D. L., Jr., and A. R. Olsen. 2003. Variance estimation for spatially balanced samples of environmental resources. Environmetrics 14:593-610.
Stevens, D. L., Jr., and A. R. Olsen. 2004. Spatially-balanced sampling of natural resources in the presence of frame imperfections. Journal of American Statistical Association:99:262-278.

SWAMP (Surface Water Ambient Monitoring Program). 2006. Water Quality Assessment of the Condition of California Coastal Waters and Wadeable Streams. The Clean Water Act 305(b) Report to the Environmental Protection Agency. Available at http://www.swrcb.ca.gov/water_issues/programs/swamp/docs/factsheets/305breport2006.pdf


Aquatic Ecological Characteristics - Water Quantity

Baldwin, C. K., F. H Wagner and U. Lall. 2003. Water resources. Pages 79-112, in Wagner, F. H. (editor). Rocky Mountain/Great Basin Regional Climate-Change Assessment. Report of the U.S. Global Change Research Program. Utah State University, Logan, UT, USA. 240 pp.
Barnett, T. P., D. W. Pierce, H. G. Hidalgo, C. Bonfils, B. D. Santer, T. Das, G. Bala, A. W. Wood, T. Nozawa, A. A. Mirin, D. R. Cayan, and M. D. Dettinger. 2008. Human-induced changes in the hydrology of the western United States. Science 319:1080-1083.
Christy, J.R. and J. J. Hnilo. 2010. Changes in snowfall in the southern Sierra Nevada of California since 1916. Energy and the Environment 21: 223-234.
DeGraff, J., D. Wagner, A. Gallegos, M. DeRose, C. Shannon, and T. Ellsworth, 2011. The remarkable occurrence of large rainfall-induced debris flows at two different locations on July 12, 2008, Southern Sierra Nevada, CA, USA. Landslides 8:343-353.
Hamlet, A. F., P. W. Mote, M. P. Clark, and D. P. Lettenmaier. 2007. Twentieth-century trends in runoff, evapotranspiration, and soil moisture in the western United States. Journal of Climate 20:1468-1486.
Huggel, C., J.J. Clague, and O. Korup. 2012. Is climate change responsible for changing landslide activity in high mountains? Earth Surface Processes and Landforms 37: 77-91.
Kaushal, S. S., G. E. Likens, N. A. Jaworski, M. L. Pace, A. M. Sides, D. Seekell, K. T. Belt, D. H. Secor, and R. L. Wingate. 2010. Rising stream and river temperatures in the United States. Frontiers in Ecology and the Environment 8:461-466.
Kim, J. 2005. A projection of the effects of the climate change induced by increased CO2 on extreme hydrologic events in the western US. Climatic Change 68:153-168.
Maurer, E. P., I. T. Stewart, C. Bonfils, P. B. Duffy, and D. Cayan. 2007. Detection, attribution, and sensitivity of trends toward earlier streamflow in the Sierra Nevada. Journal of Geophysical Research-Atmospheres 112.
McCabe, G. J., M. P. Clark, and L. E. Hay. 2007. Rain-on-snow events in the western United States. Bulletin of the American Meteorological Society 88:319-+.
Miller, N. L., K. E. Bashford and E. Strem. 2003. Potential impacts of climate change on California hydrology. Journal of the American Water Resources Association 39: 771- 784.
Moser, S., G. Franco, S. Pittiglio, W. Chou, D. Cayan. 2009. The future is now: An update on climate change science impacts and response options for California. California Climate Change Center Report CEC-500-2008-071, May 2009. California Energy Commission, Sacramento, CA.
Mote, P. W., A. F. Hamlet, M. P. Clark, and D. P. Lettenmaier. 2005. Declining mountain snowpack in western north America. Bulletin of the American Meteorological Society 86:39-+.
Null, S. E., J. H. Viers, and J. F. Mount. 2010. Hydrologic Response and Watershed Sensitivity to Climate Warming in California's Sierra Nevada. Plos One 5.
Pagano, T. and D. Garen. 2005. A recent increase in western US streamflow variability and persistence. Journal of Hydrometeorology 6:173-179.
Reba, M. L., D. Marks, A. Winstral, T. E. Link, and M. Kumar. 2011. Sensitivity of the snowcover energetics in a mountain basin to variations in climate. Hydrological Processes 25:3312-3321.
Regonda, S. K., B. Rajagopalan, M. Clark, and J. Pitlick. 2005. Seasonal cycle shifts in hydroclimatology over the western United States. Journal of Climate 18:372-384.
Stewart, I.T., D. R. Cayan, and M. D. Dettinger. 2005. Changes toward earlier streamflow timing across western North America. Journal of Climate 18: 1136-1155.
Young, C. A., M. I. Escobar-Arias, M. Fernandes, B. Joyce, M. Kiparsky, J. F. Mount, V. K. Mehta, D. Purkey, J. H. Viers, and D. Yates. 2009. Modeling the Hydrology of Climate Change in California's Sierra Nevada for Subwatershed Scale Adaptation1. Journal of the American Water Resources Association 45:1409-1423.

Amphibian Characteristics Literature Cited

AmphibiaWeb. Information on amphibian biology and conservation. [web application]. 2009. Berkeley, California: AmphibiaWeb. Available: http://amphibiaweb.org/. (Accessed: Feb 15, 2013).
Knapp, R.A.; Briggs, C.J.; Smith, T.C.; Maurer, J.R. 2011. Nowhere to hide: impact of a temperature-sensitive amphibian pathogen along an elevation gradient in the temperate zone. Ecosphere. 2:1–26.
Pope, K. and J. Long. 2013. Lakes: recent research and restoration strategies. Pages xxx-xxxin: Long, Jonathan; Skinner, Carl; North, Malcolm; Winter, Pat; Zielinski, Bill; Hunsaker, Carolyn; Collins, Brandon; Keane, John; Lake, Frank; Wright, Jessica; Moghaddas, Emily; Jardine, Angela; Hubbert, Ken; Pope, Karen; Bytnerowicz, Andrzej; Fenn, Mark; Busse, Matt; Charnley, Susan; Patterson, Trista; Quinn-Davidson, Lenya; Safford, Hugh; chapter authors and Synthesis team members. Bottoms, Rick; Hayes, Jane; team coordination and review. Meyer, Marc; Herbst, David; Matthews, Kathleen; additional contributors. USDA Forest Service Pacific Southwest Research Station. 2013. Science Synthesis to support Forest Plan Revision in the Sierra Nevada and Southern Cascades. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station. 504 p.
Sodhi N.S., Bickford D., Diesmos A.C., Lee T.M., Koh L.P., et al. 2008 Measuring the Meltdown: Drivers of Global Amphibian Extinction and Decline. PLoS ONE 3(2): e1636. doi:10.1371/journal.pone.0001636

Water Temperature Characteristics Literature Cited

Armour, C.L. 1991. Guidance for evaluating and recommending temperature regimes to protect fish. Instream Flow Information Paper 27. Biological Report 90(22). U.S. Fish and Wildlife Service, National Ecology Research Center, Fort Collins, CO.
Broadmeadow, S. B., J. G. Jones, T. E. L. Langford, P. J. Shaw, and T. R. Nisbet. 2011. The influence of riparian shade on lowland stream water temperatures in southern England and their viability for brown trout. River Res. Applic., 27: 226–237.
California Department of Fish and Game. 2010. Effects of water temperature on anadromous salmonids in the San Joaquin River Basin, DFG Exhibit 4, prepared for the informational proceeding to develop flow criteria for the delta ecosystem necessary to protect public trust resources before the State Water Resources Control Board. Retrieved February 7, 2013 from http://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=17962
Caissie, D. 2006. The thermal regime of rivers—A review: Freshwater Biology, v. 51, p. 1389-1406.
Coutant ,C.C. 1977. Compilation of temperature preference data. Journal of the Fisheries Research Board of Canada, 34, 739–745.
Coutant, C.C. 1999. Perspective on Temperature in the Pacific Northwest’s Fresh Water. Environmental Sciences Division, Publication No. 4849, Oak Ridge National Laboratory, ORNL/TM-1999/44. Oak Ridge National Laboratory, Oak Ridge, Tennessee, 109 p.
Dunham, J.B., M. M. Peacock, B.E. Rieman, R.E. Schroeter, and G.L. Vinyard. 1999. Local and geographic variability in the distribution of stream-living Lahontan cutthroat trout. Transactions of the American Fisheries Society 128:875-889.
Dunhan, J., B. Rieman, and G. Chandler. 2001. Development of field-based models of suitable thermal regimes for interior Columbia Basin salmonids. Boise, ID: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. Final Report RMRS-00-IA-11222014-521. 79 p.
Eaton, J.G., J. H. McCormick, B. E. Goodno, D. G. O'Brien, H. G. Stefany, M. Hondzo & R. M. Scheller. 1995. A field information-based system for estimating fish temperature tolerances. Fisheries 20(4):10-18.
Ebersole, J.L., W.J. Liss, and C.A. Frissell. 2001. Relationship between stream temperature, thermal refugia, and rainbow trout Oncorhynchus mykiss abundance in arid-land streams of the northwestern United States. Ecology of Freshwater Fish 10:1-10.
Elliott, J.M. 1981. Some aspects of thermal stress on freshwater teleosts. Pages 209-245 in A. D. Pickering, editor. Stress and Fish. Academic Press, London.
Fausch, K.D., S. Nakano and K. Ishigaki. 1994. Distribution of two congeneric charrs in streams of Hokkaido Island, Japan: considering multiple factors across scales. Oecologia 100:1-12.
Flebbe, P.A. 1994. A regional view of the margin: salmonid abundance and distribution in the southern Appalachian mountains of North Carolina and Virginia. Transactions of the American Fisheries Society 123:657-667.
Fry, F. E. J. 1967. Responses of poikilotherms to temperature. Pages 375-709 in A. H. Rose, ed. Thermobiology. Academic Press, San Diego, Calif. 653 pp.
Fry, F. E. J. 1971. The effect of environmental factors on the physiology of fish. Pages l-98 in W. S. Hoar and D. J. Randall, eds. Fish physiology. Vol. VI. Environmental relations and behavior. Academic Press, San Diego, Calif. 559 pp.
Hawkins C.P., J.N. Nogue, L.M. Decker and J.W. Feminella. 1997. Channel morphology, water temperature, and assemblage structure of stream insects. Journal of the North American Benthological Society, 16, 728–749.
Hutchinson, V. H. 1976. Factors influencing thermal tolerances of individual organisms. Pages 10-16 in Proceedings of the Second Sauana River Ecology Laboratory Conference, April 1975, Augusta, Georgia. Available from NTIS, CONF.- 750425.
Hynes, H.B.N. 1960. The Biology of Polluted Waters. Liverpool University Press, Liverpool, 202 p.
Johnson, S.L. 2004. Factors influencing stream temperatures in small streams: substrate effects and a shading experiment. Canadian Journal of Fish and Aquatic Sciences. 61: 913–923.
Lowney, C.L. 2000. Stream temperature variation in regulated rivers: evidence for a spatial pattern in daily minimum and maximum magnitudes. Water Resources Research, 36, 2947–2955.
Magnuson, J.J., L.B. Crowder, and P.A. Medvick. 1979. Temperature as an ecological resource. American Zoologist 19:331-343.
Nakano, S., F. Kitano, and K. Maekawa. 1996. Potential fragmentation and loss of thermal habitats for charrs in the Japanese archipelago due to climatic warming. Freshwater Biology 36:711-722.
Nielsen, J.L., T.E. Lisle, and V. Ozaki. 1994. Thermally stratified pools and their use by steelhead in northern California streams. Transactions of the American Fisheries Society 123:613-626.
Peterson, J.T., and C.F. Rabeni. 1996. Natural thermal refugia for temperate warmwater stream fishes. North American Journal of Fisheries Management 16: 738-746.
Poole, G.C. and C.H. Berman. 2001. An ecological perspective on instream temperature: natural heat dynamics and mechanisms of human-caused thermal degradation. Environ. Manag. 27: 787–802.
Poole, G., J. Risley, and M. Hicks. 2001. Spatial and Temporal Patterns of Stream Temperature (Revised). Issue Paper 3 Prepared as Part of EPA Region 10 Temperature Water Quality Criteria Guidance Development Project. EPA-910-D-01-003.
Rieman, B.E., D.C. Lee, and R.F. Thurow. 1997. Distribution, status, and likely future trends of bull trout within the Columbia River and Klamath Basins. North American Journal of Fisheries Management 17:1111-1125.
Sinokrot, B.A. and J.S. Gulliver. 2000. In-stream flow impact on river water temperatures. Journal of Hydraulic Research, 38, 339–349.
Stanford, J. A., and F. R. Hauer. 1992. Mitigating the impacts of stream and lake regulation in the Flathead River catchment, Montana, USA: An ecosystem perspective. Aquatic Conservation: Marine and Freshwater Ecosystems 2:35– 63.
Stoneman, C.L. and L.J. Michael. 1996. A simple method to classify stream thermal stability with single oberservations of daily maximum water and air temperature. North Am J Fish Manage 16:728-737.
Thomas, L. 2005. Keeping it cool: unraveling the influences on stream temperature. Pacific Northwest Research Station Science Findings, Issue 73.
Troxler, R.W. and E.L. Thackston. 1977. Predicting the rate of warming of rivers below hydro-electric installations. Journal of the Water Pollution Control Federation, August, 1902–1912.
Vannote R.L., G.W. Minshall, K.W. Cummins, J.R. Sedell and C.E. Cushing. 1980. The river continuum concept. Canadian Journal of Fisheries and Aquatic Sciences, 37, 130–137.
Ward, J. V., and J. A. Stanford. 1995. Ecological connectivity in alluvial river ecosystems and its disruption by flow regulation. Regulated Rivers: Research and Management 11:105–119.
Webb, B.W. and D.E. Walling. 1993. Temporal variability in the impact of river regulation on thermal regime and some biological implications. Freshwater Biology, 29, 167–182.
Webb, B.W. and D.E. Walling. 1996. Long-term variability in the thermal impact of river impoundment and regulation. Applied Geography, 16, 211–227.
Webb, B.W. and Y. Zhang. 1997. Spatial and seasonal variability in the components of the river heat budget. Hydrol Proc 11:79-101.

Macroinvertebrate and Algae Characteristics Literature Cited

Blinn, D.W. and D.B. Herbst. 2003. Use of diatoms and soft algae as indicators of stream abiotic determinants in the Lahontan Basin, USA. Final Report to the California Regional Water Quality Control Board, Lahontan Region and the California State Water Resources Control Board. Contract #01-119-160-0.
Blinn, D.W. and D.B. Herbst. 2007. Preliminary Index of Biological Integrity (IBI) for periphyton in the eastern Sierra Nevada, California – Unpublished, Draft Report.
EPA. 2006. Wadeable Streams Assessment: A Collaborative Survey of the Nation’s Streams, Office of Research and Development, Office of Water Washington, DC 20460; EPA 841-B-06-002. Available at __http://www.epa.gov/owow/streamsurvey/__

EPA. 2009. National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes. EPA 841-R-09-001. U.S. Environmental Protection Agency, Office of Water and Office of Research and Development, Washington, D.C.

EPA. 2011. 2012 National Lakes Assessment. Field Operations Manual. EPA 841-B-11-003. U.S. Environmental Protection Agency, Washington, DC. Available at http://www.cpcb.ku.edu/research/assets/2012_lakes/NLA%202012%20Field%20Operations%20Manual%202012.03.22.pdf

Fetscher, A.E., L. Busse, and P. R. Ode. 2009. Standard Operating Procedures for Collecting Stream Algae Samples and Associated Physical Habitat and Chemical Data for Ambient Bioassessments in California. California State Water Resources Control Board Surface Water Ambient Monitoring Program (SWAMP) Bioassessment SOP 002.

Hawkins, C.P., R.H. Norris, J.N. Hogue and J.W. Feminella. 2000. Development and evaluation of predictive models for measuring the biological integrity of streams. Ecological Applications 10:1456-1477.

Karr, J. R. 1991. Biological integrity: A long-neglected aspect of water resource management. Ecol. Appl. 1:66–84.

Karr, J. R., K. D. Fausch, P. L. Angermeier, P. R. Yant, and I. J. Schlosser. 1986. Assessing biological integrity in running waters: a method and its rationale. Ill. Nat. Hist. Surv. Spec. Publ. 5, Urbana, Ill. 28pp.

Moyle, P.B., 2002. Inland Fishes of California, Revised and Expanded. University of California Press, Berkeley. 502 pp.

Moyle, P.B., J.V.E. Katz, and R.M. Quiñones. 2011. Rapid decline of California’s native inland fishes: A status assessment. Biological Conservation 144:2414–2423.

Ode, P.R., T.M. Kincaid, T. Fleming and A.C. Rehn. 2011. Ecological Condition Assessments of California’s Perennial Wadeable Streams: Highlights from the Surface Water Ambient Monitoring Program’s Perennial Streams Assessment (PSA) (2000-2007). A collaboration between the State Water

Resources Control Board’s Non-Point Source Pollution Control Program (NPS Program), Surface Water Ambient Monitoring Program (SWAMP), California Department of Fish and Game Aquatic Bioassessment Laboratory, and the U.S. Environmental Protection Agency. Available at http://www.swrcb.ca.gov/water_issues/programs/swamp/docs/reports/psa_smmry_rpt.pdf.

Ode. P.R., A.C. Rehn and J.T. May. 2005. A quantitative tool for assessing the integrity of southern coastal California streams. Environmental Management 35:493-504.

Ode, P.R. and K. Schiff. 2009. Recommendations for the development and maintenance of a reference condition management program (RCMP) to support biological assessment of California’s wadeable streams. Report to the State Water Resources Control Board’s Surface Water Ambient Monitoring

Program (SWAMP), Sacramento, CA. Available at http://www.waterboards.ca.gov/water_issues/programs/swamp/docs/qamp/wadestreams_rcmpfinal.pdf

Olsen, A.R. 2008a. USFS Region 5, Sierra Nevada National Forests, Stream Survey Design 2008. Environmental Protection Agency - National Health and Environmental Effects Research Laboratory, Western Ecology Division, Corvallis, OR

Olsen, A.R. 2008b. USFS Region 5, Sierra Nevada National Forests, Lake Survey Design 2008. Environmental Protection Agency - National Health and Environmental Effects Research Laboratory, Western Ecology Division, Corvallis, OR

Plafkin, J.L., M.T. Barbour, K.D. Porter, S.K. Gross, and R.M. Hughes. 1989. Rapid bioassessment protocols for use in streams and rivers: Benthic macroinvertebrates and fish. U.S. Environmental Protection Agency, Office of Water Regulations and Standards, Washington, D.C. EPA 440-4-89-001.

Poff, N.L., Allan J.D., Bain M.B., Karr J.R., Prestegaard K.L., Richter B.D., Sparks R.E. & Stromberg J.C. 1997. The natural flow regime: a paradigm for river conservation and restoration. Bioscience, 47, 769–784.

Poff, N.L., M.M. Brinson and J.W. Day, Jr. 2002. Aquatic Ecosystems & Global Climate Change. Potential Impacts on Inland Freshwater and Coastal Wetland Ecosystems in the United States. Special Publication prepared for the Pew Center on Global Climate Change, Available at
__http://www.w.pewtrusts.com/uploadedFiles/wwwpewtrustsorg/Reports/Protecting_ocean_life/env_climate_aquaticecosystems.pdf__

Rehn, A.C. 2009. Benthic macroinvertebrates as indicators of biological condition below hydropower dams on west slope Sierra Nevada streams, California, USA. River Research and Applications 25:208-228.

Resh, V.H. 1979. Sampling variability and life history features: Basic consideration in the design of aquatic insect studies. Journal of the Fisheries Research Board of Canada 36:290-311.

Resh, V.H. and J.K. Jackson. 1993. Rapid assessment approaches to biomonitoring using benthic macroinvertebrates. Pages 195-233 in D.M. Rosenberg and V.H. Resh (editors). Freshwater biomonitoring and benthic macroinvertebrates. Chapman and Hall, New York.

Stevens, D. L., Jr., and A. R. Olsen. 2003. Variance estimation for spatially balanced samples of environmental resources. Environmetrics 14:593-610.

Stevens, D. L., Jr., and A. R. Olsen. 2004. Spatially-balanced sampling of natural resources in the presence of frame imperfections. Journal of American Statistical Association:99:262-278.

SWAMP (Surface Water Ambient Monitoring Program). 2006. Water Quality Assessment of the Condition of California Coastal Waters and Wadeable Streams. The Clean Water Act 305(b) Report to the Environmental Protection Agency. Available at http://www.swrcb.ca.gov/water_issues/programs/swamp/docs/factsheets/305breport2006.pdf

Special Aquatic Habitat Literature Cited

Barbour, Michael G. and Jack Major (eds.). 1990. Terrestrial Vegetation of California. California Native Plant Society (CNPS) Special Publication No. 9. Sacramento, CA 95814.

Erman, D.C. and N.A. Erman. 1975. Macroinvertebrate composition and production in some Sierra Nevada Minerotrophic peatlands. Ecology 56:591-603.

Erman, N.A. 1996. Status of aquatic invertebrates. Pages 987-1008 In Sierra Nevada Ecosystem Project: Final Report to Congress, Assessments and scientific basis for management options. Vol II, chp 35. University of California, Centers for Water and Wildland Resources, Davis, CA 95616-8750.

Erman, N.A. and D.C. Erman. 1990. Biogeography of caddisfly (Trichoptera) assemblages in cold springs of the Sierra Nevada (California, USA). Contribution 200. University of California, California Water Resources Center, Davis, CA 95616. 28 pages.

Erman, N.A. and D.C. Erman. 1995. Spring permanence, Trichoptera species richness, and the role of drought. Biodiversity of Aquatic Insects and Other Invertebrates. Journal of the Kansas Entomological Society 68(2):50-64 supplement.

Frest, T.J. and E.J. Johannes. 2006. Progress Report Freshwater Mollusk Survey of northern Sierra Nevada National Forests, 2006. USDA Forest Service, PSW Regional Office, Vallejo, CA. 10 pp.

Frest, T.J. and E.J. Johannes. 2007. Progress Report on 2006 Freshwater Mollusk Fieldwork in Sierra Nevada National Forests, California. USDA Forest Service, PSW Regional Office, Vallejo, CA. 20 pp.

Hynes, H.B.N. 1970. The Ecology of Running Waters. Liverpool University Press, Liverpool, England. 555 pages.

Moyle, P.B. 1996. Status of aquatic habitat types. Pages 945-952 In Sierra Nevada Ecosystem Project, Final Report to Congress, Vol. II, Assessments and scientific basis for management options. University of California, Centers for Water and Wildland Resources, Davis. CA. 95616.

Sada, D.W. and K.F. Pohlmann. 2002. Spring Inventory and Monitoring Protocols. Conference Proceedings. Spring-fed Wetlands: Important Scientific and Cultural Resources of the Intermountain Region. Available at __http://www.wetlands.dri.edu__ .

Shepard, W.D. 1993. Desert springs- both rare and endangered. Aquatic Conservation: Marine and Freshwater Ecosystems 3:351-359.


Habitat Fragmentation Literature Cited

Brown, K. D., A. A. Echelle, D. L. Propst, J. E. Brooks, andW. L. Fisher. 2001. Catastrophic wildfire and number of populations as factors influencing risk of extinction for gila trout. Western North American Naturalist 61:139–148.

Dunham, J. B., A. E. Rosenberger, C. H. Luce, and B. E. Rieman. 2007. Influences of wildfire and channel reorganization on spatial and temporal variation in stream temperature and the distribution of fish and amphibians. Ecosystems 10:335–346.

Malison, R.L., and C.V. Baxter. 2010. The fire pulse: wildfire stimulates flux of aquatic prey to terrestrial habitats driving increases in riparian consumers. Canadian Journal of Fisheries and Aquatic Sciences 67: 570-579.

Moyle, P.B., Williams, J.E., 1990. Biodiversity loss in the temperate zone: decline of the native fish fauna of California. Conserv. Biol. 4(3), 275-284.

Moyle, P.B., Yoshiyama, R.M., Knapp, R.A., 1996. Status of fish and fisheries. Sierra Nevada Ecosystem Project: Final Report to Congress. Volume II. Centers for Water and Wildland Resources, University of California, Davis, pp. 953-973.

Moyle, P.B. and P.J. Randall. 1996. Biotic Integrity of Watersheds. Sierra Nevada Ecosystem Project: Final Report to Congress. Volume II. Centers for Water and Wildland Resources, University of California, Davis, pp. 975-983.

Rieman, B. E., D. Lee, G. Chandler, and D. Myers. 1997. Does wildfire threaten extinction for salmonids: responses of redband trout and bull trout following recent large fires on the Boise National Forest. Pages 47–57 in J. Greenlee, editor. Proceedings of the symposium on fire effects on threatened and endangered species and habitats. International Association of Wildland Fire, Fairfield, Washington.

Rieman, B.E., Dunham, J.B., 2000. Metapopulation and salmonids: a synthesis of life history patterns and empirical observations. Ecol. Freshw. Fish 9, 51-64.

Rieman, B. E., D. Lee, D. Burns, R. Gresswell, M. K. Young, R. Stowell, J. Rinne, and P. Howell. 2003. Status of native fishes in the western United States and issues for fire and fuels management. Forest Ecology and Management 178:197–211.


Sestrich, C.M., T.E. McMahon, and M.K. Young. 2011. Influence of fire on native and nonnative salmonid populations and habitat in a western Montana basin. Transactions of the American Fisheries Society 140: 136-146.

Spina, A.P., and Tormey, D.R., 2000. Postfire sediment deposition in geographically restricted steelhead habitat. N. Amer J. Fish. Manage. 20:562–569.

TACCIMO Climate Change Tool Literature http://goo.gl/Lg3Bn

TACCIMO – Fish Information
Jager, H. I., van Winkle, W., & Holcomb, B. D. 1999. Would hydrologic climate changes in Sierra Nevada streams influence trout persistence? Transactions of the American Fisheries Society, 128, 222-240.
Katz, J., Moyle, P. B., Quinones, R. M., Israel, J. & Purdy, S. 2012. Impending extinction of salmon, steelhead, and trout (Salmonidae) in California. Environmental Biology of Fishes, DOI 10.1007/s10641-012-9974-8
Kiernan, J. D. & Moyle, P. B. 2012. Flows, droughts, and aliens: factors affecting the fish assemblage in a Sierra Nevada, California, stream. Ecological Applications, 22 (4),1146 – 1161.
Marchetti, M. P. & Moyle, P. B. 2001. Effects of flow regime on fish assemblages in a regulated California stream. Ecological Applications, 11 (2), 530-539.
Meyers, E. M., Dobrowski, B., Tague, C. L. 2010. Climate Change Impacts on Flood Frequency, Intensity, and Timing May Affect Trout Species in Sagehen Creek, California. Transactions of the American Fisheries Society, 139 (6), 1657-1664.
Moyle, P. B., Kiernan, J. D., Crain, P. K. & Quicones, R. M. 2012. Projected effects of future climates on freshwater fishes of California. California Energy Commission. Publication number: CEC-500-2012-028.
Null, S. E., Viers, J. H., Deas, M. L., Tanaka, S. K. & Mount, J. F. 2012. Stream temperature sensitivity to climate warming in California’s Sierra Nevada: impacts to coldwater habitat. Climatic Change, DOI 10.1007/s10584-012-0459-8
Rahel, F. J., Bierwagen, B., & Taniguchi, Y. 2008. Managing aquatic species of conservation concern in the face of climate change and invasive species. Conservation Biology, 22(3), 551-561.

TACCIMO – Amphibians Information
Blaustein, A. R., Walls, S. C., Bancroft, B. A., Lawler, J. J., Searle, C. L., & Gervasi, S. S. 2010. Direct and indirect effects of climate change on amphibian populations. Diversity, 2(2), 281-313. doi:10.3390/d2020281
Davidson, C., Shaffer, H. B. & Jennings, M. R. 2001. Declines of the California red-legged frog: Climate, UV-B, habitat, and pesticides hypotheses. Ecological Applications, 11(2), 464 – 479.
Davidson, C., Shaffer, H. B. & Jennings, M. R. 2002. Spatial tests of the pesticide drift, habitat destruction, UV-B, and climate-change hypotheses for California amphibian declines. Conservation Biology, 16(6), 1588 – 1601.
Lacan, I., Matthews, K. & Feldman, K. 2008 Interaction of an introduced predator with future effects of climate change in the recruitment dynamics of the imperiled Sierra Nevada yellow-legged frog (Rana sierra). Herpetological Conservation and Biology, 3 (2), 211 – 223.
Wake, D. B. & Vredenburg. 2008. Are we in the midst of the sixth mass extinction? A view from the world of amphibians. Proceedings of the National Academy of Science, 105 (Suppl 1), 11466-11473.

TACCIMO – Invertebrate Information
Herbst, D. B. & Cooper, S. D. 2010. Before and after the deluge: rain-on-snow flooding effects on aquatic invertebrate communities of small streams in the Sierra Nevada, California. Journal of the North American Benthological Society, 29(4), 1354 – 1366. DOI: 10.1899/09-185.1

Additional References added from SFL's Conservation Strategy

Derlet, R. W., Goldman, C. and Conner, M. J. 2010. Reducing the impact of summer cattle grazing on water quality in the Sierra NevadaMountains of California: a proposal. Journal of Water and Health 8(2):326-333.
Furniss, M., Roelofs, J. T. D. and Yee, C. S. 1991. Road Construction and Maintenance. In: Influences of Forest and Rangeland Management. Meehan, W. R. ed. Bethesda, Maryland: American Fisheries Society Special Publication 19. pp. 297-324.
Frissell, C.A., Scurlock, M. and Kattelman, R. 2012. SNEP Plus 15 Years: Ecological & Conservation Science for Freshwater ResourceProtection & FederalLand Management in the Sierra Nevada. Summary report for a scientific workshop held at Davis, California, 12-13 December 2011. Pacific Rivers Council Science Publication 12-001. 39 pp.
Gucinski, H., Furniss, M. J., Ziemer, R. R. and Brookes, M. H. 2001. Forest Roads: A Synthesis of Scientific Information. Gen. Tech. Rep. PNWGTR-509. U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, Portland, OR.
Scurlock, M. and Frissell, C. 2012. Conservation of Freshwater Ecosystems on Sierra Nevada National Forests: Policy Analysis and Recommendations for the Future. Pacific Rivers Council. June, 2012.
Siegel, R. B. and DeSante, D. F. 1999. Draft avian conservation plan for the Sierra Nevada Bioregion: conservation priorities and strategies for safeguarding Sierra bird populations. Institute for Bird Populations report to California Partners in Flight. Version 1.0.
Thompson, L.C., Escobar, M.I., Mosser, C.M., Purkey, D.R., Yates, D., Moyle, P.B. 2011. Water management adaptations to prevent loss of spring-run Chinook salmon in California under climate change. J. Water Resour. Plann. Manage., 10.1061/(ASCE)WR.1943-5452.0000194.
USDA Forest Service and USDI Fish and Wildlife Service 1995. PACFISH - Implementation of Interim Strategies for Managing Anadromous Fish-Producing Watersheds in Eastern Oregon and Washington, Idaho, and portions of California. February 24, 1995.
USDA Forest Service Watershed Condition Advisory Team 2011. Watershed Condition Framework: A Framework for Assessing and Tracking Changes to Watershed Condition, FS-977. http://www.fs.fed.us/publications/watershed/Watershed_Condition_Framework.pdf
United States Environmental Protection Agency (USEPA) 2008. Comments on Western Oregon Plan Revisions. January 9, 2008.
Williamson, C. E., Dodds, W., Kratz, T. K., and Palmer, M. A. 2008. Lakes and streams as sentinels of environmental change in terrestrial and atmospheric processes. Front. Ecol. Environ. 6:247–254.
Williamson, C. E., Saros, J. E., and Schindler, D. W. 2009. Sentinels of change. Science 323:887–889.

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