Effects of unregulated tributaries on a regulated mainstem

Ecogeomorphology 2009, UC Davis, CA Nicholas Buckmaster, Adam Clause, Tyler Hatch, Heather Jackson, Anna Stephenson Table of Contents: List of Figures……………………………………………………..3 Introduction……………………………………………………....4 Tuolumne River System………………………………………....5 Physical Template………………………………………….……9 Climate…………………………………………….……...9 Geomorphology………………………………………….10 Hydrograph……………………………………………....13 Water Quality…………………………………………….16 Biological Systems ……………………………………………...19 Riparian Vegetation……………………………………...20 In-stream Production..………………………………...…23 Consumers………………………………………………..24 Benthic Macroinvertebrates……………………....24 Amphibians……………………………………….30 Fishes……………………………………………...32 Conclusion………………………………………………………..43 Literature Cited……………………………………………………44

2 List of Figures  FIGURE 1. General Conceptual Model  FIGURE 2. Generalized geologic map of the Tuolumne watershed  FIGURE 3. Tuolumne River Water and Power Infrastructure (Null et al. 2009)  FIGURE 4. Map of the Tuolumne Watershed  FIGURE 5a. Detailed conceptual models of individual tributary interactions  FIGURE 5b. Detailed conceptual model of mainstem interactions  FIGURE 6. Graph of average daily discharge in the Tuolumne, Clavey and North Fork.  FIGURE 7. Temperature of Mainstem and Tributaries taken every ½ hr  FIGURE 8. An example of a ‘recruitment box.’  FIGURE 9. Riparian diversity of all species identified  FIGURE 10. Invertebrate functional feeding group percentages  FIGURE 11. Relative abundances of macroinvertebrates in the middle Tuolumne  FIGURE 12 Family-level richness of macroinvertebrates in the middle Tuolumne system  FIGURE 13. Percent Ephemeroptera, Plecoptera and Trichoptera in the middle Tuolumne  FIGURE 14. Invertebrate drift at Indian Bar.  FIGURE 15: Fish species present in the mainstem of the Tuolumne river  FIGURE 16. Spawning (blocks) and optimal temperatures (lines) for the fish common to the Tuolumne  FIGURE 17. Clavey River average Monthly Temperatures and Flows  FIGURE 18. 2008-2009 Hydrograph and Thermograph of the Mainstem (At Lumsden)  FIGURE 19 North Fork of the Tuolumne Hydrograph  FIGURE 20 Survey Locations on Clavey  FIGURE 21. Clavey River fish surveys above and below the falls  FIGURE 22. Survey locations on the North Fork  FIGURE 23. North Fork dive data above and below the falls List of Tables  TABLE 1 Water quality parameters from June 2009  TABLE 2 Dominant plant communities of the middle reaches of the Tuolumne River watershed

3 Introduction River ecosystems are complex, with the physical template defining the biological interactions that occur (Vannote et al. 1980). On a broad scale these biological interactions have been described as a continuum, varying in tandem with physical changes along the length of a river system (Vannote et al. 1980). In the Sierra Nevada of California, anthropogenic forces such as dams and species introductions also strongly shape these systems. Dams can severely modify a river ecosystem, shifting the patterns of physical and biological continuums up or down river of a natural state (Ward and Stanford 1995). Unregulated tributaries can provide important heterogeneity to these regulated rivers, and may ameliorate the influence of upstream impoundments on a mainstem (Ward and Stanford 1995, Stevens et al. 1997, Takao et al. 2008). In an effort to explicitly examine how these physical, biological, and anthropogenic forces interact to shape the ecology and geomorphology of river systems, we developed a conceptual model of the Tuolumne River and two of its major unregulated tributaries. Specifically, we looked at the potential influences of the North Fork Tuolumne River and the Clavey River on the middle reaches of the mainstem of the Tuolumne River (Figure 1).

FIGURE 1: Generalized conceptual model of the impact of tributaries on the middle reaches of the Tuolumne River.

4 The Tuolumne River System The Tuolumne River is located on the West slope of the central Sierra Nevada, with headwaters in the famous Yosemite National Park. The Sierras consist of many different rock types, but granite dominates at higher elevations, overlain in areas by tertiary volcanics. In the foothill metamorphic belt, accreted terrains and low grade metamorphics become predominant (Figure 2). Veins of quartz and gold associated with the famous motherload brought miners to foothill reaches in the mid to late 1800s. Mining activity drove the construction of early diversion dams in the Tuolumne foothills in the 1850s. Later, hydraulic mining activities generated a vast amount of gravel in tailing piles, which were often washed into the river.

FIGURE 2: Generalized geologic map of the Tuolumne watershed (Mount et al. 2009)

As the population of California increased, so did the demand for pure drinking water and electrical power. Eleanor Dam was constructed in 1918, followed by O’Shaughnessy Dam, finished in 1924 to create the hotly debated Hetch Hetchy Reservoir. In 1938 the San Francisco Power and Utility Commission (SFPUC) raised O’Shaughnessy Dam to 430ft, increasing the reservoir capacity to 360,360 acre feet. And finally, in 1955 SFPUC finished Cherry Dam to

5 create a third major impoundment in the central Sierras to supply the San Francisco Bay area with power and water. In conjunction with these three dams, the SFPUC infrastructure also includes six bay area reservoirs, three powerhouses and an array of tunnels and aqueducts. The Turlock and Modesto Irrigation Districts also own and operate aspects of the greater Tuolumne “plumbing system,” including the La Grange and New Don Pedro Dams, to generate power and provide water for people and crops in the fertile central valley of California (Figure 3) (Null et al 2009).

Cherry Creek Tuolumne Eleanor Creek River

O'SHAUGHNESSY ELEANOR DAM DAM CHERRY DAM Kirkwood Powerhouse Cherry Power Lower Cherry Tunnel Canyon Tunnel Aqueduct Mountain Tunnel Holm Lower Cherry Tuolumne Powerhouse Diversion Dam River Early Intake

Cherry Creek Tuolumne Mountain Tunnel River NEW DON PEDRO Priest Reservoir RESERVOIR & POWERHOUSE Foothill Tunnel

Moccasin La Grange Dam Reservoir & Powerhouse Modesto Turlock Canal Canal San Joaquin Pipelines 1,2,3 Ag. & Urban Ag. & Urban Demand Demand

San Joaquin River

LEGEND l s e g n n i n r u

p Other Bay T

S

s Area Cities l Reservoir s a t a

s LOCAL p y y r SAN FRANCISCO Powerhouse B C RESERVOIRS River

Pipeline Non-storage Reservoir SFPUC Demand Regions

Treatment Plant

FIGURE 3: Tuolumne River Water and Power Infrastructure (Null et al. 2009)

6 The Tuolumne River is joined by several tributaries below O’Shaughnessy Dam, including Cherry Creek (also regulated by SFPUC), the South and Middle Forks, Clavey River, and the North Fork (Figure 4). The impacts of the latter two tributaries are the focus of the conceptual model described here. Cherry Creek Clavey North River Fork

Tuolumne Mainstem

Middle & South Forks

FIGURE 4: Map of the Tuolumne Watershed, with major subwatersheds shown; red lines represent major dams in the system.

The generalized conceptual, shown above in Figure 1, illustrates the basic physical and biological factors as well as their interactions, both within the regulated mainstem and the unregulated tributaries. The large arrows in the center of the model highlight the most important ecogeomorphic subsidies from these unregulated systems that impact the regulated mainstem. Because each of these stream systems have slightly different physical and biological factors, Figure 5 shows more detailed models of the interactions within each tributary system and the mainstem. By creating these higher resolution models, we were able to more clearly demonstrate the differences between the impacts of each tributary. While each detailed model includes the same generalized factors and influences, the pattern and magnitude of those interactions varies across the systems. It is also important to note that this model is in no way a complete representation of the riverine system – it has been refined to emphasize the factors deemed most important with respect to the effects of unregulated tributaries on the regulated mainstem.

7 FIGURE 5a: Detailed conceptual models of individual tributary interactions

8 FIGURE 5b: Detailed conceptual model of mainstem interactions

Physical Template The primary physical drivers in this system include climate, geomorphology of the region, hydrograph of each river, and water quality parameters throughout the system. These four physical factors form a template on which the biotic interactions take place. They interact with one another, and can also be influenced by biotic feedback loops. Each one of these factors, their interactions with other physical drivers, and their role in the ecosystem as a whole are discussed here in more detail.

Climate The west slope of the central Sierra Nevada experiences a Mediterranean climate, with cool wet winters and hot dry summers. Because this mountain range is relatively tall and located near the edge of the continental plate, water that evaporates from the ocean moves inland until it reaches the Sierras where the air is forced up and drops its moisture. The higher reaches of the watershed receive this precipitation as snow, while the lower reaches receive it as winter rains. Variability in precipitation type and resulting flow events causes many of the differences that we see in the hydrographs and temperatures of Sierra streams. Air temperature is also a

9 driving force determining the water temperature of these aquatic systems. As the river drops below the snow line (3000-4000ft), the air temperatures, and thus water temperatures, are warmed. A majority of the North Fork Tuolumne is at these lower elevations, contributing to noticeably higher water temperatures in this tributary. Climate has also played a large role in shaping the geomorphology of the central sierras over the course of geologic time. During the most recent ice age (>1 mya – 10,000 ya) glaciers covered most of the high peaks in the Sierra Nevada. The movement of these massive blocks of ice carved huge valleys and removed much of the granite bedrock, creating glacial moraines (or sediment deposits) that today are sources of sediment for the river systems. These climatic weathering processes, such as freeze/thaw cycles, continue to add sediment to the system today.

Geomorphology Geomorphology refers to the study of landforms and the processes which create them. The different aquatic and riparian habitats present along the Tuolumne River are a direct result of geomorphic factors, such as the sediment load of the river and the shape of the channel. Sediment is contributed to the river primarily through the slow weathering of bedrock and boulders. In the case of the Tuolumne this rock is generally granitic (intrusive igneous) or metamorphic. Where and how this sediment is deposited is a function of the hydrograph and variation in the sediment capacity of the river, which is often a function of channel shape. In turn, channel shape is determined by the geologic history of a region and the erosional resistance of the bedrock through which the river flows. A few characteristic channel formations that appear within the Tuolumne watershed include steep canyons, meanders and bends, widening and narrowing of the stream bed (properly termed channel expansions and contractions), waterfalls at tributary confluences, and bars within the channel. Each of these formations combine with the sediment load to create different types of habitat, and thus influence the biological community of the watershed. The primary formations and correlated habitat types are summarized below. Steep, straight canyons are characteristic of historic glaciation, and are found in the bedrock dominated reaches of the Tuolumne and Clavey rivers. These canyons are carved by large masses of ice and snow that, because of their massive size, move in a relatively straight path downslope. As they advance, they pluck off rock from the sides and floor of the canyon, and can transport these huge boulders long distances. Channels carved by glaciation generally remain

10 straight after the retreat of the glaciers because the bedrock into which they are incised is very resistant to erosion and to the creation of new meanders. These straight channels promote fast currents, increasing the ability of the river to move sediment, while decreasing available velocity refuges for biota. Meanders and bends are found in a river channel in places where the water runs into highly resistant bedrock formations. These outcrops block the fast moving water, and it is deflected towards nearby softer materials which erode more quickly, forming a bend in the channel. In the Tuolumne watershed, volcanic activity in the tertiary period deposited more resistant rock in the form of pyroclastic flows and lahars (volcanic mudflows) which filled ancestral river channels. Preferential erosion of the weaker rock surrounding these deposits created what is known as inverted topography – when ancient low points (i.e river channels) are filled with harder rock which is slowly exposed over time and today remain as high plateaus. One of these examples of inverted topography is located near the confluence of the mainstem Tuolumne and the South Fork, and another forms the ridge between the Clavey and the North Fork. Both of these flows caused the historic river to shift, and form several large bends as the river eroded new channels along the side of the volcanic flow. Each of these major bends also altered the shape of the channel downstream as the momentum of the water “ricocheted” back and forth between banks and meandered down the canyon. Today this same process facilitates the formation of expansion and/or alternating bars in some sections of the Tuolumne mainstem. Channel expansion and contraction can arise at the confluence of a tributary. When the tributary joins the mainstem at such an angle to allow a separation of flow, a channel contraction can occur. The flow separation usually occurs on the same side of the river as the tributary, causing an eddy current where sediments from both the mainstem and the tributary are deposited. This sedimentation causes a narrowing of the mainstem channel, which can in turn increase the velocity through the area. This phenomenon can be seen at the confluence of the Clavey River with the mainstem. Tributary confluences can also cause channel expansions just upstream of the confluence as a result of the additional water joining up with the channel. Changes in the channel width (expansions and contractions) can also be caused by a change in the gradient of the channel or in the degree to which canyon walls are resistant to erosion. A lower gradient channel will have lower velocities, and thus a lower capacity to carry sediment. As the sediment settles out, the channel becomes shallower and often wider. This can be seen on the mainstem of the Tuolumne in Poopenaut Valley where a large wet meadow has

11 been created in an area with reduced gradient. (Interestingly, this reduced gradient resulted from the pattern of glacial erosion and the deposition of a terminal moraine at the end of the last ice age (McBain and Trush 2007)). The opposite can occur when the bedrock of the canyon walls resists erosion and can limit channel width. In the Tuolumne system, the most resistant formations are often intrusive igneous (mostly granite-granidiorite) or metamorphic rocks formations brought to the surface by tectonic uplift. Bars are another common feature in river channels, often caused by forces such as flow separations, flow conditions, and channel roughness. Flow separations that occur on the interior edge of a large bend create areas of slower velocity and allow sediment to deposit along a gradient, with larger cobbles at the upstream end and closer to the main channel profile. Flow conditions can also create bars within the channels, or relocate those that already exist. When several large boulders or large woody debris (LWD) are deposited together, a small pocket of low velocity water can form behind them, allowing smaller rocks and sand to also deposit. This eventually can form a mid-channel bar, among other things. Finally, channel roughness also influences the occurrence and persistence of bars in a channel. As channel roughness increases, bedload becomes more resistant to movement and more sediment can be deposited in the recirculation zones created by large roughness elements (boulders or bedrock outcroppings). This is because roughness reduces the velocity at the surface of the stream bed boundary layer. One important source of channel roughness is encroaching riparian vegetation, such as the young willows lining Indian Bar on the mainstem of the Tuolumne. Encroachment of vegetation is more common in the regulated mainstem than the unregulated tributaries due to a lower frequency of scouring flows in the winter, and minimum base flows in the summer. Indian bar on the mainstem of the Tuolumne. Waterfalls are another important geomorphic feature seen in the Tuolumne watershed. These waterfalls are most likely the result of resistant bedrock formations eroding slower than surrounding bedrock. Falls can also result from flow obstruction caused by large boulders deposited by glacial activity or transported into the river by landslides. As the water flows over or around these impediments it can result in downstream incision, creating the relief necessary to produce a waterfall. These falls occur on both the North Fork and the Clavey rivers, most likely due to the tough pyroclastic flows which filled in ancient river valleys.

12 On the mainstem of the Tuolumne we see many steep, straight canyons in the upper reaches due to the important role of glaciation at higher elevations. This reduces the number of bends and meanders, and in turn reduces the flow separations and eddies which allow for sediment deposition. Ultimately we may see fewer sand and gravel bars in the upper reaches of the Tuolumne because of these geomorphic processes, a situation which is enhanced by the low sediment load typical of a bedrock system. Additionally, the mainstem will have even less sediment available for deposition due to trapping effects by upstream dams. The reduced capacity for sediment transport by flow regulation also increases the probability that gravel will be become armored, or at least will be refreshed less frequently (Mcbain and Trush 2007). Both of the unregulated tributaries have headwaters beginning at lower elevations than the mainstem, thus they show less influence from glaciation and more influence from volcanic flows. In general, both the Clavey and the North Fork Tuolumne have much higher tortuosity in the lower reaches near their confluences with the Mainstem Tuolumne. Both the Clavey River and the North Fork Tuolumne also have more waterfalls in the lower reaches due to greater variation in bedrock resistance. The unregulated hydrograph of these rivers and the stronger influence of rain events on their discharge results in more frequent episodic flow events which transport more sediment downstream. This increased sediment transport provides the mainstem with a sediment subsidy, evidenced by the formation of classic tributary bars at the confluences from sediment washed out of the watershed.

Hydrograph The timing, frequency, duration and magnitude of flows combine to form a river’s hydrograph. The hydrograph is one of the important factors affecting the biological patterns in a river system and is influenced primarily by the size of the watershed, the precipitation pattern, the capacity for groundwater storage, and the presence or absence of regulation. The size of a watershed will determine, in part, the amount of water captured from precipitation and thus the annual discharge from that basin. The pattern of precipitation is important in determining the timing and pattern of discharge. In the Sierras, the precipitation falls primarily during the winter as either snow or rain, resulting in either a snowmelt hydrograph, a hydrograph dominated by rain events, or a mixture of the two. A watershed with a slowly melting snowpack, or a high capacity for groundwater storage, will show a slow spring recession as the frozen or stored water slowly flows out. The fractured granite bedrock of the Sierra does not hold water well, resulting

13 in a shorter, quick spring recession in the absence of snow pack, and low base flows in late summer and fall for all three of our systems. The type of regulation and the capacity of the impoundments in the system also severely affect the hydrograph. Each of the three systems show different hydrographs, based upon differences in these four main factors. The Tuolumne watershed covers about 1500 sq mi, and has a mean annual discharge of 1,800,000 acre-ft/year. The hydrograph of the mainstem Tuolumne is driven by snowmelt, but dominated by the influence of O’Shaughnessy, Cherry, and Eleanor dams. The purpose of these dams is to hold water during the wet months and release it slowly for urban and agricultural use, power generation, and limited flood control. The network of dams retain much of the flow from snowmelt and rain events, either in the upper sierras or farther downstream at New Don Pedro. The water stored in the upper impoundments is then released during the summer in a daily cycle to generate maximum power during times of peak electricity demand. The timing and volume of water released is also managed to provide desirable flows for recreational rafters. Dams change the natural flow regime by reducing the average magnitude of high winter flows, creating diel pulse flows for the powerhouses and rafters, and reducing or eliminating the gradual spring snowmelt recession. These lower flows reduce the transport capacity of the river, affecting the channel shape and patterns of sediment transport. Lower capacity allows for bars to persist for longer periods of time than predicted under historical flows. This may allow for vegetation to encroach on the stream bank, or for the stream bed to become armored. It also results in infrequent refreshment of sands and gravels, which in turn reduces the available habitat for riparian vegetation, benthic macroinvertebrates, and for spawning fishes. The unregulated Clavey River contrasts with the regulated mainstem. It has a watershed that covers about 157sq mi within the total Tuolumne watershed, and shows a much smaller mean annual discharge than the mainstem Tuolumne, at around 50,000 ac ft/yr. While the Clavey hydrograph is similarly driven by snowmelt, the lower elevation of the headwaters give rise to more frequent rain events and these events have a larger influence on the hydrograph pattern. The natural flow regime of the Clavey creates higher transport capacity during winter and spring flows, capable of refreshing sand and gravel bars. The flow regime is also important for triggering biotic responses, tuned to reproduce in sync with historical, somewhat predictable, flow recession. The North Fork watershed is the smallest of the three systems, with an area of about 110 sq mi of the total Tuolumne watershed, approximately two thirds of the size of the Clavey. The

14 mean annual discharge of the North Fork is also much smaller than that of the mainstem Tuolumne, at around 30,000 acre ft/yr. Due to the lower elevation of the North Fork, the hydrograph shows considerable influence from rain events with a small snowmelt recession in the spring. While this is a different hydrograph than the Clavey, this natural flow regime still provides significant transport capacity during the winter and spring flows, capable of naturally refreshing sand and gravel bars to create healthy habitat for riparian vegetation and aquatic organisms. These flow regimes are also important cues for biota, although the higher water temperatures cause different species to be present in the North Fork than in the Clavey. Both of these tributaries have much smaller mean annual discharges than the mainstem of the Tuolumne. However, the temporal differences between high flows of the tributaries and the mainstem result in a potentially significant influence of the tributary discharges during the late winter and early spring when the reservoirs are filling and the tributaries are high. Because the North Fork experiences more precipitation as rain, it contributes proportionally more water to the mainstem than the Clavey does in late winter, while the Clavey contributes proportionally more in late spring (Figure 6).

Average Daily 7000 Discharge Clavey River_Buck Mdw_60-95 6000 North Fork_long barn_62-86 Tuolumne River_buck_mdw_10-36 5000

4000

3000

2000

1000

0 0 100 200 300 400 Day of Water Year

FIGURE 6: Graph of average daily discharge in the Tuolumne, Clavey and North Fork.

15 Water Quality Water quality parameters, including temperature, available nutrients, and pH, vary between the tributaries (Clavey River and North Fork Tuolumne) and the mainstem Tuolumne, as well as along the longitudinal gradients of the three systems. These parameters are determined in part by other physical drivers, but are also influenced by biotic patterns. Another water quality parameter often of importance is dissolved oxygen (DO), although DO is not usually a limiting factor in the Tuolumne watershed. DO is kept near saturation because of aeration due to the turbulence and high velocity caused by steep gradients in all three systems. Turbidity, an important water quality parameter in other systems, is low throughout the entire system due to the low sediment load of these bedrock streams. Water temperature in a river system is determined by the water’s source (snow melt, rain fall, or dam releases), air temperature, amount of sunlight penetration, and water velocity (Allan 1995). Historically, water in the mainstem above Clavey River was derived mostly from snowmelt. However, in the present regulated system this snowmelt is impounded in Hetch Hetchy, Cherry, and Eleanor reservoirs before being released downstream (Null et al. 2009). In the reservoir, water has a greater surface area and a longer residence time than free flowing water, increasing the amount of sunlight penetration and thus the water temperatures at the surface. However, water is released from O’Shaughnessy Dam from a point lower in the water column where temperatures are nearly always between 6-8°C (McGurk 2009). These consistent temperatures contrast with the seasonal variability that would be seen in natural hydrograph, such as those of the Clavey or North Fork Tuolumne Rivers (Figure 7) (McGurk 2009). After release from the dam, water flows at a relatively high velocity through the steep canyon, reducing the opportunities for solar radiation to increase water temperature.

16 30 Mainstem Tuolumne above Clavey River Clavey River

) 25 )

) Mainstem Tuolumne ) ) at Indian Campsite

C North Fork Tuolumne °

( 20

e r u t

a 15 r e p

m 10 e T

5

0 4/25/09 5/5/09 5/15/09 5/25/09 6/4/09 6/14/09 6/24/09 0:00 0:00 0:00 0:00 0:00 0:00 0:00 Date/Time

FIGURE 7: Temperature data taken every half hour at four locations. Mainstem Tuolumne shows a smaller temperature range, but Clavey and North Fork show higher temperatures with more variation.

The water in the Clavey River comes primarily from snowmelt, resulting in generally cold water temperatures. The Clavey also has a relatively steep canyon and high gradient, resulting in hill slope shading and high velocity flows, and thus cool average temperatures. However, there is much more seasonal variation in water temperature on the unregulated Clavey than on the mainstem, with warmer waters in the summer and colder water in the winter (Figure 7). Due to the lower total volume of water in the tributary, the impact of the Clavey on the mainstem water temperature is likely to be rather small and limited to the area near the confluence. In Figure 7, the two graphs of the mainstem temperatures are almost identical. Indian campsite is below the Clavey confluence and only shows slightly higher temperatures than the mainstem above the Clavey confluence. However, there may be times when the mainstem has low flow and the Clavey has high flows which could lead to more influence from this tributary on the mainstem Tuolumne. The North Fork most often shows higher temperatures than either Clavey River or the mainstem Tuolumne. These higher temperatures occur because it acts as a rain-fed system, has higher average air temperatures, and is located at a lower elevation. However, the hill slope still shades some of the river, and the similar gradient of the streambed to that of the Clavey River results in fast moving water, reducing the amount of sunlight penetration. Like the Clavey, the

17 North Fork shows more seasonal variation in temperature because it is an unregulated river (Figure 7). As Tuolumne flows to lower elevations it becomes exposed to warmer air temperatures, naturally increasing the water temperature (Hauer and Lanberti 1996). This confounds the impact of slightly warmer water flowing in from the Clavey and the North Fork tributaries during most parts of the year, making it difficult to quantify the importance of tributary effects on the water temperature of the mainstem. We expect that the tributaries contribute some temperature heterogeneity to the mainstem, providing more diverse habitats for organisms to occupy. However, these effects may only be limited to the confluences because of the low relative flow of the tributaries as compared to the mainstem. Availability of nutrients is a water quality parameter that can serve as an important indicator of the ability of a habitat to support primary producers and their associated food web. Nitrogen and phosphorous are the two nutrients commonly limiting in aquatic systems. The former naturally comes from the decomposition of organic matter or from animal waste, and the latter arises mainly from erosion of rocks and soils or pollution from anthropogenic sources (Hauer and Lanberti 1996). The Tuolumne watershed is not a system naturally rich in nutrients, and what nutrients are contributed from upstream are blocked by dams. Further, there is a relatively small contribution of terrestrial organic matter from the narrow strip of available riparian habitat and a low concentration of primary producers, which reduces the cycling of organic nitrogen. Low phosphorus is also evident in the Tuolumne system, primarily due to the geology of the region. The recreational uses of the rivers (primarily rafting) and land use along side the North Fork (primarily grazing) may be yet other factors which contributes low amounts of nitrogen to the system. The high capacity of all three systems can also reduce the residence time of nutrients, and allow the tributaries to contribute nutrients to the mainstem as a subsidy to the relatively nutrient poor system. Finally, it is interesting to note that there is a disparity between the pH levels of the mainstem (close to neutral) and tributaries (somewhat basic) (FERC 1994). This difference is likely due to the influence of limestone (mainly calcium carbonate) in the tributaries, which when weathered can cause water to become more basic (Allan 1995). A slight increase in pH is seen at the confluences, but the mainstem returns to a neutral pH as it moves farther downstream from either tributary.

18 Table 1 depicts some of the water quality parameters discussed and how those parameters vary as the river flows downstream. The first location listed in the table (Tuolumne River at Meral’s Pool) is the highest upstream point and each subsequent location is further downstream. The warmer temperatures of the tributaries as compared to the mainstem are evident. After each tributary, there is a general increase in temperature of the mainstem due to inputs of the tributaries but also due to the natural increase in temperature at lower elevations. Effects from the tributaries are most likely a small part of the increase in mainstem water temperature. Also, the data on pH clearly shows the tributaries as more basic than the mainstem, but they have little affect on the mainstem.

TABLE 1: Water quality data showing variations along the Tuolumne River and affects of tributaries from June 2009

Sample Location Date/Time Temp (°C) pH Conductivity Dissolved Oxygen (uS/cm) (mg/L) Tuolumne River at Meryl's Pool 6/16/09 0940 11.4 6.3 14 10.9 ------Tuolumne River Above Clavey 6/17/09 0815 11.1 7.3 13 11.4 Confluence 6/16/09 1445 13.9 7.2 13 10.0 6/16/09 2000 13.3 7.2 12 11.6 Clavey River 6/17/09 0830 16.0 7.5 24 8.2 6/16/09 1500 17.9 7.3 24 10.5 6/16/09 2015 17.7 7.5 23 9.7 Tuolumne River at Indian campsite 6/24/09 0753 13.3 7.4 14 - below Clavey River 6/23/09 1448 15.0 7.3 14 ------North Fork Tuolumne River - - - - - 6/23/09 1252 21.5 8.0 85 - 6/16/09 1700 21.8 8.2 80 11.0 Tuolumne River below North Fork - - - - - 6/23/09 1258 15.5 7.3 17 - 6/16/09 1700 16.0 7.5 20 9.8

Biological Systems There are many organisms living within the Tuolumne watershed. The identity and patterns of abundance of these organisms are determined by the physical factors described above and by interactions among species. We have grouped the biota into the following broad categories in our conceptual model: vegetation of the riparian zone, particulate organic matter, aquatic primary producers, primary consumers, and higher order consumers. For each of these groups, the factors that determine their presence, abundance, and ecosystem function are discussed in more detail.

19 Riparian Vegetation The geomorphology and hydrograph of the Tuolumne system are the primary factors determining the vegetation communities present within the watershed. Riparian species include a variety of willow as well as alder, aspen, cottonwood, and maple. These species are adapted to Mediterranean hydrographs, with high winter flood flows and low summer base flows (Storer et al 2004). Between elevations of 500 and 3,000 ft, the dominant upland plant communities include the Lower Yellow Pine Belt, Chaparral, and Foothill Woodlands, as described in Table 2 (Storer et al 2004). These upland plants also show adaptations for a Mediterranean climate with dry, hot summers and mild winters, as demonstrated by the abundance of species with evergreen foliage and small leaves with thick cuticles to reduce water loss.

TABLE 2. Dominant plant communities of the middle reaches of the Tuolumne River watershed, with dominant woody species (based on Storer et al 2004).

Dominant Plant Community Elevation Vegetation Ponderosa Pine Lower Yellow Pine Belt 2500 - 4000 ft Black Oak Douglas Fir

Grey Pine Chaparral 1000 - 2500 ft Chamise Manzanita

Grey Pine Foothill Woodland 500 - 1000 ft Interior Live Oak Blue Oak Poison Oak Buckeye

Willow Spp. Riparian Zone --- Alder Cottonwood Aspen Big Leaf Maple Oregon Ash

20 The confined, bedrock nature of the Tuolumne River and low volume of sediment limit the formation of sand bars along the mainstem. This reduces the quantity and heterogeneity of habitat available for riparian vegetation, resulting in a generally narrow strip of riparian at the water’s edge. These geomorphic factors reduce the overall abundance of riparian vegetation in the system. However, despite this reduced abundance, riparian plants play an important role in stabilizing stream banks and gravel bars, and providing habitat for aquatic biota. Narrow riparian zones, resulting from confined canyons and low levels of sediment, also define most of the tributaries that enter the river Photo: P.F. Hilton between O’Shaughnessy Dam and the New Don Pedro reservoir, including both the Clavey and the North Fork. However each of these tributaries have slightly higher sediment loads, due in part to the connection to their respective headwaters. The North Fork also has a lower total discharge, allowing it to retain more sediment in pockets and eddies. This increased sedimentation may be partly responsible for the increased abundance of riparian vegetation in the North Fork system. The abundance and diversity of riparian vegetation can have important consequences for the amount of leaf-litter contributed to the aquatic system. The hydrograph of a river also drives the diversity and abundance of riparian vegetation. On the Tuolumne mainstem the hydrograph shows a reduced springtime recession limb and summer pulse flows for power generation (McBain and Trush 2007). Natural snowmelt recession is required for the successful regeneration of many riparian species. In a natural snowmelt hydrograph, peak flows in early spring clear new habitat for young species such as cottonwood or willow, and as flows begin to ebb, seeds or suckers are deposited. If a new sapling takes root as the water table gradually drops, the taproot can follow the receding water and the young tree can establish. The term ‘recruitment box’ describes this specific combination of scouring flows and gradual recession required by each species for regeneration (Figure 8) (Yarnell 2009).

21 FIGURE 8. An example of a ‘recruitment box.’ For successful recruitment, cottonwoods need scouring flows and a gradual recession with wet gravel bars when the seeds are sprouting. These conditions are only realized in the mixed rain-snow and the snow-dominated hydrographs in the above diagram.

Regulation of the mainstem could eliminate the occurrence of specific recruitment boxes, thus reducing the ability of some species to establish and resulting in lower diversity of the mainstem riparian community. On both tributaries the hydrographs will pass through these recruitment boxes more frequently, resulting in higher diversities (Figure 9).

Riparian Diversity 70

60 Herbaceous Shrub 50 .

Tree

s

e 40 i c e p

S 30

#

20

10

0 Clavey North Fork Indian

FIGURE 9. Riparian diversity of all species identified at Clavey River, North Fork of the Tuolumne River, and at Indian Bar on the mainstem of the Tuolumne River. Species are divided by life form.

22 In-stream Production Primary producers are aquatic organisms which use photosynthesis to create their own source of energy. Most aquatic primary producers need moderate to high levels of sunlight, enough nutrients available to uptake from the water column, and relatively warm temperatures. Many also need low water velocities (greater water residence time) which allow them to attach to substrate without experiencing extreme shearing forces (Allan 1995). The middle reaches of the mainstem Tuolumne and Clavey river watersheds, on average, have a low availability of nutrients (especially nitrogen), cold water temperatures, and fast water velocities with daily fluctuations. These fluctuations can scour periphyton (algae that is attached to substrate) at high flows and then desiccate it at low flows. These physical drivers make the Tuolumne a system with low in-stream productivity. The North Fork, however, is an exception. With warmer waters, more nutrients, more areas of slower pool habitat, and a higher pH, the North Fork appears to have a higher abundance of algae and macrophytes. A high pH promotes greater rates of primary productivity (Cushing & Allan 2001). As seen from the data in Table 1, the pH of the North Fork is the greatest, and thus, suggests that this is good habitat for primary producers. However, due to the physical drivers of the mainstem, the higher levels of local primary productivity in the North Fork do not contribute significant energy to the mainstem system. Despite an overall low abundance of primary producers in the Tuolumne system, they continue to fill an important role in the aquatic food web. Many herbivorous and omnivorous consumers graze on algae and filter organic matter from the water column. These producers also contribute particulate organic matter to the system when they die – either naturally, or due to scouring or desiccation from diel pulse flows. Resulting CPOM (>1mm) can be colonized by bacteria and diatoms or broken down by other detritivores or by physical processes of the river. CPOM if further broken down to form FPOM (0.5μm - 1mm) becomes available to filter feeding benthic macroinvertebrates (Allan 1995). Particulate organic matter and primary producers together serve as the base of the aquatic food web, and in the Tuolumne they seem to exert bottom-up forces, limiting the total biomass of the system.

23 Consumers There are multiple orders of consumers found in the aquatic systems of the Tuolumne watershed. Our model summarizes them in two groups for simplicity’s sake: primary consumers and higher order consumers. The primary consumers specifically considered here include several guilds of benthic macroinvertebrates, herbivorous terrestrial arthropods, larval amphibians, and herbivorous and omnivorous species of fishes. The higher order consumers include predatory aquatic and terrestrial macroinvertebrates, adult amphibians, omnivorous and carnivorous fishes, and terrestrial predators. Each of these taxonomic groups play different roles in the aquatic food web, and in addition the distribution and abundance of each are influenced by various physical factors. Because similar factors influence each group, often across trophic levels, the following discussion is organized according to taxonomic rather than trophic divisions.

Benthic macroinvertebrates Benthic macroinvertebrates are organisms that lack backbones, reach sizes of 0.5 millimeters or greater, and reside for at least part of their lives in freshwater. Most are insects, of which the majority are aquatic organisms during their early life stages (egg, larval, and pupal stages), after which the winged adult stage moves into the riparian zone. Because of the aquatic nature of our conceptual model, emphasis will be placed on these earlier life stages. In a generalized system the aquatic stages are important for controlling the abundance of in-stream primary productivity, for processing particulate organic matter, and as a food source for higher consumers. A wide variety of life histories exist among such invertebrates, and they can be important indicators of water quality and other conditions within an aquatic ecosystem. One method for grouping invertebrate species is by their feeding modality. The larvae can be classified into four main groups: collector/filterers (which use FPOM as a primary energy source), scraper/grazers (which remove algae and periphyton from surfaces), shredders (which process CPOM into FPOM), and predators (which feed on members of all other guilds). The relative abundances of these groups relate to the abundance and type of food resources available. In the Clavey, North Fork, and mainstem, the relative abundances of the different groups are similar (Figure 10). Collector/filterers dominate, followed by predators, scraper/grazers, and a few shredders. This guild composition suggests that the middle Tuolumne system is driven primarily by particulate matter.

24 Functional Feeding Group Percentages

100%

90%

80%

70%

60% Shredders Scraper/Grazers 50% Predators Collector/Filterers 40%

30%

20%

10%

0% Clavey North Fork Mainstem

FIGURE 10. Invertebrate functional feeding group percentages. Data derived from 5 kicknet riffle samples from each of the three systems. Taxa excluded from this graph (representing a tiny minority) were those for which feeding modality could not be ascertained due to taxonomic ID coarsity. Feeding modalities follow those reported in Merritt and Cummins (2008).

The distribution and abundance of invertebrates is influenced by a river’s hydrograph and other physical factors. During lower flows in the summer and fall, the hydrograph on the mainstem is impaired by reservoir ramping. Diel fluctuations on the mainstem alternately scour and desiccate those organisms not mobile enough to move with oscillating water levels. Hydropeaking is also detrimental to mobile taxa, forcing frequent expenditure of valuable energy. These effects are most pronounced in the egg and larval stages of invertebrates, and are consistent across most taxonomic groups (Stark 2002). For this reason, the mainstem is modestly lower in both abundance and family-level diversity when compared with the Clavey and North Fork (Figures 11 and 12). However, excellent water quality and limited additional physical disturbance on the mainstem Tuolumne still allows for the persistence of several sensitive taxa. Mayflies (Ephemeroptera), stoneflies (Plecoptera) and caddisflies (Trichoptera) are widely viewed as intolerant of environmental disturbance, yet are all found within the mainstem Tuolumne. In fact, the percent composition of these three orders is virtually identical in samples

25 across the mainstem, Clavey, and North Fork (Figure 13). It should be noted, however, that this data was gathered prior to the initiation of summer ramping, so the invertebrate assemblage had not yet been subjected to this depressant influence. An impaired hydrograph likely exerts a sharply negative pressure on the system’s invertebrate assemblage when compared with the Clavey and North Fork.

Relative Macroinvertebrate Abundance

70

60

50 e l p

m 40 a S / s l a u

d 30 i v i d n I 20

10

0 Clavey North Fork Mainstem

FIGURE 11. Relative abundances of macroinvertebrates in the middle Tuolumne, represented as individuals per kicksample. Data derived from 5 kicknet riffle samples for each river system. For each sample, all invertebrates were exhaustively removed and recorded (no subsampling was undertaken).

Macroinvertebrate Family-Level Richness

20

18

16

14 s e i l

i 12 m a F

f 10 o

r e

b 8 m u N 6

4

2

0 Clavey North Fork Mainstem

FIGURE 12. Family-level richness of macroinvertebrates in the middle Tuolumne system. Data derived from 5 kicknet riffle samples for each river system. In each sample, all invertebrates were exhaustively removed and recorded (no subsampling was undertaken).

26 Percent EPT

100%

90%

80%

70%

60%

Non-EPT Taxa 50% EPT Taxa

40%

30%

20%

10%

0% Clavey North Fork Mainstem

FIGURE 13. Percent Ephemeroptera, Plecoptera and Trichoptera in the middle Tuolumne. Data derived from 5 kicknet riffle samples for each river system. In each sample, all invertebrates were exhaustively removed and recorded (no subsampling was undertaken). All samples taken when mainstem flow ramping was not being implemented. Note overall high EPT percentage in all three systems (indicative of relatively pristine physical conditions), and lack of any significant intersystem percentage differences.

Geomorphology, including channel shape and sediment deposition, is another important physical driver of invertebrate distribution patterns. Higher levels of heterogeneity in a river channel often lead to a higher diversity of organisms (Svendsen et al. 2009). As discussed above, the geomorphic processes acting upon the tributaries result in increased sinuosity and higher sediment loads, resulting in more abundant sand and gravel bars. Multiple microhabitats are found in these areas, including pools, which allow a larger number of niche specialists to occupy a given area. The greater predominance of slow-water habitat in the tributaries thus encourages persistence of more lentic species, such as dragonflies, damselflies, and water scavenger beetles, when compared to the mainstem and its well-defined channel and high flow velocities. A third physical driver that directly influences the abundance and distribution of invertebrates is water quality. In the Tuolumne system, where water quality is generally good, the primary parameter is water temperature. Invertebrates have species-specific optimal temperatures for reproduction, egg survival, and larval growth (Vannote and Sweeney 1980). A site with high levels of microhabitat heterogeneity, such as that commonly found at tributary confluences, will be more likely to provide areas with each of those ideal temperatures. This heterogeneity allows for a higher diversity of species to pack together into the same total area

27 (McBain and Trush 2007, Rice et al. 2001). In addition to the importance of confluence areas in providing local habitat heterogeneity and velocity refuge for sensitive species, tributaries may also provide significant macroinvertebrate subsidies to the regulated system of the mainstem. Larval forms (particularly baetid mayflies) regularly drift downstream in large numbers to escape predatory invertebrates and to exploit new food resources. Such drift primarily occurs at night (Figure 14), to minimize piscine predation. Conversely, adult forms often migrate upstream to compensate for drift, and this may serve as a consistent reciprocal subsidy between the mainstem and tributaries. The negative effects of artificial flow pulses likely dictate the ultimate character of the mainstem assemblage. Biological subsidies to the mainstem, however high, will not be longitudinally stable if the physical template is not conducive to their survival. Nonetheless, at certain times of the year (prior to summer flow ramping, for example), intersystem subsidies could be substantial.

Drift at Indian Bar

0.012

0.01

0.008

Other Taxa 0.006 Baetid Mayflies

0.004

0.002

0 Day Night Time

FIGURE 14. Invertebrate drift at Indian Bar. Data derived from two samples, one taken for an hour at sunrise, the other for an identical duration after sunset. Both samples were gathered at the same location under identical flow velocities, when flow ramping was not being implemented.

Trophic interactions affecting invertebrates in an aquatic ecosystem are an important link influencing the system’s total productivity. Primary consumers of the Tuolumne depend upon healthy populations of primary producers. As discussed above, the alternating scouring and

28 desiccating flows of the regulated mainstem reduce the total amount of periphyton in the system. This acts as a bottom-up force, reducing the abundance of primary consumers such as grazing and scraping invertebrates. Because the regulated diel flows do not affect the tributaries, both should have weaker bottom-up forces controlling the abundance of invertebrates. However, other forces (such as colder temperatures in the Clavey) might still reduce the periphyton community found in the tributaries. Our model predicts that there will be greater productivity in the tributaries and immediately downstream of their confluences. This is especially true for the North Fork, due to its alluvial character and extensive emergent vegetation. Observational evidence, substantiated by quantitative data, indicates that the North Fork is more productive overall than the Clavey or the mainstem. Black flies (Simuliidae) and limnephilid caddisflies are abundant in the pools and bedrock riffles of this system. Tributary contribution of CPOM and FPOM to the mainstem also likely represents a prominent biological subsidy to the mainstem. As discussed above, the mainstem has lower levels of CPOM/FPOM than the tributaries due to differences in riparian habitat, flow velocities, and trapping of LWD and organic matter behind O’Shaughnessey Dam. The small size and ubiquitous nature of most invertebrates inevitably makes them an intermediate link in the flow of energy up a food web. Some invertebrates can also be important predators, including larval dragonflies and damselflies (Odonata), perlid and perlodid stoneflies (Plecoptera), and dobsonflies (Megaloptera). Larval odonates are typically found in areas with ponds and slower water, so they occur primarily in the tributaries—where such lentic habitats are more abundant. Stoneflies and dobsonflies, in contrast, are better adapted to lotic habitats, and so are more commonly observed in riffles throughout the Tuolumne system. Benthic macroinvertebrates are an important food source for vertebrate predators, such as adult amphibians and insectivorous fish. The importance of terrestrial arthropods in the diet of aquatic vertebrate predators is not as well documented. It is possible that pulses of aquatic and terrestrial invertebrates occur successively, providing a consistent food source throughout the year. In stream systems with thick overhanging vegetation, the contribution of terrestrial arthropods to the diet of insectivorous fishes has been shown to be significant (Nakano and Murakami 2001). Due to the sparse riparian vegetation along the Tuolumne and the tributaries we are unsure of the role that terrestrial insects may play in the food web of this aquatic system.

29 Amphibians Five species of aquatic amphibians are found in the middle reaches of the Tuolumne system: the generalist Pacific treefrog (Pseudacris regilla), the uncommon foothill yellow- legged frog (Rana boylii), the introduced American bullfrog (Rana (Lithobates) catesbeiana), the warty California toad (Bufo boreas halophilus), and the toxic Sierra newt (Taricha sierrae) (Stebbins 2003). Other amphibian species (including several salamanders) exist in the watershed, but the five listed above are the only ones that depend upon bodies of water to breed. Hence, they are the only species directly relevant to our model. This quintet of species varies in the environmental cues and physical features required for successful reproduction. As a result, they are distributed differently within the system. A primary indicator of suitable breeding habitat for all of these amphibians is flow velocity, considered on a local scale. The Pacific treefrog, California toad, and American bullfrog all prefer pools or well-vegetated eddies for egg deposition and larval rearing (Stebbins 2003). Throughout the Tuolumne system, there are sites of sufficiently lentic nature for these three species to successfully reproduce—as long as other physiological parameters are met. The foothill yellow-legged frog and Sierra newt, on the other hand, prefer flowing water and are also more sensitive to flow regulation. Foothill yellow-legged frog tadpoles maintain their position by using their large mouths to suction onto rocks, while Sierra newt larvae cling to rocks with their feet to maintain position in the river (Stebbins 2003). Thus, while these latter two species prefer lotic environments, neither can tolerate high-velocity flows. Because of these narrow flow requirements, daily fluctuations due to the regulated hydrograph of the mainstem have serious ramifications for successful recruitment of aquatic amphibians. Foothill yellow-legged frogs, for example, are completely dependent on a natural hydrograph for breeding success (Yarnell et al. 2009, Kupferberg 1996, Jennings and Hayes 1994). In the Tuolumne system, foothill yellow-legged frogs are triggered to spawn by warming temperatures coupled with the smooth spring-snowmelt recession. As the water levels begin to decline, these frogs attach their eggs to submerged cobbles, newly scoured by winter flow peaks. In the Clavey, they position their eggs in more sheltered locations on the underside of large boulders—presumably due to high spring flows (Yarnell, pers. comm.). This hydrologic combination, with scouring peak flows in the winter followed by a gradual snowmelt recession, creates a “recruitment box” that encourages successful egg and larval development, through minimizing exposure to environmental stresses (Yarnell 2009). Diel hydropower releases, such

30 as those that occur on the mainstem beginning in early summer, disrupt this adaptation. For the sensitive yellow-legged frog, such cyclic scouring and desiccation has prohibited spawning success, leading to their virtual extirpation from the mainstem. While not as strongly cued, reproductively, to the spring snowmelt recession, all other mainstem amphibians will be impacted by its artificial flow regime in similarly negative ways. Their populations will be reduced in size and number, being largely restricted to sheltered microhabitats. Only the Pacific treefrog will remain largely unaffected by flow regulation on the mainstem. This species’ remarkably fast developmental rate, affording individuals the ability to transform from egg to adult in just 2 months (Nussbaum et al. 1983), allows it to largely escape the negative effects of flow pulses. A dependable food source is another limiting factor that dictates amphibian distributions. Frog and toad tadpoles require substantial primary production and are specialized to scrape algae and bacteria from rocks and other substrates. Sierra newt larvae, on the other hand, feed exclusively on aquatic invertebrates (Lannoo 2005). Both species’ lifecycles are influenced by the hydrograph, temperature, nutrients, and shading as discussed above. Predation of amphibian eggs and larvae by invertebrates, fishes, and terrestrial vertebrates also impacts amphibian distribution. Dragonfly larvae (Odonata), predaceous diving beetles (Dytiscidae), and dobsonflies (Megaloptera) are all invertebrate groups that contribute to egg predation. The former two types are primarily found in slower waters, so they may be more important in the tributaries. The latter order is stream-dwelling, and will be found in the Clavey, North Fork, and mainstem. Crayfish are another invertebrate that heavily consume early amphibian life stages. The high density of invasive crayfish in the lower North Fork may limit the reproductive success of amphibians in that system. Among vertebrate predators, centrarchids are reported to show a strong preference for amphibian eggs and larvae and can severely impact populations (Werschkel and Christiansen, 1977). This may be a serious issue in the North Fork, where non-native smallmouth bass (Micropterus dolomieu) are present. Recovery of a tadpole from the stomach of a smallmouth bass in the North Fork demonstrates this interaction (Buckmaster, Stouthamer, and Young, pers. comm.). Terrestrial vertebrates, such as garter snakes, herons, and otters will also readily predate upon larval and adult amphibians. Sierra garter snakes (Thamnophis couchii) appear to be common in the middle Tuolumne system, particularly the lower Clavey. Native predators such as this snake, however, are indicative of healthy amphibian populations—rather than being a prohibitive influence like bass and crayfish.

31 The negative effects of a regulated hydrograph on reproduction and food resources, coupled with the rarity of pools combine to create a low abundance and diversity of amphibians in the mainstem. The amphibian populations in the tributaries are sheltered from the effects of flow regulation and have access to greater food resources, generating patches of high abundance and species diversity. However, each tributary is affected by other unique factors. The Clavey, for instance, has higher water velocities, while the North Fork has introduced piscine and crustacean predators. Even though the tributaries are relatively rich with amphibians, amphibian population subsidies to the mainstem are unlikely. Adults are generally non-migratory and poorly vagile. While high-flow events regularly wash larvae into the mainstem, there is relatively low survival of such an ordeal. The tributaries may thus represent a genetic bank for amphibians, but it is not likely that there is sufficient dispersal for them to serve as a strong source of new individuals or populations.

Fishes In the 1850s, the construction of the Tuolumne River’s first diversion dam at La Grange obstructed the passage of fish, most notably of anadromous salmonids, effectively isolating the system from the Sacramento-San Joaquin Delta and the Pacific Ocean. The construction of additional dams in subsequent years provided further barriers to fish passage, and altered the natural hydrograph. In spite of this, the fish species currently found in the middle reaches of the Tuolumne River closely resembles historical assemblages. Species present in this reach include the occasional non-native brook trout, brown trout, and smallmouth bass; and the native California roach, hardhead, rainbow trout, Sacramento pikeminnow, and Sacramento sucker. Figure 15 shows a distribution map of the predominant species in the middle reach of the mainstem of the Tuolumne River. A brief description of these fish, their spawning requirements, and their habitat preferences will serve as an introduction. This will be followed by a further discussion of how physical and biological drivers have shaped the abundance and diversity of fishes in the Tuolumne system. These species comprise two main assemblages: the pikeminnow – hardhead – sucker assemblage and the rainbow trout assemblage. The term ‘assemblage’ refers to species of a specific taxon—in this case, fish—that occur in the same geographical area, and presumably have developed both extensive habitat segregation and complex ecological interactions over

32 evolutionary time. Although the two assemblages that occur in the Tuolumne River possess some distinctive habitat requirements, considerable overlap exists within this reach, as the habitat conditions accommodate both the upstream limits of the pikeminnow—hardhead—sucker assemblage and the downstream limits of the rainbow trout assemblage.

FIGURE 15: Fish species present in the mainstem of the Tuolumne river from Lumsden to the mouth of New Don Pedro Reservoir. Note the presence of native species despite the flow alterations, as well as the two invaders (smallmouth and brown trout).

Representatives of the pikeminnow—hardhead—sucker assemblage in the middle Tuolumne reach include smallmouth bass, hardhead, California roach, Sacramento pikeminnow, Sacramento sucker, and rainbow trout. The invasive smallmouth bass is a popular game fish native to southeastern North America. Adult smallmouth bass prefer warm waters, but require cooler waters to spawn. They are voracious ambush predators that will consume anything small enough to fit into their mouths. Hardhead and California roach are omnivorous native minnow species. Although they occupy a similar ecological niche, these species possess quite different physiological tolerances. The California roach can survive in a broader range of water temperatures whereas the hardhead are restricted to narrower thermal requirements. For spawning, hardhead prefer water temperatures around 15-20 C, whereas roach successfully

33 spawn in waters ranging from 16-24 C. Another native minnow, the Sacramento pikeminnow, acts as the dominant piscivore in the middle reaches of the Tuolumne. Pikeminnow are relatively poor swimmers, relying on ambush tactics to capture prey. Like other fish in the assemblage, Sacramento pikeminnow prefer warmer water (relative to the trout), with optimal spawning temperatures ranging from 15 to 20 C (Figure 16). A third omnivorous native minnow, the Sacramento sucker, also occurs in this assemblage. Unlike the largely pelagic hardhead and California roach, the Sacramento sucker predominantly occupies the benthos, where it forages for algae and macroinvertebrates. Sacramento suckers display a wide range of tolerances to many water quality parameters. Suckers are found from the cold trout streams of the Sierra Nevada to the brackish, warm waters of Suisun Marsh (Moyle 2002). Rising water temperature (Figure 16), a rising hydrograph, and other unknown cues trigger spawning in Sacramento suckers (Moyle 2002). The modern rainbow trout assemblage in the middle reaches of the Tuolumne includes the Sacramento sucker (discussed above), rainbow trout, brown trout, and (occasionally) brook trout. Riffle sculpin, though a historical component of the assemblage has never been shown to be present. This notable absence may be due to flow peaking and high temperatures in the tributaries. The most renowned game fish of the Sierra Nevada, rainbow trout are a ‘typical’ cold water fish. Rainbow trout are strong swimmers and successful roving predators, consuming both invertebrates and smaller fish. The relative importance of each to a trout’s diet depends on the individual’s size and the availability of the prey (Moyle 2002). Brown trout also now occur in the foothill reaches of the Tuolumne River. Native to Europe, the brown trout was introduced to California because of its popularity as a game fish. The date of introduction is difficult to determine due to the largely undocumented stocking practices of the early 1900s. Like rainbow trout, brown trout are strong swimmers and voracious predators. However, they generally prefer colder water and a more piscivorous diet than the native rainbow trout (Moyle 2002). Native to eastern North America, the brook trout is a cold water specialist that has been widely introduced as a game fish. While no official records of brook trout exist in the middle reaches of the Tuolumne River, during the course of our surveys we did individuals in these middle reaches. Brook trout have been known to outcompete other trout species in cold, spring fed tributaries (the species name, Salvelinus fontinalis refers to their preference for spring fed waters), however at even slightly higher temperatures rainbow trout and brown trout outcompete them (Moyle 2002). Due to the thermal requirements of brook trout, it

34 is unlikely they are self-sustaining in the Lumsden reaches of the Tuolumne, and the adults observed most likely originated in the spring fed tributaries of the Clavey.

FIGURE 16. Spawning (blocks) and optimal temperatures (lines) for the fish common to the middle reach of the Tuolumne River and its tributaries. Little data is available for hardhead, but temperature requirements are assumed similar to pikeminnow (Moyle 2002), due to the close relationship between them. It is notable that these are not lethal maximum temperatures and minimum thermal temperatures on the graph. NOTE: Hydrographs also impact spawning a juvenile survival.

All fish have evolved in concordance with specific stream conditions and are adapted to the intricacies of those streams. On the west slope of the Sierra Nevada, fish are adapted for rivers with large spring flows which gradually recede to low summer and fall base flows (Moyle 2002). Species-specific physical cues trigger spawning at a time when the eggs and young will experience optimal growth temperatures, flow velocities, and food resources. When the physical nature of the stream is altered by impoundment and regulation the same cues can become maladaptive and fish populations are unable to persist in many areas (Osmundon 2002). Fish species that have evolved outside a given drainage are likely to be maladapted to the stream flows and temperatures. As a result, they are often unsuccessful in unregulated systems (Moyle 2002). Disturbances and regulation thus often make a river less suitable to native fishes and more suitable to invasive fishes.

35 The Clavey River is undammed and relatively pristine (FERC 1994). As a result, the Clavey River fish assemblage shows a high proportion of native fish (examples include the native minnows, Sacramento suckers, and rainbow trout), which have a high probability for successful recruitment. Invasives, such as brown trout, experience low recruitment success, having evolved under other conditions (Figure 17). In contrast, the mainstem is a heavily regulated and disturbed system that ultimately allows only a handful of species to be self- sustaining within it (Figure 18). The North Fork of the Tuolumne is a bit of an enigma, although it is an unimpaired stream, warm water temperatures and downstream reservoirs allow for the success of non-native centrarchids (smallmouth bass) (Figure 19) (Moyle 2002, FERC 1994). This invasive has a negative effect on native cyprinids in the stream.

CARO

PM/HH

Brown Trout Sac Sucker Rainbow Trout

FIGURE 17: Clavey River average Monthly Temperatures and Flows-adapted from FERC 1994 Spawning temperature requirement of the predominant fish of the Clavey are shown plotted above. The boxes are representative of the spawning times, while the arrows represent the time required for the offspring to emerge as mobile larva (data cited in Moyle 2002). The average hydrograph (black bars) shows the advantage of the native fishes. As spring spawners, the native fishes’ eggs and larva have a lower chance of encountering high flow runoff events and thus a higher chance of not being scoured. The lone invasive (brown trout) in this reach has a high likelihood of redd scour as it’s spawning requirements occur immediately before the months of the highest runoff events.

36 PM/HH CARO

Rainbow Trout Sacramento Suckers

Brown Trout

FIGURE 18: 2008-2009 Hydrograph and Thermograph of the Mainstem (At Lumsden) The spikes of the ‘regulated’ hydrograph occur during most recruitment windows and rearing stages of the fish within the reach. The spawning windows of each species are drawn based on thermal requirements, and rearing times based on species averages in Moyle 2002. As a result, of this interaction, recruitment in most species will be reduced. Rainbow trout and Sacramento Suckers have the best chance, as several of their brief windows appear followed by calm. Pikeminnow and hardhead, spawning right before the floe peaking in July do not have a good chance of successful recruitment. Brown trout are also at a disadvantage. It is important to note this is an annual hydrograph, and not a averaged one, as a result, some features this year will be muted in others, and species will have good years.

FIGURE 19 North Fork of the Tuolumne Hydrograph Monthly temperature data for the North Fork is unavailable, however, due to the early onset of summer base flow, (marked in red), and the watershed geomorphology the summer temperatures reach up to around 90 F (32 C). As a result the North Fork is not suitable for year round establishment of salmonids (Figure 16). Native cyprinids would have been successful in this stream. The shape of the NF hydrograph is superficially similar to the Clavey’s, though the peak flows are earlier due to a more pluvial dominated system. As a result, native species would be successful and self-sustaining. Rainbow trout from the mainstem likely spawn in the North Fork and migrate out before summer low flows make the water quality unsuitable. Do to predatous smallmouth, native fish are not hugely successful in the North Fork.

37 Outside of the spawning period there are also physiological stressors (both natural and unnatural) that can negatively impact fish populations. Historically, the Sierra foothill’s Mediterranean climate presents a harsh environment dominated by two extremes in which Tuolumne fishes must survive. These include high flows, typically occurring in winter and early spring, which wash adults out of a stream or demand a high output of energy for the fish to remain in place. Winter and spring runoff peaks precede the onset of summer ‘base flows’ during which temperatures rise to potentially lethal levels (FERC 1994). During this time, deep pools become important thermal refuges for fish. Due to the regulation of the mainstem flow regime, these extremes are modified, with low flows uncommon and high flows unpredictable. Another important factor in determining the success of fish populations is the heterogeneity of available habitat (Moyle 2002). In order to mitigate the aforementioned stressors, fish require both velocity and thermal refuges. Both the middle reach of the Tuolumne and the tributaries have relatively constant longitudinal gradients, meaning that high velocity flows will likely remain constant throughout the watershed. This increases the importance of smaller scale geomorphic features (which can create areas of low velocity, and thus serve as a velocity refuge) such as bends, meanders, channel bars, and boulders. Many of which are influenced by the amount of sediment available for transportation by the river. In addition, many of these geomorphic features channel high flows into specific locals. This creates areas of maximum scour during high flows, which, in turn, provides deep pools for refuge in low flows. Riparian vegetation can also play a critical role in creating habitat heterogeneity for fish, either through the contribution of large woody debris, or by providing cover during a high water event or as predation refuges. While physical constraints may dictate the presence of specific fish species, the availability of food resources will determine abundances. Areas with low primary productivity, such as the mainstem of the Tuolumne, will support low levels of fish species, with omnivorous generalists fairing the best (i.e. Sacramento suckers). Low FPOM and CPOM levels in the Tuolumne also reduce herbivorous macroinvertebrates as discussed above, which will cascade up the food web and reduce abundances of primary consumers and piscivorous fish (Osmundson 2002). Top-down regulation from top tier piscivores also can control fish abundance, but depends upon the suitability of the riparian zone as habitat for the terrestrial species (birds and mammals), as well as sufficient biomass to support populations of these predators. Top tier

38 predators are not particularly abundant on the Tuolumne in this reach with the possible exception of the North Fork. This is likely a reflection of riparian habitat quality and the low biomass of fish in the mainstem. Because of the productivity of each stream, the Clavey has a higher abundance of fish than the mainstem and the North Fork will have the highest abundance of fishes because it has the largest amount of primary productivity. However, each tributary has a different degree of evenness and species composition. The warmer waters of the North Fork also allow for the persistence of the invasive smallmouth bass. This piscivore typically displaces or reduces the native minnows of the system (roach and hardhead), and severely limits pikeminnow through competition for resources (Moyle 2002). Because smallmouth bass are extremely efficient predators of native minnows, this trophic interaction is enough to dictate the presence or absence of native minnows (Moyle 2002). Despite the habitat of the North Fork being suitable for native minnows, studies show that they cannot occur sympatrically with the bass. Brown (and Brook) trout in the mainstem, though invasive, have a minimal effect, due to low abundance. There is competition with rainbows; however, brown trout occur sympatrically with rainbows and Brook trout are exceedingly rare (Moyle 2002). Ultimately, both physical and biological interactions determine the distribution and abundance of fish in the Tuolumne River and its tributaries. Recruitment of young into a population is the most sensitive life stage for most species, and is also one of the most important in determining the potential for a population to be self-sustaining. This life stage is most dependent upon an appropriate hydrograph and thermograph of a river reach, and the presence of suitable substrate. Larval and fry life stages are also sensitive to these factors, and often require low velocity flow areas and predation refuges to rear in. For adults, there are also many limiting factors, both physical and biological, such as high temperatures and high flow events. Some of these factors impose absolute limits, such as lethal temperatures, while others vary in their strength, such as scouring flows or competition for energy resources. Because of the unpredictability of the mainstem flows, tributaries are the only locations in the watershed where native fishes consistently spawn successfully. As a result, there is a spawning migration of native fishes (cypriniformes and salmonids) up the streams, when high waters in the tributaries make passage possible, into the favorable spawning habitat both in the Clavey and the North Fork. In addition, juvenile cyprinids and salmonids in the tributaries migrate into the mainstem during the summer or early fall at the onset of low summer flows.

39 The outmigration of juveniles provides a source of young of year to the mainstem, where the species experience limited recruitment due to flow peaking and regulation. Sampling in the Clavey below a barrier falls (Figures 20 and 21) showed the absence of juvenile rainbow trout, and high numbers of Sacramento sucker and pikeminnow young of year (YOY) as well as much higher numbers of adult pikeminnow (Figure 21) when compared to sampling above the fish barrier. The pikeminnow also demonstrated spawning behavior during dives. The large pikeminnow migrate up from the mainstem to spawn, due largely to the sharp drop off in abundances seen above the falls. The presence of sucker YOY and low abundance of adult suckers also implies that suckers also migrate up the Clavey to spawn. Rainbow trout are capable of rearing and out migrating out of the system rapidly. The absence of rainbow trout less than six inches below the Clavey implies either they moved of the stream by the time we surveyed or predation by adult pikeminnow reduced their numbers. North Fork surveys show the presence of adult smallmouth bass as well as rainbow trout below the barrier falls (Figures 22 and 23), and an absence above the falls. Surveys also showed that California roach and hardhead, two species which do not occur sympatrically with smallmouth bass occur above the fish barrier. Sacramento sucker YOY were also observed below the falls, as well as smallmouth bass YOY. Adult bass were observed, however Sacramento sucker adults were not observed, and it is likely that the North Fork serves as seasonal habitat for the suckers. Cyprinids were not observed in high densities in habitat occupied by smallmouth bass, and no cyprinid YOY were found in the lower reaches of the North Fork. It is thus unlikely that there is a large spawning population of Cyprinid adults migrating up the North Fork. As discussed above, the low primary production of the mainstem is subsidized by FPOM and CPOM inputs from the tributaries, which will (via bottom up trophic control) increase the biomass of fish in the mainstem. Similar subsidies of aquatic invertebrates are important to fish in the mainstem. Riparian habitat of the North Fork may also provide seasonal influxes of terrestrial invertebrates, which subsidizes both mainstem and North Fork fish populations. The sediment influx from the tributaries leads to an increase in habitat complexity below the tributary mouth. The habitat complexity provides velocity refuge for mainstem fish during the mainstem’s unpredictable high flow events. LWD from the tributaries also will add to the habitat complexity of the mainstem.

40 FIGURE 20 Survey Locations on Clavey

Clavey River Dive Observations Adult Fishes Observed Above below Falls Clavey Fish Barrier

CAR CAR RBT RBT SKR SKR SPM SPM

Dive Observations in Clavey Dive Observations in Clavey River River below Falls below Falls

30 30 25 CAR 20 CAR 20 RBT RBT 15 10 SKR 10 SKR 0 5 SPM SPM <6" 6-12" 12- >18" 0 18" <6" 6-12" 12-18" >18"

FIGURE 21. Clavey River fish surveys above and below the falls. YOY were not plotted on the charts below, but samples taken showed California Roach, Sacramento sucker and Sacramento pikeminnow YOY to be present in the Clavey in high numbers

41 FIGURE 22. Survey locations on the North Fork Due to time constraints, only one sample was taken above the barrier falls.

North Fork Adult Fish Species below barrier North Fork Adult Fish Species Observed above Barrier

CAR RBT CAR SMB HRD SPM SPM

Size Distribution of Fished in North Fork Observed While Diving Size Distribution of Fished in North Fork Observed While Diving Below Barrier Above Barrier

30 14 12

d 25 d e e v v

r 10 CAR r e 20 e

s CAR s b RBT b 8 O 15 O HRD

r SMB r 6 e e

b SPM 10 SPM b m m 4 u u N 5 N 2 0 0 <6" 6-12" 12-18" >18" <6" 6-12" 12-18" >18" Size Catagory Size Catagory

FIGURE 23. North Fork dive data above and below the falls. YOY were not included in the plots in order to show the abundances of adult fish. YOY Sacramento sucker and smallmouth bass were identified from the sample taken back for identification.

42 Conclusion The physical and biological dynamics of a river ecosystem are inextricably linked. Modification of the template of a system, through the construction of a dam or biological introductions, results in far-reaching effects. As in the majority of Sierran watersheds, anthropogenic forces of this nature are evident on the Tuolumne River. In this conceptual model, we have addressed the impacts of these forces as they relate to the physical features and biotic composition of the middle Tuolumne watershed. We have focused our attention on how unregulated tributaries are able to modulate the regulated nature of the mainstem. Temporal variance in the magnitude of tributary effects is evident, as is the scale at which the interaction is examined. Locally, subsidies from any given tributary are generally insubstantial, and not longitudinally stable. Yet taken in aggregate, the Tuolumne’s unregulated tributaries play a more significant role in alleviating the effects of regulation on the river’s mainstem. From any perspective, however, this modulation is symptomatic and fails to truly correct the disruptions caused by flow regulation. The consistently depauperate biological assemblage on the mainstem, relative to tributaries such as the Clavey and the North Fork, is clear evidence of this. While the Tuolumne is still relatively pristine, retaining most of its key ecological functions and physical character, human actions nevertheless constrain the system in major ways. We hope that this model will help interested parties minimize these impairments, for the benefit of both river users and the biota.

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