Estimation of rearing habitat requirements of San Joaquin River Chinook salmon using the Emigrating Salmonid Habitat Estimation (ESHE) Model

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1 Estimation of rearing habitat requirements of San Joaquin River Chinook salmon using the Emigrating Salmonid Habitat Estimation (ESHE) Model California Central Valley Cramer Fish Sciences *Draft conceptual ideas not meant for public review

2 Introduction A fundamental concept in relating salmonid production to stream habitat is that stream-dwelling salmonids either defend d or rely on food from a characteristic ti area of territory (space). We assume that juvenile salmon will only rear (and setup territories) in habitat that meets their preferred range of non-consumable habitat conditions (Temperature, Depth, Velocity), defined as Available Suitable Habitat (ASH). We assume that the maximum number of individuals that a habitat t area can support is limited it by the territory size of the fish and ASH: Capacity = ASH / Territory Size

3 Introduction The goal of ESHE is to enumerate the amount of rearing habitat required to support management goal estimates of abundance. Therefore, we organize the equation to predict the required ASH to support production target abundance levels: ASH = Abundance Territory Size In stationary systems, it is relatively easy to calculate territory size and population habitat needs. However, In dynamic systems emigration and emigration timing, initial size, growth, habitat quality, and mortality all act together to influence how much territory is needed at a given location in the system at a given time.

4 Introduction Early in the year, juvenile Chinook are relatively small and can be found in upstream reaches As time (i.e., days) progress, juvenile Chinook increase in size and move through the system R i d t it i Required territory increases with increases in size

5 Introduction ESHE models the rearing and emigration of individual daily cohorts of juvenile Chinook salmon, and tracks their average growth, emigration, territory size, and ultimately t l the amount of ASH required to sustain the number of juvenile salmon present within a model reach, on a given day throughout the rearing and emigration period. Important to remember that ASH is a minor component of the amount of river channel, riparian vegetation, sediment input etc. needed to support that area of suitable habitat. t

6 Introduction Example depicting 2-D modeling of habitat suitability (indexed by depth and velocity) for a reach of the American River at three different flow levels. Total habitat required to support suitable habitat (yellow to red areas) is substantial. For instance at 6000 cfs only 6% of the area demonstrates suitable habitat. Combined Suitability 1200 cfs 100 cfs 6000 cfs

7 Introduction The goal of our modeling efforts is to support San Joaquin restoration project by enumerating the amount of ASH required to support restoration ti production targets t for spring-run and fall-run. Our estimates of required ASH paired with 2D hydrologic modeling of various alternative restoration scenarios will help in the selection of management strategies that best meet rearing and emigration habitat needs of future restored salmon populations.

8 The ESHE model tracks salmon abundance and habitat needs from the end of the spawning grounds to the end of the restoration reaches. End of Restoration Reaches End of Spawning Grounds

9 Step 1. Estimate initial juvenile abundance at bottom of spawning grounds by backcalculating from production targets and applying most appropriate survival data. Production Targets SR: 44, million FR: 6,000-70,000 Initial Juvenile Abundance SR:?? FR:??

10 Step 1. Estimate initial juvenile abundance at bottom of spawning grounds by backcalculating from production targets and applying most appropriate survival data. Production Targets SR: 44, million FR: 6,000-70,000 Reach % survival/km Source: VAMP acoustic data (Lathrop to Stockton) Reach % 100% survival/km Source: Stanislaus River tagging data Initial Juvenile Abundance SR:?? FR:?? Reach % survival/km Source: Stanislaus River Rotary Screw Trap

11 Step 1. Estimate initial juvenile abundance at bottom of spawning grounds by backcalculating from production targets and applying most appropriate survival data. Production Targets SR: 44, million FR: 6,000-70,000 Monte Carlo simulations used to resample from reach-specific survival data to select the survival path (across all reaches) that estimates the initial abundance that will meet low production target 9% of the time. Initial Juvenile Abundance SR: 121 million FR: 17 million

12 The SJRRP FMP designates a goal of 10% yearlings for spring-run. Therefore, for modeling pre-yearling emigrants we removed 10% of our estimated initial juvenile abundance of million, and estimated habitat needs for million pre- yearling spring-run. Production Targets SR: 44, million FR: 6,000-70,000 Yearling habitat needs will be modeled separately. Initial Juvenile Abundance SR: 109 million FR: 17 million

13 Step 2. Estimate entry timing and initial size of emigrants as they leave the spawning grounds under high and low flow conditions.

14 Step 2. Estimate entry timing and initial size of emigrants as they leave the spawning grounds under high and low flow conditions. Entry Timing Fall-Run Spring-Run Source: Stanislaus River RST Source: Feather River RST Above Flow Years Below Flow Years

15 Step. Move emigrants downstream at an average migration speed dependent on flow and fish size as observed in San Joaquin Basin empirical studies. Migration Speed Source: Stanislaus River Tagging Studies Smolts (>70 mm): High flow year: 18. km/day Low flow year: 7.11 km/day Pre-smolts ( 70 mm): High flow year: km/day Low flow year: 4.14 km/day

16 Step 4. Apply survival rates as emigrants move downstream. Modeled a low survival scenario (meeting low production target) and a high survival scenario (meeting high production target) for each race by applying survival paths from Monte Carlo output. Production Targets SR: 44, million FR: 6,000-70,000 Reach % survival/km Source: VAMP acoustic data (Lathrop to Stockton) Reach % 100% survival/km Source: Stanislaus River tagging data Reach % survival/km Source: Stanislaus River Rotary Screw Trap

17 Step. Apply daily growth as emigrants move downstream. Growth Source: Sacramento River fall-run Chinook (Fisher 1992)

18 Step 6. Estimate territory size requirements as emigrants move downstream. Fish territory size is calculated daily based on a length-territory size relationship for salmonids from Grant and Kramer (1990).

19 Uncertainty in relationship a function of habitat quality complexity, food abundance. We apply the mean relationship (assuming average habitat quality) to best compare to habitat estimates from 2D output.

20 In summary, we model the rearing and emigration of individual daily cohorts of juvenile Chinook salmon, and track their survival, movement, average growth, territory size, and ultimately the amount of suitable habitat required to sustain the number of juvenile salmon present within a model reach, on a given day.

21 Preliminary Results Reach Number of Salmon Present

22 Preliminary Results Reach Required Suitable Habitat Max = 18 acres

23 Preliminary Results Maximum required suitable rearing habitat (acres) Suitable Habitat Reach Spring Run Fall Run Both Runs Lower Total ,226

24 Preliminary Results Important to remember that our model estimates suitable habitat that meets preferred depths and velocities and is of average quality (complexity and food abundance). This suitable habitat is only a fraction of the total habitat required to support it. Also, we are modeling an average population, with average timing i and migration speed. Therefore, our estimates of habitat in each particular reach should be assumed to be flexible i.e. due to the unpredictable nature of fish populations, habitat could be available downstream or upstream and still meet the needs of the salmon population.

25 Preliminary Results Our estimates of suitable habitat needs will be compared to 2D hydrologic estimates of suitable habitat availability across the SJRRP reaches to identify reaches where a deficit of suitable habitat may occur. Management scenarios can then be chosen (i.e. levee set-backs, habitat alteration) to best satisfy apparent gaps in suitable habitat t availability.

Are Juvenile Chinook Salmon Entrained at Unscreened Diversions in Direct Proportion to the Volume of Water Diverted?

Are Juvenile Chinook Salmon Entrained at Unscreened Diversions in Direct Proportion to the Volume of Water Diverted? Charles H. Hanson Abstract Mark-recapture experiments were used to test the null hypothesis