DOI: 10.5061/dryad.cjsxksn7b
title: Quantification of thermal impacts across freshwater life stages to improve temperature management for anadromous salmonids

description: Water temperature is the major controlling factor that shapes the
 physiology, behavior, and ultimately, survival of aquatic ectotherms. Here
 we examine temperature effects on the survival of Chinook salmon
 (Oncorhynchus tshawytscha), a species of high economic and conservation
 importance. We implement a framework to assess how incremental changes in
 temperature impact survival across populations that is based on thermal
 performance models for three freshwater life stages of Chinook salmon.
 These temperature-dependent models were combined with local spatial
 distribution and phenology data to translate spatial-temporal stream
 temperature data into maps of life stage-specific physiological
 performance in space and time. Specifically, we converted
 temperature-dependent performance (i.e., energy used by pre-spawned
 adults, mortality of incubating embryos, and juvenile growth rate) into a
 common currency that measures survival in order to compare thermal effects
 across life stages. Based on temperature data from two abnormally warm and
 dry years for three managed rivers in the Central Valley, California,
 temperature-dependent mortality during pre-spawning holding was higher
 than embryonic mortality or juvenile mortality prior to smolting. However,
 we found that local phenology and spatial distribution helped to mitigate
 negative thermal impacts. In a theoretical application, we showed that
 high temperatures may inhibit successful reintroduction of threatened
 Central Valley spring-run Chinook salmon to two rivers where they have
 been extirpated. To increase Chinook salmon population sizes, especially
 for the threatened and declining spring-run, our results indicate that
 adults may need more cold-water holding habitat than currently available
 in order to reduce pre-spawning mortality stemming from high temperatures.
 To conclude, our framework is an effective way to calculate thermal
 impacts on multiple salmonid populations and life stages within a river
 over time, providing local managers the information to minimize negative
 thermal impacts on salmonid populations, particularly important during
 years when cold-water resources are scarce.
description: <strong>Daily predicted stream
 temperature</strong> We predicted stream
 temperature during a period of hot, intense drought in California, years
 2013-2014 on three rivers in the Central Valley: Clear Creek, Stanislaus
 River, and Tuolumne River Daily. Observed mean daily temperatures were
 extracted for each river from the temperature monitors used in the NorWest
 project (downloaded from
 https://www.fs.fed.us/rm/boise/AWAE/projects/NorWeST/StreamTemperatureDataSummaries.shtml) using ArcMap. To obtain daily stream temperatures for all river kilometers, we linearly interpolated actual stream temperature observations to create stream temperatures along a river that matched the spatial-temporal resolution of the spatial and phenological data (i.e., 1km/daily). Gaps of less than 30 days were linearly interpolated for all monitors before spatial interpolation. In the rare instance where more than one temperature recording was present per river kilometer for a specific date, we took the average. Daily stream temperature was then the input into salmonid thermal performance models. <br><br><strong>Framework - Thermal survival models</strong> We developed a framework to quantify thermal impacts across salmonid life stages using thermal performance curves (TPCs) for each life stage, local phenological and spatial data to determine when and where each life stage occurs, and water temperature along that river. First, water temperatures are used as inputs in various life stage-specific TPCs that relate temperature to instantaneous physiological performance. Second, these TPCs are combined with local spatial distribution and phenology data and stream temperature to translate spatial-temporal temperature data into maps of life stage-specific performance in space and time. Third, thermal performance was compared between life stages by estimating how effects on physiological rates are translated to reductions in survival; this important step helps elucidate which life stages are the most vulnerable to negative thermal impacts. Additionally, we compared thermal survival with and without local fish data, allowing us to quantify if local behaviors help to mitigate negative thermal impacts. We examined thermal effects for pre-spawn adults, embryos, and juveniles using the best TPCs currently available for Chinook salmon (Oncorhynchus tshawytscha). This comparative framework using continuous TPCs to quantify temperature-dependent survival across life stages can ultimately help prioritize cold water resources to minimize negative impacts on salmonid populations, especially in years when thermal criteria cannot be met. For additional modeling details for each TPC, see the published paper. 
description: Attached are files for data reproduction or to expand this
 research to other populations. The R script is written to replicate our
 results for Clear Creek spring-run Chinook salmon. The user will need to
 read "ClearCreek_streamtemperature.csv" (attached) into the R
 script prior to running. To replicate results from other rivers, the user
 will need to upload the new stream temperature dataset
 ("StanislausR_streamtemp.csv" or
 "TuolumneR_streamtemp.csv"), alter the time period of interest
 (code lines 15-18), and change the salmon phenology and spatial
 distributions for the appropriate population (code lines 40-48) from data
 in Tables S3.1 and S3.2 (linked research article). See associated README
 file for details.