Redband Trout Cardiac Function under Hypoxic and Thermal Stress
	Preliminary dataset supports the findings from the graduate dissertation of Carlie Sharpes: https://www.proquest.com/pagepdf/2672045313?accountid=14551
	Dataset currently does not have a DOI

Dataset published to support the following Graduate Dissertation:
	Title: Swimming in 'thin air': Evaluating the combination of hypoxic and thermal stress as an additive or synergistic effect
	University: University of Idaho
		
Data Use:
	Data is availabe to share internally with GEM3 participants, and will be publicly released once submitted for peer-review.

Data and Code Files:
	1. bpm_aov
		bpm_graph.r: r script to provide code to run analysis associated with data in bpm_aov.csv.
		bpm_aov.csv: Heart rate data for all redband trout individuals used for analyses of variance and figures
			Header Key:
				Fish: Unique numerical assignment for individual fish identification
				Temp: (°C) ambient water temperature recorded at the time of experiment 
				temp_cor: (°C)corrected temperature to account for trials where a non-calibrated thermometer was used 
				temp_rd: temperature rounded to the nearest whole number after correction (used for figures and Anova calculations)
				fhmax_raw: (seconds/10 beats) heart rate observed from electrocardiogram
				fhmax_bpm: (beats/minute)
				mass: (grams) body mass of fish, measured in grams
				ln.mass: (grams) natural log of body mass of fish 
				bpm_cor: (beats per minute)heart rate corrected for body mass of fish
				Ecotype: Categorical assignment based on the ecotype the fish belongs to
					Values:
						desert: warm desert
						cool: cool montane
						cold: cold montane
				Acc_Temp: Temperature at which that fish was acclimated (°C)
					Values:
						15: 15°C
						21: 21°C
				Treatment: oxygen treatment fish was exposed to during experimentation
					Values:
						normoxia: fully saturated water
						hypoxia: 50% DO saturation
		hr_process.pdf: Heart rate Measurement process protocol file.
		hypoxia_no_temp_increase.csv: a short experiment with a population of 4 individuals showing the cardiac response during no temperature increase (constant 15°C) but only DO decrease.
			Header Key:
				Fish ID: Unique numerical assignemnt for individual fish identification 
				pre-atropine: Heart rate (seconds per every 10 beats) prior to atropine injection. 
				15 min after atropine: Heart rate 15 min after atropine injection
				15 min after isoproterenol 87.5% DO: Effect of Isoproterenol to prevent bradycardia. Since there is not	a large effect, it is justified to have only used atropine for the majority of the experimental trials.
				85.00%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				77%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				70%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				61%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				46%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				42%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				36%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				33%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				20%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				18%: DO saturation of 15°C water in an open system. Corresponding numbers are heart rates of individual fish at each DO saturation 		(seconds per 10 beats)
				acc temp: Temperature at which that fish was acclimated (°C)
				ecotype: Categorical assignment based on the ecotype the fish belongs to
					Values:
						desert: warm desert
						cold: cold montane
	2. DO_Temp
		DOandTemp.r: r script for analysis of data within littlejacks1_clean.csv and littlejacks2_clean.csv
		littlejacks1_clean.csv: Dissolved oxygen and temperature readings from data logger in Little Jacks Creek. Observations taken at 15 minute intervals from 2020-09-17T13:00 to 2020-11-17T11:15. Placed at the edge of a pool in Little Jack's creek
			Header Key:
				obs: Integer based assignment for each unique observation during deployment.
				Date_Time: date and time when observation was measured. datetime in ISO8601 format yyyy-mm-ddTHH:MM with time in 24-hour clock format and recorded in the USA Mountain Timezone (-06:00 GMT)
				DO_conc: (mg/L) Dissolved oxygen concentration in 
				Temp: temperature in degrees celsius
		littlejacks2_clean.csv: Dissolved oxygen and temperature readings from data logger installed the center of a pool at Little Jacks Creek. Observations taken at 15 minute intervals from 2020-09-17T13:00 to 2020-11-17T11:15. 
	3. DOconc
		DOconc.r: r script for analysis of data within hypoxiado.csv
		hypoxiado.csv: DO % saturation and relative DO concentration (mg/L) at a either 15°C or 21°C at which fish exhibited LOE as ambient DO decreased at a constant rate of 1.5% DO saturation per minute
			Header Key:
				%: (percent air saturation) dissolved oxygen saturation in ambient water at fish's loss of equilibrium (LOE)
				DO: (mg/L) dissolved oxygen concentration at fish's LOE
				sex: Categorical assignment based on the gender of the sampled fish
					Values:
						M: male
						F: female
						NA: data not available
				ecotype: Categorical assignment based on the ecotype the fish belongs to
					Values:
						desert: warm desert
						cool: cool montane
						cold: cold montane 
				PIT: Unique individualized fish passive integrated transponder (PIT) number
				AccTemp: Temperature each fish was acclimated to in the common garden
					Values:
						15¬∞C: 15°C
						21¬∞C: 21°C
				weight: (grams) body mass of fish, measured in grams
				ln.weight: (grams) natual log of body mass of fish
	4. hypoxiatol
		hypoxiatol.csv: data for the hypoxia tolerance experiment with time at loss of equilibrium (LOE) as the response variable to decrease of DO at 1.5% air saturation per minute for fish in their given acclimation temperature. 
			Header Key:
				LOE_time: (minutes) time at fish's LOE
				sex: Categorical assignment based on the gender of the sampled fish
					Values:
						M: male
						F: female
						NA: data not available
				ecotype: Categorical assignment based on the ecotype the fish belongs to
					Values:
						desert: warm desert
						cool: cool montane
						cold: cold montane 
				AccTemp: Temperature each fish was acclimated to in the common garden
					Values:
						15¬∞C: 15°C
						21¬∞C: 21°C
				weight: (grams) body mass of fish
				ln(weight): (grams) natural log of body mass of fish
		HypoxiaTol.r: r script for analysis of data within hypoxiatol.csv
	5. q10
		Q10.r: r script for anlysis of data within q10.csv
		q10.csv: data for the temperature coefficient, Q10. Q10 measures the degree of temperature dependence on heart rate over the change of 10°C. Q10 is the response variable to the acute temperature increase and oxygen treatment.
			Header Key:
				fish: Unique numerical assignment for individual fish identification
				temp: acute temperature ramp from 15-29°C
				Q10: response variable; temperature coefficient; Q10 = (R2/R1)^(10/(T2-T1)); R2=heart rate 2, R1 = heart rate 1, T2= temperature 2, T1 = temperature 1.
				ecotype: Categorical assignment based on the ecotype the fish belongs to
					Values:
						desert: warm desert
						cool: cool montane
						cold: cold montane
				treatment: oxygen treatment fish was exposed to during experimentation
					Values:
						normoxia: fully saturated water
						hypoxia: 50% DO saturation
				Acc_Temp: Temperature each fish was acclimated to in the common garden
					Values:
						15: 15°C
						18: 18°C
						21: 21°C
				mass: body mass of fish, measured in grams
	6. raw_data
		hypoxia_hr_raw.csv: All data for redband heart rates under acute temperature increase AND 50% dissolved oxygen treatment
			Header Key:
				Fish ID #: Unique numerical assignemnt for individual fish identification 
				pre-atropine: Heart rate (seconds per every 10 beats) prior to atropine injection. Ambient water temperature 15°C
				15 min after atropine: Heart rate (seconds per every 10 beats)presumably after the atropine has taken effect. Ambient water temperature 15°C
				50% DO @ 15¬∞C: Effect that  50% dissolved oxygen has on the fish’s heart rate at 15°C
				16¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				17¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				18¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				19¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				20¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				21¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				22¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				23¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				24¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				25¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				26¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				27¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				28¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				29¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate 
				Acclimation Temp: Temperature at which that fish was acclimated (°C)
				Ecotype: Categorical assignment based on the ecotype the fish belongs to
					Values:
						desert: warm desert
						cool: cool montane
						cold: cold montane
				Population: Categorical assignment based on the creek/population where this fish was originally collected
					Values:
						Boulder: Boulder Creek Idaho
						Duncan: Duncan Creek Idaho
						Fawn: Fawn Creek Idaho
						Keithley: Keithley Creek Idaho
						Little_Jacks: Little Jacks Creek Idaho
						no-tag:
						Trail: Trail Creek Idaho
						Upper_Mann: Upper Mann Creek Idaho
						Whiskey Jack: Whiskey Jack Creek Idaho
						Williams: Williams Creek Idaho
		normoxia_hr_raw.csv: All data for redband heart rates under acute temperature increase and normoxic water, meaning fully saturated with dissolved oxygen (DO)
			Header Key:
				FISH # ID: Unique numerical assignemnt for individual fish identification
				Pre-atropine: Heart rate (seconds per every 10 beats) prior to atropine injection. Ambient water temperature 15°C
				15¬∞C: Heart rate (seconds per every 10 beats) presumably after the atropine has taken effect, 15 minutes after injection. Ambient water temperature is 15°C.
				16¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				17¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				18¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				19¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				20¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				21¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				22¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				23¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				24¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				25¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				26¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				27¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				28¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				29¬∞C: Heart rates at the given temperatures. These are steps on a ramping scale that increased ~1°C every 7 minutes. “NA” = fish has already reached the temperature at their peak heart rate
				Acclimation Temp: Temperature each fish was acclimated to in the common garden
					Values:
						15: 15°C
						18: 18°C
						21: 21°C
				Ecotype: Categorical assignment based on the ecotype the fish belongs to
					Values:
						desert: warm desert
						cool: cool montane
						cold: cold montane
				Population: Categorical assignment based on the creek/population where this fish was originally collected
					Values:
						Boulder: Boulder Creek Idaho
						Duncan: Duncan Creek Idaho
						Fawn: Fawn Creek Idaho
						Keithley: Keithley Creek Idaho
						Little_Jacks: Little Jacks Creek Idaho
						no-tag:
						Trail: Trail Creek Idaho
						Upper_Mann: Upper Mann Creek Idaho
						Whiskey Jack: Whiskey Jack Creek Idaho
						Williams: Williams Creek Idaho
	7. id_data_original.csv: individual identification data 
		Header Key:
			Fish ID: Unique fish identification numbers
			PIT tag: Unique individualized fish passive integrated transponder (PIT) number
			Mass (g): Wet body mass of fish in grams
			Length (cm): Length of fish in centimeters
			Atropine (ul): Microliters of atropine solution mixed with saline injected into inter peritoneal cavity; varies by body mass
			Date: Date the data was collected. yyyy-mm-dd
			Time: Approximate time the experiment began. HH:MM in 24-hour clock format. All time recorded in the USA Mountain Timezone (MT).
			Tank: Integer based tank assignemnt
			Ecotype: Categorical assignment based on the ecotype the fish belongs to
				Values:
					desert: warm desert
					cool: cool montane
					cold: cold montane 
			Color: Corresponds with the color of the Visible Implant Elastomer (VIE) tags that indicated what population or creek a fish  came from within each ecotype
				Values:
					red:s Upper Mann Creek (for cold montane fish);Trail Creek (for cool montane fish); Duncan Creek (for warm desert fish)
					green:Boulder Creek (for cold montane fish); Whiskey Jack Creek (for cool montane fish); Little Jack's Creek (for warm desert fish)
					orange: Fawn Creek (for cold montane fish);Keithley Creek (for cool montane fish); William's Creek (for warm desert fish)
					no_tag:tag wore off and was not available; specific population could not be identified
			Population: Categorical assignment based on the creek/population where this fish was originally collected
				Values:
					Boulder: Boulder Creek Idaho
					Duncan: Duncan Creek Idaho
					Fawn: Fawn Creek Idaho
					Keithley: Keithley Creek Idaho
					Little_Jacks: Little Jacks Creek Idaho
					no-tag:
					Trail: Trail Creek Idaho
					Upper_Mann: Upper Mann Creek Idaho
					Whiskey Jack: Whiskey Jack Creek Idaho
					Williams: Williams Creek Idaho
			Acclimation Temp. °C: Temperature each fish was acclimated to in the common garden
				Values:
					15: 15°C
					18: 18°C
					21: 21°C
			Treatment: oxygen treatment fish was exposed to during experimentation
				Values:
					normoxia: fully saturated water
					hypoxia: 50% DO saturation
			Temp. reader (1,2,3,4): Integer based assignment based on thermometer used during experimentation. This was used for corrections to temperature at peak heart rate response parameters.
			Peak HR: Water temperature in the system at the fish’s peak heart rate in °C
			Type of Heart Failure: Categorical assignment based on the type of heart failure on the ECG output
				Values:
					HR slowed: the heart rate began to slow down after the peak
					arrhythmia: the fish had cardiac arrhythmia
					skip beat: the fish skipped a heart beat
			Max HR (seconds/10 beats): peak heart rate shown in seconds per 10 beats
	8. mass_correction_fhmax.csv: shows calculations converting units of heart rate and correcting heart rate with body mass of individuals based on the average body mass. 
		Header Key:
			FISH: Unique fish identification numbers
			mass (g): body mass of fish, measured in grams
			fhmax (seconds/10beats): peak heart rate of fish measured in seconds for every 10 beats
			fhmax (bpm): peak heart rate measured in beats per minute
			fhmax corrected: peak heart rate for each fish corrected for body mass
			median mass:
	9. readme.txt
	10. tempatpeak
		Temp_at_peak.r: r script for analysis of data within tempatpeak_nooutlier.csv
		tempatpeak_nooutlier.csv: temperature at peak heart rate in response to ramping temperature and normoxia or hypoxia treatment; outlier/data collection mistake was removed from this dataset
			Header Key:
				fish: Unique numerical assignemnt for individual fish identification
				ecotype: Categorical assignment based on the ecotype the fish belongs to
					Values:
						desert: warm desert
						cool: cool montane
						cold: cold montane
				acclimation: Temperature each fish was acclimated to in the common garden
					Values:
						15: 15°C
						18: 18°C
						21: 21°C
				oxygen: oxygen treatment fish was exposed to during experimentation
					Values:
						normoxia: fully saturated water
						hypoxia: 50% DO saturation
				peak: (°C)temperature at peak heart rate; this is the fastest heart rate a fish can attain before cardiac failure; this value was corrected after experimentation date by looking at electrocardiograms and calculating approximate temperature using rate of increase and time stamp on the document; This number is considered to be the most precise and accurate in comparison to temperature at peak heart rate values expressed on raw data files. 
				sex: Categorial gender assignment for fish sampled
					Values:
						XX: Female
						XY: Male
				Mass: (grams) body mass of fish
				ln.Mass: (grams) natural log of body mass of fish 

Resource URL: ### Data is not yet availabe from a public repository

Creator(s):	
	1. Carlie Sharpes
		ORCiD: NULL
		Affiliation: University of Idaho
	2. Zhongqi Chen
		ORCid: https://orcid.org/0000-0003-0575-7013
		Affiliation: University of Idaho
	3. Brian C. Small
		ORCid: https://orcid.org/0000-0003-4854-4261
		Affiliation: University of Idaho
	
Other Contributor(s): NA

Description/Abstract:
	**Abstract**
	Aquatic hypoxia, or dissolved oxygen (DO) deficiency, has increased in frequency with rising water temperatures as a result of climate change. Temperature and DO are important factors that can affect many biotic processes for salmonids. Fish can adjust to environmental variables such as temperature change and hypoxia using phenotypic plasticity. Redband trout (Oncorhynchus mykiss gairdneri) have desert, cool montane, and cold montane ecotypes in Idaho. This research analyzed the effects of hypoxia and thermal stress, both in combined and isolated tests, on age-1 redband trout. These fish have been acclimated in a common garden at 21°C and 15°C, to model desert and cold montane habitats, respectively. The experiment examined cardiac phenotypic response using an electrocardiogram (ECG) to measure the heart rate of individuals when exposed to hypoxic conditions and acute thermal stress. The treatment started each individual’s acclimation temperature and 100% DO saturation. Hypoxia was initiated by bubbling N2 gas into the water at a constant rate to reduce DO to 50% saturation. The redband trout then experienced a temperature increase until their ECG displays arrhythmia, which marks the endpoint of the study. The results will show the heart rate at cardiac arrhythmia for each individual. Phenotypic plasticity is possible for hypoxia and acute temperature tolerance in redband trout. This could imply persistence for the species. However, if the combination of hypoxic and thermal stress has a synergistic effect, climate change could have worse consequences for fish than previously understood.
 
Publisher: NULL

Publication Year: NULL

Language(s): American English

Subject(s): 
	1. Natural Sciences
		1.6 Biological sciences
	
Keywords/Tags: adaptation, climate change, common garden, drought, gene/genome/genotype-environment interaction (GxE), morphology, Oncorhynchus mykiss gairdneri (Redband Trout), phenotype, phenotypic plasticity, physiology, resilience, restoration, survival, sustainability, target populations, vulnerability, wildlife, cardiac function, hypoxia tolerance, thermal tolerance, cardiac performance, synergistic, acute thermal stress, chronic thermal stress, acclimation, ecotype, dissolved oxygen

Resource Type General: Dataset
		
Dates: NA	

Date available for the public: Pending Peer-Review

Sizes: 778KB
 
Format(s): csv, txt, r
 
Version: NA

Funding References: 
	US NSF
		OIA-1757324
			RII Track-1: Linking Genome to Phenome to Predict Adaptive Responses of Organisms to Changing Landscapes
			https://www.nsf.gov/awardsearch/showAward?AWD_ID=1757324
		 
Spatial/Geographical Coverage Location: 
	Study Area Description: Idaho USA
	Fields Sites: Little Jacks Creek, Duncan Creek, Williams Creek, Keithley Creek, Whiskey Jack Creek, Trail Creek, Fawn Creek, Upper Mann Creek, Boulder Creek	
	Research Labs: Hagerman Fish Culture Experiment Station, Uiversity of Idaho 

Temporal Coverage: 
	Start Date: 2021-02-03
	End Date: 2021-04-14
 
License: NULL
    
Granularity of the Data: NULL
 
Contact Info: 
	Contact Name: Brian Small
	Contact Email: bcsmall@uidaho.edu
 
Related Content: NULL