Data and code from: Spatially-explicit foraging by an apex predator linked to nearshore prey and their accessibility in lakes
Data files
Apr 10, 2025 version files 1.91 GB
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01-library-oikos.Rmd
5.41 KB
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02-temp-do-oikos.Rmd
12.90 KB
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03-slope-calculations-oikos.Rmd
12.21 KB
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04-nearshore-prey-oikos.Rmd
18.61 KB
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05-lavage-oikos.Rmd
15.03 KB
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06-read-vps-oikos.Rmd
15.83 KB
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07-read-vr2-oikos.Rmd
15.47 KB
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08-spatial-processing-oikos.Rmd
11.53 KB
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09-hyp1-oikos.Rmd
21.59 KB
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10-hyp2-hyp3-oikos.Rmd
13.71 KB
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all37303.csv
142.86 MB
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all37304.csv
199.02 MB
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all37305.csv
226.87 MB
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all62601.csv
75.21 MB
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all62602.csv
251.61 MB
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Diversion_Fish_Data.csv
52.39 KB
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L373_L626_LT_lavage_fish_data_2021-22.csv
8.50 KB
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L373_L626_LT_surgery_fish_data_2022.csv
9.45 KB
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L626_VR2_Data_Processed_2024.csv
514.81 MB
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Lavage_Weigh_Sheet_Oikos.csv
23.51 KB
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Minnow_Trap_Collections_-_Fall_Data_Entry_TR.csv
23.73 KB
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Minnow_Trap_Collections.xlsx_-_Animals_(5).csv
147.88 KB
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Minnow_Trap_Collections.xlsx_-_Subsampling.csv
1.95 KB
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Nautical_Twilight_2021_NRC.csv
14.18 KB
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Nautical_Twilight_2022_NRC.csv
14.18 KB
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RBR_YSI_TempDO_L373_L626_2021-2022.csv
47.32 KB
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README.md
18.08 KB
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stations373.csv
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stations626.csv
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TempLogs_L626_2021-2022.csv
1.33 MB
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Volumes_2023-03-09.csv
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VR2_Data_up_to_2022_TR_20240319.csv
493.01 MB
Abstract
Habitat coupling – where mobile predators forage over broad spatial scales and, in doing so, link food webs from semi-discrete habitat patches – has emerged as a major structuring force in lake ecosystems. For the cold-water apex predator lake trout (Salvelinus namaycush), food-web structure and morphometry-driven accessibility to nearshore areas in summer strongly determine the degree of littoral-pelagic habitat coupling across lakes. Much of the evidence for habitat coupling, however, is based on stable isotopes of carbon to estimate littoral energy acquisition, whereas spatial data directly linking fish movements and foraging behaviour in lakes, on which this theory is based – are limited. Here we estimated nearshore prey abundance at sites of different thermal accessibility and collected stomach content data, which we combined with three-dimensional acoustic telemetry positioning and acceleration data to directly measure the spatial location of summer foraging movements and habitat coupling by lake trout in lakes with and without an offshore prey fish. Both study lakes contained higher abundances of nearshore prey fish at the most thermally accessible (i.e., steep) sites monitored. Nearshore occupancy accounted for a small proportion of lake trout positions in both lakes (<5%), although prey fish were present in most (72%) diets sampled. High acceleration events indicative of foraging were concentrated in steep, thermally accessible nearshore areas in the lake where offshore forage fish were absent, but were located further offshore in the lake with offshore prey fish. We directly demonstrate that habitat coupling by a wild, apex predator is driven by habitat and prey accessibility.
Dataset DOI: https://doi.org/10.5061/dryad.g1jwstr0v
Description of the data and file structure
This data set includes the temperature and telemetry data for Lakes 373 and 626 at IISD-Experimental Lakes Area used to analyse lake trout behaviour for the summers of 2021 and 2022. Data are owned by IISD-ELA except for the NRC sunrise and sunset data, which are downloaded from the NRC website. Code was written by Tazi Rodrigues and all authors collected the diet data.
Files and variables
File: RBR_YSI_TempDO_L373_L626_2021-2022.csv
Description: Temperature and dissolved oxygen measurements for the study lakes in the study years.
Variables
- TimeStamp: time of measurement
- Lake: location of measurement
- Average Depth (m): depth in metres of measurement
- Average Temperature (C): average temperature reading over measurement
- Dissolved Oxygen (mg/L): average dissolved oxygen reading over measurement
- Comments: any additional comments
File: Nautical_Twilight_2021_NRC.csv
Description: sunrise and sunset times observed near IISD-ELA in 2021
Variables
- Date: date of observation
- Nautical Twilight start: time that nautical twilight begins
- Sunrise: sunrise time
- Sunset: sunset time
- Nautical Twilight end: time that nautical twilight ends
File: Nautical_Twilight_2022_NRC.csv
Description: sunrise and sunset times observed near IISD-ELA in 2022
Variables
- Date: date of observation
- Nautical Twilight start: time that nautical twilight begins
- Sunrise: sunrise time
- Sunset: sunset time
- Nautical Twilight end: time that nautical twilight ends
File: Volumes_2023-03-09.csv
Description: lake volumes by bathymetric contour
Variables
- depth: lake depth
- Lake: lake identity
- monitoring_location_name: location if not just lake identity
- activity_start_date: time measurement began
- depth_upper: upper depth of lake layer
- depth_lower: lower depth of lake layer
- area_interval: area of lake layer
- volume_interval: volume of lake layer
- update_date: date measurements last updated
- Volume: 1/10 of the volume of each layer
File: TempLogs_L626_2021-2022.csv
Description: temperature logs from temperature strings set in Lake 626 at depth increments indicated in the second row
Variables
- Date Time, GMT-05:00: date and time of measurement
- P-01m through to P-11m: temperature at given depth (i.e., P-01 m == 1 m depth)
File: Diversion_Fish_Data.csv
Description: metadata for fish with telemetry tags
Variables
- Lake: location of fish
- Year: year that fish was tagged
- Tag_Num: telemetry tag number
- Fish_ID: fish identifier
- Tag Snb: serial number of tag
- TagType: type of telemetry tag
- Frequency: frequency at which tag signals
- Sensor: integrated sensors that align with tag identity
- Pulse rate: pulse rate of tag
- Species: species of fish tagged
- Date Tagged: date that fish was tagged
- Date_Released: date that fish was released after tagging
- Time_Released: time that fish was released after tagging
- PIT#: unique identifier for each fish
- Total length (mm): total length of each tagged fish, to end of caudal fin
- Fork length (mm): length of each tagged fish to fork in caudal fin, if appropriate
- Weight (g): weight of tagged fish at time of tagging
- Time in Anaesthetic: length of time tagged fish spent in anaesthetic bath
- Surgery start: surgery start time
- Surgery end: surgery end time
- Time for surgery: length of time fish spent in surgery
- Sex: sex of tagged fish if known
- Current Condition: tag condition - dead, alive, or failed
- Date_Dead: date that tag died or failed
- Time_Dead: time that tag died or failed
- Surgeon: researcher who conducted the surgery
- General Comments: any other comments
File: L373_L626_LT_surgery_fish_data_2022.csv
Description: metadata for fish tagged in the last year of this study
Variables
- Lake: location of fish
- Year: year that fish was tagged
- Tag_Num: telemetry tag number
- Fish_ID: fish identifier
- Tag Snb: serial number of tag
- TagType: type of telemetry tag
- Frequency: frequency at which tag signals
- Sensor: integrated sensors that align with tag identity
- Pulse rate: pulse rate of tag
- Species: species of fish tagged
- Date Tagged: date that fish was tagged
- Date_Released: date that fish was released after tagging
- Time_Released: time that fish was released after tagging
- PIT#: unique identifier for each fish
- Total length (mm): total length of each tagged fish, to end of caudal fin
- Fork length (mm): length of each tagged fish to fork in caudal fin, if appropriate
- Weight (g): weight of tagged fish at time of tagging
- Time in Anaesthetic: length of time tagged fish spent in anaesthetic bath
- Surgery start: surgery start time
- Surgery end: surgery end time
- Time for surgery: length of time fish spent in surgery
- Sex: sex of tagged fish if known
- Current Condition: tag condition - dead, alive, or failed
- Date_Dead: date that tag died or failed
- Time_Dead: time that tag died or failed
- Surgeon: researcher who conducted the surgery
- General Comments: any other comments
File: all37303.csv
Description: VPS readings from Lake 373. All files that begin with “all” follow the same variable format. Characters 4-6 of each file name indicate the lake name.
Variables
- Transmitter: human-assigned name for transmitter
- FullId: code-assigned name for transmitter
- Id: short form of FullId
- Time: time detected
- X: x coordinate
- Y: y coordinate
- Z: z coordinate
- Longitude: longitude of detection
- Latitude: latitude of detection
- Depth: depth of detection
- Station: NA
- HPE: horizontal position error
- HPEm: horizontal position error (m)
- RMSE: root mean squared error
- TempData: temperature data, where sensor was integrated (NA)
- DepthData: depth data, where sensor was integrated
- AccelData: accelerometer data, where sensor was integrated
- RxDetected: receivers that detected signal
- nRxDetected: number of receivers that detected signal
- RxUsed: receivers that were used to triangulate position
- nRxUsed: number of receivers that were used to triangulate position
File: all37304.csv
Description: VPS readings from Lake 373. All files that begin with “all” follow the same variable format. Characters 4-6 of each file name indicate the lake name.
Variables
- Transmitter: human-assigned name for transmitter
- FullId: code-assigned name for transmitter
- Id: short form of FullId
- Time: time detected
- X: x coordinate
- Y: y coordinate
- Z: z coordinate
- Longitude: longitude of detection
- Latitude: latitude of detection
- Depth: depth of detection
- Station: NA
- HPE: horizontal position error
- HPEm: horizontal position error (m)
- RMSE: root mean squared error
- TempData: temperature data, where sensor was integrated (NA)
- DepthData: depth data, where sensor was integrated
- AccelData: accelerometer data, where sensor was integrated
- RxDetected: receivers that detected signal
- nRxDetected: number of receivers that detected signal
- RxUsed: receivers that were used to triangulate position
- nRxUsed: number of receivers that were used to triangulate position
File: all37305.csv
Description: VPS readings from Lake 373. All files that begin with “all” follow the same variable format. Characters 4-6 of each file name indicate the lake name.
Variables
- Transmitter: human-assigned name for transmitter
- FullId: code-assigned name for transmitter
- Id: short form of FullId
- Time: time detected
- X: x coordinate
- Y: y coordinate
- Z: z coordinate
- Longitude: longitude of detection
- Latitude: latitude of detection
- Depth: depth of detection
- Station: NA
- HPE: horizontal position error
- HPEm: horizontal position error (m)
- RMSE: root mean squared error
- TempData: temperature data, where sensor was integrated (NA)
- DepthData: depth data, where sensor was integrated
- AccelData: accelerometer data, where sensor was integrated
- RxDetected: receivers that detected signal
- nRxDetected: number of receivers that detected signal
- RxUsed: receivers that were used to triangulate position
- nRxUsed: number of receivers that were used to triangulate position
File: all62601.csv
Description: VPS readings from Lake 626. All files that begin with “all” follow the same variable format. Characters 4-6 of each file name indicate the lake name.
Variables
- Transmitter: human-assigned name for transmitter
- FullId: code-assigned name for transmitter
- Id: short form of FullId
- Time: time detected
- X: x coordinate
- Y: y coordinate
- Z: z coordinate
- Longitude: longitude of detection
- Latitude: latitude of detection
- Depth: depth of detection
- Station: NA
- HPE: horizontal position error
- HPEm: horizontal position error (m)
- RMSE: root mean squared error
- TempData: temperature data, where sensor was integrated (NA)
- DepthData: depth data, where sensor was integrated
- AccelData: accelerometer data, where sensor was integrated
- RxDetected: receivers that detected signal
- nRxDetected: number of receivers that detected signal
- RxUsed: receivers that were used to triangulate position
- nRxUsed: number of receivers that were used to triangulate position
File: all62602.csv
Description: VPS readings from Lake 626. All files that begin with “all” follow the same variable format. Characters 4-6 of each file name indicate the lake name.
Variables
- Transmitter: human-assigned name for transmitter
- FullId: code-assigned name for transmitter
- Id: short form of FullId
- Time: time detected
- X: x coordinate
- Y: y coordinate
- Z: z coordinate
- Longitude: longitude of detection
- Latitude: latitude of detection
- Depth: depth of detection
- Station: NA
- HPE: horizontal position error
- HPEm: horizontal position error (m)
- RMSE: root mean squared error
- TempData: temperature data, where sensor was integrated (NA)
- DepthData: depth data, where sensor was integrated
- AccelData: accelerometer data, where sensor was integrated
- RxDetected: receivers that detected signal
- nRxDetected: number of receivers that detected signal
- RxUsed: receivers that were used to triangulate position
- nRxUsed: number of receivers that were used to triangulate position
File: stations373.csv
Description: acoustic telemetry receiver station metadata
Variables
- Serial: serial number of receiver
- StationName: human-assigned station name
- Start: date of deployment
- End: date receiver pulled, if applicable
- Latitude: latitude of receiver
- Longitude: longitude of receiver
- Depth: depth of receiver
- X: x coordinate used for positioning
- Y: y coordinate used for positioning
- Z: depth reading used for positioning
File: stations626.csv
Description: acoustic telemetry receiver station metadata
Variables
- Serial: serial number of receiver
- StationName: human-assigned station name
- Start: date of deployment
- End: date receiver pulled, if applicable
- Latitude: latitude of receiver
- Longitude: longitude of receiver
- Depth: depth of receiver
- X: x coordinate used for positioning
- Y: y coordinate used for positioning
- Z: depth reading used for positioning
File: VR2_Data_up_to_2022_TR_20240319.csv
Description: processed telemetry detections from VR2 receivers
Variables
- Transmitter: transmitter ID for tagged fish
- SensorType: type of sensor reading, if applicable
- Slope: slope for calculating readings in meaningful units
- Intercept: intercept for calculating readings in meaningful units
- Sensor.Value: value transmitted by sensor
- Sensor.Unit: unit that applies to sensor type
- DateTime: date and time of detection
- diff: difference in seconds from previous reading
- FISH: short ID from transmitter
- True.Sensor.Value: calibrated sensor value
File: L626_VR2_Data_Processed_2024.csv
Description: processed telemetry detections from VR2 receivers
Variables
- Transmitter: transmitter ID for tagged fish
- SensorType: type of sensor reading, if applicable
- Slope: slope for calculating readings in meaningful units
- Intercept: intercept for calculating readings in meaningful units
- Sensor.Value: value transmitted by sensor
- Sensor.Unit: unit that applies to sensor type
- DateTime: date and time of detection
- diff: difference in seconds from previous reading
- FISH: short ID from transmitter
- True.Sensor.Value: calibrated sensor value
File: Minnow_Trap_Collections.xlsx_-_Subsampling.csv
Description: minnow trap data for traps where subsampling occurred
Variables
- Lake: where the minnow traps were located
- Date: date of collection
- Crew: initials of people involved in field sampling that day
- Access: one of low, medium, or high related to thermal accessibility
- Depth: depth of minnow trap
- Contour: bathymetric contour at which minnow trap was set
- Species: species code
- Total Number: tallied number of fish + 30
- Tally (alive): number of fish after 30 that were alive, of that species and trap
- Tally (dead): number of fish that were dead of that species and trap
- Notes: any extra comments
File: Minnow_Trap_Collections_-_Fall_Data_Entry_TR.csv
Description: minnow trap metadata
Variables
- Date Set: date minnow trap was set
- Lake: where minnow trap was set
- Access: thermal accessibility of minnow trap set (low, medium, or high)
- Contour: bathymetric contour where minnow trap was set
- Set: which day of the three consecutive days the minnow trap was set
- Time Set: time that minnow trap was set
- Date Collected: date that minnow trap was collected
- Time Collected: time that minnow trap was collected
File: Lavage_Weigh_Sheet_Oikos.csv
Description: weights of diet items from gastric lavage
Variables
- Lake: where fish was caught
- Date: which date fish was caught
- PIT: unique identifier for each fish
- Sample: sample number
- Sample ID: lake and sample number
- Taxon: identification of lavage item
- Tin ID: letter written on tin to keep track in oven
- Tin Mass: how much the tin weighed
- DateTime In: when the tin was put in oven
- Wet + Tin (g): weight of tin and wet sample
- DateTime Out: when the tin was taken from oven
- Dry + Tin (g): weight of tin and dry sample
- Notes: extra comments
- Number: number of prey items
- SecondTin: dry weight of tin, if taken separately
File: L373_L626_LT_lavage_fish_data_2021-22.csv
Description: metadata for fish included in gastric lavage sampling
Variables
- LAKE: lake where sample was taken
- SPECIES: species of fish from which sample was taken
- sample ID: unique number for sample
- DATE: date that sample was taken
- YEAR: year that sample was taken
- CREW: initials of people involved in field work that day
- PIT: unique identifier for fish
- WEIGHT (g): mass of fish
- Total lemgth (mm): length of fish to tip of tail
- Fork length (mm): length of fish to fork in caudal fin
- SEX: sex of fish if known
- GUT CONTENT DESCRIP: field comments regarding gut contents
- MULTIPLE?: whether fish had already been sampled
- COMMENTS: extra comments
File: Minnow_Trap_Collections.xlsx_-Animals(5).csv
Description: measurements for animals collected in minnow traps
Variables
- Lake: lake where sample was taken
- Date: date on which sample was taken
- Crew: people involved in field work that day
- Access: thermal accessibility (low, medium, high)
- Depth: depth at which minnow trap was set
- Contour: bathymetric contour where minnow trap was set
- Species: fish species
- Mass: mass of each individual fish
- Standard Length: standard length of individual fish
- Fork Length: length to fork in caudal fin of individual fish, if appropriate
- Sex: sex of individual fish, if known
- Dead: whether or not the fish was dead at time of sampling
- Notes: extra comments
- SIA: whether or not the fish was taken for stable isotope analysis
- Confirmed: if data input was triple-checked
File: 01-library-oikos.Rmd
Description: Establishes functions that are used in the remaining R Markdown files.
File: 02-temp-do-oikos.Rmd
Description: Reads and processes temperature and dissolved oxygen files.
File: 03-slope-calculations-oikos.Rmd
Description: Calculates slope values for the lake rasters.
File: 04-nearshore-prey-oikos.Rmd
Description: Processing and analysis of data associated with the minnow trap data collection.
File: 05-lavage-oikos.Rmd
Description: Processing and analysis of data associated with gastric lavage.
File: 06-read-vps-oikos.Rmd
Description: Reads and processes spatial lake trout movement data.
File: 07-read-vr2-oikos.Rmd
Description: Reads and processes detection data for lake trout.
File: 08-spatial-processing-oikos.Rmd
Description: Spatial processing of spatial lake trout movement data, including assigning slope values and distance to shore to each position.
File: 09-hyp1-oikos.Rmd
Description: Produces Figure 1 of associated paper and performs kernel-based calculations.
File: 10-hyp2-hyp3-oikos.Rmd
Description: Analysis of the effect of slope on lake trout movement patterns.
Code/software
To view these data, use the associated R Markdown files using the programming language R. Scripts should be read in numbered order from 1-10. Bathymetric data used in these scripts can be found at the following location:
IISD Experimental Lakes Area. 2022. IISD Experimental Lakes Area: Bathymetry Data Package, 1968-2022 ver 3. Environmental Data Initiative. https://doi.org/10.6073/pasta/e9898c78448cbbe544057e689d3c06df.
These data include acoustic telemetry observations and diet relating to lake trout in two small boreal lakes at IISD-Experimental Lakes Area, temperature and dissolved oxygen readings for the same lakes, and the code used to process and analyse them.