Description of the data and file structure

• This repository holds replication Data for:
  • Bzonek, P.B., Midwood, J.D., Mandrak. N.E. 2025. Dispersal of an invasive cyprinid: movement patterns correlated with morphology but not a lab-expressed behavioural syndrome. Environmental Biology of Fishes. 10.1007/s10641-025-01716-5

Data collection

• The fish collected in this dataset were captured at the Royal Botanical Gardens fishway in Cootes Paradise, Hamilton, Ontario.
• Laboratory trials were conducted at the ECCC Aquatic Life Research Facility in Burlington, Ontario, Canada.
• Telemetry data was gathered in Hamilton Harbour, Hamilton, Ontario, using the GLATOS telemetry array.

General overview

•  This data includes 5 independent R project folders, each containing their associated raw data and R scripts. The photographs and .tps files used in the morphometric analysis are also included in a second zip file.
  • Morphometric Photos
    • Folder containing all .jpeg photos of Common Carp and their associated .tps files used to identify landmark features. Each .tps file is organized in its own subfolder with associated photos.
  • 01 - Morphology
    • Format landmark TPS data into R, conduct procrustes analyses, and produce geomorphological PCA loadings.
  • 02 - Lab Behaviour
    • Format DeepLabCut outputs to generate summaries of behaviour and movement data from video-recorded lab trials.
  • 03 – Telemetry
    • Generate monthly movement summaries for telemetry-tracked individual throughout Hamilton Harbour.
  • 04 – Repeatability
    • Standardize Lab, Field, and Morphology metrics then assess repeatability with {rptR} package
  • 05 – Syndrome
    • Construct a Multivariate Mixed Model to assess a behavoural syndrome in repeatable traits. Generate additional post-hoc visualiztaions and metrics.

Files and variables

File: Morphometric Photos

• .tps
  • File containing the x and y pixel coordinates of the 45 positional landmarks along the eye, operculum, and dorsal and ventral surfaces of every fish. Also included is the referenced picture ID, Individual ID, and image scaling factor.
• jpeg
  • Raw photos of the individuals described with geometric morphometrics.

File: Replication Data and Code

01 - Morphology

• Morph_Script1.1.R
  • This script processes fish shape data. It cleans and combines landmark data from fish photos with metadata like length and weight. It runs a Principal Component Analysis (PCA) to identify shape differences. The final dataset is filtered to remove faulty or hybrid samples and saved for further analysis.
• Data
  • Landmark data
    • raw .tps files that can be read into R
  • data_rawfishdetails.csv: Biological data from fish capture at Royal Botannical Gardens, including associated photos and tag numbers.
    • Photos: photo ID number
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • PIT Tag: PIT tag ID number
    • ALRF: Binary category describing if fish were brought into the lab
    • Hybrid: Binary category describing if fish as a pure Common Carp, or a Common Carp x Goldfish hybrid
    • Length: Fork length in mm
    • Fish Weight: Wet weight in g
    • Detection: Count of PIT tag detections at nearby PIT tag gate
    • Comments: Relevant comments about fish capture 
  • data_rawHamiltonHarbour.csv: Fish capture data from electrofishing throughout Hamilton Harbour.
    • Length: Fork length in mm
    • Photo: photo ID number
    • PIT: PIT tag ID number
    • Comments: Identifying where the fish were captured
  • data_rawphotoID.csv: Key to match photo ID values between photo name and fish ID.
    • Photos: Photo ID number
    • Photos 2: Fish Id number
  • data_rawtreatment.csv: Biological data from fish capture at Royal Botannical Gardens, including associated photos and tag numbers.
    • Photos: photo ID number
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Length: Fork length in mm
    • Fish Weight: Wet weight in g
• Outputs
  • data_PCA.csv: Output created by R script to summarize principal component loadings of a morphology PCA per fish.
    • PhotoName: Name of the corresponding photo
    • PhotoNumber: Number of corresponding fish
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Length: Fork length in mm
    • Weight: wet weight in g
    • Stimulus: Whether a deterrent was active at the fishway during capture or not.
    • PIT: PIT tag ID number
    • ALRF: Binary category describing if fish were brought into the lab
    • Hybrid: Binary category describing if fish as a pure Common Carp, or a Common Carp x Goldfish hybrid
    • Detection: the number of times a fish was detected
    • Comments: Relevant comments about fish capture and tagging
    • Comp1: Loading values from morphology principal component analysis
    • Comp2: Loading values from morphology principal component analysis
    • Comp3: Loading values from morphology principal component analysis
    • Comp4: Loading values from morphology principal component analysis
    • Comp5: Loading values from morphology principal component analysis

02 - Lab Behaviour

• Behaviour_script1.1.R
  • This script loads and processes fish tracking data from DeepLabCut to calculate how much each fish moved, how long it stayed near a mirror (for sociability), and how long it hid (for boldness), then summarizes and exports these behavioral metrics per trial.
• Data
  • Tracked fish (subset)
    • Trial 30 Aug 16 PMDLC_resnet50_Training 1Jun8shuffle1_200000.csv: Example of a DeepLabCut output of a tracked fish trial
      • Coords: coordinates of various body parts:
        • X: x coordinates
        • Y: y coordinates
        • Bodyparts:
          • Nose: anterior tip of fish
          • Fin_left: left fin
          • Fin_right: right fin
          • Tail: Posterior tip of caudal fin
  • Data_rawtrial.csv: Trial data from observations of the fish behaviors during the course of each trial
    • Trial Number: A number assigned to each individual trial
    • Date: Date of corresponding trial
    • Observer: Initials of who made the recording
    • Rack: Experimental Tank
    • PIT tag: PIT tag ID number
    • Water temp: the temperature of the water at the time of the trial
    • Acclimation Start Time: The time the fish began to acclimate to its new environment
    • Trial start time: Time the trial began
    • Refuge Exit Time: The time the fish left the refuge
    • Sociability Start Time: Time fish began socializing  
    • Trial End Time: The time the trial concluded
    • Failure to exit refuge: Describes if the fish failed to leave the refuge during the length of the trial
    • Trial Artificially Ended: Describes if the trial was ended by the researcher or by the original parameters
    • Comments: Relevant comments over the course of the trial
• Outputs
  • Data_labbehaviour1.1.csv: Output from R script. Behavioural summaries per fish and trial
    • Trial: Behavioural trial number
    • PIT: PIT tag ID number
    • Dist: Total distance travelled
    • MirrorTime: Time the fish spent interacting with the mirror recorded in seconds
    • RefugeTime: Time fish spent in the refuge recorded in seconds
    • Latency: Time spent in refuge before first exit
    • TrialNumber: corresponding trial number

03 – Telemetry

• Telemetry Script1.1.R
  • This project tracks fish movements in Hamilton Harbour to understand their travel patterns, home areas, and how they use different parts of the environment, including industrial zones and wetlands, by analyzing location data collected over several months.
• Data
  • Shapefiles
    • HH_Industry: Shapefile of the industrial shoreline of Hamilton Harbour
    • Lake_Ontario: Shapefile of Lake Ontario
  • data_fishsummary.csv: Biological data from tagged fish
    • Telemetry Tag 1: The telemetry tag number 
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Gate: Capture gate at fishway
    • Stimulus: Whether a deterrent was active at the fishway during capture or not.
    • PIT Tag: PIT tag ID number
    • Photo: corresponding photo numbers
    • Comments: Relevant comments and observation about the fish’s health and sutures
    • Mass: mass of fish in g
    • Total Weight: total wet weight in g
    • Length: Fork length in mm
  • data_PCA.csv: Dataset from morphology script
    • PhotoName: Name of the corresponding photo
    • PhotoNumber: Number of corresponding fish
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Length: Fork length in mm
    • Weight: wet weight in g
    • Stimulus Whether a deterrent was active at the fishway during capture or not.
    • PIT: PIT tag ID number
    • ALRF: Binary category describing if fish were brought into the lab
    • Hybrid: Binary category describing if fish as a pure Common Carp, or a Common Carp x Goldfish hybrid
    • Detection: the number of times a fish was detected
    • Comments: Relevant comments about fish capture and tagging
    • Comp1: Loading values from morphology principal component analysis
    • Comp2: Loading values from morphology principal component analysis
    • Comp3: Loading values from morphology principal component analysis
    • Comp4: Loading values from morphology principal component analysis
    • Comp5: Loading values from morphology principal component analysis
  • Data_rawtelemetry1.1.csv: Raw telemetry detection data from HAMLO GLATOS array.*
    • Animal_id: ID number which corresponds with a tagged fish
    • Detection_timestamp_utc: The date and time when a detection event occurred, recorded in Coordinated Universal Time (UTC)
    • Glatos_array: The name or code of the GLATOS receiver array where the fish detection occurred.
    • Station_no: The station number where the fish detection occurred
    • Transmitter_codespace: the Transmitter codespace number which is responsible for the detected fish
    • Transmitter_id: the Transmitter ID number which is responsible for the detected fish
    • sensor_value: outputs for sensor tags (not used in this study)
    • deploy_lat: The latitude coordinate where the acoustic receiver responsible for the detection was deployed.
    • deploy_long: The longitude coordinate where the acoustic receiver responsible for the detection was deployed.
    • Receiver_sn: The receiver serial number responsible for the detection
    • Common name: Common name of the fish species detected
    • Release location: The location the fish was released at the time of tagging
    • utc_release_date_time: The date and time the tagged fish was released recorded in Coordinated Universal Time (UTC)
    • glatos_project_transmitter: All receivers belong to the HAMLO project
    • glatos_project_receiver: All receivers belong to the HAMLO project
    • glatos_tag_recovered: Describing if the tag was recovered or not
    • station: the name of the station the fish was detected at
    • min_lag: minimum detection lag for ping
  • Function**Network_Analysis_Bzonek*.R*
    • This R script combines, constructs a function to be used in the main telemetry script. This function script generates a network analysis plot for fish movements between receivers.
• Outputs
  • Data_telemetrysummary1.csv: Output from R script. Summary acoustic telemetry movement data for Hamilton Harbour Common Carp.
    • PIT: PIT tag ID number
    • Transmitter: Transmitter ID number
    • Month: Month of detection
    • Tdist: Total distance travelled
    • Clippedhomerange95: 95% minimum convex polygon (home range) size
    • Clippedhomerange50: 50% minimum convex polygon (core range) size
    • Ddist: Daily distance travelled
    • Tracktime: Total time tracked per month (days)
    • Dispersal: Eucledian distance (m) between monthly center of activity and release site.
    • Industrial: Eucledian distance (m) between monthly center of activity and the industrial shoreline.
    • Detections: Number of detections of fish
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Stimulus: Whether a deterrent was active at the fishway during capture or not.
    • Weight: wet weight in
    • Length: Fork length in
    • Comp1: Loading values from morphology principal component analysis
    • Comp2: Loading values from morphology principal component analysis
    • Comp3: Loading values from morphology principal component analysis
    • Wetland: Monthly binary value for if fish breached the wetland barrier or not.

04 – Repeatability

• Repeatability_Script1.1.R
  • This R script combines, rescales, and cleans data from laboratory behavior tests, telemetry tracking, and morphological measurements to analyze and visualize consistent individual differences in fish behavior and movement patterns over time.
• Data
  • Data_labbehaviour1.1.csv: Output from behaviour section. Behavioural summaries per fish and trial
    • Trial: Behavioural trial number
    • PIT: PIT tag ID number
    • Dist: Total distance travelled
    • MirrorTime: Time the fish spent interacting with the mirror recorded in seconds
    • RefugeTime: Time fish spent in the refuge recorded in seconds
    • Latency: Time spent in refuge before first exit
    • TrialNumber: corresponding trial number
  • data_PCA.csv: Output from morphology section. Summarize principal component loadings of a morphology PCA per fish.
    • PhotoName: Name of the corresponding photo
    • PhotoNumber: Number of corresponding fish
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Length: Fork length in mm
    • Weight: wet weight in g
    • Stimulus: Whether a deterrent was active at the fishway during capture or not.
    • PIT: PIT tag ID number
    • ALRF: Binary category describing if fish were brought into the lab
    • Hybrid: Binary category describing if fish as a pure Common Carp, or a Common Carp x Goldfish hybrid
    • Detection: the number of times a fish was detected
    • Comments: Relevant comments about fish capture and tagging
    • Comp1: Loading values from morphology principal component analysis
    • Comp2: Loading values from morphology principal component analysis
    • Comp3: Loading values from morphology principal component analysis
    • Comp4: Loading values from morphology principal component analysis
    • Comp5: Loading values from morphology principal component analysis
  • Data_telemetrysummary1.csv: Output from Telemetry section. Summary acoustic telemetry movement data for Hamilton Harbour Common Carp.*
    • PIT: PIT tag ID number
    • Transmitter: Transmitter ID number
    • Month: Month of detection
    • Tdist: Total distance travelled
    • Clippedhomerange95: 95% minimum convex polygon (home range) size
    • Clippedhomerange50: 50% minimum convex polygon (core range) size
    • Ddist: Daily distance travelled
    • Tracktime: Total time tracked per month (days)
    • Dispersal: Eucledian distance (m) between monthly center of activity and release site.
    • Industrial: Eucledian distance (m) between monthly center of activity and the industrial shoreline.
    • Detections: Number of detections of fish
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Stimulus: Whether a deterrent was active at the fishway during capture or not.
    • Weight: wet weight in
    • Length: Fork length in
    • Comp1: Loading values from morphology principal component analysis
    • Comp2: Loading values from morphology principal component analysis
    • Comp3: Loading values from morphology principal component analysis
    • Wetland: Monthly binary value for if fish breached the wetland barrier or not.
• Outputs
  • Data_syndrome1.1.csv: Output from R script. Summary statistics for repeatable behavioural metrics that may constitute a behavioural syndrome. All values have been standardized and rescaled, so values are unitless and can be compared within and amongst individuals and other behaviours.
    • PIT: PIT tag ID number
    • RepNumber: Number of repeats (lab trial) or month ID (telemetry)
    • Activity: Total movement
    • Sociability: Time the fish spent interacting with the mirror recorded in seconds
    • Boldness: Time fish spent in the refuge recorded in seconds
    • Distance: Total distance travelled
    • Dispersal: Distance between monthly center of activity and release site
    • Stelco: Distance between monthly center of activity and release site
    • HR95: 95% minimum convex polygon (home range) size
    • HR50: 50% minimum convex polygon (core range) size
    • Comp1: Loading values from morphology principal component analysis
    • Comp2: Loading values from morphology principal component analysis
    • Length: Fork length in mm
    • Weight: wet weight in g
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Stimulus: Whether a deterrent was active at the fishway during capture or not
    • Wetland: Whether individual breached the barrier
    • Detections: Number of detections
    • LabTrial: Trial number
    • Transmitter: Acoustic telemetry transmitter number
    • Month: month of detection
    • Detections: Number of detections of fish
    • TrackTime: Total time tracked per month

05 – Syndrome

• Syndrome_script1.1.R
  • This R script follows Houslay and Wilson 2017 to generate a MCMCglmm Multivariate Mixed Model to assess a possible behavioural syndrome across lab, field, and morphologyical metrics. Pairwise post-hoc correlations are assessed and visualized.
• Data
  • Data_syndrome1.1.csv: Output from Repeatability section. Summary statistics for repeatable behavioural metrics that may constitute a behavioural syndrome. All values have been standardized and rescaled, so values are unitless and can be compared within and amongst individuals and other behaviours.
    • PIT: PIT tag ID number
    • RepNumber: Number of repeats (lab trial) or month ID (telemetry)
    • Activity: Total movement. NAs for repeat numbers above 3, as there were only 3 trials.
    • Sociability: Time the fish spent interacting with the mirror recorded in seconds. NAs for repeat numbers above 3, as there were only 3 trials.
    • Boldness: Time fish spent in the refuge recorded in seconds. NAs for repeat numbers above 3, as there were only 3 trials.
    • Distance: Total distance travelled
    • Dispersal Distance between monthly center of activity and release site
    • Stelco: Distance between monthly center of activity and release site
    • HR95: 95% minimum convex polygon (home range) size
    • HR50: 50% minimum convex polygon (core range) size
    • Comp1: Loading values from morphology principal component analysis
    • Comp2: Loading values from morphology principal component analysis
    • Length: Fork length in mm
    • Weight: Wet weight in g
    • Treatment: Deterrent exposure treatment during capture at the RBG fishway
    • Stimulus: Whether a deterrent was active at the fishway during capture or not
    • Wetland: Whether individual breached the barrier
    • Detections: Number of detections
    • LabTrial: Trial number
    • Transmitter: Acoustic telemetry transmitter number
    • Month: Month of detection
    • Detections: Number of detections of fish
    • TrackTime: Total time tracked per month

Software

• R version 4.4.2 (2024-10-31)
  • Platform x86_64-w64-mingw32/x64