Data from: Spatiotemporal variation in marine mammal antipredator behaviors resulting from a predation pinch point
Data files
Feb 09, 2026 version files 879.51 MB
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2008044_iknos_raw_data.csv
30.37 MB
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2009040_iknos_raw_data.csv
30.39 MB
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2011014_iknos_raw_data.csv
30.41 MB
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2014019_iknos_raw_data.csv
30.34 MB
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data_dive_RSB_2025_10_29.rds
191.47 MB
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data_wrangling_RSB_2025_10_29.qmd
9.80 KB
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dist2land_tweak.R
4.24 KB
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FiguresForMS_11_21_2025_RSB.qmd
93.40 KB
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orca_area.kml
2.21 KB
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R_Table.png
344.87 KB
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README.md
10.44 KB
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shark_area.kml
1.78 KB
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TV4_DiveStatType_CMH_2025_07_14.txt
566.04 MB
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TV4_SealInfo_CMH_2025_07_14.txt
15.60 KB
Abstract
Predator-prey relationships are fundamental aspects of ecological systems that determine the behavior and distribution of animals across time and space. Variation in predation risk can be used to explore when and why individuals perform antipredator behaviors. In marine environments, it is difficult to observe predation and antipredator behaviors. Fortunately, biologgers have long been used to study the distribution and dive behaviors of northern elephant seals (Mirounga angustirostris) on their twice-yearly foraging trips. Here, we analyzed the horizontal and vertical movements of 353 adult female seals across 17 years to investigate how they move through a “predation pinch point” - an area where predators and prey co-occur due to habitat features. Specifically, we explored the diel timing of departure from and arrival to the colony and spatial concentrations in benthic diving (diving close to/along the seafloor). Benthic diving and temporal concentrations in movement to and from the colony may serve antipredator functions, such as minimizing detection and ambush by predators. We found that only the timing of departure from, and not arrival to, the colony showed any significant temporal pattern. Seals tended to depart during the late afternoon or at night but arrived throughout the day. Spatially, there were consistent patterns of benthic dives during the first and final parts of their trips as seals crossed the continental shelf. By combining dive, location, bathymetry, and predator data we were able to identify how seals modified behaviors that likely help them avoid predators. These findings illustrate how animals respond to varying levels of predation risk and can be used to develop more precise dynamic landscapes of fear.
Dataset DOI: 10.5061/dryad.mkkwh71bh
Publication DOI: https://doi.org/10.1002/ece3.72841
Description of the data and file structure
Summary
This repository contains the code used to create figures in Hale et al., 2026
The script 'FiguresForMS_11_21_2025_RSB.qmd" contains the tools/functions necessary to recreate the figures in the associated manuscript.
Preliminary steps [in 'data_wrangling_RSB_2025_10_29.qmd'] are required to ensure that the data is processed correctly and that bathymetry and predator data are included.
Files and variables
Data File Details
Details for: TV4_DiveStatType_CMH_2025_07_14.txt
Description: a .txt file containing raw data that was processed for analysis. This file can be opened in any plain text editor. Data are separated by commas.
Variables within 'TV4_DiveStatType_CMH_2025_07_14.txt':
- id = seal identification code (a seven-digit number [e.g., 2004001] where the first two digits designate the species [20 is northern elephant seal], digits 3-4 indicate the year [e.g., 04 is 2004], and digits 5–7 are the deployment serial number [001 is the first deployment for a given year and species])
- DiveNumber = count of the dive
- JulDate = Julian date; extracted from MATLAB and converted to POSITXct time using the function in 'data_wrangling_RSB 2025_10_29.qmd'
- Maxdepth = maximum depth reached during the associated DiveNumber (i.e., dive 1 was 36 meters, dive 2 was 48.5 meters, etc.); measured in meters
- Dduration = dive duration for the associated dive (i.e., dive 1 was 624 seconds, dive 2 was 576 seconds, etc.); measured in seconds
- Bottime = bottom time for the associated dive; measured in seconds
- DescRate, AscRate = descent and ascent rates for the associated dive; measured in m/s
- PDI (post-dive interval) = time spend at the surface following the prior dive (e.g., dive 1 was 624 seconds and the post-dive interval was 64 seconds); measured in seconds
- DateTime = date and time of associated dive; DD-M-YYYY, HH:MM:SS
- Lat = latitude of associated dive
- Long = longitude of associated dive
- Lat_se_km, Lon_se_km = standard error associated with latitude/longitude of associated dive; measured in km
- SolarEl = angle of solar elevation during the associated dive; units are degrees
- Lon360 = converts longitude values from -180;180 to 0:360 (see https://dankelley.github.io/oce/reference/lon360.html)
- DiveTypeName = name type of the associated dive; determined as described in the manuscript
Details for: data_wrangling_RSB_2025_10_29.qmd
Description: a quarto markdown file containing the tools/functions necessary to recreate the figures in the associated manuscript. This file can be opened using RStudio (ver. 2023.06).
Variables within 'data_wrangling_RSB_2025_10_29.qmd':
- TV4_DiveStatType_CMH_2025_07_14.txt = described above
- shark_area.kml = described in detail below
- orca_area.kml = described in detail below
- dist2land_tweak.R = described in detail below
Details for: FiguresForMS_11_21_2025_RSB.qmd
Description: a quarto markdown file containing the tools/functions necessary to recreate the figures in the associated manuscript. This file can be opened using RStudio (ver. 2023.06).
Variables within 'FiguresForMS_11_21_2025_RSB.qmd':
- data_dive_RSB_2025_10_29.rds = described in detail below
Details for: *_iknos_raw_data.csv
Description: .csv files containing the raw time-depth records for the four seals included in Figure 1. Files are included separately as: 2008044_iknos_raw_data.csv, 2009040_iknos_raw_data.csv, 2011014_iknos_raw_data.csv, and 2014019_iknos_raw_data.csv.
Variables within '*_iknos_raw_data.csv':
- CorrectedDepth = corrected depth of the recorded dive (for more information about this please see Costa et al., 2024); in meters
- time = time the dive took place; must be converted to POSIX time (there is a function to do this in 'FiguresForMS_11_21_2025_RSB.qmd')
- depth = depth of the recorded dive; in meters
Details for: data_dive_RSB_2025_10_29.rds
Description: an RSD file that is the output of 'data_wrangling_RSB_2025_10_29.qmd'. This file can be opened in RStudio (ver. 2023.06) using the readRDS() function.
Variables within 'data_dive_RSB_2025_10_29.rds':
- id = seal identification code (a seven-digit number [e.g., 2004001] where the first two digits designate the species [20 is northern elephant seal], digits 3-4 indicate the year [e.g., 04 is 2004], and digits 5–7 are the deployment serial number [001 is the first deployment for a given year and species])
- DiveNumber = count of the dive
- JulDate = Julian date; extracted from MATLAB and converted to POSITXct time using the function in 'data_wrangling_RSB 2025_10_29.qmd'
- Maxdepth = maximum depth reached during the associated DiveNumber (i.e., dive 1 was 36 meters, dive 2 was 48.5 meters, etc.); measured in meters
- Dduration = dive duration for the associated dive (i.e., dive 1 was 624 seconds, dive 2 was 576 seconds, etc.); measured in seconds
- Bottime = bottom time for the associated dive; measured in seconds
- DescRate, AscRate = descent and ascent rates for the associated dive; measured in m/s
- PDI (post-dive interval) = time spend at the surface following the prior dive (e.g., dive 1 was 624 seconds and the post-dive interval was 64 seconds); measured in seconds
- DateTime = date and time of associated dive; YYYY-MM-DD, HH:MM:SS
- Lat = latitude of associated dive
- Long = longitude of associated dive
- Lat_se_km, Lon_se_km = standard error associated with latitude/longitude of associated dive; measured in km
- SolarEl = angle of solar elevation during the associated dive; units are degrees
- Lon360 = converts longitude values from -180;180 to 0:360 (see https://dankelley.github.io/oce/reference/lon360.html)
- DiveTypeName = name type of the associated dive; determined as described in the manuscript
- BirthYear = year in which the associated seal was born
- SatTagType = type of satellite tag used during the deployment; described in the methods
- GPSRows = used to determine if GPS was used as well; described in methods
- DepartLoc, ArriveLoc = departure and arrival locations; has been pre-filtered to only include ANNU (Año Nuevo)
- DepartCalcMass = mass at departure for each seal; in kilograms
- trip = foraging trip type; either Post Breeding or Post Molting
- bathy = bathymetry measurement for the associated dive
- dist_dep = distance from Año Nuevo during associated dive; measured in km (used for Figure 5B)
- shark_area, orca_area, shark_and_orca, shark_or_orca = presence or absence of seals in associated area for each associated dive; 1 = presence and 0 = absence
Details for: TV4_SealInfo_CMH_2025_07_14.txt
Description: a .txt file with information used in 'FiguresForMS_11_21_2025_RSB.qmd' and 'data_wrangling_RSB_2025_10_29.qmd'. This file can be opened in any plain text editor. Data are separated by commas.
Variables within 'TV4_SealInfo_CMH_2025_07_14.txt':
- id = seal identification code (a seven-digit number [e.g., 2004001] where the first two digits designate the species [20 is northern elephant seal], digits 3-4 indicate the year [e.g., 04 is 2004], and digits 5–7 are the deployment serial number [001 is the first deployment for a given year and species])
- BirthYear = year the seal was born
- SatTagType = type of tag the seal was equipped with; described in methods
- GPSRows; used to determine if the satellite tag used Argos + GPS or only Argos; described in methods
- DepartLoc, ArriveLoc = departure and arrival locations; is later filtered to only include ANNU (Año Nuevo)
- DepartCalcMass = mass at departure for each seal; in kilograms
- trip = foraging trip type; either Post Breeding or Post Molting
Details for: R_Table.png
Description: a .png file with packages using in R; pulled from the grateful package
Details for: dist2land_tweak
Description: an R script file with code to adjust the data for Figure 5B in the associated publication; used in 'data_wrangling_RSB 2025_10_29.qmd'. This file can be opened using RStudio (ver. 2023.06).
Details for: orca_area.kml
Description: a .kml file (extracted from Google Earth) with the distribution of mammal eating orca's (adapted from Jorgensen et al., 2019); used in 'data_wrangling_RSB 2025_10_29.qmd'. This file can be opened in Google Earth Pro (ver. 7.6.3) or by using https://kmzview.com/.
Details for: shark_area.kml
Description: a .kml file (extracted from Google Earth) with the distribution of white sharks (adapted from Jorgensen et al., 2019); used in 'data_wrangling_RSB 2025_10_29.qmd'. This file can be opened in Google Earth Pro (ver. 7.6.3) or by using https://kmzview.com/.
Code/software
Data processing methods are well described in Costa et al., 2024. Secondary processing and figure creation was done in RStudio (ver. 2023.06). The script 'FiguresForMS_11_21_2025_RSB.qmd' contains the tools/functions necessary to recreate the figures in the associated manuscript. Please note that preliminary steps (in 'data_wrangling_RSB_2025_10_29.qmd') are required to ensure that the data is processed correctly and that bathymetry and predator data are included. A table that includes the R packages is included in the files (R_Table.png).
Access information
Data was derived from the following sources:
- Costa, D. P., Holser, R. R., Keates, T. R., Adachi, T., Beltran, R. S., Champagne, C. D., ... & Yoda, K. (2024). Two decades of three-dimensional movement data from adult female northern elephant seals. Scientific Data, 11(1), 1357.
We gratefully acknowledge the work the University of California Santa Cruz, Sonoma State University, and Tagging of Pacific Predators Program teams did to produce this rich dataset.
Full funding information for the dataset can be found in Costa et al., 2024
