Assessing spawning behavior at the Northern latitudinal extreme of Pacific halibut
Data files
Apr 02, 2025 version files 195.84 MB
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Archived_Data_Plotting.R
7.49 KB
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CJFAS_Tagging_summary.xlsx
26.62 KB
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CJFAScode.r
20.22 KB
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Halibut_PSAT.zip
190.06 MB
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Maturity.zip
5.72 MB
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README.md
7.45 KB
Abstract
While modern stock assessment practice often assumes spawning dynamics are consistent across a population’s range, recent studies have shown that these can vary latitudinally. As a result, regional assessment of reproductive potential may be warranted for widely distributed species that are commercially exploited, such as the Pacific halibut (Hippoglossus stenolepis). To characterize Pacific halibut spawning dynamics at the northern extreme of their range, we attached pop-up satellite telemetry tags to large females in the Northern Bering Sea (NBS), with tag reporting locations and recorded time series data being used to infer spawning behavior and identify occupied spawning habitat conditions, location, and timing. Pacific halibut in the NBS spawned later and farther north than previously believed, where spawning habitat was occupied from January through May and reached as far north as the Russian continental shelf edge. Additionally, 54% of mature individuals never occupied presumed spawning habitat, suggesting the presence of skip spawning behavior. These findings indicate that current stock assessment practice may not accurately estimate Pacific halibut reproductive potential due to latitudinal variation in spawning dynamics.
Dataset DOI: 10.5061/dryad.612jm64cq
Description of the data and file structure
These data were collected using PSAT (miniPAT) tags attached to Pacific halibut in the Northern Bering Sea. This includes time series depth and temperature data, pop-up locations, and light data (which have been processed into longitude estimates). All tagging deployments are summarized in the provided tagging summary file.
Files and variables
File: CJFAS_Tagging_summary.xlsx
Description: This file (NBS tab) summarizes all tag deployments for Pacific halibut tagged during the study, and the data received from those deployments. The spawning tab contains only individuals that were included in spawning analyses within this manuscript, along with the data for those metrics.
Variables
- Tag: ID for the tag, with the wildlife computers PTT being used.
- Year: Year the tag was deployed.
- Date Deployed: Date the tag was deployed.
- Tagging Location: General location where the tag was deployed.
- Latitude: Latitude of tag deployment.
- Longitude: Longitude of tag deployment.
- Converted Long: Longitude of tag deployment in 0‑360 format.
- Fork Length: Fork length (cm) of the tagged halibut.
- Deployment Outcome: Result of the tagging deployment, with identifiers being described in the document. These provide a quick description of what data the tag provided.
- Pop-up Date: Date the tag released from the tagged fish.
- Latitude (pop): Latitude of tag pop-up location.
- Longitude (pop): Longitude of tag pop-up location.
- Converted Long (pop): Longitude of tag pop-up location in 0‑360 format.
- Useable Location: Yes/no on if the tag provided a pop-up location.
- Useable Time Series: Yes/no on if the tag provided time series data.
- Useable HMM: Yes/no on if the Hidden Markov model analysis could be used for the tag.
- Distance (km): Great circle distance between tag deployment and pop-up locations in km.
- Messages: Number of messages sent by the tag to receiving satellites.
- Spawner or Skipped: Designation on if the tagged halibut was determined to be a spawning or skipped spawning individual.
- Date reaching 200m: First day where recorded tag depth exceeded 200 m.
- Date leaving 200m: Last day where recorded tag depth exceeded 200 m.
- Duration below 200 m: Number of days between the date reaching and date leaving 200 m.
Empty cells indicate that data is unavailable, where the tag did not report successfully and therefore provided no information. Cells with NA AND NULL indicate “Not applicable”, due to a lack of data needed for assigning that variable.
File: Halibut_PSAT.zip
Description: This file contains all raw data utilized in this study. Halibut PSAT contains four folders, representing all data from each of the tagging years. Within each of these folders is a folder containing the data for each tag, which are labeled using the Tag ID from the tagging summary data sheet. The data within these folders are raw data outputs, and are all labeled using the Tag ID followed by qualifiers to identify the data contained within. These consist of:
- CSV outputs from Wildlife Computers
- Series, containing all transmitted depth and temperature time series data
- DailyData, containing daily summaries of Series data
- Locations, containing estimated latitudes and longitudes during tag transmissions
- MinMaxDepth, containing estimated minimum and maximum occupied depths based on all available data sources
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Processed and filtered longitude estimates (LightLoc_proc) from Wildlife Computers GPE2 software
- When available, complete data from physically recovered tags are provided. These are simply labeled as out-Archive in the respective tag folder.
Variables (Only those necessary are described here, as many raw argos outputs were not used/applicable/processed herein. Despite this, these data files were left complete as they were received)
- Deploy ID/Ptt: Same as Tag ID
- GeoDay: Day of year
- GeoLong: Estimated longitude from received light data
- Date/Day: Day of data recording (provided in different formats, needed for proper analyses in Rscripts
- MinTemp: Minimum temperature (°C) recorded during a day
- MinDepth: Minimum depth (m) recorded during a day
- MinAccuracy: Accuracy of depth recording (associated error) in meters
- MinSource: Data source from the tag data
- MaxTemp: Maximum temperature (°C) recorded during a day
- MaxDepth: Maximum depth (m) recorded during a day
- MaxAccuracy: Accuracy of depth recording (associated error) in meters
- MaxSource: Data source from the tag data
- Depth: Depth (m) recording from the tag (meters)
- Temperature: Temperature (°C) recording from the tag (Celsius)
Empty cells indicate that the data are unavailable, while empty columns represent data that was not provided when the data were downloaded from Argos. Currently, all Rscripts run and pull the necessary data from these data files.
File: Maturity.zip
Description: This folder contains survey data from the International Pacific Halibut Commission setline survey (available online for download at the IPHC website), which was used to estimate maturity at length. Results for fish tagged in the study are also provided (Maturity Output.xlsx).
Variables
- Stlkey: IPHC designation for sampling events
- Year: Year of sampling
- Station: Survey station of sampling
- Halkey: IPHC identifier for captured individuals
- Skate: Skate of capture for each individuals
- Fork Length: Fork length (cm) of individual
- Sex: Sex of individual (Male (m), Female (F), or Unidentified(U))
- Maturity: Maturity designation of individual as defined by the IPHC, with immature (1), mature (2), spawning (3), or resting (4) states being identified. Unidentified maturity status (U) is also designated.
- Age: Age of individual (when available)
- Length: Fork length (cm) of tagged halibut in this study
- Probability mature: estimated maturity probability for each tagged halibut based on the maturity curve generated within this study (CJFAScode.r)
Code/software
The only software required is R (version 4.3.1). Necessary packages are included in the provided scripts, but are primarily composed of ggplot2 and tidyverse.
The provided scripts are used to estimate halibut maturity and upload all series data obtained during this study (CJFAScode). The script can then be used to group these data by spawning and non-spawning individual, summarize the data, and visualize the data. The Archived Data Plotting.r script is specifically to access the data from physically recovered tags (out-Archive), and visualize these high resolution data. This includes looking at spawning rises, which can be visualized using the provided plotting code.
Hidden Markov Model code and outputs are not provided herein due to another manuscript discussing HMM methodology and results currently being in the review process. These are available upon reasonable request, and all data required for the HMM are provided herein. This includes the estimated longitudes in the LightLoc_proc files, as well as the depth data from the MinMaxDepth files.
The data was collected using satellite telemetry (PSAT's). The data was processed primarily by summarizing and visualizing archived data.