DOI: 10.5061/dryad.612jm64cq
title: Assessing spawning behavior at the Northern latitudinal extreme of Pacific halibut

description: 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.
description: The data was collected using satellite telemetry (PSAT's). 
 The data was processed primarily by summarizing and visualizing archived
 data.  
description: # Assessing spawning behavior at the Northern latitudinal extreme of
 Pacific halibut Dataset DOI:
 [10.5061/dryad.612jm64cq](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 - 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.