DOI: 10.5061/dryad.bzkh189pw
title: Assessing the effects of changes in reproductive condition on the survival of anadromous Dolly Varden (<em>Salvelinus malma</em>) using Bayesian multistate capture-recapture modelling

description: Understanding the interrelationship between the survival and reproductive
 states of salmonids is important for both management and conservation
 purposes; however, their complex life history introduces challenges. The
 survival probabilities of anadromous Dolly Varden (Salvelinus malma) are
 influenced by their reproductive cycle, while predicting their
 reproductive state in successive years is difficult, as it can vary based
 on an individual's sex. We developed a Bayesian multi-state
 capture-recapture model that estimates reproductive state transition
 probabilities, survival probabilities, and the effect of sex on state
 transitions using the Cormack-Jolly-Seber model. We applied the model to
 Dolly Varden data collected from five river systems in the western
 Canadian Arctic. We demonstrate sex-specific state transition probability
 differences, with females exhibiting higher transition rates into
 reproductive states. Moreover, survival probabilities were influenced by
 both sex and reproductive status. Across all rivers, survival
 probabilities for both sexes decreased by approximately 50% while spawning
 compared to non-spawning. This study provides important insights into how
 reproduction and sex affect survival among stocks, which improves their
 assessment to ensure management and conservation goals.
description: # Assessing the effects of changes in reproductive condition on the
 survival of anadromous Dolly Varden (*Salvelinus malma*) using Bayesian
 multistate capture-recapture modelling Dataset DOI:
 [10.5061/dryad.bzkh189pw](10.5061/dryad.bzkh189pw) ## Description of the
 data and file structure The data were collected through long-term
 monitoring efforts conducted by Fisheries and Oceans Canada (DFO) on
 Northern Dolly Varden (*Salvelinus malma malma*) populations in the
 western Canadian Arctic rivers of the Yukon and Northwest Territories.
 Sampling years varied by river: * Firth River (2014–2020) * Joe Creek
 (2014–2020) * Babbage River (2010–2020) * Big Fish River (2009–2020) * Rat
 River (2007–2020) Fish were captured annually using seine nets, tagged,
 and released, with sex (if identified) and reproductive state recorded at
 the time of capture. These capture–recapture data were collected to study
 survival and reproductive patterns of Dolly Varden, a species of cultural
 and subsistence importance to local communities. ### Files and variables
 All variables are Fall_YYYY, and in some files, the sex of the individual.
 #### File: Big_Breeding_Data.csv **Description:** Each column represents a
 different sampling year, where 1 indicates a capture as a spawner, 2
 indicates a capture as a non-spawner, and 0 indicates not captured, for
 the Big Fish River. #### File: Big_Breeding_Sex_Data.csv
 **Description:** Each column represents a different sampling year, where 1
 indicates a capture as a spawner, 2 indicates a capture as a non-spawner,
 and 0 indicates not captured, for the Big Fish River. The sex column
 contains 1 for males, 0 for females, and NA for unknowns. #### File:
 Big_Capture_Data.csv **Description:** Each column represents a different
 sampling year, where 1 indicates captured and 0 indicates not captured,
 for the Big Fish River. #### File: Babbage_Capture_Data.csv
 **Description:** Each column represents a different sampling year, where 1
 indicates captured and 0 indicates not captured, for the Babbage River.
 #### File: Babbage_Breeding_Data.csv **Description:** Each column
 represents a different sampling year, where 1 indicates a capture as a
 spawner, 2 indicates a capture as a non-spawner, and 0 indicates not
 captured, for the Babbage River.  #### File: Babbage_Breeding_Sex_Data.csv
 **Description:** Each column represents a different sampling year, where 1
 indicates a capture as a spawner, 2 indicates a capture as a non-spawner,
 and 0 indicates not captured, for the Babbage River. The sex column
 contains 1 for males, 0 for females, and NA for unknowns. #### File:
 Firth_Breeding_Data.csv **Description:** Each column represents a
 different sampling year, where 1 indicates a capture as a spawner, 2
 indicates a capture as a non-spawner, and 0 indicates not captured, for
 the Firth River. #### File: Firth_Breeding_Sex_Data.csv
 **Description:** Each column represents a different sampling year, where 1
 indicates a capture as a spawner, 2 indicates a capture as a non-spawner,
 and 0 indicates not captured, for the Firth River. The sex column contains
 1 for males, 0 for females, and NA for unknowns. #### File:
 Firth_Capture_Data.csv **Description:** Each column represents a different
 sampling year, where 1 indicates captured and 0 indicates not captured,
 for the Firth River. #### File: Joe_Capture_Data.csv **Description:** Each
 column represents a different sampling year, where 1 indicates captured
 and 0 indicates not captured, for Joe Creek. #### File:
 Joe_Breeding_Data.csv **Description:** Each column represents a different
 sampling year, where 1 indicates a capture as a spawner, 2 indicates a
 capture as a non-spawner, and 0 indicates not captured, for Joe Creek.
 #### File: Joe_Breeding_Sex_Data.csv **Description:** Each column
 represents a different sampling year, where 1 indicates a capture as a
 spawner, 2 indicates a capture as a non-spawner, and 0 indicates not
 captured, for Joe Creek. The sex column contains 1 for males, 0 for
 females, and NA for unknowns. #### File: Rat_Capture_Data.csv
 **Description:** Each column represents a different sampling year, where 1
 indicates captured and 0 indicates not captured, for the Rat River. ####
 File: Rat_Breeding_Sex_Data.csv **Description:** Each column represents a
 different sampling year, where 1 indicates a capture as a spawner, 2
 indicates a capture as a non-spawner, and 0 indicates not captured, for
 the Rat River. The sex column contains 1 for males, 0 for females, and NA
 for unknowns. #### File: Rat_Breeding_Data.csv **Description:** Each
 column represents a different sampling year, where 1 indicates a capture
 as a spawner, 2 indicates a capture as a non-spawner, and 0 indicates not
 captured, for the Rat River. #### File: Dolly_Varden_Codes.zip
 **Description:** This zip file contains the R codes for each river and
 each model presented in the manuscript, organized separately. It also
 includes a folder named **"Prior Sensitivity"**, which contains
 two subfolders: **"Model 2 Codes"** and **"Model 3
 Codes"**. Each of these subfolders provides R codes for analyses
 using alternative priors (Beta(1,2) and Beta(2,1)) explored in this study.
 In addition, the zip file includes the R codes for the simulation studies
 conducted for Models 2 and 3. ## Code/software All data files are provided
 in CSV format, which can be opened with Microsoft Excel or any open-source
 spreadsheet software (e.g., LibreOffice Calc). All scripts used for data
 processing and analysis are included in the **“Dolly_Varden_Codes.zip”**
 folder. Analyses were conducted in **R (version 4.5.1)**. The primary R
 packages used were: * **nimble** – for Bayesian modeling and MCMC
 simulations * **tidyverse** – for data cleaning and manipulation *
 **MCMCvis** – for summarizing and visualizing MCMC outputs The workflow
 involves data cleaning with *tidyverse*, model fitting with *nimble*, and
 post-modeling summaries and diagnostics with *MCMCvis*. The scripts are
 organized to clearly show the sequence of steps from raw data to final
 results. ## Access information Other publicly accessible locations of the
 data: * NA Data was derived from the following sources: * NA