DOI: 10.5061/dryad.2280gb5z6
title: Data from: Alternative life-history strategy contributions to effective population size in a naturally spawning Salmon population

description: Alternative life history tactics are predicted to affect within-population
 genetic processes but have received little attention. For example, the
 impact of precocious males on effective population size (Ne) has not been
 quantified directly in Pacific salmon Oncorhynchus spp., even though they
 can make up a large percentage of the total male spawners. We investigated
 the contribution of precocial males ("jacks") to Ne in a
 naturally spawning population of Coho Salmon O. kisutch from the Auke
 Creek watershed in Juneau, Alaska. Mature adults that returned from 2009
 to 2019 (~8,000 individuals) were genotyped at 259 single-nucleotide
 polymorphism (SNP) loci for parentage analysis. We used demographic and
 genetic methods to estimate the effective number of breeders per year
 (Nb). Jack contribution to Nb was assessed by comparing values of Nb
 calculated with and without jacks and their offspring. Over a range of Nb
 values (108–406), the average jack contribution to Nb from 2009 to 2015
 was 12.9% (SE=3.8%). Jacks consistently made up over 20% of the total male
 spawners. The presence of jacks did not seem to influence Nb /N. The
 linkage disequilibrium Ne estimate was lower than the demographic
 estimate, possibly due to immigration effects on population genetic
 processes: based on external marks and parentage data, we estimated that
 immigrant spawners produced 4.5% of all returning offspring. Our results
 demonstrate that jacks can influence Nb and Ne and can make a substantial
 contribution to population dynamics and conservation of threatened stocks.
description: # Data from: Alternative life-history strategy contributions to effective
 population size in a naturally spawning salmon population ## Information
 for this README * File name: README.md * Authors: Erika M. King, Megan V.
 McPhee, Scott C. Vulstek, Curry J. Cunningham, Joshua R. Russell, and
 David A. Tallmon * Date created: 7/1/2023 * Date modified: 7/14/2023 ##
 Dataset Version and Release History * Current version: * Number: 1.0.0 *
 Date: 7/14/2023 * Persistent identified: DOI: 10.5061/dryad.2280gb5z6 *
 Summary of changes: n/a ## Dataset Attribution and Usage * Dataset Title:
 Dataset for the article "Alternative life-history strategy
 contributions to effective population size in a naturally spawning salmon
 population" * Dataset Contributors: * Creators: Erika M. King, Megan
 V. McPhee, Scott C. Vulstek, Curry J. Cunningham, Joshua R. Russell, and
 David A. Tallmon * Date of issue: 7/14/2023 * License: Use of these data
 is covered by the following license: * Title: Attribution 4.0
 International (CC BY 4.0) * Specification:
 [https://creativecommons.org/licenses/by/4.0/](https://creativecommons.org/licenses/by/4.0/); the authors respectfully request to be contacted by researchers interested in the re-use of these data so that the possibility of collaboration can be discussed. * Suggested Citations: * Dataset citation: &gt; King, E. M., M. V. McPhee, S. C. Vulstek, C. J. Cunningham, and J. R. Russell. 2023. Data for the article "Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population", Dryad, Dataset, [https://doi.org/10.5061/dryad.2280gb5z6](https://doi.org/10.5061/dryad.2280gb5z6). * Corresponding publication: &gt; King, E. M., M. V. McPhee, S. C. Vulstek, C. J. Cunningham, and J. R. Russell. 2023. Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population. Evolutionary Applications. [https://doi.org/10.1111/eva.13580](https://doi.org/10.1111/eva.13580) ## Contact Information * Name: Erika M. King * Email: [king.m.erika@gmail.com](mailto:king.m.erika@gmail.com) * Address: e-mail preferred * Affiliation: University of Alaska Fairbanks * ORCID ID: [https://orcid.org/0000-0002-4370-1056](https://orcid.org/0000-0002-4370-1056) * Alternative Contact: PI * Name: Megan V. McPhee * Email: [mvmcphee@alaska.edu](mailto:mvmcphee@alaska.edu) * Address: e-mail preferred * Affiliation: University of Alaska Fairbanks # Additional Dataset Metadata ## Acknowledgments * Funding sources: Alaska SeaGrant and Douglas Island Pink and Chum, Inc. ## Dates and Locations * Dates of data collection: Field data collected between May and December 2009-2020. * Geographic locations of data collection: Juneau Alaska, USA. # Methodological Information * Methods of data collection/generation: see manuscript for details # Data and File Overview ## Description This dataset contains the scripts and supplementary tables that support the findings of the article "Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population". The raw data that supports the findings of this study are available in the supplementary material of King et al. 2023 at [http://doi.org/10.1098/rsos.221271](http://doi.org/10.1098/rsos.221271). Citation for raw data: King Erika M., Tallmon David A., Vulstek Scott C., Russell Joshua R. and McPhee Megan V. 2023 Reproductive success of jack and full-size males in a wild coho salmon population. R. Soc. open sci. 10: 221271. 221271. [http://doi.org/10.1098/rsos.221271](http://doi.org/10.1098/rsos.221271). This study relies on data already published at the above citation: -Auke Creek Coho Salmon demographic and genetic data -Auke Creek Coho Salmon parentage results -Analysis of Auke Creek Coho Salmon strays and their reproductive success Using the demographic, genetic, parentage, and reproductive success data, we used the scripts and software in this repository to calculate the demographic and genetic effective number of breeders (Nb) and effective population size (Ne). See the details below for descriptions of what each file was used for. ## Summary Metrics * File count: 12 * File formats: .xlsx, .gen, .txt, .Rmd ## Naming Conventions * This manscript and dataset was the second objective of E. M. King's MS thesis, hence the file names include 'Objective_2'. ## Table of Contents * Objective_2_Analysis_Part_2.xlsx * Step_3_output_by.gen * Step_3_output_byLD.txt * Step_3_output_byNoDat.txt * age.in * gen_data_by_brood_year_2009-2015.gen * salmonNb_run_1_output * salmonNb_run_1_text.txt * Objective_2_Analysis.Rmd * Objective_2_Analysis_no_jacks.Rmd * Objective_2_Analysis_Part_2.Rmd * Objective_2_Analysis_Part_3.Rmd ## Setup * Unpacking instructions: n/a * Relationships between files/folders: Genetic_Analysis folder includes NeEstimator_LD_analysis (Step_3_output_by.gen, Step_3_output_byLD.txt, Step_3_output_byNoDat.txt) and SalmonNb_analysis (age.in, gen_data_by_brood_year_2009-2015.gen, salmonNb_run_1_output, salmonNb_run_1_text.txt). File Objective_2_Analysis_Part_2.xlsx is related to Objective_2_Analysis_Part_2.Rmd. ## Software Recommended software/tools: FRANz, SalmonNb, NeEstimator, Rstudio, and R version 4.0.3. * R / R Studio &gt; Analyses were performed using R Statistical Software (v4.0.3). &gt; Link for R software: [https://www.R-project.org/](https://www.R-project.org/) &gt; Citation for R software: R-Core-Team. 2020 R: A language and environment for statistical computing. R Foundation for Statistical Computing. * FRANz &gt; We used the program FRANz (Riester et al. 2009) to assign offspring to parents. See manuscript methods for more details. &gt; Link to FRANz software: [https://www.bioinf.uni-leipzig.de/Software/FRANz/About.html](https://www.bioinf.uni-leipzig.de/Software/FRANz/About.html) &gt; Citation for FRANz software: Riester, M., Stadler, P. F., Klemm, K. 2009 FRANz: Reconstruction of wild multi-generation pedigrees. Bioinformatics. 25, 2134-2139. (10.1093/bioinformatics/btp064) * SalmonNb &gt; We estimated the effective number of breeders using the linkage disequilibrium (LD) method (NbLD) (Hill 1981; Waples 2006b; Waples & Do 2008) as implemented in NeEstimator V2.1 (Do et al. 2014). See manuscript methods for more details. &gt; Citation for SalmonNb software: Waples, R.S., M. Masuda, and J. Pella. 2007. SALMONNb: A program for computing cohort-specific effective population sizes (Nb) in Pacific salmon and other semelparous species using the temporal method. Mol. Ecol. Notes. 7(1):21–24. * NeEstimator &gt; We estimated the effective number of breeders using the temporal method of Waples et al. (2007) in the program SALMONNb (NbS). &gt; Citation for NeEstimator software: Do, C., R.S. Waples, D. Peel, G.M. Macbeth, B.J. Tillett, and J.R. Ovenden. 2014. NeEstimator v2.0: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol. Ecol. Resour. 14(1):209–214. # File/Folder Details ## Details for Objective\_2\_Analysis\_Part\_2.xlsx * Description: Excel sheet that includes the composite life tables for Auke Creek Coho Salmon used to calculate Nb, generation length, and Ne. This excel sheet relies on the output of the script Objective_2_Analysis_Part_2.Rmd. The census population size, mean number of offspring produced, and variance in offspring produced were used to create these tables. See the methods of the manuscript for more details. There are three scenarios represented, and each has it's own tab. The first tab titled "coho_composite_sc1", is the only tab whose results were used in the manuscript. * Format(s): .xlsx * Size(s): 22 KB * Dimensions: n/a * Variables: N: Number of individuals (all age classes). Nx: Number of individuals in each age class. Age: Age of individuals in an age class (years). kbar: Mean number of offspring produced per individual. bx: Mean number of offspring produced by an individual in an age class. Bx: Total number of offspring produced by an age class. Vx: Variance in number of offspring produced by an age class. b’x: Mean number of offspring produced by an individual in an age class for a stable population. Bx’: Total number of offspring produced by an age class for a stable population. V’x: Variance in number of offspring produced by an age class for a stable population. Relcont: Relative contribution of total offspring produced by an age class (Bx’/sum(Bx’)). j: jack fsm: full-size male CV: Coefficient of variation * Other details: Blank/empty cells have no meaning. This is a workbook and not a .csv file. The workbook has multiple tables and calculations for various parameters. Please contact the author if you would like additional details. ## Details for Genetic\_Analysis folder # NeEstimator\_LD\_analysis * Step_3_output_by.gen * Description: Input data for NeEstimator. Data is formatted as a .gen file as required for NeEstimator. Data includes individuals grouped by brood year from 2009 to 2015. See methods in manuscript for more details. * Format(s): .gen * Size(s): 5.8 MB * Dimensions: n/a * Variables: n/a * Other details: n/a * Step_3_output_byLD.txt * Description: Output file automatically generated from NeEstimator. The file includes effective population size values (Estimated Ne) for each year from 2009 to 2015. We used the Lowest Allele Frequency Used of 0.050. See the manuscript methods for additional details. * Format(s): .txt * Size(s): 11 KB * Dimensions: n/a * Variables: n/a * Other details: n/a * Step_3_output_byNoDat.txt * Description: Output file automatically generated from NeEstimator. This file was not used in the manuscript. See NeEstimator manual and instructions for more details. * Format(s): .txt * Size(s): 241 KB * Dimensions: n/a * Variables: n/a * Other details: n/a # SalmonNb\_analysis * age.in * Description: Input file for SalmonNb with age distribution (ages 2-4) and years of data included (2009-2015). See SalmonNb manual and instructions for more details. * Format(s): .txt * Size(s): 55 bytes * Dimensions: n/a * Variables: n/a * Other details: n/a * gen_data_by_brood_year_2009-2015.gen * Description: Input data for SalmonNb. Data is formatted as a .gen file as required for SalmonNb. Data includes individuals grouped by brood year from 2009 to 2015. See methods in manuscript for more details. * Format(s): .gen * Size(s): 5.8 MB * Dimensions: n/a * Variables: n/a * Other details: n/a * salmonNb_run_1_output * Description: Output results from SalmonNb. We used the data under the heading "Excluding relative allele frequencies &lt; 0.050000" titled "Least-squares estimates of Nb per year". See SalmonNb methods and instructions and our manuscript methods for more details. * Format(s): .txt * Size(s): 260 KB * Dimensions: n/a * Variables: n/a * Other details: n/a * salmonNb_run_1_text.txt * Description: This file includes the run commands we used while using SalmonNb. We computed pairwise estimates of Nb from a single genotypic data file and excluded low-frequency alleles. See SalmonNb methods and instructions and our manuscript methods for more details. * Format(s): .txt * Size(s): 611 bytes * Dimensions: n/a * Variables: n/a * Other details: n/a ## Details for Objective\_2\_Analysis.Rmd * Description: This script was used to estimate the demographic effective number of breeders and population size of Auke Creek Coho Salmon. * Format(s): .Rmd * Size(s): 57 KB * Dimensions: n/a * Variables: n/a * Other details: This script uses files (number_offspring_per_parent.csv, COAUKE_Demographic_Info.csv, concat_franz.csv, and COAUKE_Genotypes_Info.csv) that can be found in the supplementary material of King et al 2023 at [http://doi.org/10.1098/rsos.221271](http://doi.org/10.1098/rsos.221271). Please see the script and manuscript methods for more details. ## Details for Objective\_2\_Analysis\_no\_jacks.Rmd * Description: This script was used to investigates the influence of removing jacks on the effective number of breeders and population size of Auke Creek Coho Salmon. This script is based on the analysis of Objective_2_Analysis.Rmd. * Format(s): .Rmd * Size(s): 17 KB * Dimensions: n/a * Variables: n/a * Other details: This script uses files (number_offspring_per_parent.csv, COAUKE_Demographic_Info.csv, concat_franz.csv, and COAUKE_Genotypes_Info.csv) that can be found in the supplementary material of King et al 2023 at [http://doi.org/10.1098/rsos.221271](http://doi.org/10.1098/rsos.221271). Please see the script and manuscript methods for more details. ## Details for Objective\_2\_Analysis\_Part\_2.Rmd * Description: This script creates life tables for Auke Creek Coho Salmon. This script was the first step in creating the composite life tables used in Objective_2_Analysis_Part_2.xlsx. * Format(s): .Rmd * Size(s): 24 KB * Dimensions: n/a * Variables: n/a * Other details: This script uses files (number_offspring_per_parent.csv, COAUKE_Demographic_Info.csv, and concat_franz.csv) that can be found in the supplementary material of King et al 2023 at [http://doi.org/10.1098/rsos.221271](http://doi.org/10.1098/rsos.221271). Please see the script and manuscript methods for more details. ## Details for Objective\_2\_Analysis\_Part\_3.Rmd * Description: This script was used to compare genetic and demographic estimates of the effective number of breeders and effective population sizes of Auke Creek Coho Salmon. * Format(s): .Rmd * Size(s): 8 KB * Dimensions: n/a * Variables: n/a * Other details: This script uses results from Objective_2_Analysis.Rmd, Objective_2_Analysis_no_jacks.Rmd, Step_3_output_byLD.txt, and salmonNb_run_1_output.