DOI: 10.5061/dryad.280gb5mxx
title: Supplementary data for: Outmigrating central valley Chinook Salmon

description: Intraspecific diversity plays a critical role in the resilience of Chinook
 salmon populations. California’s Central Valley historically hosted one of
 the most diverse population complexes of Chinook salmon in the world.
 However, anthropogenic factors have dramatically decreased this diversity,
 with severe consequences for population resilience. Here we use next
 generation sequencing and an archive of thousands of tissue samples
 collected across two decades during the juvenile outmigration to evaluate
 phenotypic diversity between and within populations of Central Valley
 Chinook salmon. To account for highly heterogeneous sample qualities in
 the archive dataset, we develop and test an approach for population and
 subpopulation assignments of Central Valley Chinook salmon that allows
 inclusion of relatively low-quality samples while controlling error rates.
 We find significantly distinct outmigration timing and body size
 distributions for each population and subpopulation. Within the archive
 dataset, spring run individuals that assigned to the Mill and Deer Creeks
 subpopulation exhibited an earlier and broader outmigration distribution
 as well as larger body sizes than individuals that assigned to the Butte
 Creek subpopulation. Within the fall run population, individuals that
 assigned to the late-fall run subpopulation also exhibited an earlier and
 broader outmigration distribution and larger body sizes than other fall
 run fish in our dataset. These results highlight the importance of
 distinct subpopulations for maintaining remaining diversity in Central
 Valley Chinook salmon, and demonstrates the power of genomics-based
 population assignments to aid the study and management of intraspecific
 diversity.
description: # Outmigrating Central Valley Chinook Salmon Access this data on Dryad
 (DOI: 10.5061/dryad.280gb5mxx) This Dryad entry contains data files and
 scripts used for analyses in Thompson et al. 2024 (Evolutionary
 Applications). Briefly, the study examines outmigration characteristics of
 juvenile Chinook salmon collecte d at Chipps Island in the Sacramento/San
 Joaquine Delta by assigning each sample to a population of origin. The
 analysis is broken down into three parts: 1) leave-one-out analyses to
 develop a population assignme nt method and evaluate its expected
 efficacy; 2) validation of the assignment method using an independent
 dataset of known-origin samples; 3) population assignment of
 unknown-origin juvenile samples collected at Chipps Island (and obtained
 from a tissue archive). This Dryad entry contains files and scripts
 necessary for that analysis, as well as the resulting output files. ##
 Data Files The following are descriptions of all data files uploaded here.
 (Note: the single read call files described below were generated from
 sequencing data using the program ANGSD
 ([https://www.popgen.dk/angsd/index.php/ANGSD](https://www.popgen.dk/angsd/index.php/ANGSD) version0.935). See Methods in Thompson et al. (2024) for full descripton of sequencing data sources/generation.) ### trainingset\_allruns\_filtered.snp\_panel.singlereadcalls.csv File with allele calls from single read sampling for all samples in the training set (sequencing data available from Meek et al., 2020) at each site in the SNP panel. Each line contains data for one SNP in the SN P panel. Allele calls are coded as 0 for the major allele, 1 for the minor allele, and -1 for missing data. See below for an explanation of column labels: **chr** Chromosome where the SNP for that line is located **pos** Position of the SNP on the chromosome **major** The major allele in A,C,G,T format **minor** The minor allele in A,C,G,T format **ind[#]** All following columns contain allele call data for individual samples. Column name corresponds to sample ID. See trainingset_allruns_filtered.pop_key.csv for specific information on each sample. ### trainingset\_allruns\_filtered.pop\_key.csv File linking training set sample IDs to true populations and subpopulations of origin. See below for column descriptions: **ibs_file_id** Sample IDs corresponding to file names in trainingset_allruns_filtered.snp_panel.singlereadcalls.csv **sample** Original sample names from Meek et al., 2020 **major_pop1** Population of origin relevant for the first population assignment step described in this manuscript **major_pop2** Population of origin relevant for the second population assignment step described in this manuscript **sup_pop** Subpopulation of origin **minor_sub_pop** Minor subpopulation of origin for individuals whose sub_pop = WildSpring_MillDeer (members of other subpopulations have NA listed in this column) ### leave\_one\_out.maj\_pop\_1.results.csv Concatenated results file containing info and population assignment posterior probabilities for the leave-one-out analysis of assignment step 1 (Winter vs. fall/late-fall/WildSpring). See below for column descrip tions: **Individual** sample ID corresponding to the IDs in trainingset_allruns_filtered.pop_key.csv **Missingness** The proportion of missing allele calls (e.g., 0.2 = 20% missing data) **Post.Fall_LateFall_WildSpring** The posterior probability from DAPC of assignment to the Fall/Late-fall/WildSpring population **Post.Winter** The posterior probability from DAPC of assignment to the Winter population **True_pop** The true population of origin for the given sample ### leave\_one\_out.maj\_pop\_2.results.csv Concatenated results file containing info and population assignment posterior probabilities for the lea ve-one-out analysis of assignment step 2 (Fall/Late-fall vs. Wild Spring). See below for column descriptions: **Individual** sample ID corresponding to the IDs in trainingset_allruns_filtered.pop_key.csv **Missingness** The proportion of missing allele calls (e.g., 0.2 = 20% missing data) **Post.Fall_LateFall** The posterior probability from DAPC of assignment to the Fall/L **ate-fall population** **Post.WildSpring** The posterior probability from DAPC of assignment to the Wild Spring population **True_pop** The true population of origin for the given sample ### leave\_one\_out.subpop\_sprButte\_V\_sprMillDeer.results.csv Concatenated results file containing info and population assignment posterior probabilities for the lea ve-one-out analysis of assignment step 3a (Spring Butte vs. Spring Mill/Deer). See below for column descriptions: **Individual** Sample ID corresponding to the IDs in trainingset_allruns_filtered.pop_key.csv **Missingness** The proportion of missing allele calls (e.g., 0.2 = 20% missing data) **Post.WildSpring_Butte** The posterior probability from DAPC of assignment to the Wild Spring Butte subpopulation **Post.WildSpring_MillDeer** The posterior probability from DAPC of assignment to the Wild Spring Mill/Deer subpopulation **True_pop** The true subpopulation of origin for the given sample ### leave\_one\_out.subpop\_fall\_V\_latefall.results.csv Concatenated results file containing info and population assignment posterior probabilities for the lea ve-one-out analysis of assignment step 3b (fall vs. late-fall). See below for column descriptions: **Individual** sample ID corresponding to the IDs in trainingset_allruns_filtered.pop_key.csv **Missingness** The proportion of missing allele calls (e.g., 0.2 = 20% missing data) **Post.Fall** The posterior probability from DAPC of assignment to the Fall subpopulation **Post.LateFall** The posterior probability from DAPC of assignment to the Late Fall subpopulation **True_pop** The true subpopulation of origin for the given sample ### validation\_set.snp\_panel.singlereadcalls.csv File with allele calls from single read sampling for all samples in the validation dataset (sequencing data available from Baerwald et al., 2023) at each site in the SNP panel. Each line contains data for one SNP in the SNP panel. Allele calls are coded as 0 for the major allele, 1 for the minor allele, and -1 for missing data. See below for descriptions of column labels: **chr** Chromosome where the SNP for that line is located **pos** Position of the SNP on the chromosome **major** The major allele in A,C,G,T format **minor** The minor allele in A,C,G,T format **ind[#]** All following columns contain allele call data for individual samples. Column name corr esponds to sample ID. See validation_set..pop_key.csv for specific information on each sample. ### validation\_set.pop\_key.csv File linking validation set sample IDs to true populations and subpopulations of origin. See below for column descriptions: **singleread_file_id** Sample IDs corresponding to file names in validation_set.snp_panel.singlereadcalls.csv **sample** Original sample names from Baerwald, et al. (2023) **major_pop1** Population of origin relevant for the first population assignment step described in this manuscript **major_pop2** Population of origin relevant for the second population assignment step described in this **manuscript** **sup_pop** Subpopulation of origin **minor_sub_pop** Minor subpopulation of origin for individuals whose sub_pop = WildSpring_MillDeer (members of other subpopulations have NA listed in this column) ### validation\_set.assignment\_results.csv File containing validation dataset population assignment results. See below for column descriptions: **Sample** Sample IDs corresponding to file names in validation_set.pop_key.csv. **Fall_LateFall_WildSpring** The posterior probability from DAPC of assignment to the Fall/Late-fall/WildSpring population in assignment step 1. **Winter** The posterior probability from DAPC of assignment to the Winter population in assignment step 1. **Fall_LateFall** The posterior probability from DAPC of assignment to the Fall/Late-fall population in assignment step 2. **WildSpring** The posterior probability from DAPC of assignment to the WildSpring population in assignment step 2. **WildSpring_Butte** The posterior probability from DAPC of assignment to the WildSpring Butte subpopulation in assignment step 3a. **WildSpring_MillDeer** The posterior probability from DAPC of assignment to the WildSpring Mill/Deer subpopulation in assignment step 3a. **Fall** The posterior probability from DAPC of assignment to the Fall subpopulation in assignment step 3b.\ **LateFall** The posterior probability from DAPC of assignment to the Late-Fall subpopulation in assignment step 3b. **Missingness** The proportion of missing data for the sample from the validation_set.snp_panel.singlereadcalls.csv file (e.g. 0.61 = 61% missing allele calls) **Maj.pop1.Call** Population call based on the greatest posterior assignment probability for assignment step 1. **Maj.pop2.Call** Population call based on the greatest posterior assignment probability for assignment step 2 (note: samples that assigned to "Winter" in step 1 were not assigned at this step and have NA listed in this column). **Spring.subpop.Call** Subpopulation call based on greatest posterior assignment probability for assignment step 3a (note: samples with a Maj.popo1.Call of "Winter" or a Maj.pop2.Call of "Fall/LateFall" were note assigned to a WildSpring subpopulation and have NA listed for this column). **Fall.subpop.Call** Subpopulation call based on greatest posterior assignment probability for assignment step 3b (note: samples with a Maj.pop1.Call of "Winter" or a Maj.pop2.Call of "WildSpring" were not assigned to a fall subpopulation and have NA listed for this column). **true_maj.pop1** The true population of origin for this sample at assignment step 1. **true_maj.pop2** The true population of origin for this sample at assignment step 2 (note: samples whose true origin is "Winter" have NA listed in this column). **true_subpop** The true subpopulation of origin of this sample (note: samples whose true origin is "Winter" are not part of a subpopulation and have NA listed in this column). ### juvenile.1kaln\_cutoff.snp\_panel.singlereadcalls.csv File with allele calls from single read sampling for samples in the archive juvenile dataset at each site in the SNP panel. Samples that failed the 1,000 properly-paired sequencing read cutoff are excluded. Each line contains data for one SNP in the SNP panel. Allele calls are coded as 0 for the major allele, 1 for the minor allele, and -1 for missing data. See below for descriptions of column labels: **chr** Chromosome where the SNP for that line is located **pos** Position of the SNP on the chromosome **major** The major allele in A,C,G,T format **minor** The minor allele in A,C,G,T format **ind[#]** All following columns contain allele call data for individual samples. Column name corr esponds to sample ID. See sample_metadata.csv for specific information on each sample. ### sample\_metadata.csv File containing metadata (collection info, phenotype data, etc.) for all archive juvenile samples. See below for column descriptions: **Order_all** Useful column for sorting samples. Number refers to the order of all samples in the DNA plates **Order_1k_cutoff** Useful column for sorting samples. Number refers to order of samples in DNA plates that passed the 1,000 sequencing read filter **Sample_ID** CDFW identification code for each sample **Plate_name** Name of the DNA plate the sample's DNA is a part of **Well** The well location of the sample within the DNA plate **Sample_name** Sample name combining DNA plate and well info **Name_in_singleread_file** The name of the sample in juvenile.1kaln_cutoff.snp_panel.singlereadcalls.csv **SampleDate** Sample collection date at Chipps Island (note: a few samples were found to have ambiguous data data after sequencing--indicated by NA's--their information is included in this spreadsheet, but they were excluded from downstream analyses) **SampleYear** Sample collection year (note: a few samples were found to have ambiguous date data after sequencing. These contain an NA in this column, and were excluded from downstream analyses) **CollLoc** Specific collection location **properpair_aligment_count** The final number of properly paired alignments to the reference genome for each sample **make_1k_cutoff?** Indicates whether the sample passed the 1,000 read filtering cutoff for inclusion in downstream analyses **CDFW_race** Population assignment based on length-at-date criteria given by CDFW to some samples at the time of collection **Fork_length** Fork lengths of each juvenile in millimeters **Ad_clip** Indicates whether an adipose fin was present when the tissue sample was collected **NC_056456.1:13427410** Genotype call for a SNP in the GREB1L region associated with run timing **greb1l_posterior** Posterior probability of the genotype call for NC_056456.1:13427410 ### juvenile.assignment\_posteriors\_calls.csv File containing archive juvenile dataset population assignment results. See below for column descriptions: **Sample** Sample name **Missingness** The proportion of missing data for a given sample from the juvenile.1kaln_cutoff.snp_panel.singlereadcalls.csv file (e.g. 0.61 = 61% missing allele calls) **Fall_LateFall_WildSpring** The posterior probability from DAPC of assignment to the Fall/L ate-fall/WildSpring population in assignment step 1. **Winter** The posterior probability from DAPC of assignment to the Winter population in assignmen t step 1. **Fall_LateFall** The posterior probability from DAPC of assignment to the Fall/Late-fall populat ion in assignment step 2. **WildSpring** The posterior probability from DAPC of assignment to the WildSpring population in assignment step 2. **WildSpring_Butte** The posterior probability from DAPC of assignment to the WildSpring But te subpopulation in assignment step 3a. **WildSpring_MillDeer** The posterior probability from DAPC of assignment to the WildSpring Mil l/Deer subpopulation in assignment step 3a. **Fall** The posterior probability from DAPC of assignment to the Fall subpopulation in assignme nt step 3b. **LateFall** The posterior probability from DAPC of assignment to the Late-Fall subpopulatio n in assignment step 3b. **Maj.pop1.Call** Population call based on the greatest posterior assignment probability for assignment step 1. **Maj.pop2.Call** Maj.pop2.Call Population call based on the greatest posterior assignment probability for assignment step 2 (note: samples assigning to "Winter" in step 1 were not assigned at step 2 and have an NA in this column). **Spring.subpop.Call** Subpopulation call based on greatest posterior assignment probability f or assignment step 3a (note: samples with a Maj.popo1.Call of "Winter" or a Maj.pop2.Call of "Fall/LateFall" were not assigned to a WildSpring subpopulation and have NA listed for this column). **Fall.subpop.Call** Subpopulation call based on greatest posterior assignment probability for assignment step 3b (note: samples with a Maj.pop1.Call of "Winter" or a Maj.pop2.Call of "WildSpring" were not assigned to a fall subpopulation and have NA listed for this column). ## Sharing/Access Infromation The training set data was derived from previously published sequencing data publicly available from Meek et al.(2020) (doi.org/10.1139/cjfas-2019-0171) The validatiaon data set was derived from previously published sequencing data publicly available from Baerwald et al. (2023) (doi.org/10.1111/1755-0998.13777) ## Code/Software The following describes scripts used for analyses, required R packages, required input files for each script, and the resulting output files. The scripts are included in this Dryad entry. All scripts are written in R, and the following R version was used when performing analyses: ``` R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics". ``` ### leave\_one\_out.winterVall.R Runs leave-one-out analyses for winter vs all other pops (assignment step 1) Required R packages (with version used at time of analysis): adegenet (2.1.6) Required input files: trainingset_allruns_filtered.snp_panel.singlereadcalls.csv trainingset_allruns_filtered.pop_key.csv Output files: leave_one_out.maj_pop_1.results.csv (concatenated) ### leave\_one\_out.flfVws.R Runs leave-one-out analyses for fall/late-fall vs. wild spring (assignment step 2) Required R packages (with version used at time of analysis): adegenet (2.1.6) Required input files: trainingset_allruns_filtered.snp_panel.singlereadcalls.csv trainingset_allruns_filtered.pop_key.csv Output files: leave_one_out.maj_pop_2.results.csv (concatenated) ### leave\_one\_out.sbVsmd.R Runs leave-one-out analyses for spring Butte vs. spring Mill/Deer (assignment step 3a) Required R packages (with version used at time of analysis): adegenet (2.1.6) Required input files: trainingset_allruns_filtered.snp_panel.singlereadcalls.csv trainingset_allruns_filtered.pop_key.csv Output files: leave_one_out.subpop_sprButte_V_sprMillDeer.results.csv (concatenated) ### leave\_one\_out.fVlf.R Runs leave-one-out analyses for fall vs. late-fall (assignment step 3b) Required R packages (with version used at time of analysis): adegenet (2.1.6) Required input files: trainingset_allruns_filtered.snp_panel.singlereadcalls.csv trainingset_allruns_filtered.pop_key.csv Output files: leave_one_out.subpop_fall_V_latefall.results.csv (concatenated) ### validation\_analyses.R Generates population assignments for validataion sample set Required R packages (with version used at time of analysis): adegenet (2.1.6) ggplot2 (3.3.6) dplyr (1.1.2) Required input files: trainingset_allruns_filtered.snp_panel.singlereadcalls.csv trainingset_allruns_filtered.pop_key.csv validation_set.snp_panel.singlereadcalls.csv validation_set.pop_key.csv Output files: validation_set.assignment_results.csv ### cv\_juv\_assignments.R Generates population assignments for archive juvenile sample set Required R packages (with version used at time of analysis): adegenet (2.1.6) dplyr (1.1.2) Required input files: trainingset_allruns_filtered.snp_panel.singlereadcalls.csv trainingset_allruns_filtered.pop_key.csv juvenile.1kaln_cutoff.snp_panel.singlereadcalls.csv Output files: juvenile.assignment_posteriors_calls.csv