Shell files with commands and parameter settings used for each STACKS run.
Maps used to select individuals and populations in STACKS runs.
Lists used to exclude certain loci in STACKS runs.
Ped and map input files and shell file with settings used by plink to estimate loci in LD.
Shell file with commands and the recoded VCF files used to estimate highly correlated loci (additional filtering step for alternative filtered dataset). Text file lists loci added for alternative dataset excluded loci list.
Shell file with commands and the recoded VCF files used to estimate low coverage genotypes and loci (first filtering step). Text file lists loci added for first list of excluded loci.
R files for running loci filtering (e.g. loci coverage depth outliers) and population genetic analyses (e.g. adegenet, LEA). I recommmend viewing original source GitHub pages and tutorials noted in each R file credits. Includes example R project and geno files for LEA analyses.
Commands and files for conducting phylogeographic model selection in delimitR. Includes observed folded multidimensional site frequency spectrum (mSFS) input file for the Recolonisation dataset.
Full sample details (Appendix A), supplementary tables and figures (Appendix B), GBS files (loci consensus sequences, genotype files, phylogenetic alignments, trees, and all commands and files provided on GitHub) are available on DataDryad: https://doi.org/10.5061/dryad.jdfn2z3bt
The supplementary information (supplementary tables and figures; Appendix B) is also hosted with the main text: https://doi.org/10.1111/mec.16535
Demultiplexed forward and reverse DNA sequence reads for the southern bull-kelp sequenced in this study are openly available on the NCBI sequence read archive (SRA) under: PRJNA769149, http://www.ncbi.nlm.nih.gov/bioproject/PRJNA769149
Available on request, and we're working to archive all southern bull kelp raw reads on NCBI in the near future.
See this page: https://sites.google.com/view/evauxlution/data