Commands and input files for population genetic analysis of Deacon Rockfish using RADseq. Used for: Vaux F, Rasmuson LK, Kautzi LA, Rankin PS, Blume MTO, Lawrence KA, Bohn S, O’Malley KG. (2019). Sex matters: otolith shape and genomic variation in deacon rockfish (Sebastes diaconus). Ecology and Evolution 9, 13153-13173. https://doi.org/10.1002/ece3.5763
Lists input commands used for the STACKS analysis and subsequent analyses used for filtering in VCFtools, plink, and paralog-finder (HDplot), as well as BWA.
Maps used to select individuals and populations in STACKS runs.
Lists used to exclude certain loci in STACKS runs.
Ped and map files used by plink to estimate loci in LD.
Maps used to select subsets of individuals for estimating HWP.
Genetic sampling, and genetic data (vcf, genepop, and structure genotype files, and the fasta consensus file for the 92 outlier loci) are available from Dryad: https://doi.org/10.5061/dryad.8kprr4xj0
Demultiplexed forward and reverse DNA sequence reads for the deacon rockfish sequenced in this study are openly available on the NCBI sequence read archive (SRA) under: PRJNA560239, http://www.ncbi.nlm.nih.gov/bioproject/560239
Available on request from Kathleen O'Malley (State Fisheries Genomics Lab, Oregon State University), https://agsci.oregonstate.edu/state-fisheries-lab/people
See this page: https://sites.google.com/view/evauxlution/data