Anita Wray's Rockfish RADseq Project - September 2020 - December 2022

Scripts from masters project on rockfish population structure in Puget Sound, WA

Objective of Project(s):

1. Investigate the effect of interspecific hybridization and introgression in Puget Sound on genetic population structure in Brown, Copper, and Quillback rockfishes
2. Provide a comprehensive survey of population structure of all common rockfishes in Puget Sound and the Washington coast, with aim to inform fisheries management and provide data for potential petitions for ESA listing of some species

Navigation of Repository

All scripts are in folders according to what program I ran them on. All post-populations SNP filtering and analyses are in the R folder.

Associated publications

1. Wray, A., Petrou, E., Nichols, K. M., Pacunski, R., Leclair, L., Andrews, K. S., Kardos, M., et al.. (2024). Contrasting effect of hybridization on genetic differentiation in three rockfish species with similar life history. Evolutionary Applications, 17(7). Open Access Link Raw Data Link

2. Wray, A., Petrou, E., Nichols, K. M., Pacunski, R., LeClair, L., Andrews, K. S., Haggarty, D., & Hauser, L. (2025). Divergent Population Structure in Five Common Rockfish Species of Puget Sound, WA Suggests the Need for Species-Specific Management. Molecular ecology, 34(1), e17590. Open Access Link NCBI SRA Link Dryad Metadata Link