Skip to main content

Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change

Cite this dataset

Fisher, Mary et al. (2022). Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change [Dataset]. Dryad.


Small and isolated peripheral populations, which are often remnants of glacial refugia, offer an opportunity to determine the magnitude and direction of fine-scale connectivity in high gene flow marine species. When located at the equatorial edge of a species’ range, these populations may also harbor genetic diversity related to survival and reproduction at higher temperatures, a critical resource for marine species facing warming ocean temperatures. Pacific cod (Gadus macrocephalus), a marine fish in the North Pacific, has already experienced major shifts in biomass and distribution linked to climate change. We estimated the magnitude and direction of connectivity between peripheral populations of Pacific cod at the southern edge of the species’ range, by conducting restriction site-associated DNA (RAD) sequencing and individual assignment on fish collected around the Korean Peninsula during the spawning season. Three populations on the western, eastern, and southern Korean coasts were highly differentiated (FST =0.025 – 0.042) and relatively small (Ne = 433-1777). Ten putative dispersers and estimates of contemporary migration rates revealed asymmetrical, west-to-east movement around the Korean Peninsula, at a higher rate than predicted by indirect estimates of connectivity (FST). Allele frequencies at 87 RAD loci were decisively correlated with strong marine temperature gradients between the warmer southern coast and the cooler waters of the eastern and western coasts. Despite relatively small sample sizes, our data suggest asymmetrical dispersal and gene flow, potentially involving adaptive alleles, between peripheral populations inhabiting markedly different thermal regimes. Our study emphasizes the conservation value of peripheral populations in high gene flow marine fish species.


Fin clips and tissue samples were collected from aggregations of Pacific cod at known spawning sites around the Korean Peninsula, during the spawning season. Restriction site-associated DNA (RAD) libraries were prepared according to Baird et al. (2008) and Etter et al. (2011), with modifications developed for North American Pacific cod samples by Drinan et al. (2018). RAD-sequencing data was processed using the Stacks v1.44 pipeline (Catchen et al., 2011; Catchen et al., 2013), Bowtie (Langmead et al., 2009), and NCBI’s Basic Local Alignment Search Tool, BLAST (Altschul et al., 1990), per Drinan et al. (2018) and Brieuc et al. (2014).

Please see the associated publication for methodology details.



Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410. doi:

Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., . . . Johnson, E. A. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3(10), e3376. doi:10.1371/journal.pone.0003376

Brieuc, M. S. O., Waters, C. D., Seeb, J. E., & Naish, K. A. (2014). A dense linkage map for Chinook salmon (Oncorhynchus tshawytscha) reveals variable chromosomal divergence After an ancestral whole genome duplication event. G3: Genes, Genomes, Genetics, 4(3), 447-460. doi:10.1534/g3.113.009316

Catchen, J. C., Amores, A., Hohenlohe, P., Cresko, W., & Postlethwait, J. (2011). Stacks: building and genotyping loci de novo for short-read sequences. G3: Genes, Genomes, Genetics, 1, 171-182.

Catchen, J. C., Hohenlohe, P., Bassham, S., Amores, A., & Cresko, W. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology, 22(11), 3124-2140.

Drinan, D. P., Gruenthal, K. M., Canino, M. F., Lowry, D., Fisher, M. C., & Hauser, L. (2018). Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus). Evolutionary Applications, 11, 1-17. doi:10.1111/eva.12639

Etter, P. D., Preston, J. L., Bassham, S., Cresko, W. A., & Johnson, E. A. (2011). Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE, 6(4), e18561. doi:10.1371/journal.pone.0018561

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-359. doi:10.1038/nmeth.1923


National Research Foundation of Korea, Award: NRF‐2012R1A1A2004830

National Institute of Fisheries Science, Award: R2021069