Korean stock structure and transoceanic divergence in Pacific cod (Gadus macrocephalus)

Abstract

Large marine populations, while inhabiting an environment with few clear barriers to gene flow, have been shown to display complex genetic structure on varying spatial scales. Although next-generation sequencing has improved our ability to discern marine population structure and the underlying genomic architecture, we still have much to learn about the evolution of genetic divergence in the marine environment, and its implications for management of exploited marine species. Pacific cod (Gadus macrocephalus) is a marine finfish targeted by economically valuable fisheries throughout its range in the northern Pacific Ocean. The species displays diverse population structure, which arises from a combination of different demographic histories and oceanographic barriers to gene flow. Such genetic structure allows for the study of adaptive divergence across large spatial scales, and carries implications for fisheries management. We first analyzed fine-scale genetic stock structure of Pacific cod around the Korean peninsula, where it is the target of a commercial fishery and is supplemented by stock enhancement programs. Our RAD sequencing results suggest that the Korean Pacific cod fishery should be managed as three genetically distinct stocks on the western, eastern, and southern Korean coasts. Although these three stocks were highly differentiated from each other, we observed a high rate of migration between different coasts during the spawning season. We then compared this Korean data set from the western Pacific with existing RAD sequencing data from eastern Pacific cod, sampled along the coasts of Alaska, British Columbia, and Washington State. We found no evidence of parallel adaptation between the highly diverged eastern and western lineages of Pacific cod, which is in contrast to reports on Atlantic cod. The number of genomic regions of elevated divergence was lowest among subpopulations in the eastern Pacific, higher in subpopulations around the Korean peninsula, and highest in the comparison between the eastern and western Pacific lineages. The majority of these differences, as well as the opposite trend in the width of genomic regions of elevated divergence, were non-significant. As the first comparison of eastern and western Pacific cod using next-generation sequencing, our study provided key information regarding the genetic characteristics and structure of Korean cod stocks, uncovered unexpected spawning migration behavior around the Korean peninsula, and provided insights into the diversity and dynamics of adaptive divergence in a marine species of considerable commercial and ecological importance.