Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges Bank

• Published in: PloS one 2019-05, Vol.14 (5), p.e0216992
• Main Authors: Clucas, G V, Kerr, L A, Cadrin, S X, Zemeckis, D R, Sherwood, G D, Goethel, D, Whitener, Z, Kovach, A I
• Format: Article
• Language: English
• Subjects: Adaptation; Adaptive structures; Analysis; Animals; Atlantic cod; Biocomplexity; Biodiversity; Biological evolution; Biology and Life Sciences; Changing environments; Chromosome Inversion - genetics; Chromosomes; Cod; Deoxyribonucleic acid; Differentiation; Divergence; DNA; DNA sequencing; Earth Sciences; Endangered & extinct species; Environmental changes; Evolution; Evolution & development; Fisheries; Fisheries management; Gadus morhua; Gadus morhua - genetics; Gene loci; Gene sequencing; Genetic aspects; Genetic diversity; Genetic polymorphisms; Genetic variation; Genetic Variation - genetics; Genetics, Population; Genome - genetics; Genomes; Genomics; Genotype; Inversions; Loci; Natural resources; Polymorphism, Single Nucleotide - genetics; Population; Population genetics; Population structure; Populations; Production management; Publishing; Resilience; Sequence Analysis, DNA; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Spawning
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0216992

Atlantic cod (Gadus morhua) populations in the Gulf of Maine (GoM) are at a fraction of their historical abundance, creating economic hardships for fishermen and putting at risk the genetic diversity of the remaining populations. An understanding of the biocomplexity among GoM populations will allow for adaptive genetic diversity to be conserved to maximize the evolutionary potential and resilience of the fishery in a rapidly changing environment. We used restriction-site-associated DNA sequencing (RADseq) to characterize the population structure and adaptive genetic diversity of five spawning aggregations from the western GoM and Georges Bank. We also analyzed cod caught in the eastern GoM, an under-sampled area where spawning aggregations have been extirpated. Using 3,128 single nucleotide polymorphisms (SNPs), we confirmed the existence of three genetically separable spawning groups: (1) winter spawning cod from the western GoM, (2) spring spawning cod, also from the western GoM, and (3) Georges Bank cod. Non-spawning cod from the eastern GoM could not be decisively linked to either of the three spawning groups and may represent a unique component of the resource, a mixed sample, or cod from other unsampled source populations. The genetic differentiation among the three major spawning groups was primarily driven by loci putatively under selection, particularly loci in regions known to contain genomic inversions on linkage groups (LG) 7 and 12. These LGs have been found to be linked to thermal regime in cod across the Atlantic, and so it is possible that variation in timing of spawning in western GoM cod has resulted in temperature-driven adaptive divergence. This complex population structure and adaptive genetic differentiation could be crucial to ensuring the long-term productivity and resilience of the cod fishery, and so it should be considered in future management plans.