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Accurate prediction of species distribution shifts in the face of climate change requires a sound understanding of population diversity and local adaptations. Previous modeling has suggested that global warming will lead to increased abundance of Atlantic cod (Gadus morhua) in the ocean around Greenland, but the dynamics of earlier abundance fluctuations are not well understood. We applied a retrospective spatiotemporal population genomics approach to examine the temporal stability of cod population structure in this region and to search for signatures of divergent selection over a 78-year period spanning major demographic changes. Analyzing >900 gene-associated single nucleotide polymorphisms in 847 individuals, we identified four genetically distinct groups that exhibited varying spatial distributions with considerable overlap and mixture. The genetic composition had remained stable over decades at some spawning grounds, whereas complete population replacement was evident at others. Observations of elevated differentiation in certain genomic regions are consistent with adaptive divergence between the groups, indicating that they may respond differently to environmental variation. Significantly increased temporal changes at a subset of loci also suggest that adaptation may be ongoing. These findings illustrate the power of spatiotemporal population genomics for revealing biocomplexity in both space and time and for informing future fisheries management and conservation efforts. [ABSTRACT FROM AUTHOR]

Recent technological developments have facilitated intensified searches for genetic markers under selection in nonmodel species. Here, we present an approach for the identification of candidate gene variation in nonmodel organisms. We report on the characterization of 82 single nucleotide polymorphisms (SNPs) and on the development of a specific genotyping assay for 30 SNPs in 18 candidate genes for growth and reproduction in Atlantic cod ( Gadus morhua). These markers can be used for scanning natural populations for signatures of selection in both contemporary and archived historical samples, for example in retrospective studies assessing the effects of environmental changes, such as increasing temperatures, and selection imposed by high fishing pressure. Furthermore, these gene markers may be of interest to aquaculture, serving as a starting point for linking phenotypic traits important for productivity with genotypes and potentially be of use for marker-assisted selection in the future. This study demonstrates that the candidate gene approach is a valuable and targeted complement to the more random approach for discovering genetic variation in the genome and transcriptome applied through high throughput methods in nonmodel species. [ABSTRACT FROM AUTHOR]