Following the collapse of the Northern cod stock, there has been much debate regarding the population structure of Canada’s Northern Atlantic cod (Gadus morhua). The objectives of the study are: 1) to determine whether the stock exhibits structure or panmixia and 2) to compare historic cod chromosomal inversion frequency (LG01) to among historic and modern cod. A whole genome scan on 119 historic cod captured between 2001 and 2003 was conducted from four locations spanning the range of the stock and two locations outside the stock. Population structure analysis using 3,907 SNPs suggests that the stock is a single panmictic population. However, additional analyses on only LG01 (15) revealed that historic cod had a higher inversion frequency than modern cod. Taken together, these results provide support for the metapopulation hypothesis and provide novel information on putative adaptive inversion allele changes over a short timeframe.
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