Hidden but revealed: After years of genetic studies behavioural monitoring combined with genomics uncover new insight into the population dynamics of Atlantic cod in Icelandic waters

Abstract

Stock structure is of paramount importance for sustainable management of exploited resources. In that context, genetic markers have been used for more than two decades to resolve spatial structure of marine exploited resources and to fully fathom stock dynamics and interactions. While genetic markers such as allozymes and RFLP dominated the debate in the early era of genetics, technology advances have provided scientists with new tools every decade to better assess stock discrimination and interactions (i.e. gene flow). Here, we provide a review of genetic studies performed to understand stock structure of Atlantic cod in Icelandic waters, from the early allozyme approaches to the genomic work currently carried out. We further highlight the importance of the generation of a chromosome-anchored genome assembly together with whole-genome population data, which drastically changed our perception of the possible management units to consider. After nearly 60 years of genetic investigation of Atlantic cod structure in Icelandic waters, genetic (and later genomic) data combined with behavioural monitoring using Data Storage Tags shifted the attention from geographical population structures to behavioural ecotypes. This review also demonstrates the need for future research to further disentangle the impact of these ecotypes (and gene flow among them) on the population structure of Atlantic cod in Icelandic waters. It also highlights the importance of whole-genome data to unravel unexpected within-species diversity related to chromosomal inversions and associated supergenes, which are important to consider for future development of sustainable management programmes of the species within the North Atlantic.

Keywords: Gadus morhua; Iceland; behavioural ecotypes; genetics/genomics; management perspective; stock structure.

FIGURE 1

Atlantic cod migration dynamic in Icelandic waters. Spawning grounds are indicated with orange areas, while feeding ground locations are indicated in green colour. The feeding migration from the southern spawning grounds is indicated by red arrows, while black arrows indicate migration from the northern spawning grounds to more localized feeding grounds.

FIGURE 2

Typical coastal (upper) and frontal (lower) data storage tags profiles. Depth is depicted in black, temperature in light grey.

FIGURE 3

Proportion of the different Pan I genotypes among the coastal and frontal ecotypes within geographical regions during spawning time (data analysed for this review, n = 172).

FIGURE 4

Majority of detected outliers' loci within the Atlantic cod genome are clustered within linkage groups (LGs) 1, 2, 7 and 12 for the migratory and nonmigratory cod including the NEAC/NCC complex (a) and the Icelandic coastal and frontal behavioural ecotypes (b) described using DSTs data (reanalysis of data from Berg et al., 2016, 2017). Cod drawing was provided by Jón Baldur Hlíðberg©. DSTs, Data Storage Tags; NCC, Norwegian coastal cod; NEAC, Northeast Arctic cod.