Response to comments by Cardinale et al. on “Local cod (Gadus morhua) revealed by egg surveys and population genetic analysis after longstanding depletion on the Swedish Skagerrak coast” by Svedäng et al. (2019)

Ticket to spawn: Combining economic and genetic data to evaluate the effect of climate and demographic structure on spawning distribution in Atlantic cod.

Abstract Climate warming and harvesting affect the dynamics of species across the globe through a multitude of mechanisms, including distribution changes. In fish, migrations to and distribution on spawning grounds are likely influenced by both climate warming and harvesting. The Northeast Arctic (NEA) cod (Gadus morhua) performs seasonal migrations from its feeding grounds in the Barents Sea to spawning grounds along the Norwegian coast. The distribution of cod between the spawning grounds has historically changed at decadal scales, mainly due to variable use of the northern and southern margins of the spawning area. Based on historical landing records, two major hypotheses have been put f…

Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod

AbstractIdentification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. In Atlantic cod – historically a major marine resource – Northeast-Arctic- and Norwegian coastal cod are recognized by fundamental differences in migratory and non-migratory behavior, respectively. However, the genomic architecture underlying such behavioral ecotypes is unclear. Here, we have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of sev…

Disentangling structural genomic and behavioural barriers in a sea of connectivity

18 pages, 4 tables, 3 figures.-- This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

Local cod (Gadus morhua) revealed by egg surveys and population genetic analysis after longstanding depletion on the Swedish Skagerrak coast

Abstract Dramatic and persistent reductions in Atlantic cod (Gadus morhua) are common in many coastal areas. While offshore cod stocks still were abundant and productive, the Swedish west coast showed signs of diminishing adult cod abundance at the beginning of the 1980s, where the local cod component was considered to be extirpated. To survey the present cod spawning activity and stock composition, we initiated egg trawling over two consecutive years (203 hauls in total) in combination with population genetic analyses (425 individually genotyped eggs). Here, we provide evidence of cod spawning at the Swedish Skagerrak coast, suggesting recolonization or that local cod has recovered from a …

Genome architecture enables local adaptation of Atlantic cod despite high connectivity

Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits. By combining population genomic analyses based on 12K single-nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show…

Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic

Significance Both theory and experiments suggest that fishing can drive the evolution of an earlier maturation age. However, determining whether changes in the wild are the result of fisheries-induced evolution has been difficult. Temporal, genome-wide datasets can directly reveal responses to selection. Here, we investigate the genomes of two wild Atlantic cod populations from samples that pre- and postdate periods of intensive fishing. Although phenotypic changes suggest fisheries-induced evolution, we do not find evidence for any strong genomic change or loss of genetic diversity. While evolution could have occurred through undetectable frequency changes at many loci, the irreversible lo…

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations.

Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population str…