Abstract
Sandeels are an ecologically important group of fishes; they are a key part of the food chain serving as food for marine mammals, seabirds and fish. Sandeels are further targeted by a large industrial fishery, which has led to concern about ecosystem effects. In the North Sea, the lesser sandeel Ammodytes marinus is by far the most prevalent species of sandeel in the fishery. Management of sandeel in the North Sea plus the Kattegat is currently divided into seven geographical areas, based on subtle differences in demography, population dynamics and results from simulations of larval dispersal. However, little is known about the underlying genetic population structure. In this study, we used 2,522 SNPs derived from restriction site‐associated DNA sequencing (RADseq) typed in 429 fish representing four main sandeel management areas. Our main results showed (a) a lack of a clear spatially defined genetic structure across the majority of genetic markers and (b) the existence of a group of at least 13 SNPs under strong linkage disequilibrium which together separate North Sea sandeel into three haplotype clusters, suggestive of one or more structural variants in the genome. Analyses of the spatial distribution of these putative structural variants suggest at least partial reproductive isolation of sandeel in the western management area along the Scottish coast, supporting a separate management. Our results highlight the importance of the application of a large number of markers to be able to detect weak patterns of differentiation. This study contributes to increasing the genetic knowledge of this important exploited species, and results can be used to improve our understanding of population dynamics and stock structure.
Highlights
This study contributes to increasing the genetic knowledge of this important exploited species, and results can be used to improve our understanding of population dynamics and stock structure
Marine fishes are often characterized by high fecundity, large ef‐ fective population sizes and high dispersal potential leading to weak patterns of genetic differentiation (Ward, Woodwark, & Skibinski, 1994)
We explored whether the genetic data from the linkage disequilibrium (LD) group aligned with the spatial location of hydrographic dispersal barriers identified through modelling of relative larval transport probability (Christensen et al, 2008; Wright et al, 2019)
Summary
Marine fishes are often characterized by high fecundity, large ef‐ fective population sizes and high dispersal potential leading to weak patterns of genetic differentiation (Ward, Woodwark, & Skibinski, 1994). In spite of the generally low differentiation observed across the genome in a number of marine fishes, sequenc‐ ing approaches allow for analyses of large numbers of DNA markers, resulting in greatly enhanced power for identifying genomic regions exhibiting genetic structure (Bernatchez et al, 2017; Nielsen et al, 2012) Such signatures may be associated with local adaptation or reveal traces of cryptic population structure obscured by gene flow across most of the genome (Duranton et al, 2018; Gagnaire et al, 2015; Nielsen et al, 2012). We aimed to (a) characterize the population struc‐ ture of lesser sandeel in the North Sea using population genomic data and (b) assess whether the management areas currently imple‐ mented for the species in the North Sea are in line with observed genetic variability
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