Abstract
Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across the species' range using a small panel of single nucleotide polymorphisms (SNPs) previously isolated from restriction‐site‐associated DNA sequencing; these SNPs were selected to maximize differentiation at a range of both broad and fine scales. After quality control and filtering, 1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The results revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea. In addition, a genetic cline across the north‐east Atlantic was revealed using both putatively neutral and outlier SNPs, but the precise driver(s) of this clinal pattern—isolation by distance, secondary contact, selection across an environmental gradient, or a combination of these factors—remains undetermined. Putatively neutral markers differentiated lobsters from Oosterschelde, an estuary on the Dutch coast, a finding likely explained by past bottlenecks and limited gene flow with adjacent North Sea populations. Building on the findings of our spatial genetic analysis, we were able to test the accuracy of assigning lobsters at various spatial scales, including to basin of origin (Atlantic or Mediterranean), region of origin and sampling location. The predictive model assembled using 79 SNPs correctly assigned 99.7% of lobsters not used to build the model to their basin of origin, but accuracy decreased to region of origin and again to sampling location. These results are of direct relevance to managers of lobster fisheries and hatcheries, and provide the basis for a genetic tool for tracing the origin of European lobsters in the food supply chain.
Highlights
Identifying distinct genetic diversity among populations and delineating biologically accurate management units are key objectives of conservation biology and fisheries management (Funk, McKay, Hohenlohe, & Allendorf, 2012; Palsbøll, Bérubé, & Allendorf, 2007)
It is important to identify stock structure and connectivity to ensure that the spatial implementation of management is commensurate with that of biological population units (Reiss, Hoarau, Dickey‐Collas, & Wolff, 2009), and to pinpoint populations that may contribute colonizers to overfished or depleted stocks (Da Silva, Appleyard, & Upston, 2015)
This study comprises the first application of single nucleotide polymorphisms (SNPs) markers isolated from RAD sequencing to investigate population genetic structure and assignment in the European lobster
Summary
Identifying distinct genetic diversity among populations and delineating biologically accurate management units are key objectives of conservation biology and fisheries management (Funk, McKay, Hohenlohe, & Allendorf, 2012; Palsbøll, Bérubé, & Allendorf, 2007). These outlier markers have the potential to aid the delineation of conservation units by identifying adaptive diversity in protected or exploited species (Barbosa et al, 2018; Flanagan, Forester, Latch, Aitken, & Hoban, 2017; Funk et al, 2012) These markers often have greater power to differentiate populations, which offers promising applications for detecting immigrants via assignment approaches (Gagnaire et al, 2015). In the north‐east Atlantic, virtually no genetic differentiation between samples of European lobster has been found using microsatellite markers (Ellis et al, 2017; Huserbraten et al, 2013; Watson, McKeown, Coscia, Wootton, & Ironside, 2016) It is uncertain whether the apparent lack of population structure across much of the European lobster's range reflects genuine panmixia via widespread dispersal (or large effective population sizes), or limitations in the analytical power provided by small arrays of microsatellites to detect weak spatial structuring. We discuss the applications of these results to inform the management, supplementation and conservation of European lobster populations
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