Population structure and genetic variability in wild and farmed Mediterranean populations of gilthead seabream and European seabass inferred from a 60K combined species SNP array

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Knowledge of population structure and genetic diversity within and between wild and farmed populations of gilthead sea bream (Sparus aurata) and European seabass (Dicentrarchus labrax) is important to achieve sustainable aquaculture production of these species and to assess the risk of genetic impacts of fish escaped from farms. Previous population genetic studies on these species have been based on a limited number of genetic markers and samples. In this study, these features were assessed using samples from 24 seabream and 25 seabass populations distributed throughout the Mediterranean Sea, and 3 wild seabream Atlantic populations. Samples were genotyped with a newly developed combined species SNP array that includes ~60K SNPs. Data from sequencing pools of individual DNA from the same populations were also used. Different approaches were employed for identifying the extent of population stratification within species. The effective population size (a parameter inversely related to the rate at which genetic variability is lost) was estimated for each population based on linkage disequilibrium. Population structure results revealed a clear differentiation between wild and farmed populations in both species. Wild populations showed a low degree of differentiation, particularly in seabream. Despite this, a slight differentiation was observed between Atlantic and Mediterranean seabream populations and between western and eastern Mediterranean seabass populations. However, farmed populations were quite heterogeneous and showed a high degree of differentiation. Some farmed populations of both species showed a genetic makeup similar to that found in wild populations. In general, the effective population size was large (> 1000) for wild and small (< 100) for farmed populations of both species. About 40% of the seabream and 80% of the seabass farmed populations had estimates of effective population size smaller than 50 highlighting the need of applying measures to control the rate at which genetic variability is lost.
This work was supported by the European Commission Horizon 2020 (H2020) Framework Programme through grant agreement no 727315 MedAID project (Mediterranean Aquaculture Integrated Development) and by MCIN/ AEI /10.13039/501100011033 (Project PID2020-114426GB-C2).