BACKGROUND: The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. METHODS: Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. RESULTS: Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. CONCLUSIONS: Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes.

Andromeda Group SA Leof Lavriou 99 190 02 Peania Greece

Centro de Investigación Mariña Facultade de Bioloxía Universidade de Vigo 36310 Vigo Spain

CETGA Cluster de Acuicultura de Galicia Punta do Couso s n 15695 Aguiño Ribeira Spain

Departament of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela 27002 Lugo Spain

Departamento de Biología Funcional Universidad de Oviedo C Julián Clavería s n 33006 Oviedo Spain

Departamento de Mejora Genética Animal INIA CSIC Ctra de La Coruña km 7 5 28040 Madrid Spain

Ferme Marine De Douhet Route du Douhet 17840 La Brée les Bains France

Geneaqua 27002 Lugo Spain

Nofima AS P O Box 210 1431 Ås Norway

South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses Faculty of Fisheries and Protection of Waters University of South Bohemia in České Budějovice Zátiší 728 2 389 25 Vodňany Czech Republic

SYSAAF Station LPGP INRAE Campus de Beaulieu 35042 Rennes France

The Roslin Institute and Royal School of Veterinary Studies University of Edinburgh Easter Bush Midlothian EH25 9RG UK

Universitá degli Studi di Padova Via 8 Febbraio 1848 2 35122 Padova PD Italy

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