title: Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius).
abstract: Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.
authors.affiliation: Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy.
authors.forename: Ilaria
authors.initials: I
authors.lastname: Milano
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Babbucci
authors.forename: Alessia
authors.initials: A
authors.lastname: Cariani
authors.forename: Miroslava
authors.initials: M
authors.lastname: Atanassova
authors.forename: Dorte
authors.initials: D
authors.lastname: Bekkevold
authors.forename: Gary R
authors.initials: GR
authors.lastname: Carvalho
authors.forename: Montserrat
authors.initials: M
authors.lastname: Espiñeira
authors.forename: Fabio
authors.initials: F
authors.lastname: Fiorentino
authors.forename: Germana
authors.initials: G
authors.lastname: Garofalo
authors.forename: Audrey J
authors.initials: AJ
authors.lastname: Geffen
authors.forename: Jakob H
authors.initials: JH
authors.lastname: Hansen
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Helyar
authors.forename: Einar E
authors.initials: EE
authors.lastname: Nielsen
authors.forename: Rob
authors.initials: R
authors.lastname: Ogden
authors.forename: Tomaso
authors.initials: T
authors.lastname: Patarnello
authors.forename: Marco
authors.initials: M
authors.lastname: Stagioni
authors.forename: Fausto
authors.initials: F
authors.lastname: Tinti
authors.forename: Luca
authors.initials: L
authors.lastname: Bargelloni
mesh_terms: D000818:Animals; D001267:Atlantic Ocean; D005398:Fisheries; D048388:Gadiformes / Q000235:genetics*; D056426:Genetic Loci; D005828:Genetics, Population; D005838:Genotype; D005843:Geography; D015810:Linkage Disequilibrium; D008522:Mediterranean Sea; D009659:North Sea; D020641:Polymorphism, Single Nucleotide
keywords: environmental correlation; genome scan; local adaptation; outlier SNPs; salinity; temperature