Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Ilaria Milano, Massimiliano Babbucci, Alessia Cariani, Miroslava Atanassova, Dorte Bekkevold, Gary R Carvalho, Montserrat Espiñeira, Fabio Fiorentino, Germana Garofalo, Audrey J Geffen, Jakob H Hansen, Sarah J Helyar, Einar E Nielsen, Rob Ogden, Tomaso Patarnello, Marco Stagioni, FishPopTrace Consortium, Fausto Tinti, Luca Bargelloni

Research output: Contribution to journalArticle

96 Citations (Scopus)

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.

LanguageEnglish
Pages118-35
Number of pages18
JournalMolecular Ecology
Volume23
Issue number1
Early online date18 Nov 2013
DOIs
Publication statusPublished - Jan 2014

Fingerprint

Merluccius merluccius
outlier
Single Nucleotide Polymorphism
population structure
loci
Population
basins
divergence
hake
adaptive radiation
commercialization
North Sea
marine fish
Portugal
surface temperature
gene frequency
genetic marker
population size
basin
seawater

Keywords

  • Animals
  • Atlantic Ocean
  • Fisheries
  • Gadiformes
  • Genetic Loci
  • Genetics, Population
  • Genotype
  • Geography
  • Linkage Disequilibrium
  • Mediterranean Sea
  • North Sea
  • Polymorphism, Single Nucleotide

Cite this

Milano, I., Babbucci, M., Cariani, A., Atanassova, M., Bekkevold, D., Carvalho, G. R., ... Bargelloni, L. (2014). Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). Molecular Ecology, 23(1), 118-35. https://doi.org/10.1111/mec.12568
Milano, Ilaria ; Babbucci, Massimiliano ; Cariani, Alessia ; Atanassova, Miroslava ; Bekkevold, Dorte ; Carvalho, Gary R ; Espiñeira, Montserrat ; Fiorentino, Fabio ; Garofalo, Germana ; Geffen, Audrey J ; Hansen, Jakob H ; Helyar, Sarah J ; Nielsen, Einar E ; Ogden, Rob ; Patarnello, Tomaso ; Stagioni, Marco ; FishPopTrace Consortium ; Tinti, Fausto ; Bargelloni, Luca. / Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). In: Molecular Ecology. 2014 ; Vol. 23, No. 1. pp. 118-35.
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Milano, I, Babbucci, M, Cariani, A, Atanassova, M, Bekkevold, D, Carvalho, GR, Espiñeira, M, Fiorentino, F, Garofalo, G, Geffen, AJ, Hansen, JH, Helyar, SJ, Nielsen, EE, Ogden, R, Patarnello, T, Stagioni, M, FishPopTrace Consortium, Tinti, F & Bargelloni, L 2014, 'Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)', Molecular Ecology, vol. 23, no. 1, pp. 118-35. https://doi.org/10.1111/mec.12568

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). / Milano, Ilaria; Babbucci, Massimiliano; Cariani, Alessia; Atanassova, Miroslava; Bekkevold, Dorte; Carvalho, Gary R; Espiñeira, Montserrat; Fiorentino, Fabio; Garofalo, Germana; Geffen, Audrey J; Hansen, Jakob H; Helyar, Sarah J; Nielsen, Einar E; Ogden, Rob; Patarnello, Tomaso; Stagioni, Marco; FishPopTrace Consortium; Tinti, Fausto; Bargelloni, Luca.

In: Molecular Ecology, Vol. 23, No. 1, 01.2014, p. 118-35.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

AU - Milano, Ilaria

AU - Babbucci, Massimiliano

AU - Cariani, Alessia

AU - Atanassova, Miroslava

AU - Bekkevold, Dorte

AU - Carvalho, Gary R

AU - Espiñeira, Montserrat

AU - Fiorentino, Fabio

AU - Garofalo, Germana

AU - Geffen, Audrey J

AU - Hansen, Jakob H

AU - Helyar, Sarah J

AU - Nielsen, Einar E

AU - Ogden, Rob

AU - Patarnello, Tomaso

AU - Stagioni, Marco

AU - FishPopTrace Consortium

AU - Tinti, Fausto

AU - Bargelloni, Luca

PY - 2014/1

Y1 - 2014/1

N2 - 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.

AB - 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.

KW - Animals

KW - Atlantic Ocean

KW - Fisheries

KW - Gadiformes

KW - Genetic Loci

KW - Genetics, Population

KW - Genotype

KW - Geography

KW - Linkage Disequilibrium

KW - Mediterranean Sea

KW - North Sea

KW - Polymorphism, Single Nucleotide

U2 - 10.1111/mec.12568

DO - 10.1111/mec.12568

M3 - Article

VL - 23

SP - 118

EP - 135

JO - Molecular Ecology

T2 - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 1

ER -