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

I. Milano, M. Babbucci, A. Cariani, M. Atanassova, Dorte Bekkevold, G.R. Carvalho, M. Espiñeira, F. Fiorentino, G. Garofalo, A.J. Geffen, J.H. Hansen, S.J. Helyar, Einar Eg Nielsen, R. Ogden, T. Patarnello, M. Stagioni, F. Tinti, L. Bargalloni

Research output: Contribution to journalJournal articleResearchpeer-review

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 largeand
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 (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT 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
Original languageEnglish
JournalMolecular Ecology
Volume23
Issue number1
Pages (from-to)118-135
ISSN0962-1083
DOIs
Publication statusPublished - 2014

Cite this

Milano, I. ; Babbucci, M. ; Cariani, A. ; Atanassova, M. ; Bekkevold, Dorte ; Carvalho, G.R. ; Espiñeira, M. ; Fiorentino, F. ; Garofalo, G. ; Geffen, A.J. ; Hansen, J.H. ; Helyar, S.J. ; Eg Nielsen, Einar ; Ogden, R. ; Patarnello, T. ; Stagioni, M. ; Tinti, F. ; Bargalloni, L. / Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). In: Molecular Ecology. 2014 ; Vol. 23, No. 1. pp. 118-135.
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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 largeand 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 (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT 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",
author = "I. Milano and M. Babbucci and A. Cariani and M. Atanassova and Dorte Bekkevold and G.R. Carvalho and M. Espi{\~n}eira and F. Fiorentino and G. Garofalo and A.J. Geffen and J.H. Hansen and S.J. Helyar and {Eg Nielsen}, Einar and R. Ogden and T. Patarnello and M. Stagioni and F. Tinti and L. Bargalloni",
year = "2014",
doi = "10.1111/mec.12568",
language = "English",
volume = "23",
pages = "118--135",
journal = "Molecular Ecology",
issn = "0962-1083",
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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, Eg Nielsen, E, Ogden, R, Patarnello, T, Stagioni, M, Tinti, F & Bargalloni, L 2014, 'Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)', Molecular Ecology, vol. 23, no. 1, pp. 118-135. https://doi.org/10.1111/mec.12568

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius). / Milano, I.; Babbucci, M.; Cariani, A.; Atanassova, M.; Bekkevold, Dorte; Carvalho, G.R.; Espiñeira, M.; Fiorentino, F.; Garofalo, G.; Geffen, A.J.; Hansen, J.H.; Helyar, S.J.; Eg Nielsen, Einar; Ogden, R.; Patarnello, T.; Stagioni, M.; Tinti, F.; Bargalloni, L.

In: Molecular Ecology, Vol. 23, No. 1, 2014, p. 118-135.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

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

AU - Milano, I.

AU - Babbucci, M.

AU - Cariani, A.

AU - Atanassova, M.

AU - Bekkevold, Dorte

AU - Carvalho, G.R.

AU - Espiñeira, M.

AU - Fiorentino, F.

AU - Garofalo, G.

AU - Geffen, A.J.

AU - Hansen, J.H.

AU - Helyar, S.J.

AU - Eg Nielsen, Einar

AU - Ogden, R.

AU - Patarnello, T.

AU - Stagioni, M.

AU - Tinti, F.

AU - Bargalloni, L.

PY - 2014

Y1 - 2014

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 largeand 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 (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT 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 largeand 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 (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT 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

U2 - 10.1111/mec.12568

DO - 10.1111/mec.12568

M3 - Journal article

C2 - 24138219

VL - 23

SP - 118

EP - 135

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 1

ER -