A genomic island linked to ecotype divergence in Atlantic cod

Jakob Hemmer Hansen, Einar Eg Nielsen, Nina O. Therkildsen, Martin I. Taylor, Rob Ogden, Audrey J. Geffen, Dorte Bekkevold, Sarah Helyar, Christophe Pampoulie, Torild Johansen, Gary R. Carvalho

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Abstract

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or ‘genomic island’, as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that ‘genomic mosaics’ of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.
Original languageEnglish
JournalMolecular Ecology
Volume22
Issue number10
Pages (from-to)2653-2667
ISSN0962-1083
DOIs
Publication statusPublished - 2013

Cite this

Hansen, J. H., Eg Nielsen, E., Therkildsen, N. O., Taylor, M. I., Ogden, R., Geffen, A. J., ... Carvalho, G. R. (2013). A genomic island linked to ecotype divergence in Atlantic cod. Molecular Ecology, 22(10), 2653-2667. https://doi.org/10.1111/mec.12284
Hansen, Jakob Hemmer ; Eg Nielsen, Einar ; Therkildsen, Nina O. ; Taylor, Martin I. ; Ogden, Rob ; Geffen, Audrey J. ; Bekkevold, Dorte ; Helyar, Sarah ; Pampoulie, Christophe ; Johansen, Torild ; Carvalho, Gary R. / A genomic island linked to ecotype divergence in Atlantic cod. In: Molecular Ecology. 2013 ; Vol. 22, No. 10. pp. 2653-2667.
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abstract = "The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or ‘genomic island’, as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that ‘genomic mosaics’ of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.",
author = "Hansen, {Jakob Hemmer} and {Eg Nielsen}, Einar and Therkildsen, {Nina O.} and Taylor, {Martin I.} and Rob Ogden and Geffen, {Audrey J.} and Dorte Bekkevold and Sarah Helyar and Christophe Pampoulie and Torild Johansen and Carvalho, {Gary R.}",
year = "2013",
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Hansen, JH, Eg Nielsen, E, Therkildsen, NO, Taylor, MI, Ogden, R, Geffen, AJ, Bekkevold, D, Helyar, S, Pampoulie, C, Johansen, T & Carvalho, GR 2013, 'A genomic island linked to ecotype divergence in Atlantic cod', Molecular Ecology, vol. 22, no. 10, pp. 2653-2667. https://doi.org/10.1111/mec.12284

A genomic island linked to ecotype divergence in Atlantic cod. / Hansen, Jakob Hemmer; Eg Nielsen, Einar; Therkildsen, Nina O.; Taylor, Martin I.; Ogden, Rob; Geffen, Audrey J.; Bekkevold, Dorte; Helyar, Sarah; Pampoulie, Christophe; Johansen, Torild; Carvalho, Gary R.

In: Molecular Ecology, Vol. 22, No. 10, 2013, p. 2653-2667.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - A genomic island linked to ecotype divergence in Atlantic cod

AU - Hansen, Jakob Hemmer

AU - Eg Nielsen, Einar

AU - Therkildsen, Nina O.

AU - Taylor, Martin I.

AU - Ogden, Rob

AU - Geffen, Audrey J.

AU - Bekkevold, Dorte

AU - Helyar, Sarah

AU - Pampoulie, Christophe

AU - Johansen, Torild

AU - Carvalho, Gary R.

PY - 2013

Y1 - 2013

N2 - The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or ‘genomic island’, as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that ‘genomic mosaics’ of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

AB - The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or ‘genomic island’, as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that ‘genomic mosaics’ of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

U2 - 10.1111/mec.12284

DO - 10.1111/mec.12284

M3 - Journal article

C2 - 23611647

VL - 22

SP - 2653

EP - 2667

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 10

ER -