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Reply to: ‘Subfunctionalization versus neofunctionalization after whole-genome duplication’

Nature Genetics volume 50, pages 910–911 (2018)Cite this article

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Braasch et al. reply: Understanding mechanisms that preserve duplicated genetic elements after whole-genome duplication (WGD) remains an unresolved issue. Sandve et al.1 compared two methods to analyze the frequency of subfunctionalization and neofunctionalization as mechanisms for the preservation of ohnologs (WGD gene duplicates) for two different WGD events2,3. They conclude that differences arose from analytical methods rather than biology. This finding is important because differences in the antiquity and possibly the origins of WGD by allo- versus autopolyploidy might result in different evolutionary patterns in different WGD events.

A problem for evaluation is distinguishing events in the preservation phase from later events in the maintenance phase. Non-functionalization occurs within a few million years of WGD6, and duplicate preservation must occur on a similar timescale. For both the teleost genome duplication (TGD; ~350 million years ago) and the salmonid genome duplication (SaGD; ~95 million years ago), ohnologs in extant fish have spent far more time in maintenance than in preservation and, hence, signatures of sub- and neofunctionalization, which refer exclusively to preservation4, can be obscured by changes in the long maintenance phase.

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Fig. 1: Models for gene evolution after whole-genome duplication.

References

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Acknowledgements

This work was supported by US National Institutes of Health grants R01 OD011116 (alias R01 RR020833) and R24 OD01119004 (J.H.P.); a Feodor Lynen Fellowship from the Alexander von Humboldt Foundation and the Volkswagen Foundation Initiative Evolutionary Biology, grant I/84 815 (I.B.); and Agence Nationale de la Recherche (ANR) grant ANR-10-GENM-017 (PhyloFish; J.B. and Y.G.).

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Authors and Affiliations

  1. Department of Integrative Biology, Michigan State University, East Lansing, MI, USA

    Ingo Braasch

  2. INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France

    Julien Bobe & Yann Guiguen

  3. Institute of Neuroscience, University of Oregon, Eugene, OR, USA

    John H. Postlethwait

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  1. Ingo Braasch
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I.B., J.B., Y.G. and J.H.P. designed studies, conducted studies, analyzed data and wrote the letter.

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Correspondence to John H. Postlethwait.

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Braasch, I., Bobe, J., Guiguen, Y. et al. Reply to: ‘Subfunctionalization versus neofunctionalization after whole-genome duplication’ . Nat Genet 50, 910–911 (2018). https://doi.org/10.1038/s41588-018-0163-3

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