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The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi

Genner, Martin J.; Turner, George F.; Hahn, Christoph; Genner, Martin J; Turner, George F; Joyce, Domino A.


Martin J. Genner

George F. Turner

Christoph Hahn

Martin J Genner

George F Turner


Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population-level RAD-seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome-level specialization for life at depth as an important process in cichlid radiation.


Genner, M. J., Turner, G. F., Hahn, C., Genner, M. J., Turner, G. F., & Joyce, D. A. (2017). The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi. Evolution Letters, 1(4), 184-198.

Journal Article Type Letter
Acceptance Date Jul 11, 2017
Online Publication Date Aug 29, 2017
Publication Date 2017-09
Deposit Date Aug 6, 2018
Publicly Available Date Aug 6, 2018
Journal Evolution Letters
Print ISSN 2056-3744
Electronic ISSN 2056-3744
Publisher Wiley
Peer Reviewed Peer Reviewed
Volume 1
Issue 4
Pages 184-198
Keywords Cichlid; Hemoglobin; Root effect; Sensory drive; Supergene
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Copyright Statement
© 2017 The Author(s). Evolution Letters published by Wiley Periodicals, Inc. on behalf of Society for the Study of Evolution (SSE) and European Society for Evolutionary Biology (ESEB).

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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