The genomic basis of adaptation to the deep water ‘twilight zone’ in Lake Malawi cichlid fishes

Christophe Hahn, Martin J Genner, George F Turner, Domino A Joyce

Research output: Contribution to journalArticle (Academic Journal)peer-review

18 Citations (Scopus)
428 Downloads (Pure)


Deep water environments are characterized by low levels of available light at increasingly narrow spectra, great hydrostatic pressure and reduced 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 100 metres. We use population-level RAD-seq data to investigate whether four endemic deep water 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. Co-localization of functionally linked genes suggests co-adapted "supergene" complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions in candidate genes. Our data provide unique insights into genomic adaptation to life at depth, and suggest genome-level specialisation for deep water habitat as an important process in cichlid radiation.
Original languageEnglish
JournalEvolution Letters
Early online date29 Aug 2017
Publication statusE-pub ahead of print - 29 Aug 2017


  • Root effect
  • supergene
  • cichlid
  • hemoglobin
  • haemoglobin
  • sensory drive


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