Phenotypic and genomic dissection of colour pattern variation in a reef fish radiation

Floriane Coulmance, Derya Akkaynak, Yann Le Poul, Marc P. Höppner, W. Owen McMillan, Oscar Puebla

Research output: Contribution to journalArticlepeer-review


Coral reefs rank among the most diverse species assemblages on Earth. A particularly striking aspect of coral reef communities is the variety of colour patterns displayed by reef fishes. Colour pattern is known to play a central role in the ecology and evolution of reef fishes through, for example, signalling or camouflage. Nevertheless, colour pattern is a complex trait in reef fishes—actually a collection of traits—that is difficult to analyse in a quantitative and standardized way. This is the challenge that we address in this study using the hamlets (Hypoplectrus spp., Serranidae) as a model system. Our approach involves a custom underwater camera system to take orientation- and size-standardized photographs in situ, colour correction, alignment of the fish images with a combination of landmarks and Bézier curves, and principal component analysis on the colour value of each pixel of each aligned fish. This approach identifies the major colour pattern elements that contribute to phenotypic variation in the group. Furthermore, we complement the image analysis with whole-genome sequencing to run a multivariate genome-wide association study for colour pattern variation. This second layer of analysis reveals sharp association peaks along the hamlet genome for each colour pattern element and allows to characterize the phenotypic effect of the single nucleotide polymorphisms that are most strongly associated with colour pattern variation at each association peak. Our results suggest that the diversity of colour patterns displayed by the hamlets is generated by a modular genomic and phenotypic architecture.

Original languageEnglish
Article numbere17047
JournalMolecular Ecology
Issue number4
Early online date20 Jun 2023
StatePublished - Feb 2024

Bibliographical note

Publisher Copyright:
© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.


  • Hypoplectrus
  • colour pattern
  • genome-wide association
  • modularity
  • radiation
  • reef fishes

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics


Dive into the research topics of 'Phenotypic and genomic dissection of colour pattern variation in a reef fish radiation'. Together they form a unique fingerprint.

Cite this