PhD opportunity at the Department of Zoology, University of Cambridge, UK
The mechanisms underlying colour polymorphisms in trumpetfish
Supervisors: Dr James Herbert-Read, Dr Josefin Stiller, Dr Martin How & Dr Sam Matchette
Project Background
Some populations contain individuals with two or more distinct colour morphs. Understanding how different colour morphs are maintained, and whether they represent discrete genetic units or variations in phenotypic plasticity, provides opportunities to understand the adaptive value of colour variation within populations.
Trumpetfish (Aulostomus maculatus) have three putative colour morphs; yellow, brown, and blue individuals. This project will investigate trumpetfish colouration at multiple biological levels. The project will quantify variation in colour and pattern among morphs, characterise pigment composition and chromatophores using histology and reflectance spectrophotometry, assess gene flow between putative morphs, and compare gene expression profiles using RNA-seq or qPCR. By integrating morphological, biochemical, and genetic data, this study will reveal whether these morphs represent distinct genetic lineages or flexible phenotypic states, advancing our understanding of how colour diversity is generated and maintained within populations.
Type of Work
The student will investigate trumpetfish colouration through a combination of field, laboratory, and data analysis. The project will begin with field surveys and specimen imaging to document and quantify colour and pattern variation across the putative yellow, brown, and blue morphs. This will involve diving under SCUBA, standardised photography, image analysis, and statistical comparisons to define morphs. In the laboratory, the student will conduct histological examinations and chromatophore identification to map the types and distributions of pigment cells in trumpetfish skin. They will use reflectance spectrophotometry to measure the spectral properties of intact skin, generating objective profiles of each morph’s colouration. There is further scope to explore properties of the morphs’ visual capabilities and relate this to their ecology and colouration.
The student will also perform molecular analyses to explore genetic and transcriptomic differences between morphs. This may include extracting DNA and RNA, preparing and processing samples for RNA-seq, conducting qPCR assays on candidate pigmentation genes, and analysing sequence or expression data to identify potential genetic drivers of colouration. Finally, the student will quantify gene flow between morphs using population genetic analyses, integrating these results with phenotypic and pigment data to assess whether morphs are genetically distinct or not.
The project will be supported by four supervisors with different expertises; Dr Herbert-Read & Dr Sam Matchette (behavioural ecology), Dr Josefin Stiller (genetics of colouration) and Dr Martin How (visual ecology). By the end of the project, the student will have developed skills in marine fieldwork, microscopy, spectrophotometry, molecular biology, bioinformatics, and statistical analysis, while contributing to a novel, multidisciplinary investigation of colour polymorphisms.
Applicants are encouraged to contact Dr James Herbert-Read jh2223@cam.ac.uk before applying. Applicants should send a copy of their CV, academic transcript and a brief cover letter outlining their interests and motivations for applying.

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