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Evolution and Development of Pigmentation Patterns in East African Cichlid fishes https://doi.org/10.17863/CAM.116084 Hickey, Aaron 0009000003606516 Santos, Emília Understanding the origin of novel phenotypic diversity remains a fundamental question in evolutionary genetics. This thesis aims to address the origin and diversification of novel traits by integrating population genomics and developmental genetics techniques. Using East African cichlid fishes as a model system, I aim to understand the evolutionary origin and diversification of anal fin egg-spots. Egg-spots are an innovation unique to the haplochromine cichlids; yellow to red annular markings typically on male anal fins, made up of orange (xanthophores) and iridescent (iridophores) pigment cell types. The functional origin of egg-spots has been implicated in courting behaviour and sexual selection. I wish to understand the genetic, developmental, and hormonal factors that contribute to the emergence and vast variation in egg-spots of East African cichlids. In the first experimental chapter, I sought to characterise egg-spot development in the ancestral proxy species, Astatotilapia calliptera. Although egg-spots are almost ubiquitous among haplochromines, their cellular level ontogeny remains unknown. Detailed imaging from embryonic to mature stages enabled the identification of relevant pigment cell types, and developmental events. It was found that egg-spots form in a permissive environment (soft-fin ray domain) mediated largely through cellular interactions, with a surprising level of developmental plasticity influenced by environmental factors. To understand the origins of egg-spots I investigated their genetic and developmental basis using transcriptomic approaches in a tissue- and sex-specific manner, followed by functional validation. I identified candidate genes involved in egg-spot development, highlighting clear tissue-specific patterns of gene expression. These findings suggest that cellular interactions are critical for trait patterning. ii To explore the genetic and developmental basis of egg-spot diversification, I undertook comparative developmental and genomic studies on Tropheops sp. “mauve”; a closely related species to A. calliptera, possessing a divergent egg-spot phenotype. Despite differences in cellular differentiation timing and rate, comparable gene expression patterns were observed between species. This suggests that early timing of cellular events (heterochrony) significantly contributes to adult phenotypic outcomes. I identified candidate genes contributing to egg-spot patterning using transcriptomic and genomic mapping techniques. Despite the genetic similarity between species and ecomorphs, significant phenotypic diversity and developmental plasticity suggests a role for non-genetic control in egg-spot development. I investigate the endocrine mechanisms mediating this developmental plasticity within and between species. My findings demonstrate thyroid hormones influence egg-spot development and I identify differentially expressed genes in the thyroid hormone pathway between A. calliptera ecomorphs, suggesting these genes play a role mediating organism-environmental alignment and potentially contribute to phenotypic variability. Furthermore, I find signatures of genetic accommodation in the regulatory region of a gene upstream in the hypothalamic- pituitary-thyroid axis between ecomorphs, implicating these genes in adaptive evolution. Additionally, I identified species-specific differences in thyroid hormone pathway gene expression during development that correlate with phenotypic differences. The results in this thesis provide an integrated perspective of the complex genetic and developmental architecture underlying the emergence and diversification of morphological novelties. Using East African cichlids as a model, this work deepens our understanding of how genetic and environmentally-mediated endocrine regulation of development contribute to morphological diversification in adaptive radiations. University of Cambridge 2024-09-26 Thesis Doctoral Doctor of Philosophy (PhD) eng A.H is supported by Balfour-Trinity PhD studentship from the department of Zoology M.E.S is supported by a NERC IRF NE/R01504X/1 https://www.repository.cam.ac.uk/handle/1810/380488 embargo 2026-02-20 https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/2f7c6868-a48f-4442-83ca-9da211f6cc90/download 3a349188170de2b3a5cda8e0eccd3ac0 https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/2896db1f-be12-40fd-84aa-37297a89314b/download 87eda9de84448d1f82354d60eee3eb5f http://purl.org/NET/rdflicense/allrightsreserved Adaptive radiation Cichlids Development Egg-spots Evolution Genetics Hormones Pigmentation