Exploring mechanisms underlying plasticity and variation in Lake Malawi cichlids

Negi, Deepti (2026) Exploring mechanisms underlying plasticity and variation in Lake Malawi cichlids. PhD thesis, University of Glasgow.

Abstract

Because natural selection operates on phenotypes, understanding the mechanisms that generate and maintain phenotypic variation is key to explaining evolutionary divergence. In this thesis, I investigate multiple sources of variation that shape diversification, focusing on phenotypic plasticity, the genetic basis of plastic responses, genotype–environment interactions, and the role of mutations. Together, these processes not only provide the raw material for natural selection but also influence the trajectory of adaptive diversification. Lake Malawi cichlids, representing the largest known extant adaptive radiation with extensive variation in their craniofacial morphology, serve as a promising model system to test these ideas.

Chapter 1 outlines the conceptual background and establishes the context for the investigations undertaken in this research. Chapter 2 tests a key hypothesis that plasticity decreases with an increase in specialisation. For this, I studied eight representative species of Malawi cichlids and conducted a geometric morphometric approach to quantify shape variation in the craniofacial region. I also conducted RNA-seq on a subset of these species to examine gene expression and its variation in response to environmental cues across species. The findings demonstrated that plasticity operates at multiple levels, from developmental gene regulation to morphology, in facilitating adaptive divergence. The integration of morphological and transcriptomic datasets revealed that species positioned centrally along the biting–suction ecomorphological axis display relatively high plasticity, whereas specialists at the ends exhibit canalisation. This correspondence supported models where plasticity is lost during ecological specialisation via genetic assimilation in an adaptive radiation.

In Chapter 3, I studied the transcription factor zeb1 as a differentially expressed gene associated with mandible shape variation and validated its functional relevance in Lake Malawi cichlids and zebrafish. Here, I conducted qPCR on Labeotropheus fuelleborni (LF) and Tropheops sp. ‘red cheek’ (TRC) embryos to test for divergence in zeb1 expression. To further elucidate the role of zeb1 in mandible formation, I genotyped wild-type and zeb1 mutant zebrafish and conducted geometric morphometrics. Experiments with zeb1 mutant zebrafish provided evidence of how zeb1 correlates with jaw-shape variation and trophic specialisation, illustrating how a specific regulatory mutation can influence ecologically relevant morphology.

Chapter 4 explores the genetic basis of adaptive plasticity by studying a candidate gene, wnt7ba. I reared wild-type and wnt7ba mutant zebrafish under alternate feeding treatments and conducted geometric morphometrics to quantify shape variation. Although the results did not yield significant genotype effects on plasticity, patterns of differences in mutant plasticity point to wnt7ba as a plausible contributor to craniofacial development and adaptive plasticity. Given its clear relevance to trophic morphology, an ecologically critical trait, wnt7ba remains a strong candidate.

In Chapter 5, I introduce a novel, cost-effective protocol for establishing primary bone cell cultures from cichlids. By isolating primary osteogenic cells from species chosen along the biting-sucking ecomorphological axis, this approach enables characterisation of their mechanotransduction pathways and comparison of osteogenic responses among species with differing trophic ecologies and plasticity. This working protocol fills a significant gap in bone biology by facilitating the study of osteocyte-independent mechanisms of bone formation and remodelling, and provides a valuable framework for linking cellular responses to mechanical stress with evolutionary patterns of craniofacial variation in divergent cichlid species.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Additional Information: Supported by funding from NERC IAPETUS2.
• Subjects: Q Science > QH Natural history > QH301 Biology; Q Science > QH Natural history > QH345 Biochemistry; Q Science > QH Natural history > QH426 Genetics; Q Science > QL Zoology
• Colleges/Schools: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Funder's Name: NERC IAPETUS2
• Supervisor's Name: Parsons, Dr. Kevin, Dalby, Professor Matthew and Lala, Professor Kevin
• Date of Award: 2026
• Depositing User: Theses Team
• Unique ID: glathesis:2026-85970
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 26 May 2026 14:32
• Last Modified: 26 May 2026 14:34
• Thesis DOI: 10.5525/gla.thesis.85970
• URI: https://theses.gla.ac.uk/id/eprint/85970