Lineage-specific neural and morphogenetic gene family expansions accompany habitat divergence in Southern African dwarf chameleons (Bradypodion)

Gene family expansions can reveal how genomes diverge in lineages shaped by ecological divergence. We examined gene family evolution in two South African dwarf chameleons, Bradypodion pumilum and B. ventrale, which occupy contrasting forested and open-canopy habitats and belong to different clades. Using newly annotated Bradypodion genomes and four published squamate genomes, we identified orthologous gene families and estimated changes in family composition within a phylogenetic framework. The Bradypodion crown group showed expansions enriched for neural connectivity, synaptic organization, cell–cell recognition, and genome maintenance, suggesting an ancestral background of neural wiring and cellular resilience. Bradypodion pumilum exhibited expansions centred on synaptic organization, postsynaptic receptor localization, and membrane-associated signalling, indicating lineage-specific functional differentiation in a forest-associated lineage. By contrast, B. ventrale showed expansions linked to neural morphogenesis, cell adhesion, tissue organization, and developmental pathways, indicating a distinct functional profile in an open-habitat lineage. These results show that habitat-associated lineages differ not simply in the presence of expanded gene families, but in the functional categories they display across expanded families. Our study highlights the value of gene family analyses for detecting lineage-specific genomic signatures in non-model taxa and underscores the importance of integrating evolutionary history with ecological context when interpreting genomic architecture in relation to diversification.