Parallel clines and sympatric divergence in ecological and mating traits shape speciation in Lake Victoria cichlids

Speciation often emerges from the complex interplay of geography, demography, ecology, and sexual selection, yet disentangling their relative contributions remains a challenge. In this study, we examine two species complexes of rock-dwelling Lake Victoria cichlids in the genera Pundamilia and Neochromis that are distributed along a continuous geographic gradient of rocky shores. Using morphometric analyses and male nuptial coloration data, we reveal clinal craniofacial divergence following an isolation by distance model of evolution, punctuated by strong local effects. While the Pundamilia cline exhibited modular shifts in craniofacial anatomy linked to diet-specific morphology, variation in the Neochromis cline was dominated by allometric constraints, suggesting different evolutionary processes at play. At the single site where the terminal populations of both clines co-occur, each pair of sister species showed pronounced divergence in morphology and male nuptial coloration, consistent with ecological and sexual character displacement facilitating co-existence. Our findings highlight that clinal morphological variation in parapatry and more abrupt shifts in sympatry interact to generate and maintain species. These rocky shore cichlids provide a rare opportunity to investigate the speciation continuum in one of the world’s youngest adaptive radiations.