Why do some fish grow huge while others stay tiny, even within the same genus? A recent study has uncovered new genomic mechanisms underlying body size evolution and rapid speciation of cichlid fishes in Lake Malawi. Scientists found that, in the predatory cichlid genus Rhamphochromis, body size differences have evolved many times, and the associated genetic variants are linked to genes involved in skeletal and nervous system development.

The study, led by Prof. HE Shunping's team from the Institute of Hydrobiology (IHB) of the Chinese Academy of Sciences, in collaboration with Prof. Martin J. Genner from the University of Bristol, UK, has been recently published in Genome Research.

Species divergence and speciation are fundamental questions in evolutionary biology and biodiversity research. Understanding how populations diverge under the combined pressures of ecological selection and genetic variation is key to explaining adaptive radiation, ecological differentiation, and patterns of genomic evolution.

Fish, with their remarkable ecological diversity, morphological plasticity, and variable evolutionary rates, offer excellent systems for studying speciation mechanisms. Among them, the rapid diversification of fishes inhabiting plateau regions under strong environmental gradients and geographic isolation, along with the extensive adaptive radiation of cichlid fishes in the three major African lakes over relatively short evolutionary timescales, are widely recognized as classic models for studying species diversification and rapid speciation.

Focusing on the predatory cichlid fishes of the genus Rhamphochromis inhabiting the open waters of Lake Malawi, the study used whole-genome sequencing data to analyze the patterns of body size divergence during the rapid radiation of this group and explored their genomic basis.

Genomic analysis revealed that major body size differences in Rhamphochromis species evolved independently multiple times during their evolutionary history and were accompanied by clear signals of ancient interspecific hybridization.

The study further identified a series of genetic variations associated with body size. These variations were mainly enriched in genes related to vertebrate skeletal development and nervous system function, indicating that body size evolution is not a change of a single trait, but is closely coupled with morphological development and behavioral regulation networks.

Scientists then focused on Lake Kingiri, a volcanic crater lake within the Lake Malawi catchment that measures only about 600 meters in diameter. Although geographically isolated from Lake Malawi, the lake remains hydrologically connected and provides an ideal natural system for studying sympatric speciation.

They identified two sympatric and ecomorphologically divergent Rhamphochromis species inhabiting Lake Kingiri—one small-bodied and the other large-bodied. Population genomic analyses showed that the two species shared a single common ancestor and diverged less than 2,000 years ago.

The study found that the large-bodied species experienced strong directional selection over this extremely short evolutionary timescale. Signatures of selection were predominantly enriched in genetic variants associated with anatomical development and nervous system function. These findings suggest that body size-related traits may play an important role in sympatric ecological divergence and speciation.

According to the scientists, the genomic evidence from this study provides strong evidence for a role of body size divergence in ecological speciation in Lake Malawi cichlids. The findings further indicate that body size-associated genetic variants have served as key targets of natural selection during the large-scale adaptive radiation of Lake Malawi cichlids. This work also provides new insights into the mechanisms underlying rapid adaptive radiation and species diversification in cichlid fishes.

Sampling sites and body size variation in Rhamphochromis cichlid fish species (Image by IHB)