Sawasawa, W. | Search bioRxiv

bioRxiv2024

Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation

Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large inversions segregating in the benthic subradiation that each suppress recombination over more than half a chromosome. Two inversions were transferred from deepwater pelagic Diplotaxodon via admixture, while the others established early in the deep benthic clade. Introgression of haplotypes from lineages inside and outside the Malawi radiation coincided with bursts of species diversification. Inversions show evidence for transient sex linkage and a striking excess of protein changing substitutions points towards selection on neuro-sensory, physiological and reproductive genes. We conclude that repeated interplay between depth adaptation and sex-specific selection on large inversions has been central to the evolution of this iconic system.

evolutionary biology↗

bioRxiv2024

Population genomic analysis reveals cryptic population structure in the commercially important Lake Malawi cichlid Copadichromis mloto

Fish is an important source of animal protein for many people living around Lake Malawi. The evaluation of population structure and genetic diversity can yield useful information for management and conservation of fish species but is complicated in Lake Malawi by the close genetic relatedness of species of the recent cichlid adaptive radiation. In this study, we analysed whole-genome sequencing data of "true utaka", a group of cichlids previously common in fisheries, but that has faced strong decline due to overfishing. Our analysis of 223 individuals collected from fishermens catches along the western shoreline of Lake Malawi confirmed that Copadichromis mloto (C. sp. "virginalis kajose") is the true utaka most targeted by fisheries. Genetic principal component analysis, phylogenetic inference, and admixture analysis revealed complex patterns of population structure. The presence of at least three geographically widespread genetic clades that have remained separate despite gene flow and partial sympatry hints at the presence of currently undescribed, cryptic species diversity in C. mloto. This result leads us to suggest that, despite the lack of obvious habitat barriers, benthic and pelagic species of Malawi cichlids might harbour unidentified species diversity and calls for further genetic and taxonomic research to define appropriate conservation units.

genomics↗