Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

• Published in: Nature ecology & evolution Vol. 2; no. 12; pp. 1940 - 1955
• Main Authors: Malinsky, Milan, Svardal, Hannes, Tyers, Alexandra M., Miska, Eric A., Genner, Martin J., Turner, George F., Durbin, Richard
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.12.2018; Nature Publishing Group
• Subjects: 45/23; 631/158/852; 631/181; 631/181/2474; 631/181/457; 631/181/759; Adaptive radiation; Animals; Biological and Physical Anthropology; Biological Evolution; Biomedical and Life Sciences; Cichlids; Cichlids - genetics; Deep water; Divergence; Ecology; Evolutionary Biology; Fish; Gene Flow; Gene sequencing; Genetic analysis; Genetic Variation; Genome; Genomes; Genomics; Heterozygosity; Lakes; Life Sciences; Malawi; Paleontology; Phylogeny; Species; Species diversity; Tanzania; Vertebrates; Whole Genome Sequencing; Zoology; Malawi; Tanzania; Lake Malawi
• ISSN: 2397-334X; 2397-334X
• DOI: 10.1038/s41559-018-0717-x

The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. The average sequence divergence between species pairs is only 0.1–0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia -like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep-water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation. Genome-sequencing data of all major cichlid fish lineages in Lake Malawi show genomic footprints of rapid species diversification.