Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

• Published in: Nature communications 2018-08, Vol.9 (1), p.3159-12, Article 3159
• Main Authors: Irisarri, Iker, Singh, Pooja, Koblmüller, Stephan, Torres-Dowdall, Julián, Henning, Frederico, Franchini, Paolo, Fischer, Christoph, Lemmon, Alan R., Lemmon, Emily Moriarty, Thallinger, Gerhard G., Sturmbauer, Christian, Meyer, Axel
• Format: Article
• Language: English
• Subjects: 45; 45/23; 631/114/739; 631/181/735; 631/181/757; 631/181/759/2467; Adaptation; Adaptation, Biological - radiation effects; Adaptive radiation; Africa, Eastern; Animals; Aquatic habitats; Biodiversity; Biological evolution; Cichlids; Cichlids - classification; Cichlids - genetics; Colonization; Color vision; Diet; DNA, Mitochondrial - genetics; Evolution; Evolution, Molecular; Family trees; Fossils; Fresh Water; Gene Flow - radiation effects; Genetic Markers; Genotype; Geological Phenomena; Humanities and Social Sciences; Hybridization; Hybridization, Genetic - radiation effects; Lakes; Models, Genetic; multidisciplinary; Phenotype; Phylogeny; Positive selection; Science; Science (multidisciplinary); Sequence Alignment; Sequence Analysis, DNA; Speciation; Species Specificity; Tanzania
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-05479-9

Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species’ dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations. Lake Tanganyika’s cichlid radiation is the main source of East African cichlid diversity. Irisarri et al. resolve its phylogenetic backbone using anchored phylogenomics and identify trans-lineage hybridization prior to major speciation bursts and adaptive loci underlying ecological innovations.