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Nat Commun. 2018 Aug 8;9(1):3159. doi: 10.1038/s41467-018-05479-9.

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

Author information

1
Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany.
2
Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid, 28006, Spain.
3
Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria.
4
Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, 21944-970, Brazil.
5
Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria.
6
OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria.
7
Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306, USA.
8
Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306, USA.
9
Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria. christian.sturmbauer@uni-graz.at.
10
Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany. axel.meyer@uni-konstanz.de.
11
Radcliffe Institute for Advanced Study, Harvard University, Cambridge, 02138, MA, USA. axel.meyer@uni-konstanz.de.

Abstract

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.

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