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

Iker Irisarri, Pooja Singh, Stephan Koblmüller, Julián Torres-Dowdall, Frederico Henning, Paolo Franchini, Christoph Fischer, Alan R Lemmon, Emily Moriarty Lemmon, Gerhard G Thallinger, Christian Sturmbauer, Axel Meyer

Research output: Contribution to journalArticleResearchpeer-review

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.

LanguageEnglish
Article number3159
JournalNature Communications
Volume9
Issue number1
DOIs
StatusPublished - 8 Aug 2018

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Cichlids
Tanzania
fishes
loci
Lakes
lakes
Fish
Radiation
radiation
Malawi
Color vision
color vision
Color Vision
habitats
Victoria
Pedigree
genes
Ecosystem
bursts
Genes

Keywords

  • Adaptation, Biological/radiation effects
  • Africa, Eastern
  • Animals
  • Biodiversity
  • Cichlids/classification
  • DNA, Mitochondrial/genetics
  • Diet
  • Evolution, Molecular
  • Fossils
  • Fresh Water
  • Gene Flow/radiation effects
  • Genetic Markers
  • Genotype
  • Geological Phenomena
  • Hybridization, Genetic/radiation effects
  • Lakes
  • Models, Genetic
  • Phenotype
  • Phylogeny
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Species Specificity
  • Tanzania

Fields of Expertise

  • Human- & Biotechnology
  • Information, Communication & Computing

Treatment code (Nähere Zuordnung)

  • Basic - Fundamental (Grundlagenforschung)

Cooperations

  • BioTechMed-Graz

Cite this

Irisarri, I., Singh, P., Koblmüller, S., Torres-Dowdall, J., Henning, F., Franchini, P., ... Meyer, A. (2018). Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. Nature Communications, 9(1), [3159]. https://doi.org/10.1038/s41467-018-05479-9

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

In: Nature Communications, Vol. 9, No. 1, 3159, 08.08.2018.

Research output: Contribution to journalArticleResearchpeer-review

Irisarri, I, Singh, P, Koblmüller, S, Torres-Dowdall, J, Henning, F, Franchini, P, Fischer, C, Lemmon, AR, Lemmon, EM, Thallinger, GG, Sturmbauer, C & Meyer, A 2018, 'Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes', Nature Communications, vol. 9, no. 1, 3159. https://doi.org/10.1038/s41467-018-05479-9
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. / Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. In: Nature Communications. 2018 ; Vol. 9, No. 1.
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