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The ecological and genomic basis of explosive adaptive radiation

Author

Listed:
  • Matthew D. McGee

    (University of Bern
    Swiss Federal Institute of Aquatic Science and Technology (EAWAG)
    Monash University)

  • Samuel R. Borstein

    (University of Michigan)

  • Joana I. Meier

    (University of Bern
    Swiss Federal Institute of Aquatic Science and Technology (EAWAG)
    University of Cambridge)

  • David A. Marques

    (University of Bern
    Swiss Federal Institute of Aquatic Science and Technology (EAWAG))

  • Salome Mwaiko

    (Swiss Federal Institute of Aquatic Science and Technology (EAWAG))

  • Anthony Taabu

    (National Fisheries Resources Research Institute)

  • Mary A. Kishe

    (Tanzania Fisheries Research Institute)

  • Brian O’Meara

    (University of Tennessee)

  • Rémy Bruggmann

    (University of Bern
    Swiss Institute of Bioinformatics)

  • Laurent Excoffier

    (Swiss Institute of Bioinformatics
    University of Bern)

  • Ole Seehausen

    (University of Bern
    Swiss Federal Institute of Aquatic Science and Technology (EAWAG))

Abstract

Speciation rates vary considerably among lineages, and our understanding of what drives the rapid succession of speciation events within young adaptive radiations remains incomplete1–11. The cichlid fish family provides a notable example of such variation, with many slowly speciating lineages as well as several exceptionally large and rapid radiations12. Here, by reconstructing a large phylogeny of all currently described cichlid species, we show that explosive speciation is solely concentrated in species flocks of several large young lakes. Increases in the speciation rate are associated with the absence of top predators; however, this does not sufficiently explain explosive speciation. Across lake radiations, we observe a positive relationship between the speciation rate and enrichment of large insertion or deletion polymorphisms. Assembly of 100 cichlid genomes within the most rapidly speciating cichlid radiation, which is found in Lake Victoria, reveals exceptional ‘genomic potential’—hundreds of ancient haplotypes bear insertion or deletion polymorphisms, many of which are associated with specific ecologies and shared with ecologically similar species from other older radiations elsewhere in Africa. Network analysis reveals fundamentally non-treelike evolution through recombining old haplotypes, and the origins of ecological guilds are concentrated early in the radiation. Our results suggest that the combination of ecological opportunity, sexual selection and exceptional genomic potential is the key to understanding explosive adaptive radiation.

Suggested Citation

  • Matthew D. McGee & Samuel R. Borstein & Joana I. Meier & David A. Marques & Salome Mwaiko & Anthony Taabu & Mary A. Kishe & Brian O’Meara & Rémy Bruggmann & Laurent Excoffier & Ole Seehausen, 2020. "The ecological and genomic basis of explosive adaptive radiation," Nature, Nature, vol. 586(7827), pages 75-79, October.
  • Handle: RePEc:nat:nature:v:586:y:2020:i:7827:d:10.1038_s41586-020-2652-7
    DOI: 10.1038/s41586-020-2652-7
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    Cited by:

    1. Mark Pagel & Ciara O’Donovan & Andrew Meade, 2022. "General statistical model shows that macroevolutionary patterns and processes are consistent with Darwinian gradualism," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Grégoire Vernaz & Milan Malinsky & Hannes Svardal & Mingliu Du & Alexandra M. Tyers & M. Emília Santos & Richard Durbin & Martin J. Genner & George F. Turner & Eric A. Miska, 2021. "Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes," Nature Communications, Nature, vol. 12(1), pages 1-13, December.

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