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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Author

Listed:
  • Rishi De-Kayne

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

  • Oliver M. Selz

    (EAWAG Swiss Federal Institute of Aquatic Science and Technology)

  • David A. Marques

    (EAWAG Swiss Federal Institute of Aquatic Science and Technology
    University of Bern
    Natural History Museum Basel)

  • David Frei

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

  • Ole Seehausen

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

  • Philine G. D. Feulner

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

Abstract

Adaptive radiations represent some of the most remarkable explosions of diversification across the tree of life. However, the constraints to rapid diversification and how they are sometimes overcome, particularly the relative roles of genetic architecture and hybridization, remain unclear. Here, we address these questions in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. We reveal that repeated ecological and morphological diversification along a common environmental axis is associated with both genome-wide allele frequency shifts and a specific, larger effect, locus, associated with the gene edar. Additionally, we highlight the possible role of introgression between species from different lake-systems in facilitating the evolution and persistence of species with unique trait combinations and ecology. These results highlight the importance of both genome architecture and secondary contact with hybridization in fuelling adaptive radiation.

Suggested Citation

  • Rishi De-Kayne & Oliver M. Selz & David A. Marques & David Frei & Ole Seehausen & Philine G. D. Feulner, 2022. "Genomic architecture of adaptive radiation and hybridization in Alpine whitefish," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32181-8
    DOI: 10.1038/s41467-022-32181-8
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    References listed on IDEAS

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    1. Heejung Shim & Daniel I Chasman & Joshua D Smith & Samia Mora & Paul M Ridker & Deborah A Nickerson & Ronald M Krauss & Matthew Stephens, 2015. "A Multivariate Genome-Wide Association Analysis of 10 LDL Subfractions, and Their Response to Statin Treatment, in 1868 Caucasians," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-20, April.
    2. Marco Todesco & Gregory L. Owens & Natalia Bercovich & Jean-Sébastien Légaré & Shaghayegh Soudi & Dylan O. Burge & Kaichi Huang & Katherine L. Ostevik & Emily B. M. Drummond & Ivana Imerovski & Kathry, 2020. "Massive haplotypes underlie ecotypic differentiation in sunflowers," Nature, Nature, vol. 584(7822), pages 602-607, August.
    3. Joana I. Meier & Rike B. Stelkens & Domino A. Joyce & Salome Mwaiko & Numel Phiri & Ulrich K. Schliewen & Oliver M. Selz & Catherine E. Wagner & Cyprian Katongo & Ole Seehausen, 2019. "The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    4. Felicity C. Jones & Manfred G. Grabherr & Yingguang Frank Chan & Pamela Russell & Evan Mauceli & Jeremy Johnson & Ross Swofford & Mono Pirun & Michael C. Zody & Simon White & Ewan Birney & Stephen Sea, 2012. "The genomic basis of adaptive evolution in threespine sticklebacks," Nature, Nature, vol. 484(7392), pages 55-61, April.
    5. Andreas F. Kautt & Claudius F. Kratochwil & Alexander Nater & Gonzalo Machado-Schiaffino & Melisa Olave & Frederico Henning & Julián Torres-Dowdall & Andreas Härer & C. Darrin Hulsey & Paolo Franchini, 2020. "Contrasting signatures of genomic divergence during sympatric speciation," Nature, Nature, vol. 588(7836), pages 106-111, December.
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    1. Marie Louis & Petra Korlević & Milaja Nykänen & Frederick Archer & Simon Berrow & Andrew Brownlow & Eline D. Lorenzen & Joanne O’Brien & Klaas Post & Fernando Racimo & Emer Rogan & Patricia E. Rosel &, 2023. "Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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