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Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population

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Listed:
  • Pierre Lesturgie

    (Dickinson Hall
    Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles
    Faculdade de Ciências da Universidade de Lisboa, Campo Grande)

  • John S. S. Denton

    (American Museum of Natural History)

  • Lei Yang

    (Dickinson Hall)

  • Shannon Corrigan

    (Dickinson Hall)

  • Jeff Kneebone

    (Anderson Cabot Center for Ocean Life at the New England Aquarium)

  • Romuald Laso-Jadart

    (Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles
    PSL Research University)

  • Arve Lynghammar

    (NO-9037 Breivika)

  • Olivier Fedrigo

    (Colossal Biosciences)

  • Stefano Mona

    (Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles
    PSL Research University)

  • Gavin J. P. Naylor

    (Dickinson Hall)

Abstract

The Thorny Skate (Amblyraja radiata) is a vulnerable species displaying a discrete size-polymorphism in the northwest Atlantic Ocean (NWA). We conducted whole genome sequencing of samples collected across its range. Genetic diversity was similar at all sampled sites, but we discovered a ~ 31 megabase bi-allelic supergene associated with the size polymorphism, with the larger size allele having introgressed in the last ~160,000 years B.P. While both Gulf of Maine (GoM) and Canadian (CAN) populations exhibit the size polymorphism, we detected a significant deficit of heterozygotes at the supergene and longer stretches of homozygosity in GoM population. This suggests inbreeding driven by assortative mating for size in GoM but not in CAN. Coalescent-based demographic modelling reveals strong migration between regions maintaining genetic variability in the recombining genome, preventing speciation between morphs. This study highlights short-term context-dependent evolutionary consequences of a size-determining supergene providing new insights for the management of vulnerable species.

Suggested Citation

  • Pierre Lesturgie & John S. S. Denton & Lei Yang & Shannon Corrigan & Jeff Kneebone & Romuald Laso-Jadart & Arve Lynghammar & Olivier Fedrigo & Stefano Mona & Gavin J. P. Naylor, 2025. "Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56126-z
    DOI: 10.1038/s41467-025-56126-z
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    References listed on IDEAS

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    1. Eckart Stolle & Rodrigo Pracana & Federico López-Osorio & Marian K. Priebe & Gabriel Luis Hernández & Claudia Castillo-Carrillo & Maria Cristina Arias & Carolina Ivon Paris & Martin Bollazzi & Anurag , 2022. "Recurring adaptive introgression of a supergene variant that determines social organization," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    2. Shin, Ji-Hyung & Blay, Sigal & McNeney, Brad & Graham, Jinko, 2006. "LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 16(c03).
    3. Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
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