IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-56126-z.html
   My bibliography  Save this article

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

Author

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-56126-z
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-56126-z?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. 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).
    2. Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
    3. 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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ya-Mei Ding & Xiao-Xu Pang & Yu Cao & Wei-Ping Zhang & Susanne S. Renner & Da-Yong Zhang & Wei-Ning Bai, 2023. "Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Romain Fournier & Zoi Tsangalidou & David Reich & Pier Francesco Palamara, 2023. "Haplotype-based inference of recent effective population size in modern and ancient DNA samples," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Javier Martínez Pacheco & Philippe Ranocha & Luciana Kasulin & Corina M. Fusari & Lucas Servi & Ariel. A. Aptekmann & Victoria Berdion Gabarain & Juan Manuel Peralta & Cecilia Borassi & Eliana Marzol , 2022. "Apoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. Juan E. Rosas & Maia Escobar & Sebastián Martínez & Pedro Blanco & Fernando Pérez & Gastón Quero & Lucía Gutiérrez & Victoria Bonnecarrère, 2020. "Epistasis and Quantitative Resistance to Pyricularia oryzae Revealed by GWAS in Advanced Rice Breeding Populations," Agriculture, MDPI, vol. 10(12), pages 1-16, December.
    5. Guangping Huang & Lingyun Song & Xin Du & Xin Huang & Fuwen Wei, 2023. "Evolutionary genomics of camouflage innovation in the orchid mantis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Legried, Brandon & Terhorst, Jonathan, 2022. "Rates of convergence in the two-island and isolation-with-migration models," Theoretical Population Biology, Elsevier, vol. 147(C), pages 16-27.
    7. Jörn Bethune & April Kleppe & Søren Besenbacher, 2022. "A method to build extended sequence context models of point mutations and indels," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    8. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
    9. Aoki, Kenichi & Wakano, Joe Yuichiro, 2022. "Hominin forager technology, food sharing, and diet breadth," Theoretical Population Biology, Elsevier, vol. 144(C), pages 37-48.
    10. Yupeng Sang & Zhiqin Long & Xuming Dan & Jiajun Feng & Tingting Shi & Changfu Jia & Xinxin Zhang & Qiang Lai & Guanglei Yang & Hongying Zhang & Xiaoting Xu & Huanhuan Liu & Yuanzhong Jiang & Pär K. In, 2022. "Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    11. Kimmel, Marek & Wojdyła, Tomasz, 2016. "Genetic demographic networks: Mathematical model and applications," Theoretical Population Biology, Elsevier, vol. 111(C), pages 75-86.
    12. Jason Flannick & Joshua M Korn & Pierre Fontanillas & George B Grant & Eric Banks & Mark A Depristo & David Altshuler, 2012. "Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-13, July.
    13. Yee Wen Low & Sitaram Rajaraman & Crystal M. Tomlin & Joffre Ali Ahmad & Wisnu H. Ardi & Kate Armstrong & Parusuraman Athen & Ahmad Berhaman & Ruth E. Bone & Martin Cheek & Nicholas R. W. Cho & Le Min, 2022. "Genomic insights into rapid speciation within the world’s largest tree genus Syzygium," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    14. José Cerca & Bent Petersen & José Miguel Lazaro-Guevara & Angel Rivera-Colón & Siri Birkeland & Joel Vizueta & Siyu Li & Qionghou Li & João Loureiro & Chatchai Kosawang & Patricia Jaramillo Díaz & Gon, 2022. "The genomic basis of the plant island syndrome in Darwin’s giant daisies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    15. Rong Wang & Chao-Nan Liu & Simon T. Segar & Yu-Ting Jiang & Kai-Jian Zhang & Kai Jiang & Gang Wang & Jing Cai & Lu-Fan Chen & Shan Chen & Jing Cheng & Stephen G. Compton & Jun-Yin Deng & Yuan-Yuan Din, 2024. "Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    16. Jerome Kelleher & Alison M Etheridge & Gilean McVean, 2016. "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-22, May.
    17. Deng, Yun & Song, Yun S. & Nielsen, Rasmus, 2021. "The distribution of waiting distances in ancestral recombination graphs," Theoretical Population Biology, Elsevier, vol. 141(C), pages 34-43.
    18. Chengqi Cui & Yanyang Liu & Yan Liu & Xianghua Cui & Zhiyu Sun & Zhenwei Du & Ke Wu & Xiaolin Jiang & Hongxian Mei & Yongzhan Zheng, 2021. "Genome-wide association study of seed coat color in sesame (Sesamum indicum L.)," PLOS ONE, Public Library of Science, vol. 16(5), pages 1-14, May.
    19. Ran Tian & Yaolei Zhang & Hui Kang & Fan Zhang & Zhihong Jin & Jiahao Wang & Peijun Zhang & Xuming Zhou & Janet M. Lanyon & Helen L. Sneath & Lucy Woolford & Guangyi Fan & Songhai Li & Inge Seim, 2024. "Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    20. Ait Kaci Azzou, S. & Larribe, F. & Froda, S., 2016. "Inferring the demographic history from DNA sequences: An importance sampling approach based on non-homogeneous processes," Theoretical Population Biology, Elsevier, vol. 111(C), pages 16-27.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56126-z. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.